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Sample records for cortical sparse distributed

  1. Sparse distributed memory overview

    NASA Technical Reports Server (NTRS)

    Raugh, Mike

    1990-01-01

    The Sparse Distributed Memory (SDM) project is investigating the theory and applications of massively parallel computing architecture, called sparse distributed memory, that will support the storage and retrieval of sensory and motor patterns characteristic of autonomous systems. The immediate objectives of the project are centered in studies of the memory itself and in the use of the memory to solve problems in speech, vision, and robotics. Investigation of methods for encoding sensory data is an important part of the research. Examples of NASA missions that may benefit from this work are Space Station, planetary rovers, and solar exploration. Sparse distributed memory offers promising technology for systems that must learn through experience and be capable of adapting to new circumstances, and for operating any large complex system requiring automatic monitoring and control. Sparse distributed memory is a massively parallel architecture motivated by efforts to understand how the human brain works. Sparse distributed memory is an associative memory, able to retrieve information from cues that only partially match patterns stored in the memory. It is able to store long temporal sequences derived from the behavior of a complex system, such as progressive records of the system's sensory data and correlated records of the system's motor controls.

  2. Sparse distributed memory

    NASA Technical Reports Server (NTRS)

    Kanerva, Pentti

    1988-01-01

    Theoretical models of the human brain and proposed neural-network computers are developed analytically. Chapters are devoted to the mathematical foundations, background material from computer science, the theory of idealized neurons, neurons as address decoders, and the search of memory for the best match. Consideration is given to sparse memory, distributed storage, the storage and retrieval of sequences, the construction of distributed memory, and the organization of an autonomous learning system.

  3. Sparse distributed memory

    SciTech Connect

    Kanerva, P.

    1988-01-01

    Theoretical models of the human brain and proposed neural-network computers are developed analytically. Chapters are devoted to the mathematical foundations, background material from computer science, the theory of idealized neurons, neurons as address decoders, and the search of memory for the best match. Consideration is given to sparse memory, distributed storage, the storage and retrieval of sequences, the construction of distributed memory, and the organization of an autonomous learning system. 63 refs.

  4. Sparse distributed memory

    NASA Technical Reports Server (NTRS)

    Denning, Peter J.

    1989-01-01

    Sparse distributed memory was proposed be Pentti Kanerva as a realizable architecture that could store large patterns and retrieve them based on partial matches with patterns representing current sensory inputs. This memory exhibits behaviors, both in theory and in experiment, that resemble those previously unapproached by machines - e.g., rapid recognition of faces or odors, discovery of new connections between seemingly unrelated ideas, continuation of a sequence of events when given a cue from the middle, knowing that one doesn't know, or getting stuck with an answer on the tip of one's tongue. These behaviors are now within reach of machines that can be incorporated into the computing systems of robots capable of seeing, talking, and manipulating. Kanerva's theory is a break with the Western rationalistic tradition, allowing a new interpretation of learning and cognition that respects biology and the mysteries of individual human beings.

  5. Sparse asynchronous cortical generators can produce measurable scalp EEG signals.

    PubMed

    von Ellenrieder, Nicolás; Dan, Jonathan; Frauscher, Birgit; Gotman, Jean

    2016-09-01

    We investigate to what degree the synchronous activation of a smooth patch of cortex is necessary for observing EEG scalp activity. We perform extensive simulations to compare the activity generated on the scalp by different models of cortical activation, based on intracranial EEG findings reported in the literature. The spatial activation is modeled as a cortical patch of constant activation or as random sets of small generators (0.1 to 3cm(2) each) concentrated in a cortical region. Temporal activation models for the generation of oscillatory activity are either equal phase or random phase across the cortical patches. The results show that smooth or random spatial activation profiles produce scalp electric potential distributions with the same shape. Also, in the generation of oscillatory activity, multiple cortical generators with random phase produce scalp activity attenuated on average only 2 to 4 times compared to generators with equal phase. Sparse asynchronous cortical generators can produce measurable scalp EEG. This is a possible explanation for seemingly paradoxical observations of simultaneous disorganized intracranial activity and scalp EEG signals. Thus, the standard interpretation of scalp EEG might constitute an oversimplification of the underlying brain activity. PMID:27262240

  6. Sparse imaging of cortical electrical current densities via wavelet transforms

    NASA Astrophysics Data System (ADS)

    Liao, Ke; Zhu, Min; Ding, Lei; Valette, Sébastien; Zhang, Wenbo; Dickens, Deanna

    2012-11-01

    While the cerebral cortex in the human brain is of functional importance, functions defined on this structure are difficult to analyze spatially due to its highly convoluted irregular geometry. This study developed a novel L1-norm regularization method using a newly proposed multi-resolution face-based wavelet method to estimate cortical electrical activities in electroencephalography (EEG) and magnetoencephalography (MEG) inverse problems. The proposed wavelets were developed based on multi-resolution models built from irregular cortical surface meshes, which were realized in this study too. The multi-resolution wavelet analysis was used to seek sparse representation of cortical current densities in transformed domains, which was expected due to the compressibility of wavelets, and evaluated using Monte Carlo simulations. The EEG/MEG inverse problems were solved with the use of the novel L1-norm regularization method exploring the sparseness in the wavelet domain. The inverse solutions obtained from the new method using MEG data were evaluated by Monte Carlo simulations too. The present results indicated that cortical current densities could be efficiently compressed using the proposed face-based wavelet method, which exhibited better performance than the vertex-based wavelet method. In both simulations and auditory experimental data analysis, the proposed L1-norm regularization method showed better source detection accuracy and less estimation errors than other two classic methods, i.e. weighted minimum norm (wMNE) and cortical low-resolution electromagnetic tomography (cLORETA). This study suggests that the L1-norm regularization method with the use of face-based wavelets is a promising tool for studying functional activations of the human brain.

  7. Sparse cortical source localization using spatio-temporal atoms.

    PubMed

    Korats, Gundars; Ranta, Radu; Le Cam, Steven; Louis-Dorr, Valérie

    2015-01-01

    This paper addresses the problem of sparse localization of cortical sources from scalp EEG recordings. Localization algorithms use propagation model under spatial and/or temporal constraints, but their performance highly depends on the data signal-to-noise ratio (SNR). In this work we propose a dictionary based sparse localization method which uses a data driven spatio-temporal dictionary to reconstruct the measurements using Single Best Replacement (SBR) and Continuation Single Best Replacement (CSBR) algorithms. We tested and compared our methods with the well-known MUSIC and RAP-MUSIC algorithms on simulated realistic data. Tests were carried out for different noise levels. The results show that our method has a strong advantage over MUSIC-type methods in case of synchronized sources. PMID:26737185

  8. Sparse cortical current density imaging in motor potentials induced by finger movement

    NASA Astrophysics Data System (ADS)

    Ding, Lei; Ni, Ying; Sweeney, John; He, Bin

    2011-06-01

    Predominant components in electro- or magneto-encephalography (EEG/MEG) are scalp projections of synchronized neuronal electrical activity distributed over cortical structures. Reconstruction of cortical sources underlying EEG/MEG can thus be achieved with the use of the cortical current density (CCD) model. We have developed a sparse electromagnetic source imaging method based on the CCD model, named as the variation-based cortical current density (VB-SCCD) algorithm, and have shown that it has much enhanced performance in reconstructing extended cortical sources in simulations (Ding 2009 Phys. Med. Biol. 54 2683-97). The present study aims to evaluate the performance of VB-SCCD, for the first time, using experimental data obtained from six participants. The results indicate that the VB-SCCD algorithm is able to successfully reveal spatially distributed cortical sources behind motor potentials induced by visually cued repetitive finger movements, and their dynamic patterns, with millisecond resolution. These findings of motor sources and cortical systems are supported by the physiological knowledge of motor control and evidence from various neuroimaging studies with similar experiments. Furthermore, our present results indicate the improvement of cortical source resolvability of VB-SCCD, as compared with two other classical algorithms. The proposed solver embedded in VB-SCCD is able to handle large-scale computational problems, which makes the use of high-density CCD models possible and, thus, reduces model misspecifications. The present results suggest that VB-SCCD provides high resolution source reconstruction capability and is a promising tool for studying complicated dynamic systems of brain activity for basic neuroscience and clinical neuropsychiatric research.

  9. Multiple sparse volumetric priors for distributed EEG source reconstruction.

    PubMed

    Strobbe, Gregor; van Mierlo, Pieter; De Vos, Maarten; Mijović, Bogdan; Hallez, Hans; Van Huffel, Sabine; López, José David; Vandenberghe, Stefaan

    2014-10-15

    We revisit the multiple sparse priors (MSP) algorithm implemented in the statistical parametric mapping software (SPM) for distributed EEG source reconstruction (Friston et al., 2008). In the present implementation, multiple cortical patches are introduced as source priors based on a dipole source space restricted to a cortical surface mesh. In this note, we present a technique to construct volumetric cortical regions to introduce as source priors by restricting the dipole source space to a segmented gray matter layer and using a region growing approach. This extension allows to reconstruct brain structures besides the cortical surface and facilitates the use of more realistic volumetric head models including more layers, such as cerebrospinal fluid (CSF), compared to the standard 3-layered scalp-skull-brain head models. We illustrated the technique with ERP data and anatomical MR images in 12 subjects. Based on the segmented gray matter for each of the subjects, cortical regions were created and introduced as source priors for MSP-inversion assuming two types of head models. The standard 3-layered scalp-skull-brain head models and extended 4-layered head models including CSF. We compared these models with the current implementation by assessing the free energy corresponding with each of the reconstructions using Bayesian model selection for group studies. Strong evidence was found in favor of the volumetric MSP approach compared to the MSP approach based on cortical patches for both types of head models. Overall, the strongest evidence was found in favor of the volumetric MSP reconstructions based on the extended head models including CSF. These results were verified by comparing the reconstructed activity. The use of volumetric cortical regions as source priors is a useful complement to the present implementation as it allows to introduce more complex head models and volumetric source priors in future studies.

  10. Distributed memory compiler design for sparse problems

    NASA Technical Reports Server (NTRS)

    Wu, Janet; Saltz, Joel; Berryman, Harry; Hiranandani, Seema

    1991-01-01

    A compiler and runtime support mechanism is described and demonstrated. The methods presented are capable of solving a wide range of sparse and unstructured problems in scientific computing. The compiler takes as input a FORTRAN 77 program enhanced with specifications for distributing data, and the compiler outputs a message passing program that runs on a distributed memory computer. The runtime support for this compiler is a library of primitives designed to efficiently support irregular patterns of distributed array accesses and irregular distributed array partitions. A variety of Intel iPSC/860 performance results obtained through the use of this compiler are presented.

  11. Statistical prediction with Kanerva's sparse distributed memory

    NASA Technical Reports Server (NTRS)

    Rogers, David

    1989-01-01

    A new viewpoint of the processing performed by Kanerva's sparse distributed memory (SDM) is presented. In conditions of near- or over-capacity, where the associative-memory behavior of the model breaks down, the processing performed by the model can be interpreted as that of a statistical predictor. Mathematical results are presented which serve as the framework for a new statistical viewpoint of sparse distributed memory and for which the standard formulation of SDM is a special case. This viewpoint suggests possible enhancements to the SDM model, including a procedure for improving the predictiveness of the system based on Holland's work with genetic algorithms, and a method for improving the capacity of SDM even when used as an associative memory.

  12. Notes on implementation of sparsely distributed memory

    NASA Technical Reports Server (NTRS)

    Keeler, J. D.; Denning, P. J.

    1986-01-01

    The Sparsely Distributed Memory (SDM) developed by Kanerva is an unconventional memory design with very interesting and desirable properties. The memory works in a manner that is closely related to modern theories of human memory. The SDM model is discussed in terms of its implementation in hardware. Two appendices discuss the unconventional approaches of the SDM: Appendix A treats a resistive circuit for fast, parallel address decoding; and Appendix B treats a systolic array for high throughput read and write operations.

  13. A view of Kanerva's sparse distributed memory

    NASA Technical Reports Server (NTRS)

    Denning, P. J.

    1986-01-01

    Pentti Kanerva is working on a new class of computers, which are called pattern computers. Pattern computers may close the gap between capabilities of biological organisms to recognize and act on patterns (visual, auditory, tactile, or olfactory) and capabilities of modern computers. Combinations of numeric, symbolic, and pattern computers may one day be capable of sustaining robots. The overview of the requirements for a pattern computer, a summary of Kanerva's Sparse Distributed Memory (SDM), and examples of tasks this computer can be expected to perform well are given.

  14. Integer sparse distributed memory: analysis and results.

    PubMed

    Snaider, Javier; Franklin, Stan; Strain, Steve; George, E Olusegun

    2013-10-01

    Sparse distributed memory is an auto-associative memory system that stores high dimensional Boolean vectors. Here we present an extension of the original SDM, the Integer SDM that uses modular arithmetic integer vectors rather than binary vectors. This extension preserves many of the desirable properties of the original SDM: auto-associativity, content addressability, distributed storage, and robustness over noisy inputs. In addition, it improves the representation capabilities of the memory and is more robust over normalization. It can also be extended to support forgetting and reliable sequence storage. We performed several simulations that test the noise robustness property and capacity of the memory. Theoretical analyses of the memory's fidelity and capacity are also presented. PMID:23747569

  15. Sparse distributed memory and related models

    NASA Technical Reports Server (NTRS)

    Kanerva, Pentti

    1992-01-01

    Described here is sparse distributed memory (SDM) as a neural-net associative memory. It is characterized by two weight matrices and by a large internal dimension - the number of hidden units is much larger than the number of input or output units. The first matrix, A, is fixed and possibly random, and the second matrix, C, is modifiable. The SDM is compared and contrasted to (1) computer memory, (2) correlation-matrix memory, (3) feet-forward artificial neural network, (4) cortex of the cerebellum, (5) Marr and Albus models of the cerebellum, and (6) Albus' cerebellar model arithmetic computer (CMAC). Several variations of the basic SDM design are discussed: the selected-coordinate and hyperplane designs of Jaeckel, the pseudorandom associative neural memory of Hassoun, and SDM with real-valued input variables by Prager and Fallside. SDM research conducted mainly at the Research Institute for Advanced Computer Science (RIACS) in 1986-1991 is highlighted.

  16. Sparse distributed memory: Principles and operation

    NASA Technical Reports Server (NTRS)

    Flynn, M. J.; Kanerva, P.; Bhadkamkar, N.

    1989-01-01

    Sparse distributed memory is a generalized random access memory (RAM) for long (1000 bit) binary words. Such words can be written into and read from the memory, and they can also be used to address the memory. The main attribute of the memory is sensitivity to similarity, meaning that a word can be read back not only by giving the original write address but also by giving one close to it as measured by the Hamming distance between addresses. Large memories of this kind are expected to have wide use in speech recognition and scene analysis, in signal detection and verification, and in adaptive control of automated equipment, in general, in dealing with real world information in real time. The memory can be realized as a simple, massively parallel computer. Digital technology has reached a point where building large memories is becoming practical. Major design issues were resolved which were faced in building the memories. The design is described of a prototype memory with 256 bit addresses and from 8 to 128 K locations for 256 bit words. A key aspect of the design is extensive use of dynamic RAM and other standard components.

  17. Sparse distributed memory prototype: Principles of operation

    NASA Technical Reports Server (NTRS)

    Flynn, Michael J.; Kanerva, Pentti; Ahanin, Bahram; Bhadkamkar, Neal; Flaherty, Paul; Hickey, Philip

    1988-01-01

    Sparse distributed memory is a generalized random access memory (RAM) for long binary words. Such words can be written into and read from the memory, and they can be used to address the memory. The main attribute of the memory is sensitivity to similarity, meaning that a word can be read back not only by giving the original right address but also by giving one close to it as measured by the Hamming distance between addresses. Large memories of this kind are expected to have wide use in speech and scene analysis, in signal detection and verification, and in adaptive control of automated equipment. The memory can be realized as a simple, massively parallel computer. Digital technology has reached a point where building large memories is becoming practical. The research is aimed at resolving major design issues that have to be faced in building the memories. The design of a prototype memory with 256-bit addresses and from 8K to 128K locations for 256-bit words is described. A key aspect of the design is extensive use of dynamic RAM and other standard components.

  18. Sparsey™: event recognition via deep hierarchical sparse distributed codes

    PubMed Central

    Rinkus, Gerard J.

    2014-01-01

    The visual cortex's hierarchical, multi-level organization is captured in many biologically inspired computational vision models, the general idea being that progressively larger scale (spatially/temporally) and more complex visual features are represented in progressively higher areas. However, most earlier models use localist representations (codes) in each representational field (which we equate with the cortical macrocolumn, “mac”), at each level. In localism, each represented feature/concept/event (hereinafter “item”) is coded by a single unit. The model we describe, Sparsey, is hierarchical as well but crucially, it uses sparse distributed coding (SDC) in every mac in all levels. In SDC, each represented item is coded by a small subset of the mac's units. The SDCs of different items can overlap and the size of overlap between items can be used to represent their similarity. The difference between localism and SDC is crucial because SDC allows the two essential operations of associative memory, storing a new item and retrieving the best-matching stored item, to be done in fixed time for the life of the model. Since the model's core algorithm, which does both storage and retrieval (inference), makes a single pass over all macs on each time step, the overall model's storage/retrieval operation is also fixed-time, a criterion we consider essential for scalability to the huge (“Big Data”) problems. A 2010 paper described a nonhierarchical version of this model in the context of purely spatial pattern processing. Here, we elaborate a fully hierarchical model (arbitrary numbers of levels and macs per level), describing novel model principles like progressive critical periods, dynamic modulation of principal cells' activation functions based on a mac-level familiarity measure, representation of multiple simultaneously active hypotheses, a novel method of time warp invariant recognition, and we report results showing learning/recognition of spatiotemporal

  19. BIRD: A general interface for sparse distributed memory simulators

    NASA Technical Reports Server (NTRS)

    Rogers, David

    1990-01-01

    Kanerva's sparse distributed memory (SDM) has now been implemented for at least six different computers, including SUN3 workstations, the Apple Macintosh, and the Connection Machine. A common interface for input of commands would both aid testing of programs on a broad range of computer architectures and assist users in transferring results from research environments to applications. A common interface also allows secondary programs to generate command sequences for a sparse distributed memory, which may then be executed on the appropriate hardware. The BIRD program is an attempt to create such an interface. Simplifying access to different simulators should assist developers in finding appropriate uses for SDM.

  20. Two demonstrators and a simulator for a sparse, distributed memory

    NASA Technical Reports Server (NTRS)

    Brown, Robert L.

    1987-01-01

    Described are two programs demonstrating different aspects of Kanerva's Sparse, Distributed Memory (SDM). These programs run on Sun 3 workstations, one using color, and have straightforward graphically oriented user interfaces and graphical output. Presented are descriptions of the programs, how to use them, and what they show. Additionally, this paper describes the software simulator behind each program.

  1. Kanerva's sparse distributed memory with multiple hamming thresholds

    NASA Technical Reports Server (NTRS)

    Pohja, Seppo; Kaski, Kimmo

    1992-01-01

    If the stored input patterns of Kanerva's Sparse Distributed Memory (SDM) are highly correlated, utilization of the storage capacity is very low compared to the case of uniformly distributed random input patterns. We consider a variation of SDM that has a better storage capacity utilization for correlated input patterns. This approach uses a separate selection threshold for each physical storage address or hard location. The selection of the hard locations for reading or writing can be done in parallel of which SDM implementations can benefit.

  2. Comparison of spike parameters from optically identified GABAergic and glutamatergic neurons in sparse cortical cultures

    PubMed Central

    Weir, Keiko; Blanquie, Oriane; Kilb, Werner; Luhmann, Heiko J.; Sinning, Anne

    2015-01-01

    Primary neuronal cultures share many typical features with the in vivo situation, including similarities in distinct electrical activity patterns and synaptic network interactions. Here, we use multi-electrode array (MEA) recordings from spontaneously active cultures of wildtype and glutamic acid decarboxylase 67 (GAD67)-green fluorescent protein (GFP) transgenic mice to evaluate which spike parameters differ between GABAergic interneurons and principal, putatively glutamatergic neurons. To analyze this question we combine MEA recordings with optical imaging in sparse cortical cultures to assign individual spikes to visually-identified single neurons. In our culture system, excitatory and inhibitory neurons are present at a similar ratio as described in vivo, and spike waveform characteristics and firing patterns are fully developed after 2 weeks in vitro. Spike amplitude, but not other spike waveform parameters, correlated with the distance between the recording electrode and the location of the assigned neuron’s soma. Cluster analysis of spike waveform properties revealed no particular cell population that may be assigned to putative inhibitory or excitatory neurons. Moreover, experiments in primary cultures from transgenic GAD67-GFP mice, which allow optical identification of GABAergic interneurons and thus unambiguous assignment of extracellular signals, did not reveal any significant difference in spike timing and spike waveform parameters between inhibitory and excitatory neurons. Despite of our detailed characterization of spike waveform and temporal spiking properties we could not identify an unequivocal electrical parameter to discriminate between individual excitatory and inhibitory neurons in vitro. Our data suggest that under in vitro conditions cellular classifications of single neurons on the basis of their extracellular firing properties should be treated with caution. PMID:25642167

  3. Multiple peaks of species abundance distributions induced by sparse interactions.

    PubMed

    Obuchi, Tomoyuki; Kabashima, Yoshiyuki; Tokita, Kei

    2016-08-01

    We investigate the replicator dynamics with "sparse" symmetric interactions which represent specialist-specialist interactions in ecological communities. By considering a large self-interaction u, we conduct a perturbative expansion which manifests that the nature of the interactions has a direct impact on the species abundance distribution. The central results are all species coexistence in a realistic range of the model parameters and that a certain discrete nature of the interactions induces multiple peaks in the species abundance distribution, providing the possibility of theoretically explaining multiple peaks observed in various field studies. To get more quantitative information, we also construct a non-perturbative theory which becomes exact on tree-like networks if all the species coexist, providing exact critical values of u below which extinct species emerge. Numerical simulations in various different situations are conducted and they clarify the robustness of the presented mechanism of all species coexistence and multiple peaks in the species abundance distributions. PMID:27627322

  4. Multiple peaks of species abundance distributions induced by sparse interactions

    NASA Astrophysics Data System (ADS)

    Obuchi, Tomoyuki; Kabashima, Yoshiyuki; Tokita, Kei

    2016-08-01

    We investigate the replicator dynamics with "sparse" symmetric interactions which represent specialist-specialist interactions in ecological communities. By considering a large self-interaction u , we conduct a perturbative expansion which manifests that the nature of the interactions has a direct impact on the species abundance distribution. The central results are all species coexistence in a realistic range of the model parameters and that a certain discrete nature of the interactions induces multiple peaks in the species abundance distribution, providing the possibility of theoretically explaining multiple peaks observed in various field studies. To get more quantitative information, we also construct a non-perturbative theory which becomes exact on tree-like networks if all the species coexist, providing exact critical values of u below which extinct species emerge. Numerical simulations in various different situations are conducted and they clarify the robustness of the presented mechanism of all species coexistence and multiple peaks in the species abundance distributions.

  5. Synaptic and Network Mechanisms of Sparse and Reliable Visual Cortical Activity during Nonclassical Receptive Field Stimulation

    PubMed Central

    Haider, Bilal; Krause, Matthew R.; Duque, Alvaro; Yu, Yuguo; Touryan, Jonathan; Mazer, James A.; McCormick, David A.

    2011-01-01

    SUMMARY During natural vision, the entire visual field is stimulated by images rich in spatiotemporal structure. Although many visual system studies restrict stimuli to the classical receptive field (CRF), it is known that costimulation of the CRF and the surrounding nonclassical receptive field (nCRF) increases neuronal response sparseness. The cellular and network mechanisms underlying increased response sparseness remain largely unexplored. Here we show that combined CRF + nCRF stimulation increases the sparseness, reliability, and precision of spiking and membrane potential responses in classical regular spiking (RSC) pyramidal neurons of cat primary visual cortex. Conversely, fast-spiking interneurons exhibit increased activity and decreased selectivity during CRF + nCRF stimulation. The increased sparseness and reliability of RSC neuron spiking is associated with increased inhibitory barrages and narrower visually evoked synaptic potentials. Our experimental observations were replicated with a simple computational model, suggesting that network interactions among neuronal subtypes ultimately sharpen recurrent excitation, producing specific and reliable visual responses. PMID:20152117

  6. An alternative design for a sparse distributed memory

    NASA Technical Reports Server (NTRS)

    Jaeckel, Louis A.

    1989-01-01

    A new design for a Sparse Distributed Memory, called the selected-coordinate design, is described. As in the original design, there are a large number of memory locations, each of which may be activated by many different addresses (binary vectors) in a very large address space. Each memory location is defined by specifying ten selected coordinates (bit positions in the address vectors) and a set of corresponding assigned values, consisting of one bit for each selected coordinate. A memory location is activated by an address if, for all ten of the locations's selected coordinates, the corresponding bits in the address vector match the respective assigned value bits, regardless of the other bits in the address vector. Some comparative memory capacity and signal-to-noise ratio estimates for the both the new and original designs are given. A few possible hardware embodiments of the new design are described.

  7. Distributed dictionary learning for sparse representation in sensor networks.

    PubMed

    Liang, Junli; Zhang, Miaohua; Zeng, Xianyu; Yu, Guoyang

    2014-06-01

    This paper develops a distributed dictionary learning algorithm for sparse representation of the data distributed across nodes of sensor networks, where the sensitive or private data are stored or there is no fusion center or there exists a big data application. The main contributions of this paper are: 1) we decouple the combined dictionary atom update and nonzero coefficient revision procedure into two-stage operations to facilitate distributed computations, first updating the dictionary atom in terms of the eigenvalue decomposition of the sum of the residual (correlation) matrices across the nodes then implementing a local projection operation to obtain the related representation coefficients for each node; 2) we cast the aforementioned atom update problem as a set of decentralized optimization subproblems with consensus constraints. Then, we simplify the multiplier update for the symmetry undirected graphs in sensor networks and minimize the separable subproblems to attain the consistent estimates iteratively; and 3) dictionary atoms are typically constrained to be of unit norm in order to avoid the scaling ambiguity. We efficiently solve the resultant hidden convex subproblems by determining the optimal Lagrange multiplier. Some experiments are given to show that the proposed algorithm is an alternative distributed dictionary learning approach, and is suitable for the sensor network environment. PMID:24733009

  8. Distributed dictionary learning for sparse representation in sensor networks.

    PubMed

    Liang, Junli; Zhang, Miaohua; Zeng, Xianyu; Yu, Guoyang

    2014-06-01

    This paper develops a distributed dictionary learning algorithm for sparse representation of the data distributed across nodes of sensor networks, where the sensitive or private data are stored or there is no fusion center or there exists a big data application. The main contributions of this paper are: 1) we decouple the combined dictionary atom update and nonzero coefficient revision procedure into two-stage operations to facilitate distributed computations, first updating the dictionary atom in terms of the eigenvalue decomposition of the sum of the residual (correlation) matrices across the nodes then implementing a local projection operation to obtain the related representation coefficients for each node; 2) we cast the aforementioned atom update problem as a set of decentralized optimization subproblems with consensus constraints. Then, we simplify the multiplier update for the symmetry undirected graphs in sensor networks and minimize the separable subproblems to attain the consistent estimates iteratively; and 3) dictionary atoms are typically constrained to be of unit norm in order to avoid the scaling ambiguity. We efficiently solve the resultant hidden convex subproblems by determining the optimal Lagrange multiplier. Some experiments are given to show that the proposed algorithm is an alternative distributed dictionary learning approach, and is suitable for the sensor network environment.

  9. Kanerva's sparse distributed memory: An associative memory algorithm well-suited to the Connection Machine

    NASA Technical Reports Server (NTRS)

    Rogers, David

    1988-01-01

    The advent of the Connection Machine profoundly changes the world of supercomputers. The highly nontraditional architecture makes possible the exploration of algorithms that were impractical for standard Von Neumann architectures. Sparse distributed memory (SDM) is an example of such an algorithm. Sparse distributed memory is a particularly simple and elegant formulation for an associative memory. The foundations for sparse distributed memory are described, and some simple examples of using the memory are presented. The relationship of sparse distributed memory to three important computational systems is shown: random-access memory, neural networks, and the cerebellum of the brain. Finally, the implementation of the algorithm for sparse distributed memory on the Connection Machine is discussed.

  10. Learning signaling network structures with sparsely distributed data.

    PubMed

    Sachs, Karen; Itani, Solomon; Carlisle, Jennifer; Nolan, Garry P; Pe'er, Dana; Lauffenburger, Douglas A

    2009-02-01

    Flow cytometric measurement of signaling protein abundances has proved particularly useful for elucidation of signaling pathway structure. The single cell nature of the data ensures a very large dataset size, providing a statistically robust dataset for structure learning. Moreover, the approach is easily scaled to many conditions in high throughput. However, the technology suffers from a dimensionality constraint: at the cutting edge, only about 12 protein species can be measured per cell, far from sufficient for most signaling pathways. Because the structure learning algorithm (in practice) requires that all variables be measured together simultaneously, this restricts structure learning to the number of variables that constitute the flow cytometer's upper dimensionality limit. To address this problem, we present here an algorithm that enables structure learning for sparsely distributed data, allowing structure learning beyond the measurement technology's upper dimensionality limit for simultaneously measurable variables. The algorithm assesses pairwise (or n-wise) dependencies, constructs "Markov neighborhoods" for each variable based on these dependencies, measures each variable in the context of its neighborhood, and performs structure learning using a constrained search.

  11. SuperLU{_}DIST: A scalable distributed-memory sparse direct solver for unsymmetric linear systems

    SciTech Connect

    Li, Xiaoye S.; Demmel, James W.

    2002-03-27

    In this paper, we present the main algorithmic features in the software package SuperLU{_}DIST, a distributed-memory sparse direct solver for large sets of linear equations. We give in detail our parallelization strategies, with focus on scalability issues, and demonstrate the parallel performance and scalability on current machines. The solver is based on sparse Gaussian elimination, with an innovative static pivoting strategy proposed earlier by the authors. The main advantage of static pivoting over classical partial pivoting is that it permits a priori determination of data structures and communication pattern for sparse Gaussian elimination, which makes it more scalable on distributed memory machines. Based on this a priori knowledge, we designed highly parallel and scalable algorithms for both LU decomposition and triangular solve and we show that they are suitable for large-scale distributed memory machines.

  12. The application of a sparse, distributed memory to the detection, identification and manipulation of physical objects

    NASA Technical Reports Server (NTRS)

    Kanerva, P.

    1986-01-01

    To determine the relation of the sparse, distributed memory to other architectures, a broad review of the literature was made. The memory is called a pattern memory because they work with large patterns of features (high-dimensional vectors). A pattern is stored in a pattern memory by distributing it over a large number of storage elements and by superimposing it over other stored patterns. A pattern is retrieved by mathematical or statistical reconstruction from the distributed elements. Three pattern memories are discussed.

  13. An empirical investigation of sparse distributed memory using discrete speech recognition

    NASA Technical Reports Server (NTRS)

    Danforth, Douglas G.

    1990-01-01

    Presented here is a step by step analysis of how the basic Sparse Distributed Memory (SDM) model can be modified to enhance its generalization capabilities for classification tasks. Data is taken from speech generated by a single talker. Experiments are used to investigate the theory of associative memories and the question of generalization from specific instances.

  14. Kriging for interpolation of sparse and irregularly distributed geologic data

    SciTech Connect

    Campbell, K.

    1986-12-31

    For many geologic problems, subsurface observations are available only from a small number of irregularly distributed locations, for example from a handful of drill holes in the region of interest. These observations will be interpolated one way or another, for example by hand-drawn stratigraphic cross-sections, by trend-fitting techniques, or by simple averaging which ignores spatial correlation. In this paper we consider an interpolation technique for such situations which provides, in addition to point estimates, the error estimates which are lacking from other ad hoc methods. The proposed estimator is like a kriging estimator in form, but because direct estimation of the spatial covariance function is not possible the parameters of the estimator are selected by cross-validation. Its use in estimating subsurface stratigraphy at a candidate site for geologic waste repository provides an example.

  15. Learning to read aloud: A neural network approach using sparse distributed memory

    NASA Technical Reports Server (NTRS)

    Joglekar, Umesh Dwarkanath

    1989-01-01

    An attempt to solve a problem of text-to-phoneme mapping is described which does not appear amenable to solution by use of standard algorithmic procedures. Experiments based on a model of distributed processing are also described. This model (sparse distributed memory (SDM)) can be used in an iterative supervised learning mode to solve the problem. Additional improvements aimed at obtaining better performance are suggested.

  16. Two alternate proofs of Wang's lune formula for sparse distributed memory and an integral approximation

    NASA Technical Reports Server (NTRS)

    Jaeckel, Louis A.

    1988-01-01

    In Kanerva's Sparse Distributed Memory, writing to and reading from the memory are done in relation to spheres in an n-dimensional binary vector space. Thus it is important to know how many points are in the intersection of two spheres in this space. Two proofs are given of Wang's formula for spheres of unequal radii, and an integral approximation for the intersection in this case.

  17. Analysis, tuning and comparison of two general sparse solvers for distributed memory computers

    SciTech Connect

    Amestoy, P.R.; Duff, I.S.; L'Excellent, J.-Y.; Li, X.S.

    2000-06-30

    We describe the work performed in the context of a Franco-Berkeley funded project between NERSC-LBNL located in Berkeley (USA) and CERFACS-ENSEEIHT located in Toulouse (France). We discuss both the tuning and performance analysis of two distributed memory sparse solvers (superlu from Berkeley and mumps from Toulouse) on the 512 processor Cray T3E from NERSC (Lawrence Berkeley National Laboratory). This project gave us the opportunity to improve the algorithms and add new features to the codes. We then quite extensively analyze and compare the two approaches on a set of large problems from real applications. We further explain the main differences in the behavior of the approaches on artificial regular grid problems. As a conclusion to this activity report, we mention a set of parallel sparse solvers on which this type of study should be extended.

  18. Distribution of cortical neurons projecting to dorsal column nuclear complex and spinal cord in the hedgehog tenrec, Echinops telfairi.

    PubMed

    Künzle, H; Rehkämper, G

    1992-01-01

    Using retrograde axonal flow and wheatgerm agglutinin conjugated to horseradish peroxidase, we studied the distribution of cortical neurons giving rise to spinal and dorsal column nuclear projections, and correlated the regions involved in the projections with the cytoarchitectonic areas recently identified in the lesser hedgehog tenrec, Echinops telfairi (Insectivora). Labeled cortical neurons were most numerous following injections of tracer into higher cervical segments, whereas almost none were found following thoracic injections. The cortical labeling appeared more prominent ipsilaterally than contralaterally after spinal injections, although it was more prominent on the contralateral side after injection into the dorsal column nuclear complex. The majority of labeled neurons found in lamina V occupied the neocortex adjacent to the interhemispheric fissure along the rostrocaudal extent of the small corpus callosum. This location corresponded to an intermediate rostrocaudal portion of the hemisphere, and particularly to area 2 of Rehkämper. In some cases, adjacent portions of areas 1 and 3 were also involved, as well as neocortical regions of the lateral hemisphere. The present data did not suggest a somatotopic organization of the projections; likewise, evidence for the presence of more than one somatosensorimotor representation was sparse.

  19. Performance analysis of distributed symmetric sparse matrix vector multiplication algorithm for multi-core architectures

    SciTech Connect

    Oryspayev, Dossay; Aktulga, Hasan Metin; Sosonkina, Masha; Maris, Pieter; Vary, James P.

    2015-07-14

    In this article, sparse matrix vector multiply (SpMVM) is an important kernel that frequently arises in high performance computing applications. Due to its low arithmetic intensity, several approaches have been proposed in literature to improve its scalability and efficiency in large scale computations. In this paper, our target systems are high end multi-core architectures and we use messaging passing interface + open multiprocessing hybrid programming model for parallelism. We analyze the performance of recently proposed implementation of the distributed symmetric SpMVM, originally developed for large sparse symmetric matrices arising in ab initio nuclear structure calculations. We also study important features of this implementation and compare with previously reported implementations that do not exploit underlying symmetry. Our SpMVM implementations leverage the hybrid paradigm to efficiently overlap expensive communications with computations. Our main comparison criterion is the "CPU core hours" metric, which is the main measure of resource usage on supercomputers. We analyze the effects of topology-aware mapping heuristic using simplified network load model. Furthermore, we have tested the different SpMVM implementations on two large clusters with 3D Torus and Dragonfly topology. Our results show that the distributed SpMVM implementation that exploits matrix symmetry and hides communication yields the best value for the "CPU core hours" metric and significantly reduces data movement overheads.

  20. Performance analysis of distributed symmetric sparse matrix vector multiplication algorithm for multi-core architectures

    DOE PAGES

    Oryspayev, Dossay; Aktulga, Hasan Metin; Sosonkina, Masha; Maris, Pieter; Vary, James P.

    2015-07-14

    In this article, sparse matrix vector multiply (SpMVM) is an important kernel that frequently arises in high performance computing applications. Due to its low arithmetic intensity, several approaches have been proposed in literature to improve its scalability and efficiency in large scale computations. In this paper, our target systems are high end multi-core architectures and we use messaging passing interface + open multiprocessing hybrid programming model for parallelism. We analyze the performance of recently proposed implementation of the distributed symmetric SpMVM, originally developed for large sparse symmetric matrices arising in ab initio nuclear structure calculations. We also study important featuresmore » of this implementation and compare with previously reported implementations that do not exploit underlying symmetry. Our SpMVM implementations leverage the hybrid paradigm to efficiently overlap expensive communications with computations. Our main comparison criterion is the "CPU core hours" metric, which is the main measure of resource usage on supercomputers. We analyze the effects of topology-aware mapping heuristic using simplified network load model. Furthermore, we have tested the different SpMVM implementations on two large clusters with 3D Torus and Dragonfly topology. Our results show that the distributed SpMVM implementation that exploits matrix symmetry and hides communication yields the best value for the "CPU core hours" metric and significantly reduces data movement overheads.« less

  1. DOA Estimation of Coherently Distributed Sources Based on Block-Sparse Constraint

    NASA Astrophysics Data System (ADS)

    Gan, Lu; Wang, Xiao Qing; Liao, Hong Shu

    In this letter, a new method is proposed to solve the direction-of-arrivals (DOAs) estimation problem of coherently distributed sources based on the block-sparse signal model of compressed sensing (CS) and the convex optimization theory. We make use of a certain number of point sources and the CS array architecture to establish the compressive version of the discrete model of coherently distributed sources. The central DOA and the angular spread can be estimated simultaneously by solving a convex optimization problem which employs a joint norm constraint. As a result we can avoid the two-dimensional search used in conventional algorithms. Furthermore, the multiple-measurement-vectors (MMV) scenario is also considered to achieve robust estimation. The effectiveness of our method is confirmed by simulation results.

  2. Human gait recognition using patch distribution feature and locality-constrained group sparse representation.

    PubMed

    Xu, Dong; Huang, Yi; Zeng, Zinan; Xu, Xinxing

    2012-01-01

    In this paper, we propose a new patch distribution feature (PDF) (i.e., referred to as Gabor-PDF) for human gait recognition. We represent each gait energy image (GEI) as a set of local augmented Gabor features, which concatenate the Gabor features extracted from different scales and different orientations together with the X-Y coordinates. We learn a global Gaussian mixture model (GMM) (i.e., referred to as the universal background model) with the local augmented Gabor features from all the gallery GEIs; then, each gallery or probe GEI is further expressed as the normalized parameters of an image-specific GMM adapted from the global GMM. Observing that one video is naturally represented as a group of GEIs, we also propose a new classification method called locality-constrained group sparse representation (LGSR) to classify each probe video by minimizing the weighted l(1, 2) mixed-norm-regularized reconstruction error with respect to the gallery videos. In contrast to the standard group sparse representation method that is a special case of LGSR, the group sparsity and local smooth sparsity constraints are both enforced in LGSR. Our comprehensive experiments on the benchmark USF HumanID database demonstrate the effectiveness of the newly proposed feature Gabor-PDF and the new classification method LGSR for human gait recognition. Moreover, LGSR using the new feature Gabor-PDF achieves the best average Rank-1 and Rank-5 recognition rates on this database among all gait recognition algorithms proposed to date.

  3. Comparison between sparsely distributed memory and Hopfield-type neural network models

    NASA Technical Reports Server (NTRS)

    Keeler, James D.

    1986-01-01

    The Sparsely Distributed Memory (SDM) model (Kanerva, 1984) is compared to Hopfield-type neural-network models. A mathematical framework for comparing the two is developed, and the capacity of each model is investigated. The capacity of the SDM can be increased independently of the dimension of the stored vectors, whereas the Hopfield capacity is limited to a fraction of this dimension. However, the total number of stored bits per matrix element is the same in the two models, as well as for extended models with higher order interactions. The models are also compared in their ability to store sequences of patterns. The SDM is extended to include time delays so that contextual information can be used to cover sequences. Finally, it is shown how a generalization of the SDM allows storage of correlated input pattern vectors.

  4. Using data tagging to improve the performance of Kanerva's sparse distributed memory

    NASA Technical Reports Server (NTRS)

    Rogers, David

    1988-01-01

    The standard formulation of Kanerva's sparse distributed memory (SDM) involves the selection of a large number of data storage locations, followed by averaging the data contained in those locations to reconstruct the stored data. A variant of this model is discussed, in which the predominant pattern is the focus of reconstruction. First, one architecture is proposed which returns the predominant pattern rather than the average pattern. However, this model will require too much storage for most uses. Next, a hybrid model is proposed, called tagged SDM, which approximates the results of the predominant pattern machine, but is nearly as efficient as Kanerva's original formulation. Finally, some experimental results are shown which confirm that significant improvements in the recall capability of SDM can be achieved using the tagged architecture.

  5. Sparse distributed memory: understanding the speed and robustness of expert memory

    PubMed Central

    Brogliato, Marcelo S.; Chada, Daniel M.; Linhares, Alexandre

    2014-01-01

    How can experts, sometimes in exacting detail, almost immediately and very precisely recall memory items from a vast repertoire? The problem in which we will be interested concerns models of theoretical neuroscience that could explain the speed and robustness of an expert's recollection. The approach is based on Sparse Distributed Memory, which has been shown to be plausible, both in a neuroscientific and in a psychological manner, in a number of ways. A crucial characteristic concerns the limits of human recollection, the “tip-of-tongue” memory event—which is found at a non-linearity in the model. We expand the theoretical framework, deriving an optimization formula to solve this non-linearity. Numerical results demonstrate how the higher frequency of rehearsal, through work or study, immediately increases the robustness and speed associated with expert memory. PMID:24808842

  6. Effective Suppression of Pathological Synchronization in Cortical Networks by Highly Heterogeneous Distribution of Inhibitory Connections

    PubMed Central

    Kada, Hisashi; Teramae, Jun-Nosuke; Tokuda, Isao T.

    2016-01-01

    Even without external random input, cortical networks in vivo sustain asynchronous irregular firing with low firing rate. In addition to detailed balance between excitatory and inhibitory activities, recent theoretical studies have revealed that another feature commonly observed in cortical networks, i.e., long-tailed distribution of excitatory synapses implying coexistence of many weak and a few extremely strong excitatory synapses, plays an essential role in realizing the self-sustained activity in recurrent networks of biologically plausible spiking neurons. The previous studies, however, have not considered highly non-random features of the synaptic connectivity, namely, bidirectional connections between cortical neurons are more common than expected by chance and strengths of synapses are positively correlated between pre- and postsynaptic neurons. The positive correlation of synaptic connections may destabilize asynchronous activity of networks with the long-tailed synaptic distribution and induce pathological synchronized firing among neurons. It remains unclear how the cortical network avoids such pathological synchronization. Here, we demonstrate that introduction of the correlated connections indeed gives rise to synchronized firings in a cortical network model with the long-tailed distribution. By using a simplified feed-forward network model of spiking neurons, we clarify the underlying mechanism of the synchronization. We then show that the synchronization can be efficiently suppressed by highly heterogeneous distribution, typically a lognormal distribution, of inhibitory-to-excitatory connection strengths in a recurrent network model of cortical neurons. PMID:27803659

  7. Sparse regression analysis of task-relevant information distribution in the brain

    NASA Astrophysics Data System (ADS)

    Rish, Irina; Cecchi, Guillermo A.; Heuton, Kyle; Baliki, Marwan N.; Apkarian, A. Vania

    2012-02-01

    One of key topics in fMRI analysis is discovery of task-related brain areas. We focus on predictive accuracy as a better relevance measure than traditional univariate voxel activations that miss important multivariate voxel interactions. We use sparse regression (more specifically, the Elastic Net1) to learn predictive models simultaneously with selection of predictive voxel subsets, and to explore transition from task-relevant to task-irrelevant areas. Exploring the space of sparse solutions reveals a much wider spread of task-relevant information in the brain than it is typically suggested by univariate correlations. This happens for several tasks we considered, and is most noticeable in case of complex tasks such as pain rating; however, for certain simpler tasks, a clear separation between a small subset of relevant voxels and the rest of the brain is observed even with multivariate approach to measuring relevance.

  8. Sequence Prediction With Sparse Distributed Hyperdimensional Coding Applied to the Analysis of Mobile Phone Use Patterns.

    PubMed

    Rasanen, Okko J; Saarinen, Jukka P

    2016-09-01

    Modeling and prediction of temporal sequences is central to many signal processing and machine learning applications. Prediction based on sequence history is typically performed using parametric models, such as fixed-order Markov chains ( n -grams), approximations of high-order Markov processes, such as mixed-order Markov models or mixtures of lagged bigram models, or with other machine learning techniques. This paper presents a method for sequence prediction based on sparse hyperdimensional coding of the sequence structure and describes how higher order temporal structures can be utilized in sparse coding in a balanced manner. The method is purely incremental, allowing real-time online learning and prediction with limited computational resources. Experiments with prediction of mobile phone use patterns, including the prediction of the next launched application, the next GPS location of the user, and the next artist played with the phone media player, reveal that the proposed method is able to capture the relevant variable-order structure from the sequences. In comparison with the n -grams and the mixed-order Markov models, the sparse hyperdimensional predictor clearly outperforms its peers in terms of unweighted average recall and achieves an equal level of weighted average recall as the mixed-order Markov chain but without the batch training of the mixed-order model.

  9. Improved mapping of information distribution across the cortical surface with the Support Vector Machine

    PubMed Central

    Xiao, Youping; Rao, Ravi; Cecchi, Guillermo; Kaplan, Ehud

    2008-01-01

    The early visual cortices represent information of several stimulus attributes, such as orientation and color. To understand the coding mechanisms of these attributes in the brain, and the functional organization of the early visual cortices, it is necessary to determine whether different attributes are represented by different compartments within each cortex. Previous studies addressing this question have focused on the information encoded by the response amplitude of individual neurons or cortical columns, and have reached conflicting conclusions. Given the correlated variability in response amplitude across neighboring columns, it is likely that the spatial pattern of responses across these columns encodes the attribute information more reliably than the response amplitude does. Here we present a new method of mapping the spatial distribution of information that is encoded by both the response amplitude and spatial pattern. This new method is based on a statistical learning approach, the Support Vector Machine (SVM). Application of this new method to our optical imaging data suggests that information about stimulus orientation and color are distributed differently in the striate cortex, and this observation is consistent with the hypothesis of segregated representations of orientation and color in this area. We also demonstrate that SVM can be used to extract ‘single-condition’ activation maps from noisy images of intrinsic optical signals. PMID:18249089

  10. Spatially Sparse, Temporally Smooth MEG Via Vector ℓ0 .

    PubMed

    Cassidy, Ben; Solo, Victor

    2015-06-01

    In this paper, we describe a new method for solving the magnetoencephalography inverse problem: temporal vector ℓ0-penalized least squares (TV-L0LS). The method calculates maximally sparse current dipole magnitudes and directions via spatial ℓ0 regularization on a cortically-distributed source grid, while constraining the solution to be smooth with respect to time. We demonstrate the utility of this method on real and simulated data by comparison to existing methods.

  11. Asteroids' physical models from combined dense and sparse photometry and scaling of the YORP effect by the observed obliquity distribution

    NASA Astrophysics Data System (ADS)

    Hanuš, J.; Ďurech, J.; Brož, M.; Marciniak, A.; Warner, B. D.; Pilcher, F.; Stephens, R.; Behrend, R.; Carry, B.; Čapek, D.; Antonini, P.; Audejean, M.; Augustesen, K.; Barbotin, E.; Baudouin, P.; Bayol, A.; Bernasconi, L.; Borczyk, W.; Bosch, J.-G.; Brochard, E.; Brunetto, L.; Casulli, S.; Cazenave, A.; Charbonnel, S.; Christophe, B.; Colas, F.; Coloma, J.; Conjat, M.; Cooney, W.; Correira, H.; Cotrez, V.; Coupier, A.; Crippa, R.; Cristofanelli, M.; Dalmas, Ch.; Danavaro, C.; Demeautis, C.; Droege, T.; Durkee, R.; Esseiva, N.; Esteban, M.; Fagas, M.; Farroni, G.; Fauvaud, M.; Fauvaud, S.; Del Freo, F.; Garcia, L.; Geier, S.; Godon, C.; Grangeon, K.; Hamanowa, H.; Hamanowa, H.; Heck, N.; Hellmich, S.; Higgins, D.; Hirsch, R.; Husarik, M.; Itkonen, T.; Jade, O.; Kamiński, K.; Kankiewicz, P.; Klotz, A.; Koff, R. A.; Kryszczyńska, A.; Kwiatkowski, T.; Laffont, A.; Leroy, A.; Lecacheux, J.; Leonie, Y.; Leyrat, C.; Manzini, F.; Martin, A.; Masi, G.; Matter, D.; Michałowski, J.; Michałowski, M. J.; Michałowski, T.; Michelet, J.; Michelsen, R.; Morelle, E.; Mottola, S.; Naves, R.; Nomen, J.; Oey, J.; Ogłoza, W.; Oksanen, A.; Oszkiewicz, D.; Pääkkönen, P.; Paiella, M.; Pallares, H.; Paulo, J.; Pavic, M.; Payet, B.; Polińska, M.; Polishook, D.; Poncy, R.; Revaz, Y.; Rinner, C.; Rocca, M.; Roche, A.; Romeuf, D.; Roy, R.; Saguin, H.; Salom, P. A.; Sanchez, S.; Santacana, G.; Santana-Ros, T.; Sareyan, J.-P.; Sobkowiak, K.; Sposetti, S.; Starkey, D.; Stoss, R.; Strajnic, J.; Teng, J.-P.; Trégon, B.; Vagnozzi, A.; Velichko, F. P.; Waelchli, N.; Wagrez, K.; Wücher, H.

    2013-03-01

    Context. The larger number of models of asteroid shapes and their rotational states derived by the lightcurve inversion give us better insight into both the nature of individual objects and the whole asteroid population. With a larger statistical sample we can study the physical properties of asteroid populations, such as main-belt asteroids or individual asteroid families, in more detail. Shape models can also be used in combination with other types of observational data (IR, adaptive optics images, stellar occultations), e.g., to determine sizes and thermal properties. Aims: We use all available photometric data of asteroids to derive their physical models by the lightcurve inversion method and compare the observed pole latitude distributions of all asteroids with known convex shape models with the simulated pole latitude distributions. Methods: We used classical dense photometric lightcurves from several sources (Uppsala Asteroid Photometric Catalogue, Palomar Transient Factory survey, and from individual observers) and sparse-in-time photometry from the U.S. Naval Observatory in Flagstaff, Catalina Sky Survey, and La Palma surveys (IAU codes 689, 703, 950) in the lightcurve inversion method to determine asteroid convex models and their rotational states. We also extended a simple dynamical model for the spin evolution of asteroids used in our previous paper. Results: We present 119 new asteroid models derived from combined dense and sparse-in-time photometry. We discuss the reliability of asteroid shape models derived only from Catalina Sky Survey data (IAU code 703) and present 20 such models. By using different values for a scaling parameter cYORP (corresponds to the magnitude of the YORP momentum) in the dynamical model for the spin evolution and by comparing synthetic and observed pole-latitude distributions, we were able to constrain the typical values of the cYORP parameter as between 0.05 and 0.6. Table 3 is available in electronic form at http://www.aanda.org

  12. Parallelizing iterative solvers for sparse systems of equations and eigenproblems on distributed-memory machines

    SciTech Connect

    Basermann, A.

    1994-12-31

    For the solution of discretized ordinary or partial differential equations it is necessary to solve systems of equations or eigenproblems with coefficient matrices of different sparsity pattern, depending on the discretization method; using the finite element method (FE) results in largely unstructured systems of equations. Sparse eigenproblems play particularly important roles in the analysis of elastic solids and structures. In the corresponding FE models, the natural frequencies and mode shapes of free vibration are determined as are buckling loads and modes. Another class of problems is related to stability analysis, e.g. of electrical networks. Moreover, approximations of extreme eigenvalues are useful for solving sets of linear equations, e.g. for determining condition numbers of symmetric positive definite matrices or for conjugate gradients methods with polynomial preconditioning. Iterative methods for solving linear systems and eigenproblems mainly consist of matrix-vector products and vector-vector operations; the main work in each iteration is usually the computation of matrix-vector products. Therein, accessing the vector is determined by the sparsity pattern and the storage scheme of the matrix.

  13. Sparse Distributed Representation of Odors in a Large-scale Olfactory Bulb Circuit

    PubMed Central

    Yu, Yuguo; McTavish, Thomas S.; Hines, Michael L.; Shepherd, Gordon M.; Valenti, Cesare; Migliore, Michele

    2013-01-01

    In the olfactory bulb, lateral inhibition mediated by granule cells has been suggested to modulate the timing of mitral cell firing, thereby shaping the representation of input odorants. Current experimental techniques, however, do not enable a clear study of how the mitral-granule cell network sculpts odor inputs to represent odor information spatially and temporally. To address this critical step in the neural basis of odor recognition, we built a biophysical network model of mitral and granule cells, corresponding to 1/100th of the real system in the rat, and used direct experimental imaging data of glomeruli activated by various odors. The model allows the systematic investigation and generation of testable hypotheses of the functional mechanisms underlying odor representation in the olfactory bulb circuit. Specifically, we demonstrate that lateral inhibition emerges within the olfactory bulb network through recurrent dendrodendritic synapses when constrained by a range of balanced excitatory and inhibitory conductances. We find that the spatio-temporal dynamics of lateral inhibition plays a critical role in building the glomerular-related cell clusters observed in experiments, through the modulation of synaptic weights during odor training. Lateral inhibition also mediates the development of sparse and synchronized spiking patterns of mitral cells related to odor inputs within the network, with the frequency of these synchronized spiking patterns also modulated by the sniff cycle. PMID:23555237

  14. Capacity for patterns and sequences in Kanerva's SDM as compared to other associative memory models. [Sparse, Distributed Memory

    NASA Technical Reports Server (NTRS)

    Keeler, James D.

    1988-01-01

    The information capacity of Kanerva's Sparse Distributed Memory (SDM) and Hopfield-type neural networks is investigated. Under the approximations used here, it is shown that the total information stored in these systems is proportional to the number connections in the network. The proportionality constant is the same for the SDM and Hopfield-type models independent of the particular model, or the order of the model. The approximations are checked numerically. This same analysis can be used to show that the SDM can store sequences of spatiotemporal patterns, and the addition of time-delayed connections allows the retrieval of context dependent temporal patterns. A minor modification of the SDM can be used to store correlated patterns.

  15. Off-Grid Direction of Arrival Estimation Based on Joint Spatial Sparsity for Distributed Sparse Linear Arrays

    PubMed Central

    Liang, Yujie; Ying, Rendong; Lu, Zhenqi; Liu, Peilin

    2014-01-01

    In the design phase of sensor arrays during array signal processing, the estimation performance and system cost are largely determined by array aperture size. In this article, we address the problem of joint direction-of-arrival (DOA) estimation with distributed sparse linear arrays (SLAs) and propose an off-grid synchronous approach based on distributed compressed sensing to obtain larger array aperture. We focus on the complex source distribution in the practical applications and classify the sources into common and innovation parts according to whether a signal of source can impinge on all the SLAs or a specific one. For each SLA, we construct a corresponding virtual uniform linear array (ULA) to create the relationship of random linear map between the signals respectively observed by these two arrays. The signal ensembles including the common/innovation sources for different SLAs are abstracted as a joint spatial sparsity model. And we use the minimization of concatenated atomic norm via semidefinite programming to solve the problem of joint DOA estimation. Joint calculation of the signals observed by all the SLAs exploits their redundancy caused by the common sources and decreases the requirement of array size. The numerical results illustrate the advantages of the proposed approach. PMID:25420150

  16. Atypical form of Alzheimer's disease with prominent posterior cortical atrophy: a review of lesion distribution and circuit disconnection in cortical visual pathways

    NASA Technical Reports Server (NTRS)

    Hof, P. R.; Vogt, B. A.; Bouras, C.; Morrison, J. H.; Bloom, F. E. (Principal Investigator)

    1997-01-01

    In recent years, the existence of visual variants of Alzheimer's disease characterized by atypical clinical presentation at onset has been increasingly recognized. In many of these cases post-mortem neuropathological assessment revealed that correlations could be established between clinical symptoms and the distribution of neurodegenerative lesions. We have analyzed a series of Alzheimer's disease patients presenting with prominent visual symptomatology as a cardinal sign of the disease. In these cases, a shift in the distribution of pathological lesions was observed such that the primary visual areas and certain visual association areas within the occipito-parieto-temporal junction and posterior cingulate cortex had very high densities of lesions, whereas the prefrontal cortex had fewer lesions than usually observed in Alzheimer's disease. Previous quantitative analyses have demonstrated that in Alzheimer's disease, primary sensory and motor cortical areas are less damaged than the multimodal association areas of the frontal and temporal lobes, as indicated by the laminar and regional distribution patterns of neurofibrillary tangles and senile plaques. The distribution of pathological lesions in the cerebral cortex of Alzheimer's disease cases with visual symptomatology revealed that specific visual association pathways were disrupted, whereas these particular connections are likely to be affected to a less severe degree in the more common form of Alzheimer's disease. These data suggest that in some cases with visual variants of Alzheimer's disease, the neurological symptomatology may be related to the loss of certain components of the cortical visual pathways, as reflected by the particular distribution of the neuropathological markers of the disease.

  17. Three-dimensional distribution of cortical synapses: a replicated point pattern-based analysis.

    PubMed

    Anton-Sanchez, Laura; Bielza, Concha; Merchán-Pérez, Angel; Rodríguez, José-Rodrigo; DeFelipe, Javier; Larrañaga, Pedro

    2014-01-01

    The biggest problem when analyzing the brain is that its synaptic connections are extremely complex. Generally, the billions of neurons making up the brain exchange information through two types of highly specialized structures: chemical synapses (the vast majority) and so-called gap junctions (a substrate of one class of electrical synapse). Here we are interested in exploring the three-dimensional spatial distribution of chemical synapses in the cerebral cortex. Recent research has showed that the three-dimensional spatial distribution of synapses in layer III of the neocortex can be modeled by a random sequential adsorption (RSA) point process, i.e., synapses are distributed in space almost randomly, with the only constraint that they cannot overlap. In this study we hypothesize that RSA processes can also explain the distribution of synapses in all cortical layers. We also investigate whether there are differences in both the synaptic density and spatial distribution of synapses between layers. Using combined focused ion beam milling and scanning electron microscopy (FIB/SEM), we obtained three-dimensional samples from the six layers of the rat somatosensory cortex and identified and reconstructed the synaptic junctions. A total volume of tissue of approximately 4500μm(3) and around 4000 synapses from three different animals were analyzed. Different samples, layers and/or animals were aggregated and compared using RSA replicated spatial point processes. The results showed no significant differences in the synaptic distribution across the different rats used in the study. We found that RSA processes described the spatial distribution of synapses in all samples of each layer. We also found that the synaptic distribution in layers II to VI conforms to a common underlying RSA process with different densities per layer. Interestingly, the results showed that synapses in layer I had a slightly different spatial distribution from the other layers.

  18. Three-dimensional distribution of cortical synapses: a replicated point pattern-based analysis

    PubMed Central

    Anton-Sanchez, Laura; Bielza, Concha; Merchán-Pérez, Angel; Rodríguez, José-Rodrigo; DeFelipe, Javier; Larrañaga, Pedro

    2014-01-01

    The biggest problem when analyzing the brain is that its synaptic connections are extremely complex. Generally, the billions of neurons making up the brain exchange information through two types of highly specialized structures: chemical synapses (the vast majority) and so-called gap junctions (a substrate of one class of electrical synapse). Here we are interested in exploring the three-dimensional spatial distribution of chemical synapses in the cerebral cortex. Recent research has showed that the three-dimensional spatial distribution of synapses in layer III of the neocortex can be modeled by a random sequential adsorption (RSA) point process, i.e., synapses are distributed in space almost randomly, with the only constraint that they cannot overlap. In this study we hypothesize that RSA processes can also explain the distribution of synapses in all cortical layers. We also investigate whether there are differences in both the synaptic density and spatial distribution of synapses between layers. Using combined focused ion beam milling and scanning electron microscopy (FIB/SEM), we obtained three-dimensional samples from the six layers of the rat somatosensory cortex and identified and reconstructed the synaptic junctions. A total volume of tissue of approximately 4500μm3 and around 4000 synapses from three different animals were analyzed. Different samples, layers and/or animals were aggregated and compared using RSA replicated spatial point processes. The results showed no significant differences in the synaptic distribution across the different rats used in the study. We found that RSA processes described the spatial distribution of synapses in all samples of each layer. We also found that the synaptic distribution in layers II to VI conforms to a common underlying RSA process with different densities per layer. Interestingly, the results showed that synapses in layer I had a slightly different spatial distribution from the other layers. PMID:25206325

  19. Three-dimensional distribution of cortical synapses: a replicated point pattern-based analysis.

    PubMed

    Anton-Sanchez, Laura; Bielza, Concha; Merchán-Pérez, Angel; Rodríguez, José-Rodrigo; DeFelipe, Javier; Larrañaga, Pedro

    2014-01-01

    The biggest problem when analyzing the brain is that its synaptic connections are extremely complex. Generally, the billions of neurons making up the brain exchange information through two types of highly specialized structures: chemical synapses (the vast majority) and so-called gap junctions (a substrate of one class of electrical synapse). Here we are interested in exploring the three-dimensional spatial distribution of chemical synapses in the cerebral cortex. Recent research has showed that the three-dimensional spatial distribution of synapses in layer III of the neocortex can be modeled by a random sequential adsorption (RSA) point process, i.e., synapses are distributed in space almost randomly, with the only constraint that they cannot overlap. In this study we hypothesize that RSA processes can also explain the distribution of synapses in all cortical layers. We also investigate whether there are differences in both the synaptic density and spatial distribution of synapses between layers. Using combined focused ion beam milling and scanning electron microscopy (FIB/SEM), we obtained three-dimensional samples from the six layers of the rat somatosensory cortex and identified and reconstructed the synaptic junctions. A total volume of tissue of approximately 4500μm(3) and around 4000 synapses from three different animals were analyzed. Different samples, layers and/or animals were aggregated and compared using RSA replicated spatial point processes. The results showed no significant differences in the synaptic distribution across the different rats used in the study. We found that RSA processes described the spatial distribution of synapses in all samples of each layer. We also found that the synaptic distribution in layers II to VI conforms to a common underlying RSA process with different densities per layer. Interestingly, the results showed that synapses in layer I had a slightly different spatial distribution from the other layers. PMID:25206325

  20. Sparse Reconstruction for Temperature Distribution Using DTS Fiber Optic Sensors with Applications in Electrical Generator Stator Monitoring

    PubMed Central

    Bazzo, João Paulo; Pipa, Daniel Rodrigues; da Silva, Erlon Vagner; Martelli, Cicero; Cardozo da Silva, Jean Carlos

    2016-01-01

    This paper presents an image reconstruction method to monitor the temperature distribution of electric generator stators. The main objective is to identify insulation failures that may arise as hotspots in the structure. The method is based on temperature readings of fiber optic distributed sensors (DTS) and a sparse reconstruction algorithm. Thermal images of the structure are formed by appropriately combining atoms of a dictionary of hotspots, which was constructed by finite element simulation with a multi-physical model. Due to difficulties for reproducing insulation faults in real stator structure, experimental tests were performed using a prototype similar to the real structure. The results demonstrate the ability of the proposed method to reconstruct images of hotspots with dimensions down to 15 cm, representing a resolution gain of up to six times when compared to the DTS spatial resolution. In addition, satisfactory results were also obtained to detect hotspots with only 5 cm. The application of the proposed algorithm for thermal imaging of generator stators can contribute to the identification of insulation faults in early stages, thereby avoiding catastrophic damage to the structure. PMID:27618040

  1. Sparse Reconstruction for Temperature Distribution Using DTS Fiber Optic Sensors with Applications in Electrical Generator Stator Monitoring.

    PubMed

    Bazzo, João Paulo; Pipa, Daniel Rodrigues; da Silva, Erlon Vagner; Martelli, Cicero; Cardozo da Silva, Jean Carlos

    2016-01-01

    This paper presents an image reconstruction method to monitor the temperature distribution of electric generator stators. The main objective is to identify insulation failures that may arise as hotspots in the structure. The method is based on temperature readings of fiber optic distributed sensors (DTS) and a sparse reconstruction algorithm. Thermal images of the structure are formed by appropriately combining atoms of a dictionary of hotspots, which was constructed by finite element simulation with a multi-physical model. Due to difficulties for reproducing insulation faults in real stator structure, experimental tests were performed using a prototype similar to the real structure. The results demonstrate the ability of the proposed method to reconstruct images of hotspots with dimensions down to 15 cm, representing a resolution gain of up to six times when compared to the DTS spatial resolution. In addition, satisfactory results were also obtained to detect hotspots with only 5 cm. The application of the proposed algorithm for thermal imaging of generator stators can contribute to the identification of insulation faults in early stages, thereby avoiding catastrophic damage to the structure. PMID:27618040

  2. Sparse Reconstruction for Temperature Distribution Using DTS Fiber Optic Sensors with Applications in Electrical Generator Stator Monitoring.

    PubMed

    Bazzo, João Paulo; Pipa, Daniel Rodrigues; da Silva, Erlon Vagner; Martelli, Cicero; Cardozo da Silva, Jean Carlos

    2016-09-07

    This paper presents an image reconstruction method to monitor the temperature distribution of electric generator stators. The main objective is to identify insulation failures that may arise as hotspots in the structure. The method is based on temperature readings of fiber optic distributed sensors (DTS) and a sparse reconstruction algorithm. Thermal images of the structure are formed by appropriately combining atoms of a dictionary of hotspots, which was constructed by finite element simulation with a multi-physical model. Due to difficulties for reproducing insulation faults in real stator structure, experimental tests were performed using a prototype similar to the real structure. The results demonstrate the ability of the proposed method to reconstruct images of hotspots with dimensions down to 15 cm, representing a resolution gain of up to six times when compared to the DTS spatial resolution. In addition, satisfactory results were also obtained to detect hotspots with only 5 cm. The application of the proposed algorithm for thermal imaging of generator stators can contribute to the identification of insulation faults in early stages, thereby avoiding catastrophic damage to the structure.

  3. Inferring learning rules from distributions of firing rates in cortical neurons.

    PubMed

    Lim, Sukbin; McKee, Jillian L; Woloszyn, Luke; Amit, Yali; Freedman, David J; Sheinberg, David L; Brunel, Nicolas

    2015-12-01

    Information about external stimuli is thought to be stored in cortical circuits through experience-dependent modifications of synaptic connectivity. These modifications of network connectivity should lead to changes in neuronal activity as a particular stimulus is repeatedly encountered. Here we ask what plasticity rules are consistent with the differences in the statistics of the visual response to novel and familiar stimuli in inferior temporal cortex, an area underlying visual object recognition. We introduce a method that allows one to infer the dependence of the presumptive learning rule on postsynaptic firing rate, and we show that the inferred learning rule exhibits depression for low postsynaptic rates and potentiation for high rates. The threshold separating depression from potentiation is strongly correlated with both mean and s.d. of the firing rate distribution. Finally, we show that network models implementing a rule extracted from data show stable learning dynamics and lead to sparser representations of stimuli. PMID:26523643

  4. Efficient packing of patterns in sparse distributed memory by selective weighting of input bits

    NASA Technical Reports Server (NTRS)

    Kanerva, Pentti

    1991-01-01

    When a set of patterns is stored in a distributed memory, any given storage location participates in the storage of many patterns. From the perspective of any one stored pattern, the other patterns act as noise, and such noise limits the memory's storage capacity. The more similar the retrieval cues for two patterns are, the more the patterns interfere with each other in memory, and the harder it is to separate them on retrieval. A method is described of weighting the retrieval cues to reduce such interference and thus to improve the separability of patterns that have similar cues.

  5. Some methods of encoding simple visual images for use with a sparse distributed memory, with applications to character recognition

    NASA Technical Reports Server (NTRS)

    Jaeckel, Louis A.

    1989-01-01

    To study the problems of encoding visual images for use with a Sparse Distributed Memory (SDM), I consider a specific class of images- those that consist of several pieces, each of which is a line segment or an arc of a circle. This class includes line drawings of characters such as letters of the alphabet. I give a method of representing a segment of an arc by five numbers in a continuous way; that is, similar arcs have similar representations. I also give methods for encoding these numbers as bit strings in an approximately continuous way. The set of possible segments and arcs may be viewed as a five-dimensional manifold M, whose structure is like a Mobious strip. An image, considered to be an unordered set of segments and arcs, is therefore represented by a set of points in M - one for each piece. I then discuss the problem of constructing a preprocessor to find the segments and arcs in these images, although a preprocessor has not been developed. I also describe a possible extension of the representation.

  6. Expression and cellular distribution of transient receptor potential vanilloid 4 in cortical tubers of the tuberous sclerosis complex.

    PubMed

    Chen, Xin; Yang, Meihua; Sun, Feiji; Liang, Chao; Wei, Yujia; Wang, Lukang; Yue, Jiong; Chen, Bing; Li, Song; Liu, Shiyong; Yang, Hui

    2016-04-01

    Cortical tubers in patients with tuberous sclerosis complex (TSC) are highly associated with intractable epilepsy. Recent evidence has shown that transient receptor potential vanilloid 4 (TRPV4) has direct effects on both neurons and glial cells. To understand the role of TRPV4 in pathogenesis of cortical tubers, we investigated the expression patterns of TRPV4 in cortical tubers of TSC compared with normal control cortex (CTX). We found that TRPV4 was clearly up-regulated in cortical tubers at the protein levels. Immunostaining indicated that TRPV4 was specially distributed in abnormal cells, including dysplastic neurons (DNs) and giant cells (GCs). In addition, double immunofluorescent staining revealed that TRPV4 was localized on neurofilament proteins (NF200) positive neurons and glial fibrillary acidic portein (GFAP) positive reactive astrocytes. Moreover, TRPV4 co-localized with both glutamatergic and GABAergic neurons. Furthermore, protein levels of protein kinase C (PKC), but not protein kinase A (PKA), the important upstream factors of the TRPV4, were significantly increased in cortical tubers. Taken together, the overexpression and distribution patterns of TRPV4 may be linked with the intractable epilepsy caused by TSC. PMID:26874068

  7. Distribution of cortical granules in bovine oocytes classified by cumulus complex.

    PubMed

    Hosoe, M; Shioya, Y

    1997-11-01

    The present study was conducted to examine distributional changes of cortical granules (CGs) during meiotic maturation and fertilisation in vitro and the developmental ability in bovine oocytes classified by cumulus cells. The oocytes were classified by the morphology of their cumulus cell layers as follows: class A, compact and thick; class B, compact but thin; class C, naked; and class D, expanded. Some of the oocytes were stained with Lens curinalis agglutinin (LCA) before and after maturation in vitro and after insemination, and then stained with orcein to observe their nuclear stages. The others were left in culture. Distributional patterns of the CGs were classified into four types: type I, CGs distributed in clusters; type II, CGs dispersed and partly clustered; type III, all CGs dispersed; and type IV, no CGs. Most of the oocytes before culture showed a type I pattern, but this decreased after maturation culture, whereas type III increased in class A. The oocytes of class B showed similar changes while the oocytes of class C did not. In class C, many oocytes showed type I after culture, indicating that cytoplasmic maturation was not completed. In class D, 80.4% of the oocytes exhibited type III before maturation culture, indicating that their cytoplasmic maturation was different from classes A-C. And about 70% of the class D oocytes were at the nuclear stage of germinal vesicle breakdown (GVBD) before culture. The developmental rates to blastocysts in classes A-D were 28.7%, 23.1%, 0.5% and 3.4% respectively. PMID:9563685

  8. LOFAR sparse image reconstruction

    NASA Astrophysics Data System (ADS)

    Garsden, H.; Girard, J. N.; Starck, J. L.; Corbel, S.; Tasse, C.; Woiselle, A.; McKean, J. P.; van Amesfoort, A. S.; Anderson, J.; Avruch, I. M.; Beck, R.; Bentum, M. J.; Best, P.; Breitling, F.; Broderick, J.; Brüggen, M.; Butcher, H. R.; Ciardi, B.; de Gasperin, F.; de Geus, E.; de Vos, M.; Duscha, S.; Eislöffel, J.; Engels, D.; Falcke, H.; Fallows, R. A.; Fender, R.; Ferrari, C.; Frieswijk, W.; Garrett, M. A.; Grießmeier, J.; Gunst, A. W.; Hassall, T. E.; Heald, G.; Hoeft, M.; Hörandel, J.; van der Horst, A.; Juette, E.; Karastergiou, A.; Kondratiev, V. I.; Kramer, M.; Kuniyoshi, M.; Kuper, G.; Mann, G.; Markoff, S.; McFadden, R.; McKay-Bukowski, D.; Mulcahy, D. D.; Munk, H.; Norden, M. J.; Orru, E.; Paas, H.; Pandey-Pommier, M.; Pandey, V. N.; Pietka, G.; Pizzo, R.; Polatidis, A. G.; Renting, A.; Röttgering, H.; Rowlinson, A.; Schwarz, D.; Sluman, J.; Smirnov, O.; Stappers, B. W.; Steinmetz, M.; Stewart, A.; Swinbank, J.; Tagger, M.; Tang, Y.; Tasse, C.; Thoudam, S.; Toribio, C.; Vermeulen, R.; Vocks, C.; van Weeren, R. J.; Wijnholds, S. J.; Wise, M. W.; Wucknitz, O.; Yatawatta, S.; Zarka, P.; Zensus, A.

    2015-03-01

    Context. The LOw Frequency ARray (LOFAR) radio telescope is a giant digital phased array interferometer with multiple antennas distributed in Europe. It provides discrete sets of Fourier components of the sky brightness. Recovering the original brightness distribution with aperture synthesis forms an inverse problem that can be solved by various deconvolution and minimization methods. Aims: Recent papers have established a clear link between the discrete nature of radio interferometry measurement and the "compressed sensing" (CS) theory, which supports sparse reconstruction methods to form an image from the measured visibilities. Empowered by proximal theory, CS offers a sound framework for efficient global minimization and sparse data representation using fast algorithms. Combined with instrumental direction-dependent effects (DDE) in the scope of a real instrument, we developed and validated a new method based on this framework. Methods: We implemented a sparse reconstruction method in the standard LOFAR imaging tool and compared the photometric and resolution performance of this new imager with that of CLEAN-based methods (CLEAN and MS-CLEAN) with simulated and real LOFAR data. Results: We show that i) sparse reconstruction performs as well as CLEAN in recovering the flux of point sources; ii) performs much better on extended objects (the root mean square error is reduced by a factor of up to 10); and iii) provides a solution with an effective angular resolution 2-3 times better than the CLEAN images. Conclusions: Sparse recovery gives a correct photometry on high dynamic and wide-field images and improved realistic structures of extended sources (of simulated and real LOFAR datasets). This sparse reconstruction method is compatible with modern interferometric imagers that handle DDE corrections (A- and W-projections) required for current and future instruments such as LOFAR and SKA.

  9. Occlusal load distribution through the cortical and trabecular bone of the human mid-facial skeleton in natural dentition: a three-dimensional finite element study.

    PubMed

    Janovic, Aleksa; Saveljic, Igor; Vukicevic, Arso; Nikolic, Dalibor; Rakocevic, Zoran; Jovicic, Gordana; Filipovic, Nenad; Djuric, Marija

    2015-01-01

    Understanding of the occlusal load distribution through the mid-facial skeleton in natural dentition is essential because alterations in magnitude and/or direction of occlusal forces may cause remarkable changes in cortical and trabecular bone structure. Previous analyses by strain gauge technique, photoelastic and, more recently, finite element (FE) methods provided no direct evidence for occlusal load distribution through the cortical and trabecular bone compartments individually. Therefore, we developed an improved three-dimensional FE model of the human skull in order to clarify the distribution of occlusal forces through the cortical and trabecular bone during habitual masticatory activities. Particular focus was placed on the load transfer through the anterior and posterior maxilla. The results were presented in von Mises stress (VMS) and the maximum principal stress, and compared to the reported FE and strain gauge data. Our qualitative stress analysis indicates that occlusal forces distribute through the mid-facial skeleton along five vertical and two horizontal buttresses. We demonstrated that cortical bone has a priority in the transfer of occlusal load in the anterior maxilla, whereas both cortical and trabecular bone in the posterior maxilla are equally involved in performing this task. Observed site dependence of the occlusal load distribution may help clinicians in creating strategies for implantology and orthodontic treatments. Additionally, the magnitude of VMS in our model was significantly lower in comparison to previous FE models composed only of cortical bone. This finding suggests that both cortical and trabecular bone should be modeled whenever stress will be quantitatively analyzed.

  10. Elastic anisotropy and off-axis ultrasonic velocity distribution in human cortical bone

    PubMed Central

    Chung, Dong Hwa; Dechow, Paul C

    2011-01-01

    Elastic structure in cortical bone is usually simplified as orthotropic or transversely isotropic, which allows estimates of three-dimensional technical constants from ultrasonic and density measurements. These elastic property estimates can then be used to study phenotypic changes in cortical bone structure and function, and to create finite element models of skeletal structures for studies of organismal variation and functional adaptation. This study examines assumptions of orthotropic or transversely isotropic material structure in cortical bone through the investigation of off-axis ultrasonic velocities in the cortical plane in 10 samples each from a human femur, mandible and cranium. Longitudinal ultrasonic velocities were measured twice through each bone sample by rotating the perimeter of each sample in 1 ° angular intervals between two ultrasonic transducers. The data were fit to sine curves f(x) = (A× sin(x+ B) + C) and the goodness of fit was examined. All the data from the femur fit closely with the ideal sine curve model, and all three coefficients were similar among specimens, indicating similar elastic properties, anisotropies and orientations of the axes of maximum stiffness. Off-axis ultrasonic velocities in the mandible largely fit the sine curve model, although there were regional variations in the coefficients. Off-axis ultrasonic velocities from the cranial vault conformed to the sine curve model in some regions but not in others, which shows an irregular and complex pattern. We hypothesize that these variations in ultrasonic velocities reflect variations in the underlying bulk microstructure of the cortical bone, especially in the three-dimensional patterns of osteonal orientation and structure. Elastic property estimates made with ultrasonic techniques are likely valid in the femur and mandible; errors in estimates from cranial bone need to be evaluated regionally. Approximate orthotropic structure in bulk cortical bone specimens should be

  11. Fracture size and transmissivity correlations: Implications for transport simulations in sparse three-dimensional discrete fracture networks following a truncated power law distribution of fracture size

    DOE PAGES

    Hyman, Jeffrey De'Haven; Aldrich, Garrett Allen; Viswanathan, Hari S.; Makedonska, Nataliia; Karra, Satish

    2016-08-25

    We characterize how different fracture size-transmissivity relationships influence flow and transport simulations through sparse three-dimensional discrete fracture networks. Although it is generally accepted that there is a positive correlation between a fracture's size and its transmissivity/aperture, the functional form of that relationship remains a matter of debate. Relationships that assume perfect correlation, semicorrelation, and noncorrelation between the two have been proposed. To study the impact that adopting one of these relationships has on transport properties, we generate multiple sparse fracture networks composed of circular fractures whose radii follow a truncated power law distribution. The distribution of transmissivities are selected somore » that the mean transmissivity of the fracture networks are the same and the distributions of aperture and transmissivity in models that include a stochastic term are also the same. We observe that adopting a correlation between a fracture size and its transmissivity leads to earlier breakthrough times and higher effective permeability when compared to networks where no correlation is used. While fracture network geometry plays the principal role in determining where transport occurs within the network, the relationship between size and transmissivity controls the flow speed. Lastly, these observations indicate DFN modelers should be aware that breakthrough times and effective permeabilities can be strongly influenced by such a relationship in addition to fracture and network statistics.« less

  12. Measurement of strain distribution in cortical bone around miniscrew implants used for orthodontic anchorage using digital speckle pattern interferometry

    NASA Astrophysics Data System (ADS)

    Kumar, Manoj; Agarwal, Rupali; Bhutani, Ravi; Shakher, Chandra

    2016-05-01

    An application of digital speckle pattern interferometry (DSPI) for the measurement of deformations and strain-field distributions developed in cortical bone around orthodontic miniscrew implants inserted into the human maxilla is presented. The purpose of this study is to measure and compare the strain distribution in cortical bone/miniscrew interface of human maxilla around miniscrew implants of different diameters, different implant lengths, and implants of different commercially available companies. The technique is also used to measure tilt/rotation of canine caused due to the application of retraction springs. The proposed technique has high sensitivity and enables the observation of deformation/strain distribution. In DSPI, two specklegrams are recorded corresponding to pre- and postloading of the retraction spring. The DSPI fringe pattern is observed by subtracting these two specklegrams. Optical phase was extracted using Riesz transform and the monogenic signal from a single DSPI fringe pattern. The obtained phase is used to calculate the parameters of interest such as displacement/deformation and strain/stress. The experiment was conducted on a dry human skull fulfilling the criteria of intact dental arches and all teeth present. Eight different miniscrew implants were loaded with an insertion angulation of 45 deg in the inter-radicular region of the maxillary second premolar and molar region. The loading of miniscrew implants was done with force level (150 gf) by nickel-titanium closed-coil springs (9 mm). The obtained results from DSPI reveal that implant diameter and implant length affect the displacement and strain distribution in cortical bone layer surrounding the miniscrew implant.

  13. Measurement of strain distribution in cortical bone around miniscrew implants used for orthodontic anchorage using digital speckle pattern interferometry

    NASA Astrophysics Data System (ADS)

    Kumar, Manoj; Agarwal, Rupali; Bhutani, Ravi; Shakher, Chandra

    2016-05-01

    An application of digital speckle pattern interferometry (DSPI) for the measurement of deformations and strain-field distributions developed in cortical bone around orthodontic miniscrew implants inserted into the human maxilla is presented. The purpose of this study is to measure and compare the strain distribution in cortical bone/miniscrew interface of human maxilla around miniscrew implants of different diameters, different implant lengths, and implants of different commercially available companies. The technique is also used to measure tilt/rotation of canine caused due to the application of retraction springs. The proposed technique has high sensitivity and enables the observation of deformation/strain distribution. In DSPI, two specklegrams are recorded corresponding to pre- and postloading of the retraction spring. The DSPI fringe pattern is observed by subtracting these two specklegrams. Optical phase was extracted using Riesz transform and the monogenic signal from a single DSPI fringe pattern. The obtained phase is used to calculate the parameters of interest such as displacement/deformation and strain/stress. The experiment was conducted on a dry human skull fulfilling the criteria of intact dental arches and all teeth present. Eight different miniscrew implants were loaded with an insertion angulation of 45 deg in the inter-radicular region of the maxillary second premolar and molar region. The loading of miniscrew implants was done with force level (150 gf) by nickel-titanium closed-coil springs (9 mm). The obtained results from DSPI reveal that implant diameter and implant length affect the displacement and strain distribution in cortical bone layer surrounding the miniscrew implant.

  14. Long-tailed distribution of synaptic strength reveals origin and functional roles of ongoing fluctuation in cortical circuit

    NASA Astrophysics Data System (ADS)

    Teramae, Jun-nosuke

    2016-06-01

    Neurons in the cortical circuit continuous to generate irregular spike firing with extremely low firing rate (about 1-2 Hz) even when animals neither receive any external stimuli nor they do not show any significant motor movement. The ongoing activity is often called neuronal noise because measured spike trains are often highly irregular and also spike timings are highly asynchronous among neurons. Many experiments imply that neural networks themselves must generate the noisy activity as an intrinsic property of cortical circuit. However, how a network of neurons sustains the irregular spike firings with low firing rate remains unclear. Recently, by focusing on long-tailed distribution of amplitude of synaptic connections or EPSP (Excitatory Post-Synaptic Potential), we successfully revealed that due to coexistence of a few extremely strong synaptic connections and majority of weak synapses, nonlinear dynamics of population of spiking neurons can have a nontrivial stable state that corresponding to the intrinsic ongoing fluctuation of the cortical circuit. We also found that due to the fluctuation fidelity of spike transmission between neurons are optimized. Here, we report our recent findings of the ongoing fluctuation from viewpoints of mathematical and computational side.

  15. Pre-cue fronto-occipital alpha phase and distributed cortical oscillations predict failures of cognitive control.

    PubMed

    Hamm, Jordan P; Dyckman, Kara A; McDowell, Jennifer E; Clementz, Brett A

    2012-05-16

    Cognitive control is required for correct performance on antisaccade tasks, including the ability to inhibit an externally driven ocular motor response (a saccade to a peripheral stimulus) in favor of an internally driven ocular motor goal (a saccade directed away from a peripheral stimulus). Healthy humans occasionally produce errors during antisaccade tasks, but the mechanisms associated with such failures of cognitive control are uncertain. Most research on cognitive control failures focuses on poststimulus processing, although a growing body of literature highlights a role of intrinsic brain activity in perceptual and cognitive performance. The current investigation used dense array electroencephalography and distributed source analyses to examine brain oscillations across a wide frequency bandwidth in the period before antisaccade cue onset. Results highlight four important aspects of ongoing and preparatory brain activations that differentiate error from correct antisaccade trials: (1) ongoing oscillatory beta (20-30 Hz) power in anterior cingulate before trial initiation (lower for error trials); (2) instantaneous phase of ongoing alpha/theta (7 Hz) in frontal and occipital cortices immediately before trial initiation (opposite between trial types); (3) gamma power (35-60 Hz) in posterior parietal cortex 100 ms before cue onset (greater for error trials); and (4) phase locking of alpha (5-12 Hz) in parietal and occipital cortices immediately before cue onset (lower for error trials). These findings extend recently reported effects of pre-trial alpha phase on perception to cognitive control processes and help identify the cortical generators of such phase effects.

  16. Neuroblast Distribution after Cortical Impact Is Influenced by White Matter Injury in the Immature Gyrencephalic Brain

    PubMed Central

    Taylor, Sabrina R.; Smith, Colin M.; Keeley, Kristen L.; McGuone, Declan; Dodge, Carter P.; Duhaime, Ann-Christine; Costine, Beth A.

    2016-01-01

    Cortical contusions are a common type of traumatic brain injury (TBI) in children. Current knowledge of neuroblast response to cortical injury arises primarily from studies utilizing aspiration or cryoinjury in rodents. In infants and children, cortical impact affects both gray and white matter and any neurogenic response may be complicated by the large expanse of white matter between the subventricular zone (SVZ) and the cortex, and the large number of neuroblasts in transit along the major white matter tracts to populate brain regions. Previously, we described an age-dependent increase of neuroblasts in the SVZ in response to cortical impact in the immature gyrencephalic brain. Here, we investigate if neuroblasts target the injury, if white matter injury influences repair efforts, and if postnatal population of brain regions are disrupted. Piglets received a cortical impact to the rostral gyrus cortex or sham surgery at postnatal day (PND) 7, BrdU 2 days prior to (PND 5 and 6) or after injury (PND 7 and 8), and brains were collected at PND 14. Injury did not alter the number of neuroblasts in the white matter between the SVZ and the rostral gyrus. In the gray matter of the injury site, neuroblast density was increased in cavitated lesions, and the number of BrdU+ neuroblasts was increased, but comprised less than 1% of all neuroblasts. In the white matter of the injury site, neuroblasts with differentiating morphology were densely arranged along the cavity edge. In a ventral migratory stream, neuroblast density was greater in subjects with a cavitated lesion, indicating that TBI may alter postnatal development of regions supplied by that stream. Cortical impact in the immature gyrencephalic brain produced complicated and variable lesions, increased neuroblast density in cavitated gray matter, resulted in potentially differentiating neuroblasts in the white matter, and may alter the postnatal population of brain regions utilizing a population of neuroblasts that

  17. Neuroblast Distribution after Cortical Impact Is Influenced by White Matter Injury in the Immature Gyrencephalic Brain

    PubMed Central

    Taylor, Sabrina R.; Smith, Colin M.; Keeley, Kristen L.; McGuone, Declan; Dodge, Carter P.; Duhaime, Ann-Christine; Costine, Beth A.

    2016-01-01

    Cortical contusions are a common type of traumatic brain injury (TBI) in children. Current knowledge of neuroblast response to cortical injury arises primarily from studies utilizing aspiration or cryoinjury in rodents. In infants and children, cortical impact affects both gray and white matter and any neurogenic response may be complicated by the large expanse of white matter between the subventricular zone (SVZ) and the cortex, and the large number of neuroblasts in transit along the major white matter tracts to populate brain regions. Previously, we described an age-dependent increase of neuroblasts in the SVZ in response to cortical impact in the immature gyrencephalic brain. Here, we investigate if neuroblasts target the injury, if white matter injury influences repair efforts, and if postnatal population of brain regions are disrupted. Piglets received a cortical impact to the rostral gyrus cortex or sham surgery at postnatal day (PND) 7, BrdU 2 days prior to (PND 5 and 6) or after injury (PND 7 and 8), and brains were collected at PND 14. Injury did not alter the number of neuroblasts in the white matter between the SVZ and the rostral gyrus. In the gray matter of the injury site, neuroblast density was increased in cavitated lesions, and the number of BrdU+ neuroblasts was increased, but comprised less than 1% of all neuroblasts. In the white matter of the injury site, neuroblasts with differentiating morphology were densely arranged along the cavity edge. In a ventral migratory stream, neuroblast density was greater in subjects with a cavitated lesion, indicating that TBI may alter postnatal development of regions supplied by that stream. Cortical impact in the immature gyrencephalic brain produced complicated and variable lesions, increased neuroblast density in cavitated gray matter, resulted in potentially differentiating neuroblasts in the white matter, and may alter the postnatal population of brain regions utilizing a population of neuroblasts that

  18. Neuroblast Distribution after Cortical Impact Is Influenced by White Matter Injury in the Immature Gyrencephalic Brain.

    PubMed

    Taylor, Sabrina R; Smith, Colin M; Keeley, Kristen L; McGuone, Declan; Dodge, Carter P; Duhaime, Ann-Christine; Costine, Beth A

    2016-01-01

    Cortical contusions are a common type of traumatic brain injury (TBI) in children. Current knowledge of neuroblast response to cortical injury arises primarily from studies utilizing aspiration or cryoinjury in rodents. In infants and children, cortical impact affects both gray and white matter and any neurogenic response may be complicated by the large expanse of white matter between the subventricular zone (SVZ) and the cortex, and the large number of neuroblasts in transit along the major white matter tracts to populate brain regions. Previously, we described an age-dependent increase of neuroblasts in the SVZ in response to cortical impact in the immature gyrencephalic brain. Here, we investigate if neuroblasts target the injury, if white matter injury influences repair efforts, and if postnatal population of brain regions are disrupted. Piglets received a cortical impact to the rostral gyrus cortex or sham surgery at postnatal day (PND) 7, BrdU 2 days prior to (PND 5 and 6) or after injury (PND 7 and 8), and brains were collected at PND 14. Injury did not alter the number of neuroblasts in the white matter between the SVZ and the rostral gyrus. In the gray matter of the injury site, neuroblast density was increased in cavitated lesions, and the number of BrdU(+) neuroblasts was increased, but comprised less than 1% of all neuroblasts. In the white matter of the injury site, neuroblasts with differentiating morphology were densely arranged along the cavity edge. In a ventral migratory stream, neuroblast density was greater in subjects with a cavitated lesion, indicating that TBI may alter postnatal development of regions supplied by that stream. Cortical impact in the immature gyrencephalic brain produced complicated and variable lesions, increased neuroblast density in cavitated gray matter, resulted in potentially differentiating neuroblasts in the white matter, and may alter the postnatal population of brain regions utilizing a population of neuroblasts that

  19. Distribution of cerebello-olivary degeneration in idiopathic late cortical cerebellar atrophy: clinicopathological study of four autopsy cases.

    PubMed

    Ota, Satoru; Tsuchiya, Kuniaki; Anno, Midori; Niizato, Kazuhiro; Akiyama, Haruhiko

    2008-02-01

    Late cortical cerebellar atrophy (LCCA) is a neurodegenerative disease which presents with slowly progressive cerebellar ataxia as a prominent symptom and is characterized neuropathologically by a limited main lesion to the cerebellar cortex and inferior olivary nucleus. To elucidate the features of lesions in the cerebellar cortex and inferior olivary nucleus, four autopsy cases suffering from idiopathic LCCA without other cortical cerebellar atrophies, such as alcoholic cerebellar degeneration, phenytoin intoxication, or hereditary cerebellar atrophy including spinocerebellar ataxia type 6, were examined. All affected patients had identical distinct features of cerebellar cortical lesions. In all four cases, the most obvious pathological finding throughout the cerebellum was loss of Purkinje cells, but the rarefaction of granular cell layers was observed only where loss of Purkinje cells was very severe, and thinning of the molecular layer was seen only where the rarefaction of granular cell layers was moderate to severe. Two patients presented with vermis dominant cerebellar cortical lesions, but the other two patients showed hemispheric dominant pathological changes. Neuronal loss of the inferior olivary nucleus was observed in the three autopsy cases. Two of the three cases had a prominent lesion in the dorsal part of the inferior olive and the cerebellar cortical lesion disclosed the vermis dominance, but the other patient, showing prominent neuronal loss in the ventral olivary nucleus, had a cerebellar hemisphere dominant lesion. The patient without neuronal loss in the inferior olivary nucleus had suffered from a shorter period of disease than the others and the rarefaction of granular cell layers and narrowing of the molecular layer of the cerebellar cortex were mild. Therefore, it is obvious that there are two types of cerebellar cortex lesions in idiopathic LCCA; one is vermis dominant and the other is cerebellar hemispheric dominant. The lesion of the

  20. Distribution of Response Time, Cortical, and Cardiac Correlates during Emotional Interference in Persons with Subclinical Psychotic Symptoms

    PubMed Central

    Holper, Lisa K. B.; Aleksandrowicz, Alekandra; Müller, Mario; Ajdacic-Gross, Vladeta; Haker, Helene; Fallgatter, Andreas J.; Hagenmuller, Florence; Kawohl, Wolfram; Rössler, Wulf

    2016-01-01

    A psychosis phenotype can be observed below the threshold of clinical detection. The study aimed to investigate whether subclinical psychotic symptoms are associated with deficits in controlling emotional interference, and whether cortical brain and cardiac correlates of these deficits can be detected using functional near-infrared spectroscopy (fNIRS). A data set derived from a community sample was obtained from the Zurich Program for Sustainable Development of Mental Health Services. 174 subjects (mean age 29.67 ± 6.41, 91 females) were assigned to four groups ranging from low to high levels of subclinical psychotic symptoms (derived from the Symptom Checklist-90-R). Emotional interference was assessed using the emotional Stroop task comprising neutral, positive, and negative conditions. Statistical distributional methods based on delta plots [behavioral response time (RT) data] and quantile analysis (fNIRS data) were applied to evaluate the emotional interference effects. Results showed that both interference effects and disorder-specific (i.e., group-specific) effects could be detected, based on behavioral RTs, cortical hemodynamic signals (brain correlates), and heart rate variability (cardiac correlates). Subjects with high compared to low subclinical psychotic symptoms revealed significantly reduced amplitudes in dorsolateral prefrontal cortices (interference effect, p < 0.001) and middle temporal gyrus (disorder-specific group effect, p < 0.001), supported by behavioral and heart rate results. The present findings indicate that distributional analyses methods can support the detection of emotional interference effects in the emotional Stroop. The results suggested that subjects with high subclinical psychosis exhibit enhanced emotional interference effects. Based on these observations, subclinical psychosis may therefore prove to represent a valid extension of the clinical psychosis phenotype. PMID:27660608

  1. The influence of chronic fluorosis on mitochondrial dynamics morphology and distribution in cortical neurons of the rat brain.

    PubMed

    Lou, Di-Dong; Guan, Zhi-Zhong; Liu, Yan-Jie; Liu, Yan-Fei; Zhang, Kai-Lin; Pan, Ji-Gang; Pei, Jin-Jing

    2013-03-01

    The present study was designed to evaluate the effects of chronic fluorosis on the dynamics (including fusion and fission proteins), fragmentation, and distribution of mitochondria in the cortical neurons of the rat brain in an attempt to elucidate molecular mechanisms underlying the brain damage associated with excess accumulation of fluoride. Sixty Sprague-Dawley rats were divided randomly into three groups of 20 each, that is, the untreated control group (drinking water naturally containing <0.5 mg fluoride/l, NaF), the low-fluoride group (whose drinking water was supplemented with 10 mg fluoride/l) and the high-fluoride group (50 mg fluoride/l). After 6 months of exposure, the expression of mitofusin-1 (Mfn1), fission-1 (Fis1), and dynamin-related protein-1 (Drp1) at both the protein and mRNA levels were detected by Western blotting, immunohistochemistry, and real-time PCR, respectively. Moreover, mitochondrial morphology and distribution in neurons were observed by transmission electron or fluorescence microscopy. In the cortices of the brains of rats with chronic fluorosis, the level of Mfn1 protein was clearly reduced, whereas the levels of Fis1 and Drp1 were elevated. The alternations of expression of the mRNAs encoding all three of these proteins were almost the same as the corresponding changes at the protein levels. The mitochondria were fragmented and the redistributed away from the axons of the cortical neurons. These findings indicate that chronic fluorosis induces abnormal mitochondrial dynamics, which might in turn result in a high level of oxidative stress.

  2. Distribution of Response Time, Cortical, and Cardiac Correlates during Emotional Interference in Persons with Subclinical Psychotic Symptoms.

    PubMed

    Holper, Lisa K B; Aleksandrowicz, Alekandra; Müller, Mario; Ajdacic-Gross, Vladeta; Haker, Helene; Fallgatter, Andreas J; Hagenmuller, Florence; Kawohl, Wolfram; Rössler, Wulf

    2016-01-01

    A psychosis phenotype can be observed below the threshold of clinical detection. The study aimed to investigate whether subclinical psychotic symptoms are associated with deficits in controlling emotional interference, and whether cortical brain and cardiac correlates of these deficits can be detected using functional near-infrared spectroscopy (fNIRS). A data set derived from a community sample was obtained from the Zurich Program for Sustainable Development of Mental Health Services. 174 subjects (mean age 29.67 ± 6.41, 91 females) were assigned to four groups ranging from low to high levels of subclinical psychotic symptoms (derived from the Symptom Checklist-90-R). Emotional interference was assessed using the emotional Stroop task comprising neutral, positive, and negative conditions. Statistical distributional methods based on delta plots [behavioral response time (RT) data] and quantile analysis (fNIRS data) were applied to evaluate the emotional interference effects. Results showed that both interference effects and disorder-specific (i.e., group-specific) effects could be detected, based on behavioral RTs, cortical hemodynamic signals (brain correlates), and heart rate variability (cardiac correlates). Subjects with high compared to low subclinical psychotic symptoms revealed significantly reduced amplitudes in dorsolateral prefrontal cortices (interference effect, p < 0.001) and middle temporal gyrus (disorder-specific group effect, p < 0.001), supported by behavioral and heart rate results. The present findings indicate that distributional analyses methods can support the detection of emotional interference effects in the emotional Stroop. The results suggested that subjects with high subclinical psychosis exhibit enhanced emotional interference effects. Based on these observations, subclinical psychosis may therefore prove to represent a valid extension of the clinical psychosis phenotype. PMID:27660608

  3. Distribution of Response Time, Cortical, and Cardiac Correlates during Emotional Interference in Persons with Subclinical Psychotic Symptoms

    PubMed Central

    Holper, Lisa K. B.; Aleksandrowicz, Alekandra; Müller, Mario; Ajdacic-Gross, Vladeta; Haker, Helene; Fallgatter, Andreas J.; Hagenmuller, Florence; Kawohl, Wolfram; Rössler, Wulf

    2016-01-01

    A psychosis phenotype can be observed below the threshold of clinical detection. The study aimed to investigate whether subclinical psychotic symptoms are associated with deficits in controlling emotional interference, and whether cortical brain and cardiac correlates of these deficits can be detected using functional near-infrared spectroscopy (fNIRS). A data set derived from a community sample was obtained from the Zurich Program for Sustainable Development of Mental Health Services. 174 subjects (mean age 29.67 ± 6.41, 91 females) were assigned to four groups ranging from low to high levels of subclinical psychotic symptoms (derived from the Symptom Checklist-90-R). Emotional interference was assessed using the emotional Stroop task comprising neutral, positive, and negative conditions. Statistical distributional methods based on delta plots [behavioral response time (RT) data] and quantile analysis (fNIRS data) were applied to evaluate the emotional interference effects. Results showed that both interference effects and disorder-specific (i.e., group-specific) effects could be detected, based on behavioral RTs, cortical hemodynamic signals (brain correlates), and heart rate variability (cardiac correlates). Subjects with high compared to low subclinical psychotic symptoms revealed significantly reduced amplitudes in dorsolateral prefrontal cortices (interference effect, p < 0.001) and middle temporal gyrus (disorder-specific group effect, p < 0.001), supported by behavioral and heart rate results. The present findings indicate that distributional analyses methods can support the detection of emotional interference effects in the emotional Stroop. The results suggested that subjects with high subclinical psychosis exhibit enhanced emotional interference effects. Based on these observations, subclinical psychosis may therefore prove to represent a valid extension of the clinical psychosis phenotype.

  4. Distributions of Cells and Neurons across the Cortical Sheet in Old World Macaques.

    PubMed

    Turner, Emily C; Young, Nicole A; Reed, Jamie L; Collins, Christine E; Flaherty, David K; Gabi, Mariana; Kaas, Jon H

    2016-01-01

    According to previous research, cell and neuron densities vary across neocortex in a similar manner across primate taxa. Here, we provide a more extensive examination of this effect in macaque monkeys. We separated neocortex from the underlying white matter in 4 macaque monkey hemispheres (1 Macaca nemestrina, 2 Macaca radiata, and 1 Macaca mulatta), manually flattened the neocortex, and divided it into smaller tissue pieces for analysis. The number of cells and neurons were determined for each piece across the cortical sheet using flow cytometry. Primary visual cortex had the most densely packed neurons and primary motor cortex had the least densely packed neurons. With respect to differences in brain size between cases, there was little variability in the total cell and neuron numbers within specific areas, and overall trends were similar to what has been previously described in Old World baboons and other primates. The average hemispheric total cell number per hemisphere ranged from 2.9 to 3.7 billion, while the average total neuron number ranged from 1.3 to 1.7 billion neurons. The visual cortex neuron densities were predictably higher, ranging from 18.2 to 34.7 million neurons/cm2 in macaques, in comparison to a range of 9.3-17.7 million neurons/cm2 across cortex as a whole. The results support other evidence that neuron surface densities vary across the cortical sheet in a predictable pattern within and across primate taxa. PMID:27547956

  5. A Markov model for interspike interval distributions of auditory cortical neurons that do not show periodic firings.

    PubMed

    Britvina, Tatiana; Eggermont, Jos J

    2007-02-01

    Spontaneous firing properties of individual auditory cortical neurons are interpreted in terms of local and global order present in functioning brain networks, such as alternating "up" and "down" states. A four-state modulated Markov process is used to model neuronal firings. The system alternates between a bound and an unbound state, both with Poisson-distributed lifetimes. During the unbound state, active and closed states alternate with Poisson-distributed lifetimes. Inside the active state, spikes are generated as a realization of a Poisson process. This combination of processes constitutes a four-state modulated Markov process, determined by five independent parameters. Analytical expressions for the probability density functions (pdfs) that describe the interspike interval (ISI) distribution and autocorrelation function are derived. The pdf for the ISI distribution is shown to be a linear combination of three exponential functions and is expressed through the five system parameters. Through fitting experimental ISI histograms by the theoretical ones, numerical values of the system parameters are obtained for the individual neurons. Both Monte Carlo simulations and goodness-of-fit tests are used to validate the fitting procedure. The values of the estimated system parameters related to the active-closed and bound-unbound processes and their independence on the neurons' mean firing rate suggest that the underlying quasi-periodic processes reflect properties of the network in which the neurons are embedded. The characteristic times of autocorrelations, determined by the bound-unbound and active-closed processes, are also independent of the neuron's firing rate. The agreement between experimental and theoretical ISI histograms and autocorrelation functions allows interpretation of the system parameters of the individual neurons in terms of slow and delta waves, and high-frequency oscillations observed in cortical networks. This procedure can identify and track

  6. Regional and laminar distribution of cortical neurons projecting to either superior or inferior colliculus in the hedgehog tenrec.

    PubMed

    Künzle, H

    1995-01-01

    Retrograde tracer substances were injected into either the inferior or the superior colliculus in the Madagascan hedgehog tenrec, Echinops telfairi (Insectivora), to reveal the laminar and regional distribution of corticotectal cells and to correlate the labeled areas with architectural data. The tenrecs, taken from our breeding colony, have one of the least differentiated cerebral cortices among mammals, and experimental investigations of such brains are important for the understanding of the evolution and intrinsic organization of the more highly differentiated cerebral cortex in other placental mammals. Following injections into the inferior colliculus, cortical neurons were labeled bilaterally, with an ipsilateral predominance. Most labeled cells were found in the caudolateral hemisphere, area 4 as defined by Rehkämper (1981); some were in the somatosensorimotor cortex, as defined in a previous study. The labeled neurons in area 4 were located in layers V and VI, forming two bands of cells separated from each other by a poorly labeled interspace. A further subdivision of this presumed auditory region could not be achieved. This entire area was also weakly labeled following tracer injections into the superior colliculus. The labeled cells, however, were restricted to layer V of the ipsilateral side. The most consistent sites of labeled cells following injections into the superior colliculus were found in layer V of the ipsilateral caudomedial hemisphere, Rehkämper's caudal area 3, and the transitional zone adjacent to the retrosplenial cortex. This area is small in comparison to the entire region that was found in this study to project to the superior colliculus. The superior colliculus also receives projections from the ipsilateral sensorimotor and cingulate cortices. The latter projections are particularly striking in comparison to other mammals because they originate from along the entire rostrocaudal extent of the cingulate/retrosplenial region.

  7. Trajectory and terminal distribution of single centrifugal axons from olfactory cortical areas in the rat olfactory bulb.

    PubMed

    Matsutani, S

    2010-08-11

    The olfactory bulb receives a large number of centrifugal fibers whose functions remain unclear. To gain insight into the function of the bulbar centrifugal system, the morphology of individual centrifugal axons from olfactory cortical areas was examined in detail. An anterograde tracer, Phaseolus vulgaris leucoagglutinin, was injected into rat olfactory cortical areas, including the pars lateralis of the anterior olfactory nucleus (lAON) and the anterior part of the piriform cortex (aPC). Reconstruction from serial sections revealed that the extrabulbar segments of centrifugal axons from the lAON and those from the aPC had distinct trajectories: the former tended to innervate the pars externa of the AON before entering the olfactory bulb, while the latter had extrabulbar collaterals that extended to a variety of targets. In contrast to the extrabulbar segments, no clear differences were found between the intrabulbar segments of axons from the lAON and from the aPC. The intrabulbar segments of centrifugal axons were mainly found in the granule cell layer but a few axons extended into the external plexiform and glomerular layer. Approximately 40% of centrifugal axons innervated both the medial and lateral aspects of the olfactory bulb. The number of boutons found on single intrabulbar segments was typically less than 1000. Boutons tended to aggregate and form complex terminal tufts with short axonal branches. Terminal tufts, no more than 10 in single axons from ipsilateral cortical areas, were localized to the granule cell layer with varying intervals; some tufts formed patchy clusters and others were scattered over areas that extended for a few millimeters. The patchy, widespread distribution of terminals suggests that the centrifugal axons are able to couple the activity of specific subsets of bulbar neurons even when the subsets are spatially separated.

  8. Calbindin distribution in cortical and subcortical brain structures of normal and rabies-infected mice.

    PubMed

    Torres-Fernández, Orlando; Yepes, Gloria E; Gómez, Javier E; Pimienta, Hernán J

    2005-10-01

    Rabies has been an enigmatic disease of the nervous system because microscopic findings in the brain tissue are not paralleled by the severity of the clinical illness. The calcium binding protein calbindin (CB) is a neuronal marker of great interest in neuroanatomy and neuropathology. CB-ir neurons in the striatum and cerebral cortex are gabaergic cells. In the present work CB-immunoreactivity was evaluated in brains of normal and rabies-infected mice. Rabies infection caused loss of CB-immunostaining in the cortical supragranular layers as well as in the striatum. Loss of CB in the brains of mice infected with rabies virus can produce impairment in Ca++ homeostasis and in the gabaergic neurotransmission.

  9. Microfilaments and microtubules control the shape, motility, and subcellular distribution of cortical mitochondria in characean internodal cells.

    PubMed

    Foissner, I

    2004-12-01

    The shape, motility, and subcellular distribution of mitochondria in characean internodal cells were studied by visualizing fluorescent dyes with confocal laser scanning microscopy and conducting drug-inhibitor experiments. Shape, size, number, and distribution of mitochondria varied according to the growth status and the metabolic activity within the cell. Vermiform (sausage-shaped), disc-, or amoeba-like mitochondria were present in elongating internodes, whereas very young cells and older cells that had completed growth contained short, rodlike organelles only. Mitochondria were evenly distributed and passively transported in the streaming endoplasm. In the cortex, mitochondria were sandwiched between the plasma membrane and the stationary chloroplast files and distributed in relation to the pattern of pH banding. Highest mitochondrial densities were found at the acid, photosynthetically more active regions, whereas the alkaline sites contained fewer and smaller mitochondria. In the cortex of elongating cells, small mitochondria moved slowly along microtubules or actin filaments. The shape and motility of giant mitochondria depended on the simultaneous interaction with both cytoskeletal systems. There was no microtubule-dependent motility in the cortex of nonelongating mature cells and mitochondria only occasionally travelled along actin filaments. These observations suggest that mitochondria of characean internodes possess motor proteins for microtubules and actin filaments, both of which can be used either as tracks for migration or for immobilization. The cortical cytoskeleton probably controls the spatiotemporal distribution of mitochondria within the cell and promotes their association with chloroplasts, which is necessary for exchange of metabolites during photosynthesis and detoxification.

  10. Spatiotemporal distribution of cortical processing of first and second languages in bilinguals. I. Effects of proficiency and linguistic setting.

    PubMed

    Pratt, Hillel; Abbasi, Dalal Abu-Amneh; Bleich, Naomi; Mittelman, Nomi; Starr, Arnold

    2013-11-01

    The study determined how spatiotemporal distribution of cortical activity to words in first and second language is affected by language, proficiency, and linguistic setting. Ten early bilinguals and 14 late adult bilinguals listened to pairs of words presented in Arabic (L1), Hebrew (L2), or in mixed pairs and indicated whether both words had the same meaning or not. Source current densities of event-related potentials were estimated. Activity to first words in the pair lateralized to right hemisphere, higher to L1 than L2 during early processing (<300 ms) among both groups but only among late bilinguals during late processing (>300 ms). During early and late processing, activities were larger in mixed than monolinguistic settings among early bilinguals but lower in mixed than in monolinguistic settings among late bilinguals. Late processing in auditory regions was of larger magnitude in left than right hemispheres among both groups. Activity to second words in the pair was larger in mixed than in monolinguistic settings during both early and late processing among both groups. Early processing of second words in auditory regions lateralized to the right among early bilinguals and to the left among late bilinguals, whereas late processing did not differ between groups. Wernicke's area activity during late processing of L2 was larger on the right, while on the left no significant differences between languages were found. The results show that cortical language processing in bilinguals differs between early and late processing and these differences are modulated by linguistic proficiency and setting.

  11. Effects of Habitual Physical Activity and Fitness on Tibial Cortical Bone Mass, Structure and Mass Distribution in Pre-pubertal Boys and Girls: The Look Study.

    PubMed

    Duckham, Rachel L; Rantalainen, Timo; Ducher, Gaele; Hill, Briony; Telford, Richard D; Telford, Rohan M; Daly, Robin M

    2016-07-01

    Targeted weight-bearing activities during the pre-pubertal years can improve cortical bone mass, structure and distribution, but less is known about the influence of habitual physical activity (PA) and fitness. This study examined the effects of contrasting habitual PA and fitness levels on cortical bone density, geometry and mass distribution in pre-pubertal children. Boys (n = 241) and girls (n = 245) aged 7-9 years had a pQCT scan to measure tibial mid-shaft total, cortical and medullary area, cortical thickness, density, polar strength strain index (SSIpolar) and the mass/density distribution through the bone cortex (radial distribution divided into endo-, mid- and pericortical regions) and around the centre of mass (polar distribution). Four contrasting PA and fitness groups (inactive-unfit, inactive-fit, active-unfit, active-fit) were generated based on daily step counts (pedometer, 7-days) and fitness levels (20-m shuttle test and vertical jump) for boys and girls separately. Active-fit boys had 7.3-7.7 % greater cortical area and thickness compared to inactive-unfit boys (P < 0.05), which was largely due to a 6.4-7.8 % (P < 0.05) greater cortical mass in the posterior-lateral, medial and posterior-medial 66 % tibial regions. Cortical area was not significantly different across PA-fitness categories in girls, but active-fit girls had 6.1 % (P < 0.05) greater SSIpolar compared to inactive-fit girls, which was likely due to their 6.7 % (P < 0.05) greater total bone area. There was also a small region-specific cortical mass benefit in the posterior-medial 66 % tibia cortex in active-fit girls. Higher levels of habitual PA-fitness were associated with small regional-specific gains in 66 % tibial cortical bone mass in pre-pubertal children, particularly boys.

  12. Glycolysis, but not Mitochondria, responsible for intracellular ATP distribution in cortical area of podocytes

    PubMed Central

    Ozawa, Shota; Ueda, Shuko; Imamura, Hiromi; Mori, Kiyoshi; Asanuma, Katsuhiko; Yanagita, Motoko; Nakagawa, Takahiko

    2015-01-01

    Differentiated podocytes, a type of renal glomerular cells, require substantial levels of energy to maintain glomerular physiology. Mitochondria and glycolysis are two major producers of ATP, but the precise roles of each in podocytes remain unknown. This study evaluated the roles of mitochondria and glycolysis in differentiated and differentiating podocytes. Mitochondria in differentiated podocytes are located in the central part of cell body while blocking mitochondria had minor effects on cell shape and migratory ability. In contrast, blocking glycolysis significantly reduced the formation of lamellipodia, a cortical area of these cells, decreased the cell migratory ability and induced the apoptosis. Consistently, the local ATP production in lamellipodia was predominantly regulated by glycolysis. In turn, synaptopodin expression was ameliorated by blocking either mitochondrial respiration or glycolysis. Similar to differentiated podocytes, the differentiating podocytes utilized the glycolysis for regulating apoptosis and lamellipodia formation while synaptopodin expression was likely involved in both mitochondrial OXPHOS and glycolysis. Finally, adult mouse podocytes have most of mitochondria predominantly in the center of the cytosol whereas phosphofructokinase, a rate limiting enzyme for glycolysis, was expressed in foot processes. These data suggest that mitochondria and glycolysis play parallel but distinct roles in differentiated and differentiating podocytes. PMID:26677804

  13. Topographic Distribution of Stimulus-Specific Adaptation across Auditory Cortical Fields in the Anesthetized Rat

    PubMed Central

    Nieto-Diego, Javier; Malmierca, Manuel S.

    2016-01-01

    Stimulus-specific adaptation (SSA) in single neurons of the auditory cortex was suggested to be a potential neural correlate of the mismatch negativity (MMN), a widely studied component of the auditory event-related potentials (ERP) that is elicited by changes in the auditory environment. However, several aspects on this SSA/MMN relation remain unresolved. SSA occurs in the primary auditory cortex (A1), but detailed studies on SSA beyond A1 are lacking. To study the topographic organization of SSA, we mapped the whole rat auditory cortex with multiunit activity recordings, using an oddball paradigm. We demonstrate that SSA occurs outside A1 and differs between primary and nonprimary cortical fields. In particular, SSA is much stronger and develops faster in the nonprimary than in the primary fields, paralleling the organization of subcortical SSA. Importantly, strong SSA is present in the nonprimary auditory cortex within the latency range of the MMN in the rat and correlates with an MMN-like difference wave in the simultaneously recorded local field potentials (LFP). We present new and strong evidence linking SSA at the cellular level to the MMN, a central tool in cognitive and clinical neuroscience. PMID:26950883

  14. Glycolysis, but not Mitochondria, responsible for intracellular ATP distribution in cortical area of podocytes.

    PubMed

    Ozawa, Shota; Ueda, Shuko; Imamura, Hiromi; Mori, Kiyoshi; Asanuma, Katsuhiko; Yanagita, Motoko; Nakagawa, Takahiko

    2015-12-18

    Differentiated podocytes, a type of renal glomerular cells, require substantial levels of energy to maintain glomerular physiology. Mitochondria and glycolysis are two major producers of ATP, but the precise roles of each in podocytes remain unknown. This study evaluated the roles of mitochondria and glycolysis in differentiated and differentiating podocytes. Mitochondria in differentiated podocytes are located in the central part of cell body while blocking mitochondria had minor effects on cell shape and migratory ability. In contrast, blocking glycolysis significantly reduced the formation of lamellipodia, a cortical area of these cells, decreased the cell migratory ability and induced the apoptosis. Consistently, the local ATP production in lamellipodia was predominantly regulated by glycolysis. In turn, synaptopodin expression was ameliorated by blocking either mitochondrial respiration or glycolysis. Similar to differentiated podocytes, the differentiating podocytes utilized the glycolysis for regulating apoptosis and lamellipodia formation while synaptopodin expression was likely involved in both mitochondrial OXPHOS and glycolysis. Finally, adult mouse podocytes have most of mitochondria predominantly in the center of the cytosol whereas phosphofructokinase, a rate limiting enzyme for glycolysis, was expressed in foot processes. These data suggest that mitochondria and glycolysis play parallel but distinct roles in differentiated and differentiating podocytes.

  15. Distributed Processing and Cortical Specialization for Speech and Environmental Sounds in Human Temporal Cortex

    ERIC Educational Resources Information Center

    Leech, Robert; Saygin, Ayse Pinar

    2011-01-01

    Using functional MRI, we investigated whether auditory processing of both speech and meaningful non-linguistic environmental sounds in superior and middle temporal cortex relies on a complex and spatially distributed neural system. We found that evidence for spatially distributed processing of speech and environmental sounds in a substantial…

  16. Anatomical coupling among distributed cortical regions in youth varies as a function of individual differences in vocabulary abilities.

    PubMed

    Lee, Nancy Raitano; Raznahan, Armin; Wallace, Gregory L; Alexander-Bloch, Aaron; Clasen, Liv S; Lerch, Jason P; Giedd, Jay N

    2014-05-01

    Patient lesion and functional magnetic resonance imaging (fMRI) studies have provided convincing evidence that a distributed brain network subserves word knowledge. However, little is known about the structural correlates of this network within the context of typical development and whether anatomical coupling in linguistically relevant regions of cortex varies as a function of vocabulary skill. Here we investigate the association between vocabulary and anatomical coupling in 235 typically developing youth (ages 6-19 years) using structural MRI. The study's primary aim was to evaluate whether higher vocabulary performance was associated with greater vertex-level cortical thickness covariation in distributed regions of cortex known to be associated with word knowledge. Results indicate that better vocabulary skills are associated with greater anatomical coupling in several linguistically relevant regions of cortex, including the left inferior parietal (temporal-parietal junction), inferior temporal, middle frontal, and superior frontal gyri and the right inferior frontal and precentral gyri. Furthermore, in high vocabulary scorers, stronger coupling is found among these regions. Thus, complementing patient and fMRI studies, this is the first investigation to highlight the relevance of anatomical covariance within the cortex to vocabulary skills in typically developing youth, further elucidating the distributed nature of neural systems subserving word knowledge.

  17. Anatomical coupling among distributed cortical regions in youth varies as a function of individual differences in vocabulary abilities.

    PubMed

    Lee, Nancy Raitano; Raznahan, Armin; Wallace, Gregory L; Alexander-Bloch, Aaron; Clasen, Liv S; Lerch, Jason P; Giedd, Jay N

    2014-05-01

    Patient lesion and functional magnetic resonance imaging (fMRI) studies have provided convincing evidence that a distributed brain network subserves word knowledge. However, little is known about the structural correlates of this network within the context of typical development and whether anatomical coupling in linguistically relevant regions of cortex varies as a function of vocabulary skill. Here we investigate the association between vocabulary and anatomical coupling in 235 typically developing youth (ages 6-19 years) using structural MRI. The study's primary aim was to evaluate whether higher vocabulary performance was associated with greater vertex-level cortical thickness covariation in distributed regions of cortex known to be associated with word knowledge. Results indicate that better vocabulary skills are associated with greater anatomical coupling in several linguistically relevant regions of cortex, including the left inferior parietal (temporal-parietal junction), inferior temporal, middle frontal, and superior frontal gyri and the right inferior frontal and precentral gyri. Furthermore, in high vocabulary scorers, stronger coupling is found among these regions. Thus, complementing patient and fMRI studies, this is the first investigation to highlight the relevance of anatomical covariance within the cortex to vocabulary skills in typically developing youth, further elucidating the distributed nature of neural systems subserving word knowledge. PMID:23728856

  18. Spatiotemporal distribution of cortical processing of first and second languages in bilinguals. II. Effects of phonologic and semantic priming.

    PubMed

    Pratt, Hillel; Abbasi, Dalal Abu-Amneh; Bleich, Naomi; Mittelman, Nomi; Starr, Arnold

    2013-11-01

    This study determined the effects of phonology and semantics on the distribution of cortical activity to the second of a pair of words in first and second language (mixed pairs). The effects of relative proficiency in the two languages and linguistic setting (monolinguistic or mixed) are reported in a companion paper. Ten early bilinguals and 14 late bilinguals listened to mixed pairs of words in Arabic (L1) and Hebrew (L2) and indicated whether both words in the pair had the same or different meanings. The spatio-temporal distribution of current densities of event-related potentials were estimated for each language and according to semantic and phonologic relationship (same or different) compared with the first word in the pair. During early processing (<300 ms), brain activity in temporal and temporoparietal auditory areas was enhanced by phonologic incongruence between words in the pair and in Wernicke's area by both phonologic and semantic priming. In contrast, brain activities during late processing (>300 ms) were enhanced by semantic incongruence between the two words, particularly in temporal areas and in left hemisphere Broca's and Wernicke's areas. The latter differences were greater when words were in L2. Surprisingly, no significant effects of relative proficiency on processing the second word in the pair were found. These results indicate that the distribution of brain activity to the second of two words presented bilingually is affected differently during early and late processing by both semantic and phonologic priming by- and incongruence with the immediately preceding word.

  19. Sparse Regression as a Sparse Eigenvalue Problem

    NASA Technical Reports Server (NTRS)

    Moghaddam, Baback; Gruber, Amit; Weiss, Yair; Avidan, Shai

    2008-01-01

    We extend the l0-norm "subspectral" algorithms for sparse-LDA [5] and sparse-PCA [6] to general quadratic costs such as MSE in linear (kernel) regression. The resulting "Sparse Least Squares" (SLS) problem is also NP-hard, by way of its equivalence to a rank-1 sparse eigenvalue problem (e.g., binary sparse-LDA [7]). Specifically, for a general quadratic cost we use a highly-efficient technique for direct eigenvalue computation using partitioned matrix inverses which leads to dramatic x103 speed-ups over standard eigenvalue decomposition. This increased efficiency mitigates the O(n4) scaling behaviour that up to now has limited the previous algorithms' utility for high-dimensional learning problems. Moreover, the new computation prioritizes the role of the less-myopic backward elimination stage which becomes more efficient than forward selection. Similarly, branch-and-bound search for Exact Sparse Least Squares (ESLS) also benefits from partitioned matrix inverse techniques. Our Greedy Sparse Least Squares (GSLS) generalizes Natarajan's algorithm [9] also known as Order-Recursive Matching Pursuit (ORMP). Specifically, the forward half of GSLS is exactly equivalent to ORMP but more efficient. By including the backward pass, which only doubles the computation, we can achieve lower MSE than ORMP. Experimental comparisons to the state-of-the-art LARS algorithm [3] show forward-GSLS is faster, more accurate and more flexible in terms of choice of regularization

  20. Brightness variation distributions among main belt asteroids from sparse light-curve sampling with Pan-STARRS 1

    NASA Astrophysics Data System (ADS)

    McNeill, A.; Fitzsimmons, A.; Jedicke, R.; Wainscoat, R.; Denneau, L.; Vereš, P.; Magnier, E.; Chambers, K. C.; Kaiser, N.; Waters, C.

    2016-07-01

    The rotational state of asteroids is controlled by various physical mechanisms including collisions, internal damping and the Yarkovsky-O'Keefe-Radzievskii-Paddack effect. We have analysed the changes in magnitude between consecutive detections of ˜60 000 asteroids measured by the Panoramic Survey Telescope and Rapid Response System (PanSTARRS) 1 survey during its first 18 months of operations. We have attempted to explain the derived brightness changes physically and through the application of a simple model. We have found a tendency towards smaller magnitude variations with decreasing diameter for objects of 1 < D < 8 km. Assuming the shape distribution of objects in this size range to be independent of size and composition our model suggests a population with average axial ratios 1 : 0.85 ± 0.13 : 0.71 ± 0.13, with larger objects more likely to have spin axes perpendicular to the orbital plane.

  1. Two-Dimensional DOA and Polarization Estimation for a Mixture of Uncorrelated and Coherent Sources with Sparsely-Distributed Vector Sensor Array

    PubMed Central

    Si, Weijian; Zhao, Pinjiao; Qu, Zhiyu

    2016-01-01

    This paper presents an L-shaped sparsely-distributed vector sensor (SD-VS) array with four different antenna compositions. With the proposed SD-VS array, a novel two-dimensional (2-D) direction of arrival (DOA) and polarization estimation method is proposed to handle the scenario where uncorrelated and coherent sources coexist. The uncorrelated and coherent sources are separated based on the moduli of the eigenvalues. For the uncorrelated sources, coarse estimates are acquired by extracting the DOA information embedded in the steering vectors from estimated array response matrix of the uncorrelated sources, and they serve as coarse references to disambiguate fine estimates with cyclical ambiguity obtained from the spatial phase factors. For the coherent sources, four Hankel matrices are constructed, with which the coherent sources are resolved in a similar way as for the uncorrelated sources. The proposed SD-VS array requires only two collocated antennas for each vector sensor, thus the mutual coupling effects across the collocated antennas are reduced greatly. Moreover, the inter-sensor spacings are allowed beyond a half-wavelength, which results in an extended array aperture. Simulation results demonstrate the effectiveness and favorable performance of the proposed method. PMID:27258271

  2. Two-Dimensional DOA and Polarization Estimation for a Mixture of Uncorrelated and Coherent Sources with Sparsely-Distributed Vector Sensor Array.

    PubMed

    Si, Weijian; Zhao, Pinjiao; Qu, Zhiyu

    2016-01-01

    This paper presents an L-shaped sparsely-distributed vector sensor (SD-VS) array with four different antenna compositions. With the proposed SD-VS array, a novel two-dimensional (2-D) direction of arrival (DOA) and polarization estimation method is proposed to handle the scenario where uncorrelated and coherent sources coexist. The uncorrelated and coherent sources are separated based on the moduli of the eigenvalues. For the uncorrelated sources, coarse estimates are acquired by extracting the DOA information embedded in the steering vectors from estimated array response matrix of the uncorrelated sources, and they serve as coarse references to disambiguate fine estimates with cyclical ambiguity obtained from the spatial phase factors. For the coherent sources, four Hankel matrices are constructed, with which the coherent sources are resolved in a similar way as for the uncorrelated sources. The proposed SD-VS array requires only two collocated antennas for each vector sensor, thus the mutual coupling effects across the collocated antennas are reduced greatly. Moreover, the inter-sensor spacings are allowed beyond a half-wavelength, which results in an extended array aperture. Simulation results demonstrate the effectiveness and favorable performance of the proposed method. PMID:27258271

  3. Frontal and parietal cortical interactions with distributed visual representations during selective attention and action selection.

    PubMed

    Nelissen, Natalie; Stokes, Mark; Nobre, Anna C; Rushworth, Matthew F S

    2013-10-16

    Using multivoxel pattern analysis (MVPA), we studied how distributed visual representations in human occipitotemporal cortex are modulated by attention and link their modulation to concurrent activity in frontal and parietal cortex. We detected similar occipitotemporal patterns during a simple visuoperceptual task and an attention-to-working-memory task in which one or two stimuli were cued before being presented among other pictures. Pattern strength varied from highest to lowest when the stimulus was the exclusive focus of attention, a conjoint focus, and when it was potentially distracting. Although qualitatively similar effects were seen inside regions relatively specialized for the stimulus category and outside, the former were quantitatively stronger. By regressing occipitotemporal pattern strength against activity elsewhere in the brain, we identified frontal and parietal areas exerting top-down control over, or reading information out from, distributed patterns in occipitotemporal cortex. Their interactions with patterns inside regions relatively specialized for that stimulus category were higher than those with patterns outside those regions and varied in strength as a function of the attentional condition. One area, the frontal operculum, was distinguished by selectively interacting with occipitotemporal patterns only when they were the focus of attention. There was no evidence that any frontal or parietal area actively inhibited occipitotemporal representations even when they should be ignored and were suppressed. Using MVPA to decode information within these frontal and parietal areas showed that they contained information about attentional context and/or readout information from occipitotemporal cortex to guide behavior but that frontal regions lacked information about category identity.

  4. The Spatial Distribution of the Exocyst and Actin Cortical Patches Is Sufficient To Organize Hyphal Tip Growth

    PubMed Central

    Caballero-Lima, David; Kaneva, Iliyana N.; Watton, Simon P.

    2013-01-01

    In the hyphal tip of Candida albicans we have made detailed quantitative measurements of (i) exocyst components, (ii) Rho1, the regulatory subunit of (1,3)-β-glucan synthase, (iii) Rom2, the specialized guanine-nucleotide exchange factor (GEF) of Rho1, and (iv) actin cortical patches, the sites of endocytosis. We use the resulting data to construct and test a quantitative 3-dimensional model of fungal hyphal growth based on the proposition that vesicles fuse with the hyphal tip at a rate determined by the local density of exocyst components. Enzymes such as (1,3)-β-glucan synthase thus embedded in the plasma membrane continue to synthesize the cell wall until they are removed by endocytosis. The model successfully predicts the shape and dimensions of the hyphae, provided that endocytosis acts to remove cell wall-synthesizing enzymes at the subapical bands of actin patches. Moreover, a key prediction of the model is that the distribution of the synthase is substantially broader than the area occupied by the exocyst. This prediction is borne out by our quantitative measurements. Thus, although the model highlights detailed issues that require further investigation, in general terms the pattern of tip growth of fungal hyphae can be satisfactorily explained by a simple but quantitative model rooted within the known molecular processes of polarized growth. Moreover, the methodology can be readily adapted to model other forms of polarized growth, such as that which occurs in plant pollen tubes. PMID:23666623

  5. Sparse pseudospectral approximation method

    NASA Astrophysics Data System (ADS)

    Constantine, Paul G.; Eldred, Michael S.; Phipps, Eric T.

    2012-07-01

    Multivariate global polynomial approximations - such as polynomial chaos or stochastic collocation methods - are now in widespread use for sensitivity analysis and uncertainty quantification. The pseudospectral variety of these methods uses a numerical integration rule to approximate the Fourier-type coefficients of a truncated expansion in orthogonal polynomials. For problems in more than two or three dimensions, a sparse grid numerical integration rule offers accuracy with a smaller node set compared to tensor product approximation. However, when using a sparse rule to approximately integrate these coefficients, one often finds unacceptable errors in the coefficients associated with higher degree polynomials. By reexamining Smolyak's algorithm and exploiting the connections between interpolation and projection in tensor product spaces, we construct a sparse pseudospectral approximation method that accurately reproduces the coefficients of basis functions that naturally correspond to the sparse grid integration rule. The compelling numerical results show that this is the proper way to use sparse grid integration rules for pseudospectral approximation.

  6. Estimating sparse precision matrices

    NASA Astrophysics Data System (ADS)

    Padmanabhan, Nikhil; White, Martin; Zhou, Harrison H.; O'Connell, Ross

    2016-08-01

    We apply a method recently introduced to the statistical literature to directly estimate the precision matrix from an ensemble of samples drawn from a corresponding Gaussian distribution. Motivated by the observation that cosmological precision matrices are often approximately sparse, the method allows one to exploit this sparsity of the precision matrix to more quickly converge to an asymptotic 1/sqrt{N_sim} rate while simultaneously providing an error model for all of the terms. Such an estimate can be used as the starting point for further regularization efforts which can improve upon the 1/sqrt{N_sim} limit above, and incorporating such additional steps is straightforward within this framework. We demonstrate the technique with toy models and with an example motivated by large-scale structure two-point analysis, showing significant improvements in the rate of convergence. For the large-scale structure example, we find errors on the precision matrix which are factors of 5 smaller than for the sample precision matrix for thousands of simulations or, alternatively, convergence to the same error level with more than an order of magnitude fewer simulations.

  7. Highly parallel sparse Cholesky factorization

    NASA Technical Reports Server (NTRS)

    Gilbert, John R.; Schreiber, Robert

    1990-01-01

    Several fine grained parallel algorithms were developed and compared to compute the Cholesky factorization of a sparse matrix. The experimental implementations are on the Connection Machine, a distributed memory SIMD machine whose programming model conceptually supplies one processor per data element. In contrast to special purpose algorithms in which the matrix structure conforms to the connection structure of the machine, the focus is on matrices with arbitrary sparsity structure. The most promising algorithm is one whose inner loop performs several dense factorizations simultaneously on a 2-D grid of processors. Virtually any massively parallel dense factorization algorithm can be used as the key subroutine. The sparse code attains execution rates comparable to those of the dense subroutine. Although at present architectural limitations prevent the dense factorization from realizing its potential efficiency, it is concluded that a regular data parallel architecture can be used efficiently to solve arbitrarily structured sparse problems. A performance model is also presented and it is used to analyze the algorithms.

  8. Multisnapshot Sparse Bayesian Learning for DOA

    NASA Astrophysics Data System (ADS)

    Gerstoft, Peter; Mecklenbrauker, Christoph F.; Xenaki, Angeliki; Nannuru, Santosh

    2016-10-01

    The directions of arrival (DOA) of plane waves are estimated from multi-snapshot sensor array data using Sparse Bayesian Learning (SBL). The prior source amplitudes is assumed independent zero-mean complex Gaussian distributed with hyperparameters the unknown variances (i.e. the source powers). For a complex Gaussian likelihood with hyperparameter the unknown noise variance, the corresponding Gaussian posterior distribution is derived. For a given number of DOAs, the hyperparameters are automatically selected by maximizing the evidence and promote sparse DOA estimates. The SBL scheme for DOA estimation is discussed and evaluated competitively against LASSO ($\\ell_1$-regularization), conventional beamforming, and MUSIC

  9. Structured Multifrontal Sparse Solver

    2014-05-01

    StruMF is an algebraic structured preconditioner for the interative solution of large sparse linear systems. The preconditioner corresponds to a multifrontal variant of sparse LU factorization in which some dense blocks of the factors are approximated with low-rank matrices. It is algebraic in that it only requires the linear system itself, and the approximation threshold that determines the accuracy of individual low-rank approximations. Favourable rank properties are obtained using a block partitioning which is amore » refinement of the partitioning induced by nested dissection ordering.« less

  10. Cortical dynamics revisited.

    PubMed

    Singer, Wolf

    2013-12-01

    Recent discoveries on the organisation of the cortical connectome together with novel data on the dynamics of neuronal interactions require an extension of classical concepts on information processing in the cerebral cortex. These new insights justify considering the brain as a complex, self-organised system with nonlinear dynamics in which principles of distributed, parallel processing coexist with serial operations within highly interconnected networks. The observed dynamics suggest that cortical networks are capable of providing an extremely high-dimensional state space in which a large amount of evolutionary and ontogenetically acquired information can coexist and be accessible to rapid parallel search.

  11. Modeling cortical source dynamics and interactions during seizure.

    PubMed

    Mullen, Tim; Acar, Zeynep Akalin; Worrell, Gregory; Makeig, Scott

    2011-01-01

    Mapping the dynamics and spatial topography of brain source processes critically involved in initiating and propagating seizure activity is critical for effective epilepsy diagnosis, intervention, and treatment. In this report we analyze neuronal dynamics before and during epileptic seizures using adaptive multivariate autoregressive (VAR) models applied to maximally-independent (ICA) sources of intracranial EEG (iEEG, ECoG) data recorded from subdural electrodes implanted in a human patient for evaluation of surgery for epilepsy. We visualize the spatial distribution of causal sources and sinks of ictal activity on the cortical surface (gyral and sulcal) using a novel combination of multivariate Granger-causal and graph-theoretic metrics combined with distributed source localization by Sparse Bayesian Learning applied to a multi-scale patch basis. This analysis reveals and visualizes distinct, seizure stage-dependent shifts in inter-component spatiotemporal dynamics and connectivity including the clinically-identified epileptic foci. PMID:22254582

  12. Ephrin-B1 controls the columnar distribution of cortical pyramidal neurons by restricting their tangential migration.

    PubMed

    Dimidschstein, Jordane; Passante, Lara; Dufour, Audrey; van den Ameele, Jelle; Tiberi, Luca; Hrechdakian, Tatyana; Adams, Ralf; Klein, Rüdiger; Lie, Dieter Chichung; Jossin, Yves; Vanderhaeghen, Pierre

    2013-09-18

    Neurons of the cerebral cortex are organized in layers and columns. Unlike laminar patterning, the mechanisms underlying columnar organization remain largely unexplored. Here, we show that ephrin-B1 plays a key role in this process through the control of nonradial steps of migration of pyramidal neurons. In vivo gain of function of ephrin-B1 resulted in a reduction of tangential motility of pyramidal neurons, leading to abnormal neuronal clustering. Conversely, following genetic disruption of ephrin-B1, cortical neurons displayed a wider lateral dispersion, resulting in enlarged ontogenic columns. Dynamic analyses revealed that ephrin-B1 controls the lateral spread of pyramidal neurons by limiting neurite extension and tangential migration during the multipolar phase. Furthermore, we identified P-Rex1, a guanine-exchange factor for Rac3, as a downstream ephrin-B1 effector required to control migration during the multipolar phase. Our results demonstrate that ephrin-B1 inhibits nonradial migration of pyramidal neurons, thereby controlling the pattern of cortical columns.

  13. The effects of bone density and crestal cortical bone thickness on micromotion and peri-implant bone strain distribution in an immediately loaded implant: a nonlinear finite element analysis

    PubMed Central

    2016-01-01

    Purpose This study investigated the effects of bone density and crestal cortical bone thickness at the implant-placement site on micromotion (relative displacement between the implant and bone) and the peri-implant bone strain distribution under immediate-loading conditions. Methods A three-dimensional finite element model of the posterior mandible with an implant was constructed. Various bone parameters were simulated, including low or high cancellous bone density, low or high crestal cortical bone density, and crestal cortical bone thicknesses ranging from 0.5 to 2.5 mm. Delayed- and immediate-loading conditions were simulated. A buccolingual oblique load of 200 N was applied to the top of the abutment. Results The maximum extent of micromotion was approximately 100 μm in the low-density cancellous bone models, whereas it was under 30 μm in the high-density cancellous bone models. Crestal cortical bone thickness significantly affected the maximum micromotion in the low-density cancellous bone models. The minimum principal strain in the peri-implant cortical bone was affected by the density of the crestal cortical bone and cancellous bone to the same degree for both delayed and immediate loading. In the low-density cancellous bone models under immediate loading, the minimum principal strain in the peri-implant cortical bone decreased with an increase in crestal cortical bone thickness. Conclusions Cancellous bone density may be a critical factor for avoiding excessive micromotion in immediately loaded implants. Crestal cortical bone thickness significantly affected the maximum extent of micromotion and peri-implant bone strain in simulations of low-density cancellous bone under immediate loading. PMID:27382504

  14. Sparse inpainting and isotropy

    SciTech Connect

    Feeney, Stephen M.; McEwen, Jason D.; Peiris, Hiranya V.; Marinucci, Domenico; Cammarota, Valentina; Wandelt, Benjamin D. E-mail: marinucc@axp.mat.uniroma2.it E-mail: h.peiris@ucl.ac.uk E-mail: cammarot@axp.mat.uniroma2.it

    2014-01-01

    Sparse inpainting techniques are gaining in popularity as a tool for cosmological data analysis, in particular for handling data which present masked regions and missing observations. We investigate here the relationship between sparse inpainting techniques using the spherical harmonic basis as a dictionary and the isotropy properties of cosmological maps, as for instance those arising from cosmic microwave background (CMB) experiments. In particular, we investigate the possibility that inpainted maps may exhibit anisotropies in the behaviour of higher-order angular polyspectra. We provide analytic computations and simulations of inpainted maps for a Gaussian isotropic model of CMB data, suggesting that the resulting angular trispectrum may exhibit small but non-negligible deviations from isotropy.

  15. Sparse matrix test collections

    SciTech Connect

    Duff, I.

    1996-12-31

    This workshop will discuss plans for coordinating and developing sets of test matrices for the comparison and testing of sparse linear algebra software. We will talk of plans for the next release (Release 2) of the Harwell-Boeing Collection and recent work on improving the accessibility of this Collection and others through the World Wide Web. There will only be three talks of about 15 to 20 minutes followed by a discussion from the floor.

  16. Histomorphometric Assessment of Cancellous and Cortical Bone Material Distribution in the Proximal Humerus of Normal and Osteoporotic Individuals

    PubMed Central

    Sprecher, Christoph M.; Schmidutz, Florian; Helfen, Tobias; Richards, R. Geoff; Blauth, Michael; Milz, Stefan

    2015-01-01

    Abstract Osteoporosis is a systemic disorder predominantly affecting postmenopausal women but also men at an advanced age. Both genders may suffer from low-energy fractures of, for example, the proximal humerus when reduction of the bone stock or/and quality has occurred. The aim of the current study was to compare the amount of bone in typical fracture zones of the proximal humerus in osteoporotic and non-osteoporotic individuals. The amount of bone in the proximal humerus was determined histomorphometrically in frontal plane sections. The donor bones were allocated to normal and osteoporotic groups using the T-score from distal radius DXA measurements of the same extremities. The T-score evaluation was done according to WHO criteria. Regional thickness of the subchondral plate and the metaphyseal cortical bone were measured using interactive image analysis. At all measured locations the amount of cancellous bone was significantly lower in individuals from the osteoporotic group compared to the non-osteoporotic one. The osteoporotic group showed more significant differences between regions of the same bone than the non-osteoporotic group. In both groups the subchondral cancellous bone and the subchondral plate were least affected by bone loss. In contrast, the medial metaphyseal region in the osteoporotic group exhibited higher bone loss in comparison to the lateral side. This observation may explain prevailing fracture patterns, which frequently involve compression fractures and certainly has an influence on the stability of implants placed in this medial region. It should be considered when planning the anchoring of osteosynthesis materials in osteoporotic patients with fractures of the proximal humerus. PMID:26705200

  17. Cellular Adaptation Facilitates Sparse and Reliable Coding in Sensory Pathways

    PubMed Central

    Farkhooi, Farzad; Froese, Anja; Muller, Eilif; Menzel, Randolf; Nawrot, Martin P.

    2013-01-01

    Most neurons in peripheral sensory pathways initially respond vigorously when a preferred stimulus is presented, but adapt as stimulation continues. It is unclear how this phenomenon affects stimulus coding in the later stages of sensory processing. Here, we show that a temporally sparse and reliable stimulus representation develops naturally in sequential stages of a sensory network with adapting neurons. As a modeling framework we employ a mean-field approach together with an adaptive population density treatment, accompanied by numerical simulations of spiking neural networks. We find that cellular adaptation plays a critical role in the dynamic reduction of the trial-by-trial variability of cortical spike responses by transiently suppressing self-generated fast fluctuations in the cortical balanced network. This provides an explanation for a widespread cortical phenomenon by a simple mechanism. We further show that in the insect olfactory system cellular adaptation is sufficient to explain the emergence of the temporally sparse and reliable stimulus representation in the mushroom body. Our results reveal a generic, biophysically plausible mechanism that can explain the emergence of a temporally sparse and reliable stimulus representation within a sequential processing architecture. PMID:24098101

  18. Cerebellar Functional Parcellation Using Sparse Dictionary Learning Clustering.

    PubMed

    Wang, Changqing; Kipping, Judy; Bao, Chenglong; Ji, Hui; Qiu, Anqi

    2016-01-01

    The human cerebellum has recently been discovered to contribute to cognition and emotion beyond the planning and execution of movement, suggesting its functional heterogeneity. We aimed to identify the functional parcellation of the cerebellum using information from resting-state functional magnetic resonance imaging (rs-fMRI). For this, we introduced a new data-driven decomposition-based functional parcellation algorithm, called Sparse Dictionary Learning Clustering (SDLC). SDLC integrates dictionary learning, sparse representation of rs-fMRI, and k-means clustering into one optimization problem. The dictionary is comprised of an over-complete set of time course signals, with which a sparse representation of rs-fMRI signals can be constructed. Cerebellar functional regions were then identified using k-means clustering based on the sparse representation of rs-fMRI signals. We solved SDLC using a multi-block hybrid proximal alternating method that guarantees strong convergence. We evaluated the reliability of SDLC and benchmarked its classification accuracy against other clustering techniques using simulated data. We then demonstrated that SDLC can identify biologically reasonable functional regions of the cerebellum as estimated by their cerebello-cortical functional connectivity. We further provided new insights into the cerebello-cortical functional organization in children.

  19. Cerebellar Functional Parcellation Using Sparse Dictionary Learning Clustering

    PubMed Central

    Wang, Changqing; Kipping, Judy; Bao, Chenglong; Ji, Hui; Qiu, Anqi

    2016-01-01

    The human cerebellum has recently been discovered to contribute to cognition and emotion beyond the planning and execution of movement, suggesting its functional heterogeneity. We aimed to identify the functional parcellation of the cerebellum using information from resting-state functional magnetic resonance imaging (rs-fMRI). For this, we introduced a new data-driven decomposition-based functional parcellation algorithm, called Sparse Dictionary Learning Clustering (SDLC). SDLC integrates dictionary learning, sparse representation of rs-fMRI, and k-means clustering into one optimization problem. The dictionary is comprised of an over-complete set of time course signals, with which a sparse representation of rs-fMRI signals can be constructed. Cerebellar functional regions were then identified using k-means clustering based on the sparse representation of rs-fMRI signals. We solved SDLC using a multi-block hybrid proximal alternating method that guarantees strong convergence. We evaluated the reliability of SDLC and benchmarked its classification accuracy against other clustering techniques using simulated data. We then demonstrated that SDLC can identify biologically reasonable functional regions of the cerebellum as estimated by their cerebello-cortical functional connectivity. We further provided new insights into the cerebello-cortical functional organization in children. PMID:27199650

  20. TASMANIAN Sparse Grids Module

    SciTech Connect

    and Drayton Munster, Miroslav Stoyanov

    2013-09-20

    Sparse Grids are the family of methods of choice for multidimensional integration and interpolation in low to moderate number of dimensions. The method is to select extend a one dimensional set of abscissas, weights and basis functions by taking a subset of all possible tensor products. The module provides the ability to create global and local approximations based on polynomials and wavelets. The software has three components, a library, a wrapper for the library that provides a command line interface via text files ad a MATLAB interface via the command line tool.

  1. Sparse Image Format

    2007-04-12

    The Sparse Image Format (SIF) is a file format for storing spare raster images. It works by breaking an image down into tiles. Space is savid by only storing non-uniform tiles, i.e. tiles with at least two different pixel values. If a tile is completely uniform, its common pixel value is stored instead of the complete tile raster. The software is a library in the C language used for manipulating files in SIF format. Itmore » supports large files (> 2GB) and is designed to build in Windows and Linux environments.« less

  2. TASMANIAN Sparse Grids Module

    2013-09-20

    Sparse Grids are the family of methods of choice for multidimensional integration and interpolation in low to moderate number of dimensions. The method is to select extend a one dimensional set of abscissas, weights and basis functions by taking a subset of all possible tensor products. The module provides the ability to create global and local approximations based on polynomials and wavelets. The software has three components, a library, a wrapper for the library thatmore » provides a command line interface via text files ad a MATLAB interface via the command line tool.« less

  3. Sparse Image Format

    SciTech Connect

    Eads, Damian Ryan

    2007-04-12

    The Sparse Image Format (SIF) is a file format for storing spare raster images. It works by breaking an image down into tiles. Space is savid by only storing non-uniform tiles, i.e. tiles with at least two different pixel values. If a tile is completely uniform, its common pixel value is stored instead of the complete tile raster. The software is a library in the C language used for manipulating files in SIF format. It supports large files (> 2GB) and is designed to build in Windows and Linux environments.

  4. Early asymmetries in maternal transcript distribution associated with a cortical microtubule network and a polar body in the beetle Tribolium castaneum.

    PubMed

    Peel, Andrew D; Averof, Michalis

    2010-11-01

    The localization of maternal mRNAs during oogenesis plays a central role in axial specification in some insects. Here we describe a polar body-associated asymmetry in maternal transcript distribution in pre-blastoderm eggs of the beetle Tribolium castaneum. Since the position of the polar body marks the future dorsal side of the embryo, we have investigated whether this asymmetry in mRNA distribution plays a role in dorsal-ventral axis specification. Whilst our results suggest polar body-associated transcripts do not play a significant role in specifying the DV axis, at least during early embryogenesis, we do find that the polar body is closely associated with a cortical microtubule network (CMN), which may play a role in the localization of transcripts during oogenesis. Transcripts of the gene T.c.pangolin co-localize with the CMN at the time of their anterior localization during oogenesis and their anterior localization is disrupted by the microtubule-depolymerizing agent colcemid. PMID:20857499

  5. Early asymmetries in maternal transcript distribution associated with a cortical microtubule network and a polar body in the beetle Tribolium castaneum.

    PubMed

    Peel, Andrew D; Averof, Michalis

    2010-11-01

    The localization of maternal mRNAs during oogenesis plays a central role in axial specification in some insects. Here we describe a polar body-associated asymmetry in maternal transcript distribution in pre-blastoderm eggs of the beetle Tribolium castaneum. Since the position of the polar body marks the future dorsal side of the embryo, we have investigated whether this asymmetry in mRNA distribution plays a role in dorsal-ventral axis specification. Whilst our results suggest polar body-associated transcripts do not play a significant role in specifying the DV axis, at least during early embryogenesis, we do find that the polar body is closely associated with a cortical microtubule network (CMN), which may play a role in the localization of transcripts during oogenesis. Transcripts of the gene T.c.pangolin co-localize with the CMN at the time of their anterior localization during oogenesis and their anterior localization is disrupted by the microtubule-depolymerizing agent colcemid.

  6. Sparse MEG source imaging in Landau-Kleffner syndrome.

    PubMed

    Zhu, Min; Zhang, Wenbo; Dickens, Deanna; Ding, Lei

    2011-01-01

    Epilepsy patients with Landau-Kleffner syndrome (LKS) usually have a normal brain structure, which makes it a challenge to identify the epileptogenic zone only based on magnetic resonance imaging (MRI) data. A sparse source imaging technique called variation based sparse cortical current density (VB-SCCD) imaging was adopted here to reconstruct cortical sources of magnetoencephalography (MEG) interictal spikes from an LKS patient. Realistic boundary element (BE) head and cortex models were built by segmenting structural MRI. 148-channel MEG was recorded for 10 minutes between seizures. Total 29 epileptiform spikes were selected for analysis. The primary cortical sources were observed locating at the left intra- and perisylvian cortex. Multiple extrasylvian sources were identified as the secondary sources. The spatio-temporal patterns of cortical sources provide more insights about the neuronal synchrony and propagation of epileptic discharges. Our observations were consistent with presurgical diagnosis for this patient and observation of aphasia in LKS. The present results suggest that the promising of VB-SCCD technique in assisting with presurgical planning and studying the neural network for LKS in determining the lateralization of epileptic origins. It can further be applied to non-invasively localize and/or lateralize eloquent cortex for language for epilepsy patients in general in the future.

  7. Neonatal Atlas Construction Using Sparse Representation

    PubMed Central

    Shi, Feng; Wang, Li; Wu, Guorong; Li, Gang; Gilmore, John H.; Lin, Weili; Shen, Dinggang

    2014-01-01

    Atlas construction generally includes first an image registration step to normalize all images into a common space and then an atlas building step to fuse the information from all the aligned images. Although numerous atlas construction studies have been performed to improve the accuracy of the image registration step, unweighted or simply weighted average is often used in the atlas building step. In this article, we propose a novel patch-based sparse representation method for atlas construction after all images have been registered into the common space. By taking advantage of local sparse representation, more anatomical details can be recovered in the built atlas. To make the anatomical structures spatially smooth in the atlas, the anatomical feature constraints on group structure of representations and also the overlapping of neighboring patches are imposed to ensure the anatomical consistency between neighboring patches. The proposed method has been applied to 73 neonatal MR images with poor spatial resolution and low tissue contrast, for constructing a neonatal brain atlas with sharp anatomical details. Experimental results demonstrate that the proposed method can significantly enhance the quality of the constructed atlas by discovering more anatomical details especially in the highly convoluted cortical regions. The resulting atlas demonstrates superior performance of our atlas when applied to spatially normalizing three different neonatal datasets, compared with other start-of-the-art neonatal brain atlases. PMID:24638883

  8. Sparse Hashing Tracking.

    PubMed

    Zhang, Lihe; Lu, Huchuan; Du, Dandan; Liu, Luning

    2016-02-01

    In this paper, we propose a novel tracking framework based on a sparse and discriminative hashing method. Different from the previous work, we treat object tracking as an approximate nearest neighbor searching process in a binary space. Using the hash functions, the target templates and the candidates can be projected into the Hamming space, facilitating the distance calculation and tracking efficiency. First, we integrate both the inter-class and intra-class information to train multiple hash functions for better classification, while most classifiers in previous tracking methods usually neglect the inter-class correlation, which may cause the inaccuracy. Then, we introduce sparsity into the hash coefficient vectors for dynamic feature selection, which is crucial to select the discriminative and stable features to adapt to visual variations during the tracking process. Extensive experiments on various challenging sequences show that the proposed algorithm performs favorably against the state-of-the-art methods.

  9. Regional Evaluation of Groundwater Age Distributions Using Lumped Parameter Models with Large, Sparse Datasets: Example from the Central Valley, California, USA

    NASA Astrophysics Data System (ADS)

    Jurgens, B. C.; Bohlke, J. K.; Voss, S.; Fram, M. S.; Esser, B.

    2015-12-01

    Tracer-based, lumped parameter models (LPMs) are an appealing way to estimate the distribution of age for groundwater because the cost of sampling wells is often less than building numerical groundwater flow models sufficiently complex to provide groundwater age distributions. In practice, however, tracer datasets are often incomplete because of anthropogenic or terrigenic contamination of tracers, or analytical limitations. While age interpretations using such datsets can have large uncertainties, it may still be possible to identify key parts of the age distribution if LPMs are carefully chosen to match hydrogeologic conceptualization and the degree of age mixing is reasonably estimated. We developed a systematic approach for evaluating groundwater age distributions using LPMs with a large but incomplete set of tracer data (3H, 3Hetrit, 14C, and CFCs) from 535 wells, mostly used for public supply, in the Central Valley, California, USA that were sampled by the USGS for the California State Water Resources Control Board Groundwater Ambient Monitoring and Assessment or the USGS National Water Quality Assessment Programs. In addition to mean ages, LPMs gave estimates of unsaturated zone travel times, recharge rates for pre- and post-development groundwater, the degree of age mixing in wells, proportion of young water (<60 yrs), and the depth of the boundary between post-development and predevelopment groundwater throughout the Central Valley. Age interpretations were evaluated by comparing past nitrate trends with LPM predicted trends, and whether the presence or absence of anthropogenic organic compounds was consistent with model results. This study illustrates a practical approach for assessing groundwater age information at a large scale to reveal important characteristics about the age structure of a major aquifer, and of the water supplies being derived from it.

  10. Homologs of mitochondrial transcription factor B, sparsely distributed within the eukaryotic radiation, are likely derived from the dimethyladenosine methyltransferase of the mitochondrial endosymbiont.

    PubMed

    Shutt, Timothy E; Gray, Michael W

    2006-06-01

    Mitochondrial transcription factor B (mtTFB), an essential component in regulating the expression of mitochondrial DNA-encoded genes in both yeast and humans, is a dimethyladenosine methyltransferase (DMT) that has acquired a secondary role in mitochondrial transcription. So far, mtTFB has only been well studied in Opisthokonta (metazoan animals and fungi). Here we investigate the phylogenetic distribution of mtTFB homologs throughout the domain Eucarya, documenting the first examples of this protein outside of the opisthokonts. Surprisingly, we identified putative mtTFB homologs only in amoebozoan protists and trypanosomatids. Phylogenetic analysis together with conservation of intron positions in amoebozoan and human genes supports the grouping of the putative mtTFB homologs as a distinct clade. Phylogenetic analysis further demonstrates that the mtTFB is most likely derived from the DMT of the mitochondrial endosymbiont.

  11. Spatial integration and cortical dynamics.

    PubMed Central

    Gilbert, C D; Das, A; Ito, M; Kapadia, M; Westheimer, G

    1996-01-01

    Cells in adult primary visual cortex are capable of integrating information over much larger portions of the visual field than was originally thought. Moreover, their receptive field properties can be altered by the context within which local features are presented and by changes in visual experience. The substrate for both spatial integration and cortical plasticity is likely to be found in a plexus of long-range horizontal connections, formed by cortical pyramidal cells, which link cells within each cortical area over distances of 6-8 mm. The relationship between horizontal connections and cortical functional architecture suggests a role in visual segmentation and spatial integration. The distribution of lateral interactions within striate cortex was visualized with optical recording, and their functional consequences were explored by using comparable stimuli in human psychophysical experiments and in recordings from alert monkeys. They may represent the substrate for perceptual phenomena such as illusory contours, surface fill-in, and contour saliency. The dynamic nature of receptive field properties and cortical architecture has been seen over time scales ranging from seconds to months. One can induce a remapping of the topography of visual cortex by making focal binocular retinal lesions. Shorter-term plasticity of cortical receptive fields was observed following brief periods of visual stimulation. The mechanisms involved entailed, for the short-term changes, altering the effectiveness of existing cortical connections, and for the long-term changes, sprouting of axon collaterals and synaptogenesis. The mutability of cortical function implies a continual process of calibration and normalization of the perception of visual attributes that is dependent on sensory experience throughout adulthood and might further represent the mechanism of perceptual learning. Images Fig. 1 Fig. 2 Fig. 3 Fig. 4 Fig. 5 PMID:8570604

  12. Population coding in sparsely connected networks of noisy neurons

    PubMed Central

    Tripp, Bryan P.; Orchard, Jeff

    2012-01-01

    This study examines the relationship between population coding and spatial connection statistics in networks of noisy neurons. Encoding of sensory information in the neocortex is thought to require coordinated neural populations, because individual cortical neurons respond to a wide range of stimuli, and exhibit highly variable spiking in response to repeated stimuli. Population coding is rooted in network structure, because cortical neurons receive information only from other neurons, and because the information they encode must be decoded by other neurons, if it is to affect behavior. However, population coding theory has often ignored network structure, or assumed discrete, fully connected populations (in contrast with the sparsely connected, continuous sheet of the cortex). In this study, we modeled a sheet of cortical neurons with sparse, primarily local connections, and found that a network with this structure could encode multiple internal state variables with high signal-to-noise ratio. However, we were unable to create high-fidelity networks by instantiating connections at random according to spatial connection probabilities. In our models, high-fidelity networks required additional structure, with higher cluster factors and correlations between the inputs to nearby neurons. PMID:22586391

  13. Cellular distribution of vascular endothelial growth factor A (VEGFA) and B (VEGFB) and VEGF receptors 1 and 2 in focal cortical dysplasia type IIB

    PubMed Central

    Boer, Karin; Troost, Dirk; Spliet, Wim G. M.; van Rijen, Peter C.; Gorter, Jan A.

    2008-01-01

    Members of the vascular endothelial growth factor (VEGF) family are key signaling proteins in the induction and regulation of angiogenesis, both during development and in pathological conditions. However, signaling mediated through VEGF family proteins and their receptors has recently been shown to have direct effects on neurons and glial cells. In the present study, we immunocytochemically investigated the expression and cellular distribution of VEGFA, VEGFB, and their associated receptors (VEGFR-1 and VEGFR-2) in focal cortical dysplasia (FCD) type IIB from patients with medically intractable epilepsy. Histologically normal temporal cortex and perilesional regions displayed neuronal immunoreactivity (IR) for VEGFA, VEGFB, and VEGF receptors (VEGFR-1 and VEGFR-2), mainly in pyramidal neurons. Weak IR was observed in blood vessels and there was no notable glial IR within the grey and white matter. In all FCD specimens, VEGFA, VEGFB, and both VEGF receptors were highly expressed in dysplastic neurons. IR in astroglial and balloon cells was observed for VEGFA and its receptors. VEGFR-1 displayed strong endothelial staining in FCD. Double-labeling also showed expression of VEGFA, VEGFB and VEGFR-1 in cells of the microglia/macrophage lineage. The neuronal expression of both VEGFA and VEGFB, together with their specific receptors in FCD, suggests autocrine/paracrine effects on dysplastic neurons. These autocrine/paracrine effects could play a role in the development of FCD, preventing the death of abnormal neuronal cells. In addition, the expression of VEGFA and its receptors in glial cells within the dysplastic cortex indicates that VEGF-mediated signaling could contribute to astroglial activation and associated inflammatory reactions. PMID:18317782

  14. Improved bidirectional retrieval of sparse patterns stored by Hebbian learning.

    PubMed

    Sommer, Friedrich T.; Palm, Gunther

    1999-03-01

    The Willshaw model is asymptotically the most efficient neural associative memory (NAM), but its finite version is hampered by high retrieval errors. Iterative retrieval has been proposed in a large number of different models to improve performance in auto-association tasks. In this paper, bidirectional retrieval for the hetero-associative memory task is considered: we define information efficiency as a general performance measure for bidirectional associative memory (BAM) and determine its asymptotic bound for the bidirectional Willshaw model. For the finite Willshaw model, an efficient new bidirectional retrieval strategy is proposed, the appropriate combinatorial model analysis is derived, and implications of the proposed sparse BAM for applications and brain theory are discussed. The distribution of the dendritic sum in the finite Willshaw model given by Buckingham and Willshaw [Buckingham, J., & Willshaw, D. (1992). Performance characteristics of associative nets. Network, 3, 407-414] allows no fast numerical evaluation. We derive a combinatorial formula with a highly reduced evaluation time that is used in the improved error analysis of the basic model and for estimation of the retrieval error in the naive model extension, where bidirectional retrieval is employed in the hetero-associative Willshaw model. The analysis rules out the naive BAM extension as a promising improvement. A new bidirectional retrieval algorithm - called crosswise bidirectional (CB) retrieval - is presented. The cross talk error is significantly reduced without employing more complex learning procedures or dummy augmentation in the pattern coding, as proposed in other refined BAM models [Wang, Y. F., Cruz, J. B., & Mulligan, J. H. (1990). Two coding strategies for bidirectional associative memory. IEEE Trans. Neural Networks, 1(1), 81-92; Leung, C.-S., Chan, L.-W., & Lai, E. (1995). Stability, capacity and statistical dynamics of second-order bidirectional associative memory. IEEE Trans

  15. CCD Sparse Field CTE Internal

    NASA Astrophysics Data System (ADS)

    Hernandez, Svea

    2012-10-01

    CTE measurements are made using the "internal sparse field test", along the parallelaxis. The "POS=" optional parameter, introduced during cycle 11, is used to provideoff-center MSM positioning of some slits. All exposures are internals.

  16. CCD Sparse Field CTE Internal

    NASA Astrophysics Data System (ADS)

    Wolfe, Michael

    2011-10-01

    CTE measurements are made using the "internal sparse field test", along the parallelaxis. The "POS=" optional parameter, introduced during cycle 11, is used to provideoff-center MSM positionings of some slits. All exposures are internals.

  17. CCD Sparse Field CTE Internal

    NASA Astrophysics Data System (ADS)

    Wolfe, Michael

    2010-09-01

    CTE measurements are made using the "internal sparse field test", along the parallelaxis. The "POS=" optional parameter, introduced during cycle 11, is used to provideoff-center MSM positionings of some slits. All exposures are internals.

  18. CCD Sparse Field CTE Internal

    NASA Astrophysics Data System (ADS)

    Hernandez, Svea

    2013-10-01

    CTE measurements are made using the "internal sparse field test", along the parallelaxis. The "POS=" optional parameter, introduced during cycle 11, is used to provideoff-center MSM positioning of some slits. All exposures are internals.

  19. CCD Sparse Field CTE Internal

    NASA Astrophysics Data System (ADS)

    Wolfe, Michael

    2009-07-01

    CTE measurements are made using the "internal sparse field test", along the parallelaxis. The "POS=" optional parameter, introduced during cycle 11, is used to provideoff-center MSM positionings of some slits. All exposures are internals.

  20. Threaded Operations on Sparse Matrices

    SciTech Connect

    Sneed, Brett

    2015-09-01

    We investigate the use of sparse matrices and OpenMP multi-threading on linear algebra operations involving them. Several sparse matrix data structures are presented. Implementation of the multi- threading primarily occurs in the level one and two BLAS functions used within the four algorithms investigated{the Power Method, Conjugate Gradient, Biconjugate Gradient, and Jacobi's Method. The bene ts of launching threads once per high level algorithm are explored.

  1. Sparse Methods for Biomedical Data

    PubMed Central

    Ye, Jieping; Liu, Jun

    2013-01-01

    Following recent technological revolutions, the investigation of massive biomedical data with growing scale, diversity, and complexity has taken a center stage in modern data analysis. Although complex, the underlying representations of many biomedical data are often sparse. For example, for a certain disease such as leukemia, even though humans have tens of thousands of genes, only a few genes are relevant to the disease; a gene network is sparse since a regulatory pathway involves only a small number of genes; many biomedical signals are sparse or compressible in the sense that they have concise representations when expressed in a proper basis. Therefore, finding sparse representations is fundamentally important for scientific discovery. Sparse methods based on the ℓ1 norm have attracted a great amount of research efforts in the past decade due to its sparsity-inducing property, convenient convexity, and strong theoretical guarantees. They have achieved great success in various applications such as biomarker selection, biological network construction, and magnetic resonance imaging. In this paper, we review state-of-the-art sparse methods and their applications to biomedical data. PMID:24076585

  2. Representation-Independent Iteration of Sparse Data Arrays

    NASA Technical Reports Server (NTRS)

    James, Mark

    2007-01-01

    An approach is defined that describes a method of iterating over massively large arrays containing sparse data using an approach that is implementation independent of how the contents of the sparse arrays are laid out in memory. What is unique and important here is the decoupling of the iteration over the sparse set of array elements from how they are internally represented in memory. This enables this approach to be backward compatible with existing schemes for representing sparse arrays as well as new approaches. What is novel here is a new approach for efficiently iterating over sparse arrays that is independent of the underlying memory layout representation of the array. A functional interface is defined for implementing sparse arrays in any modern programming language with a particular focus for the Chapel programming language. Examples are provided that show the translation of a loop that computes a matrix vector product into this representation for both the distributed and not-distributed cases. This work is directly applicable to NASA and its High Productivity Computing Systems (HPCS) program that JPL and our current program are engaged in. The goal of this program is to create powerful, scalable, and economically viable high-powered computer systems suitable for use in national security and industry by 2010. This is important to NASA for its computationally intensive requirements for analyzing and understanding the volumes of science data from our returned missions.

  3. Mean-field sparse optimal control

    PubMed Central

    Fornasier, Massimo; Piccoli, Benedetto; Rossi, Francesco

    2014-01-01

    We introduce the rigorous limit process connecting finite dimensional sparse optimal control problems with ODE constraints, modelling parsimonious interventions on the dynamics of a moving population divided into leaders and followers, to an infinite dimensional optimal control problem with a constraint given by a system of ODE for the leaders coupled with a PDE of Vlasov-type, governing the dynamics of the probability distribution of the followers. In the classical mean-field theory, one studies the behaviour of a large number of small individuals freely interacting with each other, by simplifying the effect of all the other individuals on any given individual by a single averaged effect. In this paper, we address instead the situation where the leaders are actually influenced also by an external policy maker, and we propagate its effect for the number N of followers going to infinity. The technical derivation of the sparse mean-field optimal control is realized by the simultaneous development of the mean-field limit of the equations governing the followers dynamics together with the Γ-limit of the finite dimensional sparse optimal control problems. PMID:25288818

  4. Wavelet Sparse Approximate Inverse Preconditioners

    NASA Technical Reports Server (NTRS)

    Chan, Tony F.; Tang, W.-P.; Wan, W. L.

    1996-01-01

    There is an increasing interest in using sparse approximate inverses as preconditioners for Krylov subspace iterative methods. Recent studies of Grote and Huckle and Chow and Saad also show that sparse approximate inverse preconditioner can be effective for a variety of matrices, e.g. Harwell-Boeing collections. Nonetheless a drawback is that it requires rapid decay of the inverse entries so that sparse approximate inverse is possible. However, for the class of matrices that, come from elliptic PDE problems, this assumption may not necessarily hold. Our main idea is to look for a basis, other than the standard one, such that a sparse representation of the inverse is feasible. A crucial observation is that the kind of matrices we are interested in typically have a piecewise smooth inverse. We exploit this fact, by applying wavelet techniques to construct a better sparse approximate inverse in the wavelet basis. We shall justify theoretically and numerically that our approach is effective for matrices with smooth inverse. We emphasize that in this paper we have only presented the idea of wavelet approximate inverses and demonstrated its potential but have not yet developed a highly refined and efficient algorithm.

  5. Sparse modeling of spatial environmental variables associated with asthma

    PubMed Central

    Chang, Timothy S.; Gangnon, Ronald E.; Page, C. David; Buckingham, William R.; Tandias, Aman; Cowan, Kelly J.; Tomasallo, Carrie D.; Arndt, Brian G.; Hanrahan, Lawrence P.; Guilbert, Theresa W.

    2014-01-01

    Geographically distributed environmental factors influence the burden of diseases such as asthma. Our objective was to identify sparse environmental variables associated with asthma diagnosis gathered from a large electronic health record (EHR) dataset while controlling for spatial variation. An EHR dataset from the University of Wisconsin’s Family Medicine, Internal Medicine and Pediatrics Departments was obtained for 199,220 patients aged 5–50 years over a three-year period. Each patient’s home address was geocoded to one of 3,456 geographic census block groups. Over one thousand block group variables were obtained from a commercial database. We developed a Sparse Spatial Environmental Analysis (SASEA). Using this method, the environmental variables were first dimensionally reduced with sparse principal component analysis. Logistic thin plate regression spline modeling was then used to identify block group variables associated with asthma from sparse principal components. The addresses of patients from the EHR dataset were distributed throughout the majority of Wisconsin’s geography. Logistic thin plate regression spline modeling captured spatial variation of asthma. Four sparse principal components identified via model selection consisted of food at home, dog ownership, household size, and disposable income variables. In rural areas, dog ownership and renter occupied housing units from significant sparse principal components were associated with asthma. Our main contribution is the incorporation of sparsity in spatial modeling. SASEA sequentially added sparse principal components to Logistic thin plate regression spline modeling. This method allowed association of geographically distributed environmental factors with asthma using EHR and environmental datasets. SASEA can be applied to other diseases with environmental risk factors. PMID:25533437

  6. Sparse modeling of spatial environmental variables associated with asthma.

    PubMed

    Chang, Timothy S; Gangnon, Ronald E; David Page, C; Buckingham, William R; Tandias, Aman; Cowan, Kelly J; Tomasallo, Carrie D; Arndt, Brian G; Hanrahan, Lawrence P; Guilbert, Theresa W

    2015-02-01

    Geographically distributed environmental factors influence the burden of diseases such as asthma. Our objective was to identify sparse environmental variables associated with asthma diagnosis gathered from a large electronic health record (EHR) dataset while controlling for spatial variation. An EHR dataset from the University of Wisconsin's Family Medicine, Internal Medicine and Pediatrics Departments was obtained for 199,220 patients aged 5-50years over a three-year period. Each patient's home address was geocoded to one of 3456 geographic census block groups. Over one thousand block group variables were obtained from a commercial database. We developed a Sparse Spatial Environmental Analysis (SASEA). Using this method, the environmental variables were first dimensionally reduced with sparse principal component analysis. Logistic thin plate regression spline modeling was then used to identify block group variables associated with asthma from sparse principal components. The addresses of patients from the EHR dataset were distributed throughout the majority of Wisconsin's geography. Logistic thin plate regression spline modeling captured spatial variation of asthma. Four sparse principal components identified via model selection consisted of food at home, dog ownership, household size, and disposable income variables. In rural areas, dog ownership and renter occupied housing units from significant sparse principal components were associated with asthma. Our main contribution is the incorporation of sparsity in spatial modeling. SASEA sequentially added sparse principal components to Logistic thin plate regression spline modeling. This method allowed association of geographically distributed environmental factors with asthma using EHR and environmental datasets. SASEA can be applied to other diseases with environmental risk factors.

  7. Sparse modeling of spatial environmental variables associated with asthma.

    PubMed

    Chang, Timothy S; Gangnon, Ronald E; David Page, C; Buckingham, William R; Tandias, Aman; Cowan, Kelly J; Tomasallo, Carrie D; Arndt, Brian G; Hanrahan, Lawrence P; Guilbert, Theresa W

    2015-02-01

    Geographically distributed environmental factors influence the burden of diseases such as asthma. Our objective was to identify sparse environmental variables associated with asthma diagnosis gathered from a large electronic health record (EHR) dataset while controlling for spatial variation. An EHR dataset from the University of Wisconsin's Family Medicine, Internal Medicine and Pediatrics Departments was obtained for 199,220 patients aged 5-50years over a three-year period. Each patient's home address was geocoded to one of 3456 geographic census block groups. Over one thousand block group variables were obtained from a commercial database. We developed a Sparse Spatial Environmental Analysis (SASEA). Using this method, the environmental variables were first dimensionally reduced with sparse principal component analysis. Logistic thin plate regression spline modeling was then used to identify block group variables associated with asthma from sparse principal components. The addresses of patients from the EHR dataset were distributed throughout the majority of Wisconsin's geography. Logistic thin plate regression spline modeling captured spatial variation of asthma. Four sparse principal components identified via model selection consisted of food at home, dog ownership, household size, and disposable income variables. In rural areas, dog ownership and renter occupied housing units from significant sparse principal components were associated with asthma. Our main contribution is the incorporation of sparsity in spatial modeling. SASEA sequentially added sparse principal components to Logistic thin plate regression spline modeling. This method allowed association of geographically distributed environmental factors with asthma using EHR and environmental datasets. SASEA can be applied to other diseases with environmental risk factors. PMID:25533437

  8. Galaxy redshift surveys with sparse sampling

    SciTech Connect

    Chiang, Chi-Ting; Wullstein, Philipp; Komatsu, Eiichiro; Jee, Inh; Jeong, Donghui; Blanc, Guillermo A.; Ciardullo, Robin; Gronwall, Caryl; Hagen, Alex; Schneider, Donald P.; Drory, Niv; Fabricius, Maximilian; Landriau, Martin; Finkelstein, Steven; Jogee, Shardha; Cooper, Erin Mentuch; Tuttle, Sarah; Gebhardt, Karl; Hill, Gary J.

    2013-12-01

    Survey observations of the three-dimensional locations of galaxies are a powerful approach to measure the distribution of matter in the universe, which can be used to learn about the nature of dark energy, physics of inflation, neutrino masses, etc. A competitive survey, however, requires a large volume (e.g., V{sub survey} ∼ 10Gpc{sup 3}) to be covered, and thus tends to be expensive. A ''sparse sampling'' method offers a more affordable solution to this problem: within a survey footprint covering a given survey volume, V{sub survey}, we observe only a fraction of the volume. The distribution of observed regions should be chosen such that their separation is smaller than the length scale corresponding to the wavenumber of interest. Then one can recover the power spectrum of galaxies with precision expected for a survey covering a volume of V{sub survey} (rather than the volume of the sum of observed regions) with the number density of galaxies given by the total number of observed galaxies divided by V{sub survey} (rather than the number density of galaxies within an observed region). We find that regularly-spaced sampling yields an unbiased power spectrum with no window function effect, and deviations from regularly-spaced sampling, which are unavoidable in realistic surveys, introduce calculable window function effects and increase the uncertainties of the recovered power spectrum. On the other hand, we show that the two-point correlation function (pair counting) is not affected by sparse sampling. While we discuss the sparse sampling method within the context of the forthcoming Hobby-Eberly Telescope Dark Energy Experiment, the method is general and can be applied to other galaxy surveys.

  9. STIS Sparse Field CTE test

    NASA Astrophysics Data System (ADS)

    Goudfrooij, Paul

    1997-07-01

    CTE measurements are made using the "sparse field test", along both the serial and parallel axes. This program needs special commanding to provide {a} off-center MSM positionings of some slits, and {b} the ability to read out with any amplifier {A, B, C, or D}. All exposures are internals.

  10. Amesos2 Templated Direct Sparse Solver Package

    2011-05-24

    Amesos2 is a templated direct sparse solver package. Amesos2 provides interfaces to direct sparse solvers, rather than providing native solver capabilities. Amesos2 is a derivative work of the Trilinos package Amesos.

  11. P-SPARSLIB: A parallel sparse iterative solution package

    SciTech Connect

    Saad, Y.

    1994-12-31

    Iterative methods are gaining popularity in engineering and sciences at a time where the computational environment is changing rapidly. P-SPARSLIB is a project to build a software library for sparse matrix computations on parallel computers. The emphasis is on iterative methods and the use of distributed sparse matrices, an extension of the domain decomposition approach to general sparse matrices. One of the goals of this project is to develop a software package geared towards specific applications. For example, the author will test the performance and usefulness of P-SPARSLIB modules on linear systems arising from CFD applications. Equally important is the goal of portability. In the long run, the author wishes to ensure that this package is portable on a variety of platforms, including SIMD environments and shared memory environments.

  12. Sparse Sensing of Aerodynamic Loads on Insect Wings

    NASA Astrophysics Data System (ADS)

    Manohar, Krithika; Brunton, Steven; Kutz, J. Nathan

    2015-11-01

    We investigate how insects use sparse sensors on their wings to detect aerodynamic loading and wing deformation using a coupled fluid-structure model given periodically flapping input motion. Recent observations suggest that insects collect sensor information about their wing deformation to inform control actions for maneuvering and rejecting gust disturbances. Given a small number of point measurements of the chordwise aerodynamic loads from the sparse sensors, we reconstruct the entire chordwise loading using sparsesensing - a signal processing technique that reconstructs a signal from a small number of measurements using l1 norm minimization of sparse modal coefficients in some basis. We compare reconstructions from sensors randomly sampled from probability distributions biased toward different regions along the wing chord. In this manner, we determine the preferred regions along the chord for sensor placement and for estimating chordwise loads to inform control decisions in flight.

  13. Finding communities in sparse networks

    NASA Astrophysics Data System (ADS)

    Singh, Abhinav; Humphries, Mark D.

    2015-03-01

    Spectral algorithms based on matrix representations of networks are often used to detect communities, but classic spectral methods based on the adjacency matrix and its variants fail in sparse networks. New spectral methods based on non-backtracking random walks have recently been introduced that successfully detect communities in many sparse networks. However, the spectrum of non-backtracking random walks ignores hanging trees in networks that can contain information about their community structure. We introduce the reluctant backtracking operators that explicitly account for hanging trees as they admit a small probability of returning to the immediately previous node, unlike the non-backtracking operators that forbid an immediate return. We show that the reluctant backtracking operators can detect communities in certain sparse networks where the non-backtracking operators cannot, while performing comparably on benchmark stochastic block model networks and real world networks. We also show that the spectrum of the reluctant backtracking operator approximately optimises the standard modularity function. Interestingly, for this family of non- and reluctant-backtracking operators the main determinant of performance on real-world networks is whether or not they are normalised to conserve probability at each node.

  14. Sparse Matrices in MATLAB: Design and Implementation

    NASA Technical Reports Server (NTRS)

    Gilbert, John R.; Moler, Cleve; Schreiber, Robert

    1992-01-01

    The matrix computation language and environment MATLAB is extended to include sparse matrix storage and operations. The only change to the outward appearance of the MATLAB language is a pair of commands to create full or sparse matrices. Nearly all the operations of MATLAB now apply equally to full or sparse matrices, without any explicit action by the user. The sparse data structure represents a matrix in space proportional to the number of nonzero entries, and most of the operations compute sparse results in time proportional to the number of arithmetic operations on nonzeros.

  15. Optimized sparse-particle aerosol representations for modeling cloud-aerosol interactions

    NASA Astrophysics Data System (ADS)

    Fierce, Laura; McGraw, Robert

    2016-04-01

    Sparse representations of atmospheric aerosols are needed for efficient regional- and global-scale chemical transport models. Here we introduce a new framework for representing aerosol distributions, based on the method of moments. Given a set of moment constraints, we show how linear programming can be used to identify collections of sparse particles that approximately maximize distributional entropy. The collections of sparse particles derived from this approach reproduce CCN activity of the exact model aerosol distributions with high accuracy. Additionally, the linear programming techniques described in this study can be used to bound key aerosol properties, such as the number concentration of CCN. Unlike the commonly used sparse representations, such as modal and sectional schemes, the maximum-entropy moment-based approach is not constrained to pre-determined size bins or assumed distribution shapes. This study is a first step toward a new aerosol simulation scheme that will track multivariate aerosol distributions with sufficient computational efficiency for large-scale simulations.

  16. Simulating Cortical Feedback Modulation as Changes in Excitation and Inhibition in a Cortical Circuit Model.

    PubMed

    Zagha, Edward; Murray, John D; McCormick, David A

    2016-01-01

    Cortical feedback pathways are hypothesized to distribute context-dependent signals during flexible behavior. Recent experimental work has attempted to understand the mechanisms by which cortical feedback inputs modulate their target regions. Within the mouse whisker sensorimotor system, cortical feedback stimulation modulates spontaneous activity and sensory responsiveness, leading to enhanced sensory representations. However, the cellular mechanisms underlying these effects are currently unknown. In this study we use a simplified neural circuit model, which includes two recurrent excitatory populations and global inhibition, to simulate cortical modulation. First, we demonstrate how changes in the strengths of excitation and inhibition alter the input-output processing responses of our model. Second, we compare these responses with experimental findings from cortical feedback stimulation. Our analyses predict that enhanced inhibition underlies the changes in spontaneous and sensory evoked activity observed experimentally. More generally, these analyses provide a framework for relating cellular and synaptic properties to emergent circuit function and dynamic modulation. PMID:27595137

  17. Simulating Cortical Feedback Modulation as Changes in Excitation and Inhibition in a Cortical Circuit Model

    PubMed Central

    Murray, John D.; McCormick, David A.

    2016-01-01

    Abstract Cortical feedback pathways are hypothesized to distribute context-dependent signals during flexible behavior. Recent experimental work has attempted to understand the mechanisms by which cortical feedback inputs modulate their target regions. Within the mouse whisker sensorimotor system, cortical feedback stimulation modulates spontaneous activity and sensory responsiveness, leading to enhanced sensory representations. However, the cellular mechanisms underlying these effects are currently unknown. In this study we use a simplified neural circuit model, which includes two recurrent excitatory populations and global inhibition, to simulate cortical modulation. First, we demonstrate how changes in the strengths of excitation and inhibition alter the input–output processing responses of our model. Second, we compare these responses with experimental findings from cortical feedback stimulation. Our analyses predict that enhanced inhibition underlies the changes in spontaneous and sensory evoked activity observed experimentally. More generally, these analyses provide a framework for relating cellular and synaptic properties to emergent circuit function and dynamic modulation.

  18. Simulating Cortical Feedback Modulation as Changes in Excitation and Inhibition in a Cortical Circuit Model.

    PubMed

    Zagha, Edward; Murray, John D; McCormick, David A

    2016-01-01

    Cortical feedback pathways are hypothesized to distribute context-dependent signals during flexible behavior. Recent experimental work has attempted to understand the mechanisms by which cortical feedback inputs modulate their target regions. Within the mouse whisker sensorimotor system, cortical feedback stimulation modulates spontaneous activity and sensory responsiveness, leading to enhanced sensory representations. However, the cellular mechanisms underlying these effects are currently unknown. In this study we use a simplified neural circuit model, which includes two recurrent excitatory populations and global inhibition, to simulate cortical modulation. First, we demonstrate how changes in the strengths of excitation and inhibition alter the input-output processing responses of our model. Second, we compare these responses with experimental findings from cortical feedback stimulation. Our analyses predict that enhanced inhibition underlies the changes in spontaneous and sensory evoked activity observed experimentally. More generally, these analyses provide a framework for relating cellular and synaptic properties to emergent circuit function and dynamic modulation.

  19. Simulating Cortical Feedback Modulation as Changes in Excitation and Inhibition in a Cortical Circuit Model

    PubMed Central

    Murray, John D.; McCormick, David A.

    2016-01-01

    Abstract Cortical feedback pathways are hypothesized to distribute context-dependent signals during flexible behavior. Recent experimental work has attempted to understand the mechanisms by which cortical feedback inputs modulate their target regions. Within the mouse whisker sensorimotor system, cortical feedback stimulation modulates spontaneous activity and sensory responsiveness, leading to enhanced sensory representations. However, the cellular mechanisms underlying these effects are currently unknown. In this study we use a simplified neural circuit model, which includes two recurrent excitatory populations and global inhibition, to simulate cortical modulation. First, we demonstrate how changes in the strengths of excitation and inhibition alter the input–output processing responses of our model. Second, we compare these responses with experimental findings from cortical feedback stimulation. Our analyses predict that enhanced inhibition underlies the changes in spontaneous and sensory evoked activity observed experimentally. More generally, these analyses provide a framework for relating cellular and synaptic properties to emergent circuit function and dynamic modulation. PMID:27595137

  20. Dose-shaping using targeted sparse optimization

    SciTech Connect

    Sayre, George A.; Ruan, Dan

    2013-07-15

    Purpose: Dose volume histograms (DVHs) are common tools in radiation therapy treatment planning to characterize plan quality. As statistical metrics, DVHs provide a compact summary of the underlying plan at the cost of losing spatial information: the same or similar dose-volume histograms can arise from substantially different spatial dose maps. This is exactly the reason why physicians and physicists scrutinize dose maps even after they satisfy all DVH endpoints numerically. However, up to this point, little has been done to control spatial phenomena, such as the spatial distribution of hot spots, which has significant clinical implications. To this end, the authors propose a novel objective function that enables a more direct tradeoff between target coverage, organ-sparing, and planning target volume (PTV) homogeneity, and presents our findings from four prostate cases, a pancreas case, and a head-and-neck case to illustrate the advantages and general applicability of our method.Methods: In designing the energy minimization objective (E{sub tot}{sup sparse}), the authors utilized the following robust cost functions: (1) an asymmetric linear well function to allow differential penalties for underdose, relaxation of prescription dose, and overdose in the PTV; (2) a two-piece linear function to heavily penalize high dose and mildly penalize low and intermediate dose in organs-at risk (OARs); and (3) a total variation energy, i.e., the L{sub 1} norm applied to the first-order approximation of the dose gradient in the PTV. By minimizing a weighted sum of these robust costs, general conformity to dose prescription and dose-gradient prescription is achieved while encouraging prescription violations to follow a Laplace distribution. In contrast, conventional quadratic objectives are associated with a Gaussian distribution of violations, which is less forgiving to large violations of prescription than the Laplace distribution. As a result, the proposed objective E{sub tot

  1. Scenario generation for stochastic optimization problems via the sparse grid method

    SciTech Connect

    Chen, Michael; Mehrotra, Sanjay; Papp, David

    2015-04-19

    We study the use of sparse grids in the scenario generation (or discretization) problem in stochastic programming problems where the uncertainty is modeled using a continuous multivariate distribution. We show that, under a regularity assumption on the random function involved, the sequence of optimal objective function values of the sparse grid approximations converges to the true optimal objective function values as the number of scenarios increases. The rate of convergence is also established. We treat separately the special case when the underlying distribution is an affine transform of a product of univariate distributions, and show how the sparse grid method can be adapted to the distribution by the use of quadrature formulas tailored to the distribution. We numerically compare the performance of the sparse grid method using different quadrature rules with classic quasi-Monte Carlo (QMC) methods, optimal rank-one lattice rules, and Monte Carlo (MC) scenario generation, using a series of utility maximization problems with up to 160 random variables. The results show that the sparse grid method is very efficient, especially if the integrand is sufficiently smooth. In such problems the sparse grid scenario generation method is found to need several orders of magnitude fewer scenarios than MC and QMC scenario generation to achieve the same accuracy. As a result, it is indicated that the method scales well with the dimension of the distribution--especially when the underlying distribution is an affine transform of a product of univariate distributions, in which case the method appears scalable to thousands of random variables.

  2. ESTIMATION OF FUNCTIONALS OF SPARSE COVARIANCE MATRICES

    PubMed Central

    Fan, Jianqing; Rigollet, Philippe; Wang, Weichen

    2016-01-01

    High-dimensional statistical tests often ignore correlations to gain simplicity and stability leading to null distributions that depend on functionals of correlation matrices such as their Frobenius norm and other ℓr norms. Motivated by the computation of critical values of such tests, we investigate the difficulty of estimation the functionals of sparse correlation matrices. Specifically, we show that simple plug-in procedures based on thresholded estimators of correlation matrices are sparsity-adaptive and minimax optimal over a large class of correlation matrices. Akin to previous results on functional estimation, the minimax rates exhibit an elbow phenomenon. Our results are further illustrated in simulated data as well as an empirical study of data arising in financial econometrics. PMID:26806986

  3. Fast generation of sparse random kernel graphs

    SciTech Connect

    Hagberg, Aric; Lemons, Nathan; Du, Wen -Bo

    2015-09-10

    The development of kernel-based inhomogeneous random graphs has provided models that are flexible enough to capture many observed characteristics of real networks, and that are also mathematically tractable. We specify a class of inhomogeneous random graph models, called random kernel graphs, that produces sparse graphs with tunable graph properties, and we develop an efficient generation algorithm to sample random instances from this model. As real-world networks are usually large, it is essential that the run-time of generation algorithms scales better than quadratically in the number of vertices n. We show that for many practical kernels our algorithm runs in time at most ο(n(logn)²). As an example, we show how to generate samples of power-law degree distribution graphs with tunable assortativity.

  4. Fast generation of sparse random kernel graphs

    DOE PAGES

    Hagberg, Aric; Lemons, Nathan; Du, Wen -Bo

    2015-09-10

    The development of kernel-based inhomogeneous random graphs has provided models that are flexible enough to capture many observed characteristics of real networks, and that are also mathematically tractable. We specify a class of inhomogeneous random graph models, called random kernel graphs, that produces sparse graphs with tunable graph properties, and we develop an efficient generation algorithm to sample random instances from this model. As real-world networks are usually large, it is essential that the run-time of generation algorithms scales better than quadratically in the number of vertices n. We show that for many practical kernels our algorithm runs in timemore » at most ο(n(logn)²). As an example, we show how to generate samples of power-law degree distribution graphs with tunable assortativity.« less

  5. Rab3A, a possible marker of cortical granules, participates in cortical granule exocytosis in mouse eggs.

    PubMed

    Bello, Oscar Daniel; Cappa, Andrea Isabel; de Paola, Matilde; Zanetti, María Natalia; Fukuda, Mitsunori; Fissore, Rafael A; Mayorga, Luis S; Michaut, Marcela A

    2016-09-10

    Fusion of cortical granules with the oocyte plasma membrane is the most significant event to prevent polyspermy. This particular exocytosis, also known as cortical reaction, is regulated by calcium and its molecular mechanism is still not known. Rab3A, a member of the small GTP-binding protein superfamily, has been implicated in calcium-dependent exocytosis and is not yet clear whether Rab3A participates in cortical granules exocytosis. Here, we examine the involvement of Rab3A in the physiology of cortical granules, particularly, in their distribution during oocyte maturation and activation, and their participation in membrane fusion during cortical granule exocytosis. Immunofluorescence and Western blot analysis showed that Rab3A and cortical granules have a similar migration pattern during oocyte maturation, and that Rab3A is no longer detected after cortical granule exocytosis. These results suggested that Rab3A might be a marker of cortical granules. Overexpression of EGFP-Rab3A colocalized with cortical granules with a Pearson correlation coefficient of +0.967, indicating that Rab3A and cortical granules have almost a perfect colocalization in the egg cortical region. Using a functional assay, we demonstrated that microinjection of recombinant, prenylated and active GST-Rab3A triggered cortical granule exocytosis, indicating that Rab3A has an active role in this secretory pathway. To confirm this active role, we inhibited the function of endogenous Rab3A by microinjecting a polyclonal antibody raised against Rab3A prior to parthenogenetic activation. Our results showed that Rab3A antibody microinjection abolished cortical granule exocytosis in parthenogenetically activated oocytes. Altogether, our findings confirm that Rab3A might function as a marker of cortical granules and participates in cortical granule exocytosis in mouse eggs. PMID:27423421

  6. Rab3A, a possible marker of cortical granules, participates in cortical granule exocytosis in mouse eggs.

    PubMed

    Bello, Oscar Daniel; Cappa, Andrea Isabel; de Paola, Matilde; Zanetti, María Natalia; Fukuda, Mitsunori; Fissore, Rafael A; Mayorga, Luis S; Michaut, Marcela A

    2016-09-10

    Fusion of cortical granules with the oocyte plasma membrane is the most significant event to prevent polyspermy. This particular exocytosis, also known as cortical reaction, is regulated by calcium and its molecular mechanism is still not known. Rab3A, a member of the small GTP-binding protein superfamily, has been implicated in calcium-dependent exocytosis and is not yet clear whether Rab3A participates in cortical granules exocytosis. Here, we examine the involvement of Rab3A in the physiology of cortical granules, particularly, in their distribution during oocyte maturation and activation, and their participation in membrane fusion during cortical granule exocytosis. Immunofluorescence and Western blot analysis showed that Rab3A and cortical granules have a similar migration pattern during oocyte maturation, and that Rab3A is no longer detected after cortical granule exocytosis. These results suggested that Rab3A might be a marker of cortical granules. Overexpression of EGFP-Rab3A colocalized with cortical granules with a Pearson correlation coefficient of +0.967, indicating that Rab3A and cortical granules have almost a perfect colocalization in the egg cortical region. Using a functional assay, we demonstrated that microinjection of recombinant, prenylated and active GST-Rab3A triggered cortical granule exocytosis, indicating that Rab3A has an active role in this secretory pathway. To confirm this active role, we inhibited the function of endogenous Rab3A by microinjecting a polyclonal antibody raised against Rab3A prior to parthenogenetic activation. Our results showed that Rab3A antibody microinjection abolished cortical granule exocytosis in parthenogenetically activated oocytes. Altogether, our findings confirm that Rab3A might function as a marker of cortical granules and participates in cortical granule exocytosis in mouse eggs.

  7. Cortical Reorganization following Injury Early in Life

    PubMed Central

    Artzi, Moran; Shiran, Shelly Irene; Weinstein, Maya; Myers, Vicki; Tarrasch, Ricardo; Schertz, Mitchell; Fattal-Valevski, Aviva; Miller, Elka; Gordon, Andrew M.; Green, Dido; Ben Bashat, Dafna

    2016-01-01

    The brain has a remarkable capacity for reorganization following injury, especially during the first years of life. Knowledge of structural reorganization and its consequences following perinatal injury is sparse. Here we studied changes in brain tissue volume, morphology, perfusion, and integrity in children with hemiplegia compared to typically developing children, using MRI. Children with hemiplegia demonstrated reduced total cerebral volume, with increased cerebrospinal fluid (CSF) and reduced total white matter volumes, with no differences in total gray matter volume, compared to typically developing children. An increase in cortical thickness at the hemisphere contralateral to the lesion (CLH) was detected in motor and language areas, which may reflect compensation for the gray matter loss in the lesion area or retention of ipsilateral pathways. In addition, reduced cortical thickness, perfusion, and surface area were detected in limbic areas. Increased CSF volume and precentral cortical thickness and reduced white matter volume were correlated with worse motor performance. Brain reorganization of the gray matter within the CLH, while not necessarily indicating better outcome, is suggested as a response to neuronal deficits following injury early in life. PMID:27298741

  8. Estimation of sparse directed acyclic graphs for multivariate counts data.

    PubMed

    Han, Sung Won; Zhong, Hua

    2016-09-01

    The next-generation sequencing data, called high-throughput sequencing data, are recorded as count data, which are generally far from normal distribution. Under the assumption that the count data follow the Poisson log-normal distribution, this article provides an L1-penalized likelihood framework and an efficient search algorithm to estimate the structure of sparse directed acyclic graphs (DAGs) for multivariate counts data. In searching for the solution, we use iterative optimization procedures to estimate the adjacency matrix and the variance matrix of the latent variables. The simulation result shows that our proposed method outperforms the approach which assumes multivariate normal distributions, and the log-transformation approach. It also shows that the proposed method outperforms the rank-based PC method under sparse network or hub network structures. As a real data example, we demonstrate the efficiency of the proposed method in estimating the gene regulatory networks of the ovarian cancer study. PMID:26849781

  9. Robust Sparse Blind Source Separation

    NASA Astrophysics Data System (ADS)

    Chenot, Cecile; Bobin, Jerome; Rapin, Jeremy

    2015-11-01

    Blind Source Separation is a widely used technique to analyze multichannel data. In many real-world applications, its results can be significantly hampered by the presence of unknown outliers. In this paper, a novel algorithm coined rGMCA (robust Generalized Morphological Component Analysis) is introduced to retrieve sparse sources in the presence of outliers. It explicitly estimates the sources, the mixing matrix, and the outliers. It also takes advantage of the estimation of the outliers to further implement a weighting scheme, which provides a highly robust separation procedure. Numerical experiments demonstrate the efficiency of rGMCA to estimate the mixing matrix in comparison with standard BSS techniques.

  10. Mesoscopic Patterns of Neural Activity Support Songbird Cortical Sequences

    PubMed Central

    Guitchounts, Grigori; Velho, Tarciso; Lois, Carlos; Gardner, Timothy J.

    2015-01-01

    Time-locked sequences of neural activity can be found throughout the vertebrate forebrain in various species and behavioral contexts. From “time cells” in the hippocampus of rodents to cortical activity controlling movement, temporal sequence generation is integral to many forms of learned behavior. However, the mechanisms underlying sequence generation are not well known. Here, we describe a spatial and temporal organization of the songbird premotor cortical microcircuit that supports sparse sequences of neural activity. Multi-channel electrophysiology and calcium imaging reveal that neural activity in premotor cortex is correlated with a length scale of 100 µm. Within this length scale, basal-ganglia–projecting excitatory neurons, on average, fire at a specific phase of a local 30 Hz network rhythm. These results show that premotor cortical activity is inhomogeneous in time and space, and that a mesoscopic dynamical pattern underlies the generation of the neural sequences controlling song. PMID:26039895

  11. Bayesian Learning in Sparse Graphical Factor Models via Variational Mean-Field Annealing

    PubMed Central

    Yoshida, Ryo; West, Mike

    2010-01-01

    We describe a class of sparse latent factor models, called graphical factor models (GFMs), and relevant sparse learning algorithms for posterior mode estimation. Linear, Gaussian GFMs have sparse, orthogonal factor loadings matrices, that, in addition to sparsity of the implied covariance matrices, also induce conditional independence structures via zeros in the implied precision matrices. We describe the models and their use for robust estimation of sparse latent factor structure and data/signal reconstruction. We develop computational algorithms for model exploration and posterior mode search, addressing the hard combinatorial optimization involved in the search over a huge space of potential sparse configurations. A mean-field variational technique coupled with annealing is developed to successively generate “artificial” posterior distributions that, at the limiting temperature in the annealing schedule, define required posterior modes in the GFM parameter space. Several detailed empirical studies and comparisons to related approaches are discussed, including analyses of handwritten digit image and cancer gene expression data. PMID:20890391

  12. A new sparse Bayesian learning method for inverse synthetic aperture radar imaging via exploiting cluster patterns

    NASA Astrophysics Data System (ADS)

    Fang, Jun; Zhang, Lizao; Duan, Huiping; Huang, Lei; Li, Hongbin

    2016-05-01

    The application of sparse representation to SAR/ISAR imaging has attracted much attention over the past few years. This new class of sparse representation based imaging methods present a number of unique advantages over conventional range-Doppler methods, the basic idea behind these works is to formulate SAR/ISAR imaging as a sparse signal recovery problem. In this paper, we propose a new two-dimensional pattern-coupled sparse Bayesian learning(SBL) method to capture the underlying cluster patterns of the ISAR target images. Based on this model, an expectation-maximization (EM) algorithm is developed to infer the maximum a posterior (MAP) estimate of the hyperparameters, along with the posterior distribution of the sparse signal. Experimental results demonstrate that the proposed method is able to achieve a substantial performance improvement over existing algorithms, including the conventional SBL method.

  13. Image fusion using sparse overcomplete feature dictionaries

    DOEpatents

    Brumby, Steven P.; Bettencourt, Luis; Kenyon, Garrett T.; Chartrand, Rick; Wohlberg, Brendt

    2015-10-06

    Approaches for deciding what individuals in a population of visual system "neurons" are looking for using sparse overcomplete feature dictionaries are provided. A sparse overcomplete feature dictionary may be learned for an image dataset and a local sparse representation of the image dataset may be built using the learned feature dictionary. A local maximum pooling operation may be applied on the local sparse representation to produce a translation-tolerant representation of the image dataset. An object may then be classified and/or clustered within the translation-tolerant representation of the image dataset using a supervised classification algorithm and/or an unsupervised clustering algorithm.

  14. Cortical Neural Computation by Discrete Results Hypothesis

    PubMed Central

    Castejon, Carlos; Nuñez, Angel

    2016-01-01

    One of the most challenging problems we face in neuroscience is to understand how the cortex performs computations. There is increasing evidence that the power of the cortical processing is produced by populations of neurons forming dynamic neuronal ensembles. Theoretical proposals and multineuronal experimental studies have revealed that ensembles of neurons can form emergent functional units. However, how these ensembles are implicated in cortical computations is still a mystery. Although cell ensembles have been associated with brain rhythms, the functional interaction remains largely unclear. It is still unknown how spatially distributed neuronal activity can be temporally integrated to contribute to cortical computations. A theoretical explanation integrating spatial and temporal aspects of cortical processing is still lacking. In this Hypothesis and Theory article, we propose a new functional theoretical framework to explain the computational roles of these ensembles in cortical processing. We suggest that complex neural computations underlying cortical processing could be temporally discrete and that sensory information would need to be quantized to be computed by the cerebral cortex. Accordingly, we propose that cortical processing is produced by the computation of discrete spatio-temporal functional units that we have called “Discrete Results” (Discrete Results Hypothesis). This hypothesis represents a novel functional mechanism by which information processing is computed in the cortex. Furthermore, we propose that precise dynamic sequences of “Discrete Results” is the mechanism used by the cortex to extract, code, memorize and transmit neural information. The novel “Discrete Results” concept has the ability to match the spatial and temporal aspects of cortical processing. We discuss the possible neural underpinnings of these functional computational units and describe the empirical evidence supporting our hypothesis. We propose that fast

  15. Miniature Laboratory for Detecting Sparse Biomolecules

    NASA Technical Reports Server (NTRS)

    Lin, Ying; Yu, Nan

    2005-01-01

    A miniature laboratory system has been proposed for use in the field to detect sparsely distributed biomolecules. By emphasizing concentration and sorting of specimens prior to detection, the underlying system concept would make it possible to attain high detection sensitivities without the need to develop ever more sensitive biosensors. The original purpose of the proposal is to aid the search for signs of life on a remote planet by enabling the detection of specimens as sparse as a few molecules or microbes in a large amount of soil, dust, rocks, water/ice, or other raw sample material. Some version of the system could prove useful on Earth for remote sensing of biological contamination, including agents of biological warfare. Processing in this system would begin with dissolution of the raw sample material in a sample-separation vessel. The solution in the vessel would contain floating microscopic magnetic beads coated with substances that could engage in chemical reactions with various target functional groups that are parts of target molecules. The chemical reactions would cause the targeted molecules to be captured on the surfaces of the beads. By use of a controlled magnetic field, the beads would be concentrated in a specified location in the vessel. Once the beads were thus concentrated, the rest of the solution would be discarded. This procedure would obviate the filtration steps and thereby also eliminate the filter-clogging difficulties of typical prior sample-concentration schemes. For ferrous dust/soil samples, the dissolution would be done first in a separate vessel before the solution is transferred to the microbead-containing vessel.

  16. Synaptic mechanisms underlying sparse coding of active touch.

    PubMed

    Crochet, Sylvain; Poulet, James F A; Kremer, Yves; Petersen, Carl C H

    2011-03-24

    Sensory information is actively gathered by animals, but the synaptic mechanisms driving neuronal circuit function during active sensory processing are poorly understood. Here, we investigated the synaptically driven membrane potential dynamics during active whisker sensation using whole-cell recordings from layer 2/3 pyramidal neurons in the primary somatosensory barrel cortex of behaving mice. Although whisker contact with an object evoked rapid depolarization in all neurons, these touch responses only drove action potentials in ∼10% of the cells. Such sparse coding was ensured by cell-specific reversal potentials of the touch-evoked response that were hyperpolarized relative to action potential threshold for most neurons. Intercontact interval profoundly influenced touch-evoked postsynaptic potentials, interestingly without affecting the peak membrane potential of the touch response. Dual whole-cell recordings indicated highly correlated membrane potential dynamics during active touch. Sparse action potential firing within synchronized cortical layer 2/3 microcircuits therefore appears to robustly signal each active touch response.

  17. Efficient particle filtering via sparse kernel density estimation.

    PubMed

    Banerjee, Amit; Burlina, Philippe

    2010-09-01

    Particle filters (PFs) are Bayesian filters capable of modeling nonlinear, non-Gaussian, and nonstationary dynamical systems. Recent research in PFs has investigated ways to appropriately sample from the posterior distribution, maintain multiple hypotheses, and alleviate computational costs while preserving tracking accuracy. To address these issues, a novel utilization of the support vector data description (SVDD) density estimation method within the particle filtering framework is presented. The SVDD density estimate can be integrated into a wide range of PFs to realize several benefits. It yields a sparse representation of the posterior density that reduces the computational complexity of the PF. The proposed approach also provides an analytical expression for the posterior distribution that can be used to identify its modes for maintaining multiple hypotheses and computing the MAP estimate, and to directly sample from the posterior. We present several experiments that demonstrate the advantages of incorporating a sparse kernel density estimate in a particle filter.

  18. Sparse representation for the ISAR image reconstruction

    NASA Astrophysics Data System (ADS)

    Hu, Mengqi; Montalbo, John; Li, Shuxia; Sun, Ligang; Qiao, Zhijun G.

    2016-05-01

    In this paper, a sparse representation of the data for an inverse synthetic aperture radar (ISAR) system is provided in two dimensions. The proposed sparse representation motivates the use a of a Convex Optimization that recovers the image with far less samples, which is required by Nyquist-Shannon sampling theorem to increases the efficiency and decrease the cost of calculation in radar imaging.

  19. Sparse Modeling for Astronomical Data Analysis

    NASA Astrophysics Data System (ADS)

    Ikeda, Shiro; Odaka, Hirokazu; Uemura, Makoto

    2016-03-01

    For astronomical data analysis, there have been proposed multiple methods based on sparse modeling. We have proposed a method for Compton camera imaging. The proposed approach is a sparse modeling method, but the derived algorithm is different from LASSO. We explain the problem and how we derived the method.

  20. Approximate inverse preconditioners for general sparse matrices

    SciTech Connect

    Chow, E.; Saad, Y.

    1994-12-31

    Preconditioned Krylov subspace methods are often very efficient in solving sparse linear matrices that arise from the discretization of elliptic partial differential equations. However, for general sparse indifinite matrices, the usual ILU preconditioners fail, often because of the fact that the resulting factors L and U give rise to unstable forward and backward sweeps. In such cases, alternative preconditioners based on approximate inverses may be attractive. We are currently developing a number of such preconditioners based on iterating on each column to get the approximate inverse. For this approach to be efficient, the iteration must be done in sparse mode, i.e., we must use sparse-matrix by sparse-vector type operatoins. We will discuss a few options and compare their performance on standard problems from the Harwell-Boeing collection.

  1. Maximum constrained sparse coding for image representation

    NASA Astrophysics Data System (ADS)

    Zhang, Jie; Zhao, Danpei; Jiang, Zhiguo

    2015-12-01

    Sparse coding exhibits good performance in many computer vision applications by finding bases which capture highlevel semantics of the data and learning sparse coefficients in terms of the bases. However, due to the fact that bases are non-orthogonal, sparse coding can hardly preserve the samples' similarity, which is important for discrimination. In this paper, a new image representing method called maximum constrained sparse coding (MCSC) is proposed. Sparse representation with more active coefficients means more similarity information, and the infinite norm is added to the solution for this purpose. We solve the optimizer by constraining the codes' maximum and releasing the residual to other dictionary atoms. Experimental results on image clustering show that our method can preserve the similarity of adjacent samples and maintain the sparsity of code simultaneously.

  2. Large-scale sparse singular value computations

    NASA Technical Reports Server (NTRS)

    Berry, Michael W.

    1992-01-01

    Four numerical methods for computing the singular value decomposition (SVD) of large sparse matrices on a multiprocessor architecture are presented. Lanczos and subspace iteration-based methods for determining several of the largest singular triplets (singular values and corresponding left and right-singular vectors) for sparse matrices arising from two practical applications: information retrieval and seismic reflection tomography are emphasized. The target architectures for implementations are the CRAY-2S/4-128 and Alliant FX/80. The sparse SVD problem is well motivated by recent information-retrieval techniques in which dominant singular values and their corresponding singular vectors of large sparse term-document matrices are desired, and by nonlinear inverse problems from seismic tomography applications which require approximate pseudo-inverses of large sparse Jacobian matrices.

  3. Scale-Invariant Sparse PCA on High Dimensional Meta-elliptical Data

    PubMed Central

    Han, Fang; Liu, Han

    2014-01-01

    We propose a semiparametric method for conducting scale-invariant sparse principal component analysis (PCA) on high dimensional non-Gaussian data. Compared with sparse PCA, our method has weaker modeling assumption and is more robust to possible data contamination. Theoretically, the proposed method achieves a parametric rate of convergence in estimating the parameter of interests under a flexible semiparametric distribution family; Computationally, the proposed method exploits a rank-based procedure and is as efficient as sparse PCA; Empirically, our method outperforms most competing methods on both synthetic and real-world datasets. PMID:24932056

  4. Towards robust and effective shape modeling: sparse shape composition.

    PubMed

    Zhang, Shaoting; Zhan, Yiqiang; Dewan, Maneesh; Huang, Junzhou; Metaxas, Dimitris N; Zhou, Xiang Sean

    2012-01-01

    Organ shape plays an important role in various clinical practices, e.g., diagnosis, surgical planning and treatment evaluation. It is usually derived from low level appearance cues in medical images. However, due to diseases and imaging artifacts, low level appearance cues might be weak or misleading. In this situation, shape priors become critical to infer and refine the shape derived by image appearances. Effective modeling of shape priors is challenging because: (1) shape variation is complex and cannot always be modeled by a parametric probability distribution; (2) a shape instance derived from image appearance cues (input shape) may have gross errors; and (3) local details of the input shape are difficult to preserve if they are not statistically significant in the training data. In this paper we propose a novel Sparse Shape Composition model (SSC) to deal with these three challenges in a unified framework. In our method, a sparse set of shapes in the shape repository is selected and composed together to infer/refine an input shape. The a priori information is thus implicitly incorporated on-the-fly. Our model leverages two sparsity observations of the input shape instance: (1) the input shape can be approximately represented by a sparse linear combination of shapes in the shape repository; (2) parts of the input shape may contain gross errors but such errors are sparse. Our model is formulated as a sparse learning problem. Using L1 norm relaxation, it can be solved by an efficient expectation-maximization (EM) type of framework. Our method is extensively validated on two medical applications, 2D lung localization in X-ray images and 3D liver segmentation in low-dose CT scans. Compared to state-of-the-art methods, our model exhibits better performance in both studies. PMID:21963296

  5. Synaptogenesis in purified cortical subplate neurons.

    PubMed

    McKellar, Claire E; Shatz, Carla J

    2009-08-01

    An ideal preparation for investigating events during synaptogenesis would be one in which synapses are sparse, but can be induced at will using a rapid, exogenous trigger. We describe a culture system of immunopurified subplate neurons in which synaptogenesis can be triggered, providing the first homogeneous culture of neocortical neurons for the investigation of synapse development. Synapses in immunopurified rat subplate neurons are sparse, and can be induced by a 48-h exposure to feeder layers of neurons and glia, an induction more rapid than any previously reported. Induced synapses are electrophysiologically functional and ultrastructurally normal. Microarray and real-time PCR experiments reveal a new program of gene expression accompanying synaptogenesis. Surprisingly few known synaptic genes are upregulated during the first 24 h of synaptogenesis; Gene Ontology annotation reveals a preferential upregulation of synaptic genes only at a later time. In situ hybridization confirms that some of the genes regulated in cultures are also expressed in the developing cortex. This culture system provides both a means of studying synapse formation in a homogeneous population of cortical neurons, and better synchronization of synaptogenesis, permitting the investigation of neuron-wide events following the triggering of synapse formation.

  6. Synaptogenesis in Purified Cortical Subplate Neurons

    PubMed Central

    Shatz, Carla J.

    2009-01-01

    An ideal preparation for investigating events during synaptogenesis would be one in which synapses are sparse, but can be induced at will using a rapid, exogenous trigger. We describe a culture system of immunopurified subplate neurons in which synaptogenesis can be triggered, providing the first homogeneous culture of neocortical neurons for the investigation of synapse development. Synapses in immunopurified rat subplate neurons are sparse, and can be induced by a 48-h exposure to feeder layers of neurons and glia, an induction more rapid than any previously reported. Induced synapses are electrophysiologically functional and ultrastructurally normal. Microarray and real-time PCR experiments reveal a new program of gene expression accompanying synaptogenesis. Surprisingly few known synaptic genes are upregulated during the first 24 h of synaptogenesis; Gene Ontology annotation reveals a preferential upregulation of synaptic genes only at a later time. In situ hybridization confirms that some of the genes regulated in cultures are also expressed in the developing cortex. This culture system provides both a means of studying synapse formation in a homogeneous population of cortical neurons, and better synchronization of synaptogenesis, permitting the investigation of neuron-wide events following the triggering of synapse formation. PMID:19029062

  7. Decoding of Covert Vowel Articulation Using Electroencephalography Cortical Currents

    PubMed Central

    Yoshimura, Natsue; Nishimoto, Atsushi; Belkacem, Abdelkader Nasreddine; Shin, Duk; Kambara, Hiroyuki; Hanakawa, Takashi; Koike, Yasuharu

    2016-01-01

    With the goal of providing assistive technology for the communication impaired, we proposed electroencephalography (EEG) cortical currents as a new approach for EEG-based brain-computer interface spellers. EEG cortical currents were estimated with a variational Bayesian method that uses functional magnetic resonance imaging (fMRI) data as a hierarchical prior. EEG and fMRI data were recorded from ten healthy participants during covert articulation of Japanese vowels /a/ and /i/, as well as during a no-imagery control task. Applying a sparse logistic regression (SLR) method to classify the three tasks, mean classification accuracy using EEG cortical currents was significantly higher than that using EEG sensor signals and was also comparable to accuracies in previous studies using electrocorticography. SLR weight analysis revealed vertices of EEG cortical currents that were highly contributive to classification for each participant, and the vertices showed discriminative time series signals according to the three tasks. Furthermore, functional connectivity analysis focusing on the highly contributive vertices revealed positive and negative correlations among areas related to speech processing. As the same findings were not observed using EEG sensor signals, our results demonstrate the potential utility of EEG cortical currents not only for engineering purposes such as brain-computer interfaces but also for neuroscientific purposes such as the identification of neural signaling related to language processing. PMID:27199638

  8. Cortical State and Attention

    PubMed Central

    Harris, Kenneth D.; Thiele, Alexander

    2012-01-01

    Preface The brain continuously adapts its processing machinery to behavioural demands. To achieve this it rapidly modulates the operating mode of cortical circuits, controlling the way information is transformed and routed. This article will focus on two experimental approaches by which the control of cortical information processing has been investigated: the study of state-dependent cortical processing in rodents, and attention in the primate visual system. Both processes involve a modulation of low-frequency activity fluctuations and spiking correlation, and are mediated by common receptor systems. We suggest that selective attention involves processes similar to state change, operating at a local columnar level to enhance the representation of otherwise nonsalient features while suppressing internally generated activity patterns. PMID:21829219

  9. Efficient nearest neighbors via robust sparse hashing.

    PubMed

    Cherian, Anoop; Sra, Suvrit; Morellas, Vassilios; Papanikolopoulos, Nikolaos

    2014-08-01

    This paper presents a new nearest neighbor (NN) retrieval framework: robust sparse hashing (RSH). Our approach is inspired by the success of dictionary learning for sparse coding. Our key idea is to sparse code the data using a learned dictionary, and then to generate hash codes out of these sparse codes for accurate and fast NN retrieval. But, direct application of sparse coding to NN retrieval poses a technical difficulty: when data are noisy or uncertain (which is the case with most real-world data sets), for a query point, an exact match of the hash code generated from the sparse code seldom happens, thereby breaking the NN retrieval. Borrowing ideas from robust optimization theory, we circumvent this difficulty via our novel robust dictionary learning and sparse coding framework called RSH, by learning dictionaries on the robustified counterparts of the perturbed data points. The algorithm is applied to NN retrieval on both simulated and real-world data. Our results demonstrate that RSH holds significant promise for efficient NN retrieval against the state of the art.

  10. Automatic parcellation of longitudinal cortical surfaces

    NASA Astrophysics Data System (ADS)

    Alassaf, Manal H.; Hahn, James K.

    2015-03-01

    We present a novel automatic method to parcellate the cortical surfaces of the neonatal brain longitudinal atlas at different stages of development. A labeled brain atlas of newborn at 41 weeks gestational age (GA) is used to propagate labels of anatomical regions of interest to an unlabeled spatio-temporal atlas, which provides a dynamic model of brain development at each week between 28-44 GA weeks. First, labels from the cortical volume of the labeled newborn brain are propagated to an age-matched cortical surface from the spatio-temporal atlas. Then, labels are propagated across the cortical surfaces of each week of the spatio-temporal atlas by registering successive cortical surfaces using a novel approach and an energy optimization function. This procedure incorporates local and global, spatial and temporal information when assigning the labels to each surface. The result is a complete parcellation of 17 neonatal brain surfaces of the spatio-temporal atlas with similar points per labels distributions across weeks.

  11. Prefrontal cortical minicolumn: from executive control to disrupted cognitive processing

    PubMed Central

    Casanova, Manuel F.

    2014-01-01

    The prefrontal cortex of the primate brain has a modular architecture based on the aggregation of neurons in minicolumnar arrangements having afferent and efferent connections distributed across many brain regions to represent, select and/or maintain behavioural goals and executive commands. Prefrontal cortical microcircuits are assumed to play a key role in the perception to action cycle that integrates relevant information about environment, and then selects and enacts behavioural responses. Thus, neurons within the interlaminar microcircuits participate in various functional states requiring the integration of signals across cortical layers and the selection of executive variables. Recent research suggests that executive abilities emerge from cortico-cortical interactions between interlaminar prefrontal cortical microcircuits, whereas their disruption is involved in a broad spectrum of neurologic and psychiatric disorders such as autism, schizophrenia, Alzheimer’s and drug addiction. The focus of this review is on the structural, functional and pathological approaches involving cortical minicolumns. Based on recent technological progress it has been demonstrated that microstimulation of infragranular cortical layers with patterns of microcurrents derived from supragranular layers led to an increase in cognitive performance. This suggests that interlaminar prefrontal cortical microcircuits are playing a causal role in improving cognitive performance. An important reason for the new interest in cortical modularity comes from both the impressive progress in understanding anatomical, physiological and pathological facets of cortical microcircuits and the promise of neural prosthetics for patients with neurological and psychiatric disorders. PMID:24531625

  12. Anomia produced by direct cortical stimulation of the pre-supplementary motor area in a patient undergoing preoperative language mapping.

    PubMed

    Rozanski, Verena Eveline; Peraud, Aurelia; Noachtar, Soheyl

    2015-06-01

    There is sparse data on the analysis of supplementary motor area in language function using direct cortical stimulation of the supplementary motor area. Here, we report a patient who experienced isolated anomia during stimulation of the anterior supplementary motor area and discuss the role of the supplementary motor area in speech production. The role of the pre-supplementary motor· area in word selection, observed in fMRI studies, can be confirmed by direct cortical stimulation.

  13. Sparse matrix methods research using the CSM testbed software system

    NASA Technical Reports Server (NTRS)

    Chu, Eleanor; George, J. Alan

    1989-01-01

    Research is described on sparse matrix techniques for the Computational Structural Mechanics (CSM) Testbed. The primary objective was to compare the performance of state-of-the-art techniques for solving sparse systems with those that are currently available in the CSM Testbed. Thus, one of the first tasks was to become familiar with the structure of the testbed, and to install some or all of the SPARSPAK package in the testbed. A suite of subroutines to extract from the data base the relevant structural and numerical information about the matrix equations was written, and all the demonstration problems distributed with the testbed were successfully solved. These codes were documented, and performance studies comparing the SPARSPAK technology to the methods currently in the testbed were completed. In addition, some preliminary studies were done comparing some recently developed out-of-core techniques with the performance of the testbed processor INV.

  14. Responses of Neurons in Primary and Inferior Temporal Visual Cortices to Natural Scenes

    NASA Astrophysics Data System (ADS)

    Baddeley, Roland; Abbott, L. F.; Booth, Michael C. A.; Sengpiel, Frank; Freeman, Tobe; Wakeman, Edward A.; Rolls, Edmund T.

    1997-12-01

    The primary visual cortex (V1) is the first cortical area to receive visual input, and inferior temporal (IT) areas are among the last along the ventral visual pathway. We recorded, in area V1 of anaesthetized cats and area IT of awake macaque monkeys, responses of neurons to videos of natural scenes. Responses were analysed to test various hypotheses concerning the nature of neural coding in these two regions. A variety of spike-train statistics were measured including spike-count distributions, interspike interval distributions, coefficients of variation, power spectra, Fano factors and different sparseness measures. All statistics showed non-Poisson characteristics and several revealed self-similarity of the spike trains. Spike-count distributions were approximately exponential in both visual areas for eight different videos and for counting windows ranging from 50 ms to 5 seconds. The results suggest that the neurons maximize their information carrying capacity while maintaining a fixed long-term-average firing rate, or equivalently, minimize their average firing rate for a fixed information carrying capacity.

  15. Sparse High Dimensional Models in Economics.

    PubMed

    Fan, Jianqing; Lv, Jinchi; Qi, Lei

    2011-09-01

    This paper reviews the literature on sparse high dimensional models and discusses some applications in economics and finance. Recent developments of theory, methods, and implementations in penalized least squares and penalized likelihood methods are highlighted. These variable selection methods are proved to be effective in high dimensional sparse modeling. The limits of dimensionality that regularization methods can handle, the role of penalty functions, and their statistical properties are detailed. Some recent advances in ultra-high dimensional sparse modeling are also briefly discussed. PMID:22022635

  16. Sparse High Dimensional Models in Economics

    PubMed Central

    Fan, Jianqing; Lv, Jinchi; Qi, Lei

    2010-01-01

    This paper reviews the literature on sparse high dimensional models and discusses some applications in economics and finance. Recent developments of theory, methods, and implementations in penalized least squares and penalized likelihood methods are highlighted. These variable selection methods are proved to be effective in high dimensional sparse modeling. The limits of dimensionality that regularization methods can handle, the role of penalty functions, and their statistical properties are detailed. Some recent advances in ultra-high dimensional sparse modeling are also briefly discussed. PMID:22022635

  17. Enhancing Scalability of Sparse Direct Methods

    SciTech Connect

    Li, Xiaoye S.; Demmel, James; Grigori, Laura; Gu, Ming; Xia,Jianlin; Jardin, Steve; Sovinec, Carl; Lee, Lie-Quan

    2007-07-23

    TOPS is providing high-performance, scalable sparse direct solvers, which have had significant impacts on the SciDAC applications, including fusion simulation (CEMM), accelerator modeling (COMPASS), as well as many other mission-critical applications in DOE and elsewhere. Our recent developments have been focusing on new techniques to overcome scalability bottleneck of direct methods, in both time and memory. These include parallelizing symbolic analysis phase and developing linear-complexity sparse factorization methods. The new techniques will make sparse direct methods more widely usable in large 3D simulations on highly-parallel petascale computers.

  18. Visualization of Cortical Dynamics

    NASA Astrophysics Data System (ADS)

    Grinvald, Amiram

    2003-03-01

    Recent progress in studies of cortical dynamics will be reviewed including the combination of real time optical imaging based on voltage sensitive dyes, single and multi- unit recordings, LFP, intracellular recordings and microstimulation. To image the flow of neuronal activity from one cortical site to the next, in real time, we have used optical imaging based on newly designed voltage sensitive dyes and a Fuji 128x 128 fast camera which we modified. A factor of 20-40 fold improvement in the signal to noise ratio was obtained with the new dye during in vivo imaging experiments. This improvements has facilitates the exploration of cortical dynamics without signal averaging in the millisecond time domain. We confirmed that the voltage sensitive dye signal indeed reflects membrane potential changes in populations of neurons by showing that the time course of the intracellular activity recorded intracellularly from a single neuron was highly correlated in many cases with the optical signal from a small patch of cortex recorded nearby. We showed that the firing of single cortical neurons is not a random process but occurs when the on-going pattern of million of neurons is similar to the functional architecture map which correspond to the tuning properties of that neuron. Chronic optical imaging, combined with electrical recordings and microstimulation, over a long period of times of more than a year, was successfully applied also to the study of higher brain functions in the behaving macaque monkey.

  19. Cortical thinning in psychopathy

    PubMed Central

    Ly, Martina; Motzkin, Julian C.; Philippi, Carissa L.; Kirk, Gregory R.; Newman, Joseph P.; Kiehl, Kent A.; Koenigs, Michael

    2013-01-01

    Objective Psychopathy is a personality disorder associated with severely antisocial behavior and a host of cognitive and affective deficits. The neuropathological basis of the disorder has not been clearly established. Cortical thickness is a sensitive measure of brain structure that has been used to identify neurobiological abnormalities in a number of psychiatric disorders. The purpose of this study is to evaluate cortical thickness and corresponding functional connectivity in criminal psychopaths. Method Using T1 MRI data, we computed cortical thickness maps in a sample of adult male prison inmates selected based on psychopathy diagnosis (n=21 psychopathic inmates, n=31 non-psychopathic inmates). Using rest-fMRI data from a subset of these inmates (n=20 psychopathic inmates, n=20 non-psychopathic inmates), we then computed functional connectivity within networks exhibiting significant thinning among psychopaths. Results Relative to non-psychopaths, psychopaths exhibited significantly thinner cortex in a number of regions, including left insula and dorsal anterior cingulate cortex, bilateral precentral gyrus, bilateral anterior temporal cortex, and right inferior frontal gyrus. These neurostructural differences were not due to differences in age, IQ, or substance abuse. Psychopaths also exhibited a corresponding reduction in functional connectivity between left insula and left dorsal anterior cingulate cortex. Conclusions Psychopathy is associated with a distinct pattern of cortical thinning and reduced functional connectivity. PMID:22581200

  20. Cortical control of facial expression.

    PubMed

    Müri, René M

    2016-06-01

    The present Review deals with the motor control of facial expressions in humans. Facial expressions are a central part of human communication. Emotional face expressions have a crucial role in human nonverbal behavior, allowing a rapid transfer of information between individuals. Facial expressions can be either voluntarily or emotionally controlled. Recent studies in nonhuman primates and humans have revealed that the motor control of facial expressions has a distributed neural representation. At least five cortical regions on the medial and lateral aspects of each hemisphere are involved: the primary motor cortex, the ventral lateral premotor cortex, the supplementary motor area on the medial wall, and the rostral and caudal cingulate cortex. The results of studies in humans and nonhuman primates suggest that the innervation of the face is bilaterally controlled for the upper part and mainly contralaterally controlled for the lower part. Furthermore, the primary motor cortex, the ventral lateral premotor cortex, and the supplementary motor area are essential for the voluntary control of facial expressions. In contrast, the cingulate cortical areas are important for emotional expression, because they receive input from different structures of the limbic system. PMID:26418049

  1. On finding supernodes for sparse matrix computations

    SciTech Connect

    Liu, J.W.H. . Dept. of Computer Science); Ng, E.; Peyton, B.W. )

    1990-06-01

    A simple characterization of fundamental supernodes is given in terms of the row subtrees of sparse Cholesky factors in the elimination tree. Using this characterization, we present an efficient algorithm that determines the set of such supernodes in time proportional to the number of nonzeros and equations in the original matrix. Experimental results are included to demonstrate the use of this algorithm in the context of sparse supernodal symbolic factorization. 18 refs., 3 figs., 3 tabs.

  2. Finding Nonoverlapping Substructures of a Sparse Matrix

    SciTech Connect

    Pinar, Ali; Vassilevska, Virginia

    2005-08-11

    Many applications of scientific computing rely on computations on sparse matrices. The design of efficient implementations of sparse matrix kernels is crucial for the overall efficiency of these applications. Due to the high compute-to-memory ratio and irregular memory access patterns, the performance of sparse matrix kernels is often far away from the peak performance on a modern processor. Alternative data structures have been proposed, which split the original matrix A into A{sub d} and A{sub s}, so that A{sub d} contains all dense blocks of a specified size in the matrix, and A{sub s} contains the remaining entries. This enables the use of dense matrix kernels on the entries of A{sub d} producing better memory performance. In this work, we study the problem of finding a maximum number of nonoverlapping dense blocks in a sparse matrix, which is previously not studied in the sparse matrix community. We show that the maximum nonoverlapping dense blocks problem is NP-complete by using a reduction from the maximum independent set problem on cubic planar graphs. We also propose a 2/3-approximation algorithm that runs in linear time in the number of nonzeros in the matrix. This extended abstract focuses on our results for 2x2 dense blocks. However we show that our results can be generalized to arbitrary sized dense blocks, and many other oriented substructures, which can be exploited to improve the memory performance of sparse matrix operations.

  3. Sparse extreme learning machine for classification.

    PubMed

    Bai, Zuo; Huang, Guang-Bin; Wang, Danwei; Wang, Han; Westover, M Brandon

    2014-10-01

    Extreme learning machine (ELM) was initially proposed for single-hidden-layer feedforward neural networks (SLFNs). In the hidden layer (feature mapping), nodes are randomly generated independently of training data. Furthermore, a unified ELM was proposed, providing a single framework to simplify and unify different learning methods, such as SLFNs, least square support vector machines, proximal support vector machines, and so on. However, the solution of unified ELM is dense, and thus, usually plenty of storage space and testing time are required for large-scale applications. In this paper, a sparse ELM is proposed as an alternative solution for classification, reducing storage space and testing time. In addition, unified ELM obtains the solution by matrix inversion, whose computational complexity is between quadratic and cubic with respect to the training size. It still requires plenty of training time for large-scale problems, even though it is much faster than many other traditional methods. In this paper, an efficient training algorithm is specifically developed for sparse ELM. The quadratic programming problem involved in sparse ELM is divided into a series of smallest possible sub-problems, each of which are solved analytically. Compared with SVM, sparse ELM obtains better generalization performance with much faster training speed. Compared with unified ELM, sparse ELM achieves similar generalization performance for binary classification applications, and when dealing with large-scale binary classification problems, sparse ELM realizes even faster training speed than unified ELM. PMID:25222727

  4. Visual tracking via robust multitask sparse prototypes

    NASA Astrophysics Data System (ADS)

    Zhang, Huanlong; Hu, Shiqiang; Yu, Junyang

    2015-03-01

    Sparse representation has been applied to an online subspace learning-based tracking problem. To handle partial occlusion effectively, some researchers introduce l1 regularization to principal component analysis (PCA) reconstruction. However, in these traditional tracking methods, the representation of each object observation is often viewed as an individual task so the inter-relationship between PCA basis vectors is ignored. We propose a new online visual tracking algorithm with multitask sparse prototypes, which combines multitask sparse learning with PCA-based subspace representation. We first extend a visual tracking algorithm with sparse prototypes in multitask learning framework to mine inter-relations between subtasks. Then, to avoid the problem that enforcing all subtasks to share the same structure may result in degraded tracking results, we impose group sparse constraints on the coefficients of PCA basis vectors and element-wise sparse constraints on the error coefficients, respectively. Finally, we show that the proposed optimization problem can be effectively solved using the accelerated proximal gradient method with the fast convergence. Experimental results compared with the state-of-the-art tracking methods demonstrate that the proposed algorithm achieves favorable performance when the object undergoes partial occlusion, motion blur, and illumination changes.

  5. Learning discriminative dictionary for group sparse representation.

    PubMed

    Sun, Yubao; Liu, Qingshan; Tang, Jinhui; Tao, Dacheng

    2014-09-01

    In recent years, sparse representation has been widely used in object recognition applications. How to learn the dictionary is a key issue to sparse representation. A popular method is to use l1 norm as the sparsity measurement of representation coefficients for dictionary learning. However, the l1 norm treats each atom in the dictionary independently, so the learned dictionary cannot well capture the multisubspaces structural information of the data. In addition, the learned subdictionary for each class usually shares some common atoms, which weakens the discriminative ability of the reconstruction error of each subdictionary. This paper presents a new dictionary learning model to improve sparse representation for image classification, which targets at learning a class-specific subdictionary for each class and a common subdictionary shared by all classes. The model is composed of a discriminative fidelity, a weighted group sparse constraint, and a subdictionary incoherence term. The discriminative fidelity encourages each class-specific subdictionary to sparsely represent the samples in the corresponding class. The weighted group sparse constraint term aims at capturing the structural information of the data. The subdictionary incoherence term is to make all subdictionaries independent as much as possible. Because the common subdictionary represents features shared by all classes, we only use the reconstruction error of each class-specific subdictionary for classification. Extensive experiments are conducted on several public image databases, and the experimental results demonstrate the power of the proposed method, compared with the state-of-the-arts.

  6. Robust face recognition via sparse representation.

    PubMed

    Wright, John; Yang, Allen Y; Ganesh, Arvind; Sastry, S Shankar; Ma, Yi

    2009-02-01

    We consider the problem of automatically recognizing human faces from frontal views with varying expression and illumination, as well as occlusion and disguise. We cast the recognition problem as one of classifying among multiple linear regression models and argue that new theory from sparse signal representation offers the key to addressing this problem. Based on a sparse representation computed by l{1}-minimization, we propose a general classification algorithm for (image-based) object recognition. This new framework provides new insights into two crucial issues in face recognition: feature extraction and robustness to occlusion. For feature extraction, we show that if sparsity in the recognition problem is properly harnessed, the choice of features is no longer critical. What is critical, however, is whether the number of features is sufficiently large and whether the sparse representation is correctly computed. Unconventional features such as downsampled images and random projections perform just as well as conventional features such as Eigenfaces and Laplacianfaces, as long as the dimension of the feature space surpasses certain threshold, predicted by the theory of sparse representation. This framework can handle errors due to occlusion and corruption uniformly by exploiting the fact that these errors are often sparse with respect to the standard (pixel) basis. The theory of sparse representation helps predict how much occlusion the recognition algorithm can handle and how to choose the training images to maximize robustness to occlusion. We conduct extensive experiments on publicly available databases to verify the efficacy of the proposed algorithm and corroborate the above claims.

  7. Parathyroid hormone treatment improves the cortical bone microstructure by improving the distribution of type I collagen in postmenopausal women with osteoporosis.

    PubMed

    Ascenzi, Maria-Grazia; Liao, Vivian P; Lee, Brittany M; Billi, Fabrizio; Zhou, Hua; Lindsay, Robert; Cosman, Felicia; Nieves, Jeri; Bilezikian, John P; Dempster, David W

    2012-03-01

    Although an important index, the level of bone mineral density (BMD) does not completely describe fracture risk. Another bone structural parameter, the orientation of type I collagen, is known to add to risk determination, independently of BMD, ex vivo. We investigated the Haversian system of transiliac crest biopsies from postmenopausal women before and after treatment with parathyroid hormone (PTH). We used the birefringent signal of circularly polarized light and its underlying collagen arrangements by confocal and electron microscopy, in conjunction with the degree of calcification by high-resolution micro-X-ray. We found that PTH treatment increased the Haversian system area by 11.92 ± 5.82 mm² to 12.76 ± 4.50 mm² (p = 0.04); decreased bright birefringence from 0.45 ± 0.02 to 0.40 ± 0.01 (scale zero to one, p = 0.0005); increased the average percent area of osteons with alternating birefringence from 48.15% ± 10.27% to 66.33% ± 7.73% (p = 0.034); and nonsignificantly decreased the average percent area of semihomogeneous birefringent osteons (8.36% ± 10.63% versus 5.41% ± 9.13%, p = 0.40) and of birefringent bright osteons (4.14% ± 8.90% versus 2.08% ± 3.36%, p = 0.10). Further, lamellar thickness significantly increased from 3.78 ± 0.11 µm to 4.47 ± 0.14 µm (p = 0.0002) for bright lamellae, and from 3.32 ± 0.12 µm to 3.70 ± 0.12 µm (p = 0.045) for extinct lamellae. This increased lamellar thickness altered the distribution of birefringence and therefore the distribution of collagen orientation in the tissue. With PTH treatment, a higher percent area of osteons at the initial degree of calcification was observed, relative to the intermediate-low degree of calcification (57.16% ± 3.08% versus 32.90% ± 3.69%, p = 0.04), with percentage of alternating osteons at initial stages of calcification increasing from 19.75 ± 1.22 to 80.13 ± 6.47, p = 0.001. In conclusion, PTH treatment increases heterogeneity of collagen orientation, a starting

  8. Scenario generation for stochastic optimization problems via the sparse grid method

    DOE PAGES

    Chen, Michael; Mehrotra, Sanjay; Papp, David

    2015-04-19

    We study the use of sparse grids in the scenario generation (or discretization) problem in stochastic programming problems where the uncertainty is modeled using a continuous multivariate distribution. We show that, under a regularity assumption on the random function involved, the sequence of optimal objective function values of the sparse grid approximations converges to the true optimal objective function values as the number of scenarios increases. The rate of convergence is also established. We treat separately the special case when the underlying distribution is an affine transform of a product of univariate distributions, and show how the sparse grid methodmore » can be adapted to the distribution by the use of quadrature formulas tailored to the distribution. We numerically compare the performance of the sparse grid method using different quadrature rules with classic quasi-Monte Carlo (QMC) methods, optimal rank-one lattice rules, and Monte Carlo (MC) scenario generation, using a series of utility maximization problems with up to 160 random variables. The results show that the sparse grid method is very efficient, especially if the integrand is sufficiently smooth. In such problems the sparse grid scenario generation method is found to need several orders of magnitude fewer scenarios than MC and QMC scenario generation to achieve the same accuracy. As a result, it is indicated that the method scales well with the dimension of the distribution--especially when the underlying distribution is an affine transform of a product of univariate distributions, in which case the method appears scalable to thousands of random variables.« less

  9. Lineage-specific laminar organization of cortical GABAergic interneurons.

    PubMed

    Ciceri, Gabriele; Dehorter, Nathalie; Sols, Ignasi; Huang, Z Josh; Maravall, Miguel; Marín, Oscar

    2013-09-01

    In the cerebral cortex, pyramidal cells and interneurons are generated in distant germinal zones, and so the mechanisms that control their precise assembly into specific microcircuits remain an enigma. Here we report that cortical interneurons labeled at the clonal level do not distribute randomly but rather have a strong tendency to cluster in the mouse neocortex. This behavior is common to different classes of interneurons, independently of their origin. Interneuron clusters are typically contained within one or two adjacent cortical layers, are largely formed by isochronically generated neurons and populate specific layers, as revealed by unbiased hierarchical clustering methods. Our results suggest that different progenitor cells give rise to interneurons populating infra- and supragranular cortical layers, which challenges current views of cortical neurogenesis. Thus, specific lineages of cortical interneurons seem to be produced to primarily mirror the laminar structure of the cerebral cortex, rather than its columnar organization.

  10. Merlin/ERM proteins establish cortical asymmetry and centrosome position

    PubMed Central

    Hebert, Alan M.; DuBoff, Brian; Casaletto, Jessica B.; Gladden, Andrew B.; McClatchey, Andrea I.

    2012-01-01

    The ability to generate asymmetry at the cell cortex underlies cell polarization and asymmetric cell division. Here we demonstrate a novel role for the tumor suppressor Merlin and closely related ERM proteins (Ezrin, Radixin, and Moesin) in generating cortical asymmetry in the absence of external cues. Our data reveal that Merlin functions to restrict the cortical distribution of the actin regulator Ezrin, which in turn positions the interphase centrosome in single epithelial cells and three-dimensional organotypic cultures. In the absence of Merlin, ectopic cortical Ezrin yields mispositioned centrosomes, misoriented spindles, and aberrant epithelial architecture. Furthermore, in tumor cells with centrosome amplification, the failure to restrict cortical Ezrin abolishes centrosome clustering, yielding multipolar mitoses. These data uncover fundamental roles for Merlin/ERM proteins in spatiotemporally organizing the cell cortex and suggest that Merlin's role in restricting cortical Ezrin may contribute to tumorigenesis by disrupting cell polarity, spindle orientation, and, potentially, genome stability. PMID:23249734

  11. Synapse-Centric Mapping of Cortical Models to the SpiNNaker Neuromorphic Architecture.

    PubMed

    Knight, James C; Furber, Steve B

    2016-01-01

    While the adult human brain has approximately 8.8 × 10(10) neurons, this number is dwarfed by its 1 × 10(15) synapses. From the point of view of neuromorphic engineering and neural simulation in general this makes the simulation of these synapses a particularly complex problem. SpiNNaker is a digital, neuromorphic architecture designed for simulating large-scale spiking neural networks at speeds close to biological real-time. Current solutions for simulating spiking neural networks on SpiNNaker are heavily inspired by work on distributed high-performance computing. However, while SpiNNaker shares many characteristics with such distributed systems, its component nodes have much more limited resources and, as the system lacks global synchronization, the computation performed on each node must complete within a fixed time step. We first analyze the performance of the current SpiNNaker neural simulation software and identify several problems that occur when it is used to simulate networks of the type often used to model the cortex which contain large numbers of sparsely connected synapses. We then present a new, more flexible approach for mapping the simulation of such networks to SpiNNaker which solves many of these problems. Finally we analyze the performance of our new approach using both benchmarks, designed to represent cortical connectivity, and larger, functional cortical models. In a benchmark network where neurons receive input from 8000 STDP synapses, our new approach allows 4× more neurons to be simulated on each SpiNNaker core than has been previously possible. We also demonstrate that the largest plastic neural network previously simulated on neuromorphic hardware can be run in real time using our new approach: double the speed that was previously achieved. Additionally this network contains two types of plastic synapse which previously had to be trained separately but, using our new approach, can be trained simultaneously.

  12. Synapse-Centric Mapping of Cortical Models to the SpiNNaker Neuromorphic Architecture

    PubMed Central

    Knight, James C.; Furber, Steve B.

    2016-01-01

    While the adult human brain has approximately 8.8 × 1010 neurons, this number is dwarfed by its 1 × 1015 synapses. From the point of view of neuromorphic engineering and neural simulation in general this makes the simulation of these synapses a particularly complex problem. SpiNNaker is a digital, neuromorphic architecture designed for simulating large-scale spiking neural networks at speeds close to biological real-time. Current solutions for simulating spiking neural networks on SpiNNaker are heavily inspired by work on distributed high-performance computing. However, while SpiNNaker shares many characteristics with such distributed systems, its component nodes have much more limited resources and, as the system lacks global synchronization, the computation performed on each node must complete within a fixed time step. We first analyze the performance of the current SpiNNaker neural simulation software and identify several problems that occur when it is used to simulate networks of the type often used to model the cortex which contain large numbers of sparsely connected synapses. We then present a new, more flexible approach for mapping the simulation of such networks to SpiNNaker which solves many of these problems. Finally we analyze the performance of our new approach using both benchmarks, designed to represent cortical connectivity, and larger, functional cortical models. In a benchmark network where neurons receive input from 8000 STDP synapses, our new approach allows 4× more neurons to be simulated on each SpiNNaker core than has been previously possible. We also demonstrate that the largest plastic neural network previously simulated on neuromorphic hardware can be run in real time using our new approach: double the speed that was previously achieved. Additionally this network contains two types of plastic synapse which previously had to be trained separately but, using our new approach, can be trained simultaneously.

  13. Synapse-Centric Mapping of Cortical Models to the SpiNNaker Neuromorphic Architecture.

    PubMed

    Knight, James C; Furber, Steve B

    2016-01-01

    While the adult human brain has approximately 8.8 × 10(10) neurons, this number is dwarfed by its 1 × 10(15) synapses. From the point of view of neuromorphic engineering and neural simulation in general this makes the simulation of these synapses a particularly complex problem. SpiNNaker is a digital, neuromorphic architecture designed for simulating large-scale spiking neural networks at speeds close to biological real-time. Current solutions for simulating spiking neural networks on SpiNNaker are heavily inspired by work on distributed high-performance computing. However, while SpiNNaker shares many characteristics with such distributed systems, its component nodes have much more limited resources and, as the system lacks global synchronization, the computation performed on each node must complete within a fixed time step. We first analyze the performance of the current SpiNNaker neural simulation software and identify several problems that occur when it is used to simulate networks of the type often used to model the cortex which contain large numbers of sparsely connected synapses. We then present a new, more flexible approach for mapping the simulation of such networks to SpiNNaker which solves many of these problems. Finally we analyze the performance of our new approach using both benchmarks, designed to represent cortical connectivity, and larger, functional cortical models. In a benchmark network where neurons receive input from 8000 STDP synapses, our new approach allows 4× more neurons to be simulated on each SpiNNaker core than has been previously possible. We also demonstrate that the largest plastic neural network previously simulated on neuromorphic hardware can be run in real time using our new approach: double the speed that was previously achieved. Additionally this network contains two types of plastic synapse which previously had to be trained separately but, using our new approach, can be trained simultaneously. PMID:27683540

  14. Synapse-Centric Mapping of Cortical Models to the SpiNNaker Neuromorphic Architecture

    PubMed Central

    Knight, James C.; Furber, Steve B.

    2016-01-01

    While the adult human brain has approximately 8.8 × 1010 neurons, this number is dwarfed by its 1 × 1015 synapses. From the point of view of neuromorphic engineering and neural simulation in general this makes the simulation of these synapses a particularly complex problem. SpiNNaker is a digital, neuromorphic architecture designed for simulating large-scale spiking neural networks at speeds close to biological real-time. Current solutions for simulating spiking neural networks on SpiNNaker are heavily inspired by work on distributed high-performance computing. However, while SpiNNaker shares many characteristics with such distributed systems, its component nodes have much more limited resources and, as the system lacks global synchronization, the computation performed on each node must complete within a fixed time step. We first analyze the performance of the current SpiNNaker neural simulation software and identify several problems that occur when it is used to simulate networks of the type often used to model the cortex which contain large numbers of sparsely connected synapses. We then present a new, more flexible approach for mapping the simulation of such networks to SpiNNaker which solves many of these problems. Finally we analyze the performance of our new approach using both benchmarks, designed to represent cortical connectivity, and larger, functional cortical models. In a benchmark network where neurons receive input from 8000 STDP synapses, our new approach allows 4× more neurons to be simulated on each SpiNNaker core than has been previously possible. We also demonstrate that the largest plastic neural network previously simulated on neuromorphic hardware can be run in real time using our new approach: double the speed that was previously achieved. Additionally this network contains two types of plastic synapse which previously had to be trained separately but, using our new approach, can be trained simultaneously. PMID:27683540

  15. Inversion of magnetotelluric data in a sparse model domain

    NASA Astrophysics Data System (ADS)

    Nittinger, Christian G.; Becken, Michael

    2016-06-01

    The inversion of magnetotelluric data into subsurface electrical conductivity poses an ill-posed problem. Smoothing constraints are widely employed to estimate a regularized solution. Here, we present an alternative inversion scheme that estimates a sparse representation of the model in a wavelet basis. The objective of the inversion is to determine the few non-zero wavelet coefficients which are required to fit the data. This approach falls into the class of sparsity constrained inversion schemes and minimizes the combination of the data misfit in a least squares ℓ2 sense and of a model coefficient norm in a ℓ1 sense (ℓ2-ℓ1 minimization). The ℓ1 coefficient norm renders the solution sparse in a suitable representation such as the multi-resolution wavelet basis, but does not impose explicit structural penalties on the model as it is the case for ℓ2 regularization. The presented numerical algorithm solves the mixed ℓ2-ℓ1 norm minimization problem for the non-linear magnetotelluric inverse problem. We demonstrate the feasibility of our algorithm on synthetic 2-D MT data as well as on a real data example. We found that sparse models can be estimated by inversion and that the spatial distribution of non-vanishing coefficients indicates regions in the model which are resolved.

  16. Inversion of magnetotelluric data in a sparse model domain

    NASA Astrophysics Data System (ADS)

    Nittinger, Christian G.; Becken, Michael

    2016-08-01

    The inversion of magnetotelluric data into subsurface electrical conductivity poses an ill-posed problem. Smoothing constraints are widely employed to estimate a regularized solution. Here, we present an alternative inversion scheme that estimates a sparse representation of the model in a wavelet basis. The objective of the inversion is to determine the few non-zero wavelet coefficients which are required to fit the data. This approach falls into the class of sparsity constrained inversion schemes and minimizes the combination of the data misfit in a least-squares ℓ2 sense and of a model coefficient norm in an ℓ1 sense (ℓ2-ℓ1 minimization). The ℓ1 coefficient norm renders the solution sparse in a suitable representation such as the multiresolution wavelet basis, but does not impose explicit structural penalties on the model as it is the case for ℓ2 regularization. The presented numerical algorithm solves the mixed ℓ2-ℓ1 norm minimization problem for the nonlinear magnetotelluric inverse problem. We demonstrate the feasibility of our algorithm on synthetic 2-D MT data as well as on a real data example. We found that sparse models can be estimated by inversion and that the spatial distribution of non-vanishing coefficients indicates regions in the model which are resolved.

  17. Treatment of non-sparse cratering in planetary surface dating

    NASA Astrophysics Data System (ADS)

    Kneissl, T.; Michael, G. G.; Schmedemann, N.

    2016-10-01

    We here propose a new technique to derive crater size-frequency distributions (CSFDs) from non-sparsely cratered surfaces, by accounting for the loss of craters due to subsequent crater/ejecta coverage. This approach, which we refer to as the buffered non-sparseness correction (BNSC), relates each crater to a measurement area found by excluding regions in the study area that have been resurfaced by larger craters and their ejecta blankets. The approach includes the well-known buffered crater counting (BCC) technique in order to consider the potential identification of craters whose centers are located outside the counting area. We demonstrate the new approach at two test sites on the Moon, one on the ancient lunar highlands outside the South Pole Aitken basin and the other on the much younger surface of lunar Mare Serenitatis. As expected, the correction has a much stronger effect on ancient, densely cratered surfaces than on younger, sparsely cratered surfaces. Furthermore, these first results indicate that the shapes of CSFDs on ancient terrains are actually very similar to the shapes of CSFDs on younger terrains.

  18. Purely Cortical Anaplastic Ependymoma

    PubMed Central

    Romero, Flávio Ramalho; Zanini, Marco Antônio; Ducati, Luis Gustavo; Vital, Roberto Bezerra; de Lima Neto, Newton Moreira; Gabarra, Roberto Colichio

    2012-01-01

    Ependymomas are glial tumors derived from ependymal cells lining the ventricles and the central canal of the spinal cord. It may occur outside the ventricular structures, representing the extraventicular form, or without any relationship of ventricular system, called ectopic ependymona. Less than fifteen cases of ectopic ependymomas were reported and less than five were anaplastic. We report a rare case of pure cortical ectopic anaplastic ependymoma. PMID:23119204

  19. Purely cortical anaplastic ependymoma.

    PubMed

    Romero, Flávio Ramalho; Zanini, Marco Antônio; Ducati, Luis Gustavo; Vital, Roberto Bezerra; de Lima Neto, Newton Moreira; Gabarra, Roberto Colichio

    2012-01-01

    Ependymomas are glial tumors derived from ependymal cells lining the ventricles and the central canal of the spinal cord. It may occur outside the ventricular structures, representing the extraventicular form, or without any relationship of ventricular system, called ectopic ependymona. Less than fifteen cases of ectopic ependymomas were reported and less than five were anaplastic. We report a rare case of pure cortical ectopic anaplastic ependymoma.

  20. Stochastic Computations in Cortical Microcircuit Models

    PubMed Central

    Maass, Wolfgang

    2013-01-01

    Experimental data from neuroscience suggest that a substantial amount of knowledge is stored in the brain in the form of probability distributions over network states and trajectories of network states. We provide a theoretical foundation for this hypothesis by showing that even very detailed models for cortical microcircuits, with data-based diverse nonlinear neurons and synapses, have a stationary distribution of network states and trajectories of network states to which they converge exponentially fast from any initial state. We demonstrate that this convergence holds in spite of the non-reversibility of the stochastic dynamics of cortical microcircuits. We further show that, in the presence of background network oscillations, separate stationary distributions emerge for different phases of the oscillation, in accordance with experimentally reported phase-specific codes. We complement these theoretical results by computer simulations that investigate resulting computation times for typical probabilistic inference tasks on these internally stored distributions, such as marginalization or marginal maximum-a-posteriori estimation. Furthermore, we show that the inherent stochastic dynamics of generic cortical microcircuits enables them to quickly generate approximate solutions to difficult constraint satisfaction problems, where stored knowledge and current inputs jointly constrain possible solutions. This provides a powerful new computing paradigm for networks of spiking neurons, that also throws new light on how networks of neurons in the brain could carry out complex computational tasks such as prediction, imagination, memory recall and problem solving. PMID:24244126

  1. Increased temporolimbic cortical folding complexity in temporal lobe epilepsy

    PubMed Central

    Voets, N.L.; Bernhardt, B.C.; Kim, H.; Yoon, U.

    2011-01-01

    Objective: Converging evidence suggests that abnormalities of brain development may play a role in the pathogenesis of temporal lobe epilepsy (TLE). As sulco-gyral patterns are thought to be a footprint of cortical development, we set out to quantitatively map folding complexity across the neocortex in TLE. Additionally, we tested whether there was a relationship between cortical complexity and features of hippocampal maldevelopment, commonly referred to as malrotation. Methods: To quantify folding complexity, we obtained whole-brain surface-based measures of absolute mean cortical curvature from MRI scans acquired in 43 drug-resistant patients with TLE with unilateral hippocampal atrophy, and 40 age- and sex-matched healthy controls. In patients, we correlated changes in cortical curvature with 3-dimensional measures of hippocampal positioning. Results: We found increased folding complexity in the temporolimbic cortices encompassing parahippocampal, temporopolar, insular, and fronto-opercular regions. Increased complexity was observed ipsilateral to the seizure focus in patients with left TLE (LTLE), whereas these changes were bilateral in patients with right TLE (RTLE). In both TLE groups, increased temporolimbic complexity was associated with increased hippocampal malrotation. We found tendencies for increased complexity in bilateral posterior temporal cortices in LTLE and contralateral parahippocampal cortices in RTLE to be predictive of unfavorable seizure outcome after surgery. Conclusion: The anatomic distribution of increased cortical complexity overlapping with limbic seizure networks in TLE and its association with hippocampal maldevelopment further imply that neurodevelopmental factors may play a role in the epileptogenic process of TLE. PMID:21148116

  2. Posterior Cortical Atrophy

    PubMed Central

    Crutch, Sebastian J; Lehmann, Manja; Schott, Jonathan M; Rabinovici, Gil D; Rossor, Martin N; Fox, Nick C

    2013-01-01

    Posterior cortical atrophy (PCA) is a neurodegenerative syndrome that is characterized by a progressive decline in visuospatial, visuoperceptual, literacy and praxic skills. The progressive neurodegeneration affecting parietal, occipital and occipito-temporal cortices which underlies PCA is attributable to Alzheimer's disease (AD) in the majority of patients. However, alternative underlying aetiologies including Dementia with Lewy Bodies (DLB), corticobasal degeneration (CBD) and prion disease have also been identified, and not all PCA patients have atrophy on clinical imaging. This heterogeneity has led to diagnostic and terminological inconsistencies, caused difficulty comparing studies from different centres, and limited the generalizability of clinical trials and investigations of factors driving phenotypic variability. Significant challenges remain in identifying the factors associated with both the selective vulnerability of posterior cortical regions and the young age of onset seen in PCA. Greater awareness of the syndrome and agreement over the correspondence between syndrome-and disease-level classifications are required in order to improve diagnostic accuracy, research study design and clinical management. PMID:22265212

  3. Parallel sparse matrix computations: Wavefront minimization of sparse matrices. Final report for the period ending June 14, 1998

    SciTech Connect

    Pothen, A.

    1999-02-01

    Gary Kumfert and Alex Pothen have improved the quality and run time of two ordering algorithms for minimizing the wavefront and envelope size of sparse matrices and graphs. These algorithms compute orderings for irregular data structures (e.g., unstructured meshes) that reduce the number of cache misses on modern workstation architectures. They have completed the implementation of a parallel solver for sparse, symmetric indefinite systems for distributed memory computers such as the IBM SP-2. The indefiniteness requires one to incorporate block pivoting (2 by 2 blocks) in the algorithm, thus demanding dynamic, parallel data structures. This is the first reported parallel solver for the indefinite problem. Direct methods for solving systems of linear equations employ sophisticated combinatorial and algebraic algorithms that contribute to software complexity, and hence it is natural to consider object-oriented design (OOD) in this context. The authors have continued to create software for solving sparse systems of linear equations by direct methods employing OOD. Fast computation of robust preconditioners is a priority for solving large systems of equations on unstructured grids and in other applications. They have developed new algorithms and software that can compute incomplete factorization preconditioners for high level fill in time proportional to the number of floating point operations and memory accesses.

  4. Measuring sparseness in the brain: Comment on Bowers (2009)

    PubMed Central

    Quiroga, R. Quian; Kreiman, G.

    2011-01-01

    Bowers (2009) challenged the common view in favor of distributed representations in psychological modeling and the main arguments given against localist and grandmother cell coding schemes. He revisited the results of several single-cell studies arguing that they do not support distributed representations. We praise the contribution of Bowers for joining evidence from psychological modeling and neurophysiological recordings, but disagree with several of his claims. In this comment we argue that distinctions between distributed, localist and grandmother cell coding can be troublesome with real data. Moreover, these distinctions seem to be lying within the same continuum, and we argue that it may be sensible to characterize coding schemes using a sparseness measure. We further argue that there may not be a unique coding scheme implemented in all brain areas and for all possible functions. In particular, current evidence suggests that the brain may use distributed codes in primary sensory areas and sparser and invariant representations in higher areas. PMID:20063978

  5. Associative fear learning enhances sparse network coding in primary sensory cortex

    PubMed Central

    Gdalyahu, Amos; Tring, Elaine; Polack, Pierre-Olivier; Gruver, Robin; Golshani, Peyman; Fanselow, Michael S.; Silva, Alcino J.; Trachtenberg, Joshua T.

    2012-01-01

    Summary Several models of associative learning predict that stimulus processing changes during association formation. How associative learning reconfigures neural circuits in primary sensory cortex to "learn" associative attributes of a stimulus remains unknown. Using 2-photon in-vivo calcium imaging to measure responses of networks of neurons in primary somatosensory cortex, we discovered that associative fear learning, in which whisker stimulation is paired with foot shock, enhances sparse population coding and robustness of the conditional stimulus, yet decreases total network activity. Fewer cortical neurons responded to stimulation of the trained whisker than in controls, yet their response strength was enhanced. These responses were not observed in mice exposed to a non-associative learning procedure. Our results define how the cortical representation of a sensory stimulus is shaped by associative fear learning. These changes are proposed to enhance efficient sensory processing after associative learning. PMID:22794266

  6. Sparse source configurations for asteroid tomography

    NASA Astrophysics Data System (ADS)

    Pursiainen, S.; Kaasalainen, M.

    2014-04-01

    The objective of our recent research has been to develop non-invasive imaging techniques for future planetary research and mining activities involving a challenging in situ environment and tight payload limits [1]. This presentation will deal in particular with an approach in which the internal relative permittivity ∈r or the refractive index n = √ ∈r of an asteroid is to be recovered based on radio signal transmitted by a sparse set [2] of fixed or movable landers. To address important aspects of mission planning, we have analyzed different signal source configurations to find the minimal number of source positions needed for robust localization of anomalies, such as internal voids. Characteristic to this inverse problem are the large relative changes in signal speed caused by the high permittivity of typical asteroid minerals (e.g. basalt), leading to strong refractions and reflections of the signal. Finding an appropriate problemspecific signaling arrangement is an important premission goal for successful in situ measurements. This presentation will include inversion results obtained with laboratory-recorded travel time data y of the form in which n δ denotes a perturbation of a refractive index n = n δ + nbg; gi estimates the total noise due to different error sources; (ybg)i = ∫Ci nbg ds is an entry of noiseless background data ybg; and Ci is a signal path. Also simulated time-evolution data will be covered with respect to potential u satisfying the wave equation ∈rδ2/δt2+ ōδu/δt-∆u = f, where ō is a (latent) conductivity distribution and f is a source term. Special interest will be paid to inversion robustness regarding changes of the prior model and source positioning. Among other things, our analysis suggests that strongly refractive anomalies can be detected with three or four sources independently of their positioning.

  7. Simultaneous EEG and MEG source reconstruction in sparse electromagnetic source imaging.

    PubMed

    Ding, Lei; Yuan, Han

    2013-04-01

    Electroencephalography (EEG) and magnetoencephalography (MEG) have different sensitivities to differently configured brain activations, making them complimentary in providing independent information for better detection and inverse reconstruction of brain sources. In the present study, we developed an integrative approach, which integrates a novel sparse electromagnetic source imaging method, i.e., variation-based cortical current density (VB-SCCD), together with the combined use of EEG and MEG data in reconstructing complex brain activity. To perform simultaneous analysis of multimodal data, we proposed to normalize EEG and MEG signals according to their individual noise levels to create unit-free measures. Our Monte Carlo simulations demonstrated that this integrative approach is capable of reconstructing complex cortical brain activations (up to 10 simultaneously activated and randomly located sources). Results from experimental data showed that complex brain activations evoked in a face recognition task were successfully reconstructed using the integrative approach, which were consistent with other research findings and validated by independent data from functional magnetic resonance imaging using the same stimulus protocol. Reconstructed cortical brain activations from both simulations and experimental data provided precise source localizations as well as accurate spatial extents of localized sources. In comparison with studies using EEG or MEG alone, the performance of cortical source reconstructions using combined EEG and MEG was significantly improved. We demonstrated that this new sparse ESI methodology with integrated analysis of EEG and MEG data could accurately probe spatiotemporal processes of complex human brain activations. This is promising for noninvasively studying large-scale brain networks of high clinical and scientific significance.

  8. Finding nonoverlapping substructures of a sparse matrix

    SciTech Connect

    Pinar, Ali; Vassilevska, Virginia

    2004-08-09

    Many applications of scientific computing rely on computations on sparse matrices, thus the design of efficient implementations of sparse matrix kernels is crucial for the overall efficiency of these applications. Due to the high compute-to-memory ratio and irregular memory access patterns, the performance of sparse matrix kernels is often far away from the peak performance on a modern processor. Alternative data structures have been proposed, which split the original matrix A into A{sub d} and A{sub s}, so that A{sub d} contains all dense blocks of a specified size in the matrix, and A{sub s} contains the remaining entries. This enables the use of dense matrix kernels on the entries of A{sub d} producing better memory performance. In this work, we study the problem of finding a maximum number of non overlapping rectangular dense blocks in a sparse matrix, which has not been studied in the sparse matrix community. We show that the maximum non overlapping dense blocks problem is NP-complete by using a reduction from the maximum independent set problem on cubic planar graphs. We also propose a 2/3-approximation algorithm for 2 times 2 blocks that runs in linear time in the number of nonzeros in the matrix. We discuss alternatives to rectangular blocks such as diagonal blocks and cross blocks and present complexity analysis and approximation algorithms.

  9. Universal Collaboration Strategies for Signal Detection: A Sparse Learning Approach

    NASA Astrophysics Data System (ADS)

    Khanduri, Prashant; Kailkhura, Bhavya; Thiagarajan, Jayaraman J.; Varshney, Pramod K.

    2016-10-01

    This paper considers the problem of high dimensional signal detection in a large distributed network whose nodes can collaborate with their one-hop neighboring nodes (spatial collaboration). We assume that only a small subset of nodes communicate with the Fusion Center (FC). We design optimal collaboration strategies which are universal for a class of deterministic signals. By establishing the equivalence between the collaboration strategy design problem and sparse PCA, we solve the problem efficiently and evaluate the impact of collaboration on detection performance.

  10. Removing sparse noise from hyperspectral images with sparse and low-rank penalties

    NASA Astrophysics Data System (ADS)

    Tariyal, Snigdha; Aggarwal, Hemant Kumar; Majumdar, Angshul

    2016-03-01

    In diffraction grating, at times, there are defective pixels on the focal plane array; this results in horizontal lines of corrupted pixels in some channels. Since only a few such pixels exist, the corruption/noise is sparse. Studies on sparse noise removal from hyperspectral noise are parsimonious. To remove such sparse noise, a prior work exploited the interband spectral correlation along with intraband spatial redundancy to yield a sparse representation in transform domains. We improve upon the prior technique. The intraband spatial redundancy is modeled as a sparse set of transform coefficients and the interband spectral correlation is modeled as a rank deficient matrix. The resulting optimization problem is solved using the split Bregman technique. Comparative experimental results show that our proposed approach is better than the previous one.

  11. Cortical Clefts and Cortical Bumps: A Continuous Spectrum

    PubMed Central

    Furruqh, Farha; Thirunavukarasu, Suresh; Vivekandan, Ravichandran

    2016-01-01

    Cortical ‘clefts’ (schizencephaly) and cortical ‘bumps’ (polymicrogyria) are malformations arising due to defects in postmigrational development of neurons. They are frequently encountered together, with schizencephalic clefts being lined by polymicrogyria. We present the case of an eight-year-old boy who presented with seizures. Imaging revealed closed lip schizencephaly, polymicrogyria and a deep ‘incomplete’ cleft lined by polymicrogyria not communicating with the lateral ventricle. We speculate that hypoperfusion or ischaemic cortical injury during neuronal development may lead to a spectrum of malformations ranging from polymicrogyria to incomplete cortical clefts to schizencephaly. PMID:27630923

  12. Cortical Clefts and Cortical Bumps: A Continuous Spectrum.

    PubMed

    Biswas, Asthik; Furruqh, Farha; Thirunavukarasu, Suresh; Vivekandan, Ravichandran

    2016-07-01

    Cortical 'clefts' (schizencephaly) and cortical 'bumps' (polymicrogyria) are malformations arising due to defects in postmigrational development of neurons. They are frequently encountered together, with schizencephalic clefts being lined by polymicrogyria. We present the case of an eight-year-old boy who presented with seizures. Imaging revealed closed lip schizencephaly, polymicrogyria and a deep 'incomplete' cleft lined by polymicrogyria not communicating with the lateral ventricle. We speculate that hypoperfusion or ischaemic cortical injury during neuronal development may lead to a spectrum of malformations ranging from polymicrogyria to incomplete cortical clefts to schizencephaly. PMID:27630923

  13. Motor and sensory cortical reorganization after bilateral forearm transplantation: Four-year follow-up fMRI case study.

    PubMed

    Hernandez-Castillo, Carlos R; Aguilar-Castañeda, Erika; Iglesias, Martin; Fernandez-Ruiz, Juan

    2016-05-01

    The objective of this study was to characterize the cortical activity pattern of one patient who received bilateral forearm transplants. Using fMRI we acquired motor and sensory brain activity every year after surgery and during three consecutive years while the patient underwent physical rehabilitation. The motor related cortical activity evaluated during the first year showed a sparse pattern involving several brain regions. Over time, the analysis showed a progressive delimitation of the motor-related areas that had significant activity. The results also showed continuous size reductions of the activated cluster in the motor cortex. The activation in the sensory cortex showed significant increases in cluster size over time. The intensity of both motor and sensory cortical activations correlated with the Disabilities of the Arm, Shoulder and Hand questionnaire. Our results show significant cortical reorganization of motor and sensory cortices after transplantation of bilateral forearm transplantation over a four-year period.

  14. A novel sparse boosting method for crater detection in the high resolution planetary image

    NASA Astrophysics Data System (ADS)

    Wang, Yan; Yang, Gang; Guo, Lei

    2015-09-01

    Impact craters distributed on planetary surface become one of the main barriers during the soft landing of planetary probes. In order to accelerate the crater detection, in this paper, we present a new sparse boosting (SparseBoost) method for automatic detection of sub-kilometer craters. The SparseBoost method integrates an improved sparse kernel density estimator (RSDE-WL1) into the Boost algorithm and the RSDE-WL1 estimator is achieved by introducing weighted l1 penalty term into the reduced set density estimator. An iterative algorithm is proposed to implement the RSDE-WL1. The SparseBoost algorithm has the advantage of fewer selected features and simpler representation of the weak classifiers compared with the Boost algorithm. Our SparseBoost based crater detection method is evaluated on a large and high resolution image of Martian surface. Experimental results demonstrate that the proposed method can achieve less computational complexity in comparison with other crater detection methods in terms of selected features.

  15. Fast wavelet based sparse approximate inverse preconditioner

    SciTech Connect

    Wan, W.L.

    1996-12-31

    Incomplete LU factorization is a robust preconditioner for both general and PDE problems but unfortunately not easy to parallelize. Recent study of Huckle and Grote and Chow and Saad showed that sparse approximate inverse could be a potential alternative while readily parallelizable. However, for special class of matrix A that comes from elliptic PDE problems, their preconditioners are not optimal in the sense that independent of mesh size. A reason may be that no good sparse approximate inverse exists for the dense inverse matrix. Our observation is that for this kind of matrices, its inverse entries typically have piecewise smooth changes. We can take advantage of this fact and use wavelet compression techniques to construct a better sparse approximate inverse preconditioner. We shall show numerically that our approach is effective for this kind of matrices.

  16. The biology and dynamics of mammalian cortical granules

    PubMed Central

    2011-01-01

    Cortical granules are membrane bound organelles located in the cortex of unfertilized oocytes. Following fertilization, cortical granules undergo exocytosis to release their contents into the perivitelline space. This secretory process, which is calcium dependent and SNARE protein-mediated pathway, is known as the cortical reaction. After exocytosis, the released cortical granule proteins are responsible for blocking polyspermy by modifying the oocytes' extracellular matrices, such as the zona pellucida in mammals. Mammalian cortical granules range in size from 0.2 um to 0.6 um in diameter and different from most other regulatory secretory organelles in that they are not renewed once released. These granules are only synthesized in female germ cells and transform an egg upon sperm entry; therefore, this unique cellular structure has inherent interest for our understanding of the biology of fertilization. Cortical granules are long thought to be static and awaiting in the cortex of unfertilized oocytes to be stimulated undergoing exocytosis upon gamete fusion. Not till recently, the dynamic nature of cortical granules is appreciated and understood. The latest studies of mammalian cortical granules document that this organelle is not only biochemically heterogeneous, but also displays complex distribution during oocyte development. Interestingly, some cortical granules undergo exocytosis prior to fertilization; and a number of granule components function beyond the time of fertilization in regulating embryonic cleavage and preimplantation development, demonstrating their functional significance in fertilization as well as early embryonic development. The following review will present studies that investigate the biology of cortical granules and will also discuss new findings that uncover the dynamic aspect of this organelle in mammals. PMID:22088197

  17. Sparse regularization for force identification using dictionaries

    NASA Astrophysics Data System (ADS)

    Qiao, Baijie; Zhang, Xingwu; Wang, Chenxi; Zhang, Hang; Chen, Xuefeng

    2016-04-01

    The classical function expansion method based on minimizing l2-norm of the response residual employs various basis functions to represent the unknown force. Its difficulty lies in determining the optimum number of basis functions. Considering the sparsity of force in the time domain or in other basis space, we develop a general sparse regularization method based on minimizing l1-norm of the coefficient vector of basis functions. The number of basis functions is adaptively determined by minimizing the number of nonzero components in the coefficient vector during the sparse regularization process. First, according to the profile of the unknown force, the dictionary composed of basis functions is determined. Second, a sparsity convex optimization model for force identification is constructed. Third, given the transfer function and the operational response, Sparse reconstruction by separable approximation (SpaRSA) is developed to solve the sparse regularization problem of force identification. Finally, experiments including identification of impact and harmonic forces are conducted on a cantilever thin plate structure to illustrate the effectiveness and applicability of SpaRSA. Besides the Dirac dictionary, other three sparse dictionaries including Db6 wavelets, Sym4 wavelets and cubic B-spline functions can also accurately identify both the single and double impact forces from highly noisy responses in a sparse representation frame. The discrete cosine functions can also successfully reconstruct the harmonic forces including the sinusoidal, square and triangular forces. Conversely, the traditional Tikhonov regularization method with the L-curve criterion fails to identify both the impact and harmonic forces in these cases.

  18. Cortical Basal Ganglionic Degeneration

    PubMed Central

    Scarmeas, Nikolaos; Chin, Steven S.; Marder, Karen

    2011-01-01

    In this case study, we describe the symptoms, neuropsychological testing, and brain pathology of a retired mason's assistant with cortical basal ganglionic degeneration (CBGD). CBGD is an extremely rare neurodegenerative disease that is categorized under both Parkinsonian syndromes and frontal lobe dementias. It affects men and women nearly equally, and the age of onset is usually in the sixth decade of life. CBGD is characterized by Parkinson's-like motor symptoms and by deficits of movement and cognition, indicating focal brain pathology. Neuronal cell loss is ultimately responsible for the neurological symptoms. PMID:14602941

  19. Tensor methods for large, sparse unconstrained optimization

    SciTech Connect

    Bouaricha, A.

    1996-11-01

    Tensor methods for unconstrained optimization were first introduced by Schnabel and Chow [SIAM J. Optimization, 1 (1991), pp. 293-315], who describe these methods for small to moderate size problems. This paper extends these methods to large, sparse unconstrained optimization problems. This requires an entirely new way of solving the tensor model that makes the methods suitable for solving large, sparse optimization problems efficiently. We present test results for sets of problems where the Hessian at the minimizer is nonsingular and where it is singular. These results show that tensor methods are significantly more efficient and more reliable than standard methods based on Newton`s method.

  20. Analog system for computing sparse codes

    DOEpatents

    Rozell, Christopher John; Johnson, Don Herrick; Baraniuk, Richard Gordon; Olshausen, Bruno A.; Ortman, Robert Lowell

    2010-08-24

    A parallel dynamical system for computing sparse representations of data, i.e., where the data can be fully represented in terms of a small number of non-zero code elements, and for reconstructing compressively sensed images. The system is based on the principles of thresholding and local competition that solves a family of sparse approximation problems corresponding to various sparsity metrics. The system utilizes Locally Competitive Algorithms (LCAs), nodes in a population continually compete with neighboring units using (usually one-way) lateral inhibition to calculate coefficients representing an input in an over complete dictionary.

  1. Efficient quantum circuits for arbitrary sparse unitaries

    SciTech Connect

    Jordan, Stephen P.; Wocjan, Pawel

    2009-12-15

    Arbitrary exponentially large unitaries cannot be implemented efficiently by quantum circuits. However, we show that quantum circuits can efficiently implement any unitary provided it has at most polynomially many nonzero entries in any row or column, and these entries are efficiently computable. One can formulate a model of computation based on the composition of sparse unitaries which includes the quantum Turing machine model, the quantum circuit model, anyonic models, permutational quantum computation, and discrete time quantum walks as special cases. Thus, we obtain a simple unified proof that these models are all contained in BQP. Furthermore, our general method for implementing sparse unitaries simplifies several existing quantum algorithms.

  2. Sparse Density Estimation on the Multinomial Manifold.

    PubMed

    Hong, Xia; Gao, Junbin; Chen, Sheng; Zia, Tanveer

    2015-11-01

    A new sparse kernel density estimator is introduced based on the minimum integrated square error criterion for the finite mixture model. Since the constraint on the mixing coefficients of the finite mixture model is on the multinomial manifold, we use the well-known Riemannian trust-region (RTR) algorithm for solving this problem. The first- and second-order Riemannian geometry of the multinomial manifold are derived and utilized in the RTR algorithm. Numerical examples are employed to demonstrate that the proposed approach is effective in constructing sparse kernel density estimators with an accuracy competitive with those of existing kernel density estimators. PMID:25647665

  3. A sparse Gaussian process framework for photometric redshift estimation

    NASA Astrophysics Data System (ADS)

    Almosallam, Ibrahim A.; Lindsay, Sam N.; Jarvis, Matt J.; Roberts, Stephen J.

    2016-01-01

    Accurate photometric redshifts are a lynchpin for many future experiments to pin down the cosmological model and for studies of galaxy evolution. In this study, a novel sparse regression framework for photometric redshift estimation is presented. Synthetic data set simulating the Euclid survey and real data from SDSS DR12 are used to train and test the proposed models. We show that approaches which include careful data preparation and model design offer a significant improvement in comparison with several competing machine learning algorithms. Standard implementations of most regression algorithms use the minimization of the sum of squared errors as the objective function. For redshift inference, this induces a bias in the posterior mean of the output distribution, which can be problematic. In this paper, we directly minimize the target metric Δz = (zs - zp)/(1 + zs) and address the bias problem via a distribution-based weighting scheme, incorporated as part of the optimization objective. The results are compared with other machine learning algorithms in the field such as artificial neural networks (ANN), Gaussian processes (GPs) and sparse GPs. The proposed framework reaches a mean absolute Δz = 0.0026(1 + zs), over the redshift range of 0 ≤ zs ≤ 2 on the simulated data, and Δz = 0.0178(1 + zs) over the entire redshift range on the SDSS DR12 survey, outperforming the standard ANNz used in the literature. We also investigate how the relative size of the training sample affects the photometric redshift accuracy. We find that a training sample of >30 per cent of total sample size, provides little additional constraint on the photometric redshifts, and note that our GP formalism strongly outperforms ANNz in the sparse data regime for the simulated data set.

  4. Infrared image recognition based on structure sparse and atomic sparse parallel

    NASA Astrophysics Data System (ADS)

    Wu, Yalu; Li, Ruilong; Xu, Yi; Wang, Liping

    2015-12-01

    Use the redundancy of the super complete dictionary can capture the structural features of the image effectively, can achieving the effective representation of the image. However, the commonly used atomic sparse representation without regard the structure of the dictionary and the unrelated non-zero-term in the process of the computation, though structure sparse consider the structure feature of dictionary, the majority coefficients of the blocks maybe are non-zero, it may affect the identification efficiency. For the disadvantages of these two sparse expressions, a weighted parallel atomic sparse and sparse structure is proposed, and the recognition efficiency is improved by the adaptive computation of the optimal weights. The atomic sparse expression and structure sparse expression are respectively, and the optimal weights are calculated by the adaptive method. Methods are as follows: training by using the less part of the identification sample, the recognition rate is calculated by the increase of the certain step size and t the constraint between weight. The recognition rate as the Z axis, two weight values respectively as X, Y axis, the resulting points can be connected in a straight line in the 3 dimensional coordinate system, by solving the highest recognition rate, the optimal weights can be obtained. Through simulation experiments can be known, the optimal weights based on adaptive method are better in the recognition rate, weights obtained by adaptive computation of a few samples, suitable for parallel recognition calculation, can effectively improve the recognition rate of infrared images.

  5. Six Principles of Visual Cortical Dynamics

    PubMed Central

    Roland, Per E.

    2010-01-01

    A fundamental goal in vision science is to determine how many neurons in how many areas are required to compute a coherent interpretation of the visual scene. Here I propose six principles of cortical dynamics of visual processing in the first 150 ms following the appearance of a visual stimulus. Fast synaptic communication between neurons depends on the driving neurons and the biophysical history and driving forces of the target neurons. Under these constraints, the retina communicates changes in the field of view driving large populations of neurons in visual areas into a dynamic sequence of feed-forward communication and integration of the inward current of the change signal into the dendrites of higher order area neurons (30–70 ms). Simultaneously an even larger number of neurons within each area receiving feed-forward input are pre-excited to sub-threshold levels. The higher order area neurons communicate the results of their computations as feedback adding inward current to the excited and pre-excited neurons in lower areas. This feedback reconciles computational differences between higher and lower areas (75–120 ms). This brings the lower area neurons into a new dynamic regime characterized by reduced driving forces and sparse firing reflecting the visual areas interpretation of the current scene (140 ms). The population membrane potentials and net-inward/outward currents and firing are well behaved at the mesoscopic scale, such that the decoding in retinotopic cortical space shows the visual areas’ interpretation of the current scene. These dynamics have plausible biophysical explanations. The principles are theoretical, predictive, supported by recent experiments and easily lend themselves to experimental tests or computational modeling. PMID:20661451

  6. Time in Cortical Circuits

    PubMed Central

    Shadlen, Michael N.; Jazayeri, Mehrdad; Nobre, Anna C.; Buonomano, Dean V.

    2015-01-01

    Time is central to cognition. However, the neural basis for time-dependent cognition remains poorly understood. We explore how the temporal features of neural activity in cortical circuits and their capacity for plasticity can contribute to time-dependent cognition over short time scales. This neural activity is linked to cognition that operates in the present or anticipates events or stimuli in the near future. We focus on deliberation and planning in the context of decision making as a cognitive process that integrates information across time. We progress to consider how temporal expectations of the future modulate perception. We propose that understanding the neural basis for how the brain tells time and operates in time will be necessary to develop general models of cognition. SIGNIFICANCE STATEMENT Time is central to cognition. However, the neural basis for time-dependent cognition remains poorly understood. We explore how the temporal features of neural activity in cortical circuits and their capacity for plasticity can contribute to time-dependent cognition over short time scales. We propose that understanding the neural basis for how the brain tells time and operates in time will be necessary to develop general models of cognition. PMID:26468192

  7. Second SIAM conference on sparse matrices: Abstracts. Final technical report

    SciTech Connect

    1996-12-31

    This report contains abstracts on the following topics: invited and long presentations (IP1 & LP1); sparse matrix reordering & graph theory I; sparse matrix tools & environments I; eigenvalue computations I; iterative methods & acceleration techniques I; applications I; parallel algorithms I; sparse matrix reordering & graphy theory II; sparse matrix tool & environments II; least squares & optimization I; iterative methods & acceleration techniques II; applications II; eigenvalue computations II; least squares & optimization II; parallel algorithms II; sparse direct methods; iterative methods & acceleration techniques III; eigenvalue computations III; and sparse matrix reordering & graph theory III.

  8. Facial expression recognition with facial parts based sparse representation classifier

    NASA Astrophysics Data System (ADS)

    Zhi, Ruicong; Ruan, Qiuqi

    2009-10-01

    Facial expressions play important role in human communication. The understanding of facial expression is a basic requirement in the development of next generation human computer interaction systems. Researches show that the intrinsic facial features always hide in low dimensional facial subspaces. This paper presents facial parts based facial expression recognition system with sparse representation classifier. Sparse representation classifier exploits sparse representation to select face features and classify facial expressions. The sparse solution is obtained by solving l1 -norm minimization problem with constraint of linear combination equation. Experimental results show that sparse representation is efficient for facial expression recognition and sparse representation classifier obtain much higher recognition accuracies than other compared methods.

  9. Cortical control of anticipatory postural adjustments prior to stepping.

    PubMed

    Varghese, J P; Merino, D M; Beyer, K B; McIlroy, W E

    2016-01-28

    Human bipedal balance control is achieved either reactively or predictively by a distributed network of neural areas within the central nervous system with a potential role for cerebral cortex. While the role of the cortex in reactive balance has been widely explored, only few studies have addressed the cortical activations related to predictive balance control. The present study investigated the cortical activations related to the preparation and execution of anticipatory postural adjustment (APA) that precede a step. This study also examined whether the preparatory cortical activations related to a specific movement is dependent on the context of control (postural component vs. focal component). Ground reaction forces and electroencephalographic (EEG) data were recorded from 14 healthy adults while they performed lateral weight shift and lateral stepping with and without initially preloading their weight to the stance leg. EEG analysis revealed that there were distinct movement-related potentials (MRPs) with concurrent event-related desynchronization (ERD) of mu and beta rhythms prior to the onset of APA and also to the onset of foot-off during lateral stepping in the fronto-central cortical areas. Also, the MRPs and ERD prior to the onset of APA and onset of lateral weight shift were not significantly different suggesting the comparable cortical activations for the generation of postural and focal movements. The present study reveals the occurrence of cortical activation prior to the execution of an APA that precedes a step. Importantly, this cortical activity appears independent of the context of the movement. PMID:26608123

  10. Security-enhanced phase encryption assisted by nonlinear optical correlation via sparse phase

    NASA Astrophysics Data System (ADS)

    Chen, Wen; Wang, Xiaogang; Chen, Xudong

    2015-03-01

    We propose a method for security-enhanced phase encryption assisted by a nonlinear optical correlation via a sparse phase. Optical configurations are established based on a phase retrieval algorithm for embedding an input image and the secret data into phase-only masks. We found that when one or a few phase-only masks generated during data hiding are sparse, it is possible to integrate these sparse masks into those phase-only masks generated during the encoding of the input image. Synthesized phase-only masks are used for the recovery, and sparse distributions (i.e., binary maps) for generating the incomplete phase-only masks are considered as additional parameters for the recovery of secret data. It is difficult for unauthorized receivers to know that a useful phase has been sparsely distributed in the finally generated phase-only masks for secret-data recovery. Only when the secret data are correctly verified can the input image obtained with valid keys be claimed as targeted information.

  11. Learning Stable Multilevel Dictionaries for Sparse Representations.

    PubMed

    Thiagarajan, Jayaraman J; Ramamurthy, Karthikeyan Natesan; Spanias, Andreas

    2015-09-01

    Sparse representations using learned dictionaries are being increasingly used with success in several data processing and machine learning applications. The increasing need for learning sparse models in large-scale applications motivates the development of efficient, robust, and provably good dictionary learning algorithms. Algorithmic stability and generalizability are desirable characteristics for dictionary learning algorithms that aim to build global dictionaries, which can efficiently model any test data similar to the training samples. In this paper, we propose an algorithm to learn dictionaries for sparse representations from large scale data, and prove that the proposed learning algorithm is stable and generalizable asymptotically. The algorithm employs a 1-D subspace clustering procedure, the K-hyperline clustering, to learn a hierarchical dictionary with multiple levels. We also propose an information-theoretic scheme to estimate the number of atoms needed in each level of learning and develop an ensemble approach to learn robust dictionaries. Using the proposed dictionaries, the sparse code for novel test data can be computed using a low-complexity pursuit procedure. We demonstrate the stability and generalization characteristics of the proposed algorithm using simulations. We also evaluate the utility of the multilevel dictionaries in compressed recovery and subspace learning applications.

  12. Multilevel sparse functional principal component analysis.

    PubMed

    Di, Chongzhi; Crainiceanu, Ciprian M; Jank, Wolfgang S

    2014-01-29

    We consider analysis of sparsely sampled multilevel functional data, where the basic observational unit is a function and data have a natural hierarchy of basic units. An example is when functions are recorded at multiple visits for each subject. Multilevel functional principal component analysis (MFPCA; Di et al. 2009) was proposed for such data when functions are densely recorded. Here we consider the case when functions are sparsely sampled and may contain only a few observations per function. We exploit the multilevel structure of covariance operators and achieve data reduction by principal component decompositions at both between and within subject levels. We address inherent methodological differences in the sparse sampling context to: 1) estimate the covariance operators; 2) estimate the functional principal component scores; 3) predict the underlying curves. Through simulations the proposed method is able to discover dominating modes of variations and reconstruct underlying curves well even in sparse settings. Our approach is illustrated by two applications, the Sleep Heart Health Study and eBay auctions. PMID:24872597

  13. Multilevel sparse functional principal component analysis

    PubMed Central

    Di, Chongzhi; Crainiceanu, Ciprian M.; Jank, Wolfgang S.

    2014-01-01

    We consider analysis of sparsely sampled multilevel functional data, where the basic observational unit is a function and data have a natural hierarchy of basic units. An example is when functions are recorded at multiple visits for each subject. Multilevel functional principal component analysis (MFPCA; Di et al. 2009) was proposed for such data when functions are densely recorded. Here we consider the case when functions are sparsely sampled and may contain only a few observations per function. We exploit the multilevel structure of covariance operators and achieve data reduction by principal component decompositions at both between and within subject levels. We address inherent methodological differences in the sparse sampling context to: 1) estimate the covariance operators; 2) estimate the functional principal component scores; 3) predict the underlying curves. Through simulations the proposed method is able to discover dominating modes of variations and reconstruct underlying curves well even in sparse settings. Our approach is illustrated by two applications, the Sleep Heart Health Study and eBay auctions. PMID:24872597

  14. Algorithms for sparse nonnegative Tucker decompositions.

    PubMed

    Mørup, Morten; Hansen, Lars Kai; Arnfred, Sidse M

    2008-08-01

    There is a increasing interest in analysis of large-scale multiway data. The concept of multiway data refers to arrays of data with more than two dimensions, that is, taking the form of tensors. To analyze such data, decomposition techniques are widely used. The two most common decompositions for tensors are the Tucker model and the more restricted PARAFAC model. Both models can be viewed as generalizations of the regular factor analysis to data of more than two modalities. Nonnegative matrix factorization (NMF), in conjunction with sparse coding, has recently been given much attention due to its part-based and easy interpretable representation. While NMF has been extended to the PARAFAC model, no such attempt has been done to extend NMF to the Tucker model. However, if the tensor data analyzed are nonnegative, it may well be relevant to consider purely additive (i.e., nonnegative) Tucker decompositions). To reduce ambiguities of this type of decomposition, we develop updates that can impose sparseness in any combination of modalities, hence, proposed algorithms for sparse nonnegative Tucker decompositions (SN-TUCKER). We demonstrate how the proposed algorithms are superior to existing algorithms for Tucker decompositions when the data and interactions can be considered nonnegative. We further illustrate how sparse coding can help identify what model (PARAFAC or Tucker) is more appropriate for the data as well as to select the number of components by turning off excess components. The algorithms for SN-TUCKER can be downloaded from Mørup (2007).

  15. Self-Control in Sparsely Coded Networks

    NASA Astrophysics Data System (ADS)

    Dominguez, D. R. C.; Bollé, D.

    1998-03-01

    A complete self-control mechanism is proposed in the dynamics of neural networks through the introduction of a time-dependent threshold, determined in function of both the noise and the pattern activity in the network. Especially for sparsely coded models this mechanism is shown to considerably improve the storage capacity, the basins of attraction, and the mutual information content.

  16. Sparse matrix orderings for factorized inverse preconditioners

    SciTech Connect

    Benzi, M.; Tuama, M.

    1998-09-01

    The effect of reorderings on the performance of factorized sparse approximate inverse preconditioners is considered. It is shown that certain reorderings can be very beneficial both in the preconditioner construction phase and in terms of the rate of convergence of the preconditioned iteration.

  17. STIS Sparse Field CTE test {Cycle 9}

    NASA Astrophysics Data System (ADS)

    Goudfrooij, Paul

    2000-07-01

    CTE measurements are made using the "sparse field test", along both the serial and parallel axes. This program needs special commanding to provide {a} off-center MSM positionings of some slits, and {b} the ability to read out with any amplifier {A, B, C, or D}. All exposures are internals.

  18. STIS Sparse Field CTE test {Cycle 8}

    NASA Astrophysics Data System (ADS)

    Goudfrooij, Paul

    1999-07-01

    CTE measurements are made using the "sparse field test", along both the serial and parallel axes. This program needs special commanding to provide {a} off-center MSM positionings of some slits, and {b} the ability to read out with any amplifier {A, B, C, or D}. All exposures are internals.

  19. SAR Image Despeckling Via Structural Sparse Representation

    NASA Astrophysics Data System (ADS)

    Lu, Ting; Li, Shutao; Fang, Leyuan; Benediktsson, Jón Atli

    2016-12-01

    A novel synthetic aperture radar (SAR) image despeckling method based on structural sparse representation is introduced. The proposed method utilizes the fact that different regions in SAR images correspond to varying terrain reflectivity. Therefore, SAR images can be split into a heterogeneous class (with a varied terrain reflectivity) and a homogeneous class (with a constant terrain reflectivity). In the proposed method, different sparse representation based despeckling schemes are designed by combining the different region characteristics in SAR images. For heterogeneous regions with rich structure and texture information, structural dictionaries are learned to appropriately represent varied structural characteristics. Specifically, each patch in these regions is sparsely coded with the best fitted structural dictionary, thus good structure preservation can be obtained. For homogenous regions without rich structure and texture information, the highly redundant photometric self-similarity is exploited to suppress speckle noise without introducing artifacts. That is achieved by firstly learning the sub-dictionary, then simultaneously sparsely coding for each group of photometrically similar image patches. Visual and objective experimental results demonstrate the superiority of the proposed method over the-state-of-the-art methods.

  20. A Comparative Study of Sparse Associative Memories

    NASA Astrophysics Data System (ADS)

    Gripon, Vincent; Heusel, Judith; Löwe, Matthias; Vermet, Franck

    2016-07-01

    We study various models of associative memories with sparse information, i.e. a pattern to be stored is a random string of 0s and 1s with about log N 1s, only. We compare different synaptic weights, architectures and retrieval mechanisms to shed light on the influence of the various parameters on the storage capacity.

  1. Spatial Learning and Action Planning in a Prefrontal Cortical Network Model

    PubMed Central

    Martinet, Louis-Emmanuel; Sheynikhovich, Denis; Benchenane, Karim; Arleo, Angelo

    2011-01-01

    The interplay between hippocampus and prefrontal cortex (PFC) is fundamental to spatial cognition. Complementing hippocampal place coding, prefrontal representations provide more abstract and hierarchically organized memories suitable for decision making. We model a prefrontal network mediating distributed information processing for spatial learning and action planning. Specific connectivity and synaptic adaptation principles shape the recurrent dynamics of the network arranged in cortical minicolumns. We show how the PFC columnar organization is suitable for learning sparse topological-metrical representations from redundant hippocampal inputs. The recurrent nature of the network supports multilevel spatial processing, allowing structural features of the environment to be encoded. An activation diffusion mechanism spreads the neural activity through the column population leading to trajectory planning. The model provides a functional framework for interpreting the activity of PFC neurons recorded during navigation tasks. We illustrate the link from single unit activity to behavioral responses. The results suggest plausible neural mechanisms subserving the cognitive “insight” capability originally attributed to rodents by Tolman & Honzik. Our time course analysis of neural responses shows how the interaction between hippocampus and PFC can yield the encoding of manifold information pertinent to spatial planning, including prospective coding and distance-to-goal correlates. PMID:21625569

  2. Cortico-cortical communication dynamics

    PubMed Central

    Roland, Per E.; Hilgetag, Claus C.; Deco, Gustavo

    2014-01-01

    In principle, cortico-cortical communication dynamics is simple: neurons in one cortical area communicate by sending action potentials that release glutamate and excite their target neurons in other cortical areas. In practice, knowledge about cortico-cortical communication dynamics is minute. One reason is that no current technique can capture the fast spatio-temporal cortico-cortical evolution of action potential transmission and membrane conductances with sufficient spatial resolution. A combination of optogenetics and monosynaptic tracing with virus can reveal the spatio-temporal cortico-cortical dynamics of specific neurons and their targets, but does not reveal how the dynamics evolves under natural conditions. Spontaneous ongoing action potentials also spread across cortical areas and are difficult to separate from structured evoked and intrinsic brain activity such as thinking. At a certain state of evolution, the dynamics may engage larger populations of neurons to drive the brain to decisions, percepts and behaviors. For example, successfully evolving dynamics to sensory transients can appear at the mesoscopic scale revealing how the transient is perceived. As a consequence of these methodological and conceptual difficulties, studies in this field comprise a wide range of computational models, large-scale measurements (e.g., by MEG, EEG), and a combination of invasive measurements in animal experiments. Further obstacles and challenges of studying cortico-cortical communication dynamics are outlined in this critical review. PMID:24847217

  3. Modeling cortical circuits.

    SciTech Connect

    Rohrer, Brandon Robinson; Rothganger, Fredrick H.; Verzi, Stephen J.; Xavier, Patrick Gordon

    2010-09-01

    The neocortex is perhaps the highest region of the human brain, where audio and visual perception takes place along with many important cognitive functions. An important research goal is to describe the mechanisms implemented by the neocortex. There is an apparent regularity in the structure of the neocortex [Brodmann 1909, Mountcastle 1957] which may help simplify this task. The work reported here addresses the problem of how to describe the putative repeated units ('cortical circuits') in a manner that is easily understood and manipulated, with the long-term goal of developing a mathematical and algorithmic description of their function. The approach is to reduce each algorithm to an enhanced perceptron-like structure and describe its computation using difference equations. We organize this algorithmic processing into larger structures based on physiological observations, and implement key modeling concepts in software which runs on parallel computing hardware.

  4. Cortical plasticity and rehabilitation.

    PubMed

    Moucha, Raluca; Kilgard, Michael P

    2006-01-01

    The brain is constantly adapting to environmental and endogenous changes (including injury) that occur at every stage of life. The mechanisms that regulate neural plasticity have been refined over millions of years. Motivation and sensory experience directly shape the rewiring that makes learning and neurological recovery possible. Guiding neural reorganization in a manner that facilitates recovery of function is a primary goal of neurological rehabilitation. As the rules that govern neural plasticity become better understood, it will be possible to manipulate the sensory and motor experience of patients to induce specific forms of plasticity. This review summarizes our current knowledge regarding factors that regulate cortical plasticity, illustrates specific forms of reorganization induced by control of each factor, and suggests how to exploit these factors for clinical benefit.

  5. A Comparison of Methods for Ocean Reconstruction from Sparse Observations

    NASA Astrophysics Data System (ADS)

    Streletz, G. J.; Kronenberger, M.; Weber, C.; Gebbie, G.; Hagen, H.; Garth, C.; Hamann, B.; Kreylos, O.; Kellogg, L. H.; Spero, H. J.

    2014-12-01

    We present a comparison of two methods for developing reconstructions of oceanic scalar property fields from sparse scattered observations. Observed data from deep sea core samples provide valuable information regarding the properties of oceans in the past. However, because the locations of sample sites are distributed on the ocean floor in a sparse and irregular manner, developing a global ocean reconstruction is a difficult task. Our methods include a flow-based and a moving least squares -based approximation method. The flow-based method augments the process of interpolating or approximating scattered scalar data by incorporating known flow information. The scheme exploits this additional knowledge to define a non-Euclidean distance measure between points in the spatial domain. This distance measure is used to create a reconstruction of the desired scalar field on the spatial domain. The resulting reconstruction thus incorporates information from both the scattered samples and the known flow field. The second method does not assume a known flow field, but rather works solely with the observed scattered samples. It is based on a modification of the moving least squares approach, a weighted least squares approximation method that blends local approximations into a global result. The modifications target the selection of data used for these local approximations and the construction of the weighting function. The definition of distance used in the weighting function is crucial for this method, so we use a machine learning approach to determine a set of near-optimal parameters for the weighting. We have implemented both of the reconstruction methods and have tested them using several sparse oceanographic datasets. Based upon these studies, we discuss the advantages and disadvantages of each method and suggest possible ways to combine aspects of both methods in order to achieve an overall high-quality reconstruction.

  6. Deploying temporary networks for upscaling of sparse network stations

    NASA Astrophysics Data System (ADS)

    Coopersmith, Evan J.; Cosh, Michael H.; Bell, Jesse E.; Kelly, Victoria; Hall, Mark; Palecki, Michael A.; Temimi, Marouane

    2016-10-01

    Soil observations networks at the national scale play an integral role in hydrologic modeling, drought assessment, agricultural decision support, and our ability to understand climate change. Understanding soil moisture variability is necessary to apply these measurements to model calibration, business and consumer applications, or even human health issues. The installation of soil moisture sensors as sparse, national networks is necessitated by limited financial resources. However, this results in the incomplete sampling of the local heterogeneity of soil type, vegetation cover, topography, and the fine spatial distribution of precipitation events. To this end, temporary networks can be installed in the areas surrounding a permanent installation within a sparse network. The temporary networks deployed in this study provide a more representative average at the 3 km and 9 km scales, localized about the permanent gauge. The value of such temporary networks is demonstrated at test sites in Millbrook, New York and Crossville, Tennessee. The capacity of a single U.S. Climate Reference Network (USCRN) sensor set to approximate the average of a temporary network at the 3 km and 9 km scales using a simple linear scaling function is tested. The capacity of a temporary network to provide reliable estimates with diminishing numbers of sensors, the temporal stability of those networks, and ultimately, the relationship of the variability of those networks to soil moisture conditions at the permanent sensor are investigated. In this manner, this work demonstrates the single-season installation of a temporary network as a mechanism to characterize the soil moisture variability at a permanent gauge within a sparse network.

  7. Analysing Local Sparseness in the Macaque Brain Network

    PubMed Central

    Singh, Raghavendra; Nagar, Seema; Nanavati, Amit A.

    2015-01-01

    Understanding the network structure of long distance pathways in the brain is a necessary step towards developing an insight into the brain’s function, organization and evolution. Dense global subnetworks of these pathways have often been studied, primarily due to their functional implications. Instead we study sparse local subnetworks of the pathways to establish the role of a brain area in enabling shortest path communication between its non-adjacent topological neighbours. We propose a novel metric to measure the topological communication load on a vertex due to its immediate neighbourhood, and show that in terms of distribution of this local communication load, a network of Macaque long distance pathways is substantially different from other real world networks and random graph models. Macaque network contains the entire range of local subnetworks, from star-like networks to clique-like networks, while other networks tend to contain a relatively small range of subnetworks. Further, sparse local subnetworks in the Macaque network are not only found across topographical super-areas, e.g., lobes, but also within a super-area, arguing that there is conservation of even relatively short-distance pathways. To establish the communication role of a vertex we borrow the concept of brokerage from social science, and present the different types of brokerage roles that brain areas play, highlighting that not only the thalamus, but also cingulate gyrus and insula often act as “relays” for areas in the neocortex. These and other analysis of communication load and roles of the sparse subnetworks of the Macaque brain provide new insights into the organisation of its pathways. PMID:26437077

  8. Analysing Local Sparseness in the Macaque Brain Network.

    PubMed

    Singh, Raghavendra; Nagar, Seema; Nanavati, Amit A

    2015-01-01

    Understanding the network structure of long distance pathways in the brain is a necessary step towards developing an insight into the brain's function, organization and evolution. Dense global subnetworks of these pathways have often been studied, primarily due to their functional implications. Instead we study sparse local subnetworks of the pathways to establish the role of a brain area in enabling shortest path communication between its non-adjacent topological neighbours. We propose a novel metric to measure the topological communication load on a vertex due to its immediate neighbourhood, and show that in terms of distribution of this local communication load, a network of Macaque long distance pathways is substantially different from other real world networks and random graph models. Macaque network contains the entire range of local subnetworks, from star-like networks to clique-like networks, while other networks tend to contain a relatively small range of subnetworks. Further, sparse local subnetworks in the Macaque network are not only found across topographical super-areas, e.g., lobes, but also within a super-area, arguing that there is conservation of even relatively short-distance pathways. To establish the communication role of a vertex we borrow the concept of brokerage from social science, and present the different types of brokerage roles that brain areas play, highlighting that not only the thalamus, but also cingulate gyrus and insula often act as "relays" for areas in the neocortex. These and other analysis of communication load and roles of the sparse subnetworks of the Macaque brain provide new insights into the organisation of its pathways.

  9. A bit allocation method for sparse source coding.

    PubMed

    Kaaniche, Mounir; Fraysse, Aurélia; Pesquet-Popescu, Béatrice; Pesquet, Jean-Christophe

    2014-01-01

    In this paper, we develop an efficient bit allocation strategy for subband-based image coding systems. More specifically, our objective is to design a new optimization algorithm based on a rate-distortion optimality criterion. To this end, we consider the uniform scalar quantization of a class of mixed distributed sources following a Bernoulli-generalized Gaussian distribution. This model appears to be particularly well-adapted for image data, which have a sparse representation in a wavelet basis. In this paper, we propose new approximations of the entropy and the distortion functions using piecewise affine and exponential forms, respectively. Because of these approximations, bit allocation is reformulated as a convex optimization problem. Solving the resulting problem allows us to derive the optimal quantization step for each subband. Experimental results show the benefits that can be drawn from the proposed bit allocation method in a typical transform-based coding application.

  10. Sparse Geologic Dictionaries for Flexible and Low-Rank Subsurface Flow Model Calibration: Field Applications

    NASA Astrophysics Data System (ADS)

    Khaninezhad, M. R. M.; Jafarpour, B.

    2014-12-01

    Inference of spatially distributed reservoir and aquifer properties from scattered and spatially limited data poses a poorly constrained nonlinear inverse problem that can have many solutions. In particular, the uncertainty in the geologic continuity model can remarkably degrade the quality of fluid displacement predictions, hence, the efficiency of resource development plans. For model calibration, instead of estimating aquifer properties for each grid cell in the model, the sparse representation of the aquifer properties is estimated from nonlinear production data. The resulting calibration problem can be solved using recent developments in sparse signal processing, widely known as compressed sensing. This novel formulation leads to a sparse data inversion technique that effectively searches for relevant geologic patterns that can explain the available spatiotemporal data. We recently introduced a new model calibration framework by using sparse geologic dictionaries that are constructed from uncertain prior geologic models. Here, we first demonstrate the effectiveness of the proposed sparse geologic dictionaries for flexible and robust model calibration under prior geologic uncertainty. We illustrate the effectiveness of the proposed approach in using limited nonlinear production data to identify a consistent geologic scenario from a number of candidate scenarios, which is usually a challenging problem in geostatistical reservoir characterization. We then evaluate the feasibility of adopting this framework for field application. In particular, we present subsurface field model calibration applications in which sparse geologic dictionaries are learned from uncertain prior information on large-scale reservoir property descriptions. We consider two large-scale field case studies, the Brugges and the Norne field examples. We discuss the construction of geologic dictionaries for large-scale problems and present reduced-order methods to speed up the computational

  11. Cortical Control of Striatal Dopamine Transmission via Striatal Cholinergic Interneurons

    PubMed Central

    Kosillo, Polina; Zhang, Yan-Feng; Threlfell, Sarah; Cragg, Stephanie J.

    2016-01-01

    Corticostriatal regulation of striatal dopamine (DA) transmission has long been postulated, but ionotropic glutamate receptors have not been localized directly to DA axons. Striatal cholinergic interneurons (ChIs) are emerging as major players in striatal function, and can govern DA transmission by activating nicotinic receptors (nAChRs) on DA axons. Cortical inputs to ChIs have historically been perceived as sparse, but recent evidence indicates that they strongly activate ChIs. We explored whether activation of M1/M2 corticostriatal inputs can consequently gate DA transmission, via ChIs. We reveal that optogenetic activation of channelrhodopsin-expressing corticostriatal axons can drive striatal DA release detected with fast-scan cyclic voltammetry and requires activation of nAChRs on DA axons and AMPA receptors on ChIs that promote short-latency action potentials. By contrast, DA release driven by optogenetic activation of intralaminar thalamostriatal inputs involves additional activation of NMDA receptors on ChIs and action potential generation over longer timescales. Therefore, cortical and thalamic glutamate inputs can modulate DA transmission by regulating ChIs as gatekeepers, through ionotropic glutamate receptors. The different use of AMPA and NMDA receptors by cortical versus thalamic inputs might lead to distinct input integration strategies by ChIs and distinct modulation of the function of DA and striatum. PMID:27566978

  12. A sparse digital signal model for ultrasonic nondestructive evaluation of layered materials.

    PubMed

    Bochud, N; Gomez, A M; Rus, G; Peinado, A M

    2015-09-01

    Signal modeling has been proven to be an useful tool to characterize damaged materials under ultrasonic nondestructive evaluation (NDE). In this paper, we introduce a novel digital signal model for ultrasonic NDE of multilayered materials. This model borrows concepts from lattice filter theory, and bridges them to the physics involved in the wave-material interactions. In particular, the proposed theoretical framework shows that any multilayered material can be characterized by a transfer function with sparse coefficients. The filter coefficients are linked to the physical properties of the material and are analytically obtained from them, whereas a sparse distribution naturally arises and does not rely on heuristic approaches. The developed model is first validated with experimental measurements obtained from multilayered media consisting of homogeneous solids. Then, the sparse structure of the obtained digital filter is exploited through a model-based inverse problem for damage identification in a carbon fiber-reinforced polymer (CFRP) plate.

  13. Synthesizing spatiotemporally sparse smartphone sensor data for bridge modal identification

    NASA Astrophysics Data System (ADS)

    Ozer, Ekin; Feng, Maria Q.

    2016-08-01

    Smartphones as vibration measurement instruments form a large-scale, citizen-induced, and mobile wireless sensor network (WSN) for system identification and structural health monitoring (SHM) applications. Crowdsourcing-based SHM is possible with a decentralized system granting citizens with operational responsibility and control. Yet, citizen initiatives introduce device mobility, drastically changing SHM results due to uncertainties in the time and the space domains. This paper proposes a modal identification strategy that fuses spatiotemporally sparse SHM data collected by smartphone-based WSNs. Multichannel data sampled with the time and the space independence is used to compose the modal identification parameters such as frequencies and mode shapes. Structural response time history can be gathered by smartphone accelerometers and converted into Fourier spectra by the processor units. Timestamp, data length, energy to power conversion address temporal variation, whereas spatial uncertainties are reduced by geolocation services or determining node identity via QR code labels. Then, parameters collected from each distributed network component can be extended to global behavior to deduce modal parameters without the need of a centralized and synchronous data acquisition system. The proposed method is tested on a pedestrian bridge and compared with a conventional reference monitoring system. The results show that the spatiotemporally sparse mobile WSN data can be used to infer modal parameters despite non-overlapping sensor operation schedule.

  14. Music emotion detection using hierarchical sparse kernel machines.

    PubMed

    Chin, Yu-Hao; Lin, Chang-Hong; Siahaan, Ernestasia; Wang, Jia-Ching

    2014-01-01

    For music emotion detection, this paper presents a music emotion verification system based on hierarchical sparse kernel machines. With the proposed system, we intend to verify if a music clip possesses happiness emotion or not. There are two levels in the hierarchical sparse kernel machines. In the first level, a set of acoustical features are extracted, and principle component analysis (PCA) is implemented to reduce the dimension. The acoustical features are utilized to generate the first-level decision vector, which is a vector with each element being a significant value of an emotion. The significant values of eight main emotional classes are utilized in this paper. To calculate the significant value of an emotion, we construct its 2-class SVM with calm emotion as the global (non-target) side of the SVM. The probability distributions of the adopted acoustical features are calculated and the probability product kernel is applied in the first-level SVMs to obtain first-level decision vector feature. In the second level of the hierarchical system, we merely construct a 2-class relevance vector machine (RVM) with happiness as the target side and other emotions as the background side of the RVM. The first-level decision vector is used as the feature with conventional radial basis function kernel. The happiness verification threshold is built on the probability value. In the experimental results, the detection error tradeoff (DET) curve shows that the proposed system has a good performance on verifying if a music clip reveals happiness emotion.

  15. Threshold partitioning of sparse matrices and applications to Markov chains

    SciTech Connect

    Choi, Hwajeong; Szyld, D.B.

    1996-12-31

    It is well known that the order of the variables and equations of a large, sparse linear system influences the performance of classical iterative methods. In particular if, after a symmetric permutation, the blocks in the diagonal have more nonzeros, classical block methods have a faster asymptotic rate of convergence. In this paper, different ordering and partitioning algorithms for sparse matrices are presented. They are modifications of PABLO. In the new algorithms, in addition to the location of the nonzeros, the values of the entries are taken into account. The matrix resulting after the symmetric permutation has dense blocks along the diagonal, and small entries in the off-diagonal blocks. Parameters can be easily adjusted to obtain, for example, denser blocks, or blocks with elements of larger magnitude. In particular, when the matrices represent Markov chains, the permuted matrices are well suited for block iterative methods that find the corresponding probability distribution. Applications to three types of methods are explored: (1) Classical block methods, such as Block Gauss Seidel. (2) Preconditioned GMRES, where a block diagonal preconditioner is used. (3) Iterative aggregation method (also called aggregation/disaggregation) where the partition obtained from the ordering algorithm with certain parameters is used as an aggregation scheme. In all three cases, experiments are presented which illustrate the performance of the methods with the new orderings. The complexity of the new algorithms is linear in the number of nonzeros and the order of the matrix, and thus adding little computational effort to the overall solution.

  16. Fault feature extraction of rolling element bearings using sparse representation

    NASA Astrophysics Data System (ADS)

    He, Guolin; Ding, Kang; Lin, Huibin

    2016-03-01

    Influenced by factors such as speed fluctuation, rolling element sliding and periodical variation of load distribution and impact force on the measuring direction of sensor, the impulse response signals caused by defective rolling bearing are non-stationary, and the amplitudes of the impulse may even drop to zero when the fault is out of load zone. The non-stationary characteristic and impulse missing phenomenon reduce the effectiveness of the commonly used demodulation method on rolling element bearing fault diagnosis. Based on sparse representation theories, a new approach for fault diagnosis of rolling element bearing is proposed. The over-complete dictionary is constructed by the unit impulse response function of damped second-order system, whose natural frequencies and relative damping ratios are directly identified from the fault signal by correlation filtering method. It leads to a high similarity between atoms and defect induced impulse, and also a sharply reduction of the redundancy of the dictionary. To improve the matching accuracy and calculation speed of sparse coefficient solving, the fault signal is divided into segments and the matching pursuit algorithm is carried out by segments. After splicing together all the reconstructed signals, the fault feature is extracted successfully. The simulation and experimental results show that the proposed method is effective for the fault diagnosis of rolling element bearing in large rolling element sliding and low signal to noise ratio circumstances.

  17. Causal Network Inference Via Group Sparse Regularization.

    PubMed

    Bolstad, Andrew; Van Veen, Barry D; Nowak, Robert

    2011-06-11

    This paper addresses the problem of inferring sparse causal networks modeled by multivariate autoregressive (MAR) processes. Conditions are derived under which the Group Lasso (gLasso) procedure consistently estimates sparse network structure. The key condition involves a "false connection score" ψ. In particular, we show that consistent recovery is possible even when the number of observations of the network is far less than the number of parameters describing the network, provided that ψ < 1. The false connection score is also demonstrated to be a useful metric of recovery in nonasymptotic regimes. The conditions suggest a modified gLasso procedure which tends to improve the false connection score and reduce the chances of reversing the direction of causal influence. Computational experiments and a real network based electrocorticogram (ECoG) simulation study demonstrate the effectiveness of the approach.

  18. Solving large sparse eigenvalue problems on supercomputers

    NASA Technical Reports Server (NTRS)

    Philippe, Bernard; Saad, Youcef

    1988-01-01

    An important problem in scientific computing consists in finding a few eigenvalues and corresponding eigenvectors of a very large and sparse matrix. The most popular methods to solve these problems are based on projection techniques on appropriate subspaces. The main attraction of these methods is that they only require the use of the matrix in the form of matrix by vector multiplications. The implementations on supercomputers of two such methods for symmetric matrices, namely Lanczos' method and Davidson's method are compared. Since one of the most important operations in these two methods is the multiplication of vectors by the sparse matrix, methods of performing this operation efficiently are discussed. The advantages and the disadvantages of each method are compared and implementation aspects are discussed. Numerical experiments on a one processor CRAY 2 and CRAY X-MP are reported. Possible parallel implementations are also discussed.

  19. Sparse representation for color image restoration.

    PubMed

    Mairal, Julien; Elad, Michael; Sapiro, Guillermo

    2008-01-01

    Sparse representations of signals have drawn considerable interest in recent years. The assumption that natural signals, such as images, admit a sparse decomposition over a redundant dictionary leads to efficient algorithms for handling such sources of data. In particular, the design of well adapted dictionaries for images has been a major challenge. The K-SVD has been recently proposed for this task and shown to perform very well for various grayscale image processing tasks. In this paper, we address the problem of learning dictionaries for color images and extend the K-SVD-based grayscale image denoising algorithm that appears in. This work puts forward ways for handling nonhomogeneous noise and missing information, paving the way to state-of-the-art results in applications such as color image denoising, demosaicing, and inpainting, as demonstrated in this paper. PMID:18229804

  20. Sparse brain network using penalized linear regression

    NASA Astrophysics Data System (ADS)

    Lee, Hyekyoung; Lee, Dong Soo; Kang, Hyejin; Kim, Boong-Nyun; Chung, Moo K.

    2011-03-01

    Sparse partial correlation is a useful connectivity measure for brain networks when it is difficult to compute the exact partial correlation in the small-n large-p setting. In this paper, we formulate the problem of estimating partial correlation as a sparse linear regression with a l1-norm penalty. The method is applied to brain network consisting of parcellated regions of interest (ROIs), which are obtained from FDG-PET images of the autism spectrum disorder (ASD) children and the pediatric control (PedCon) subjects. To validate the results, we check their reproducibilities of the obtained brain networks by the leave-one-out cross validation and compare the clustered structures derived from the brain networks of ASD and PedCon.

  1. Causal Network Inference Via Group Sparse Regularization

    PubMed Central

    Bolstad, Andrew; Van Veen, Barry D.; Nowak, Robert

    2011-01-01

    This paper addresses the problem of inferring sparse causal networks modeled by multivariate autoregressive (MAR) processes. Conditions are derived under which the Group Lasso (gLasso) procedure consistently estimates sparse network structure. The key condition involves a “false connection score” ψ. In particular, we show that consistent recovery is possible even when the number of observations of the network is far less than the number of parameters describing the network, provided that ψ < 1. The false connection score is also demonstrated to be a useful metric of recovery in nonasymptotic regimes. The conditions suggest a modified gLasso procedure which tends to improve the false connection score and reduce the chances of reversing the direction of causal influence. Computational experiments and a real network based electrocorticogram (ECoG) simulation study demonstrate the effectiveness of the approach. PMID:21918591

  2. Neural process reconstruction from sparse user scribbles.

    PubMed

    Roberts, Mike; Jeong, Won-Ki; Vázquez-Reina, Amelio; Unger, Markus; Bischof, Horst; Lichtman, Jeff; Pfister, Hanspeter

    2011-01-01

    We present a novel semi-automatic method for segmenting neural processes in large, highly anisotropic EM (electron microscopy) image stacks. Our method takes advantage of sparse scribble annotations provided by the user to guide a 3D variational segmentation model, thereby allowing our method to globally optimally enforce 3D geometric constraints on the segmentation. Moreover, we leverage a novel algorithm for propagating segmentation constraints through the image stack via optimal volumetric pathways, thereby allowing our method to compute highly accurate 3D segmentations from very sparse user input. We evaluate our method by reconstructing 16 neural processes in a 1024 x 1024 x 50 nanometer-scale EM image stack of a mouse hippocampus. We demonstrate that, on average, our method is 68% more accurate than previous state-of-the-art semi-automatic methods. PMID:22003670

  3. Fingerprint Compression Based on Sparse Representation.

    PubMed

    Shao, Guangqi; Wu, Yanping; A, Yong; Liu, Xiao; Guo, Tiande

    2014-02-01

    A new fingerprint compression algorithm based on sparse representation is introduced. Obtaining an overcomplete dictionary from a set of fingerprint patches allows us to represent them as a sparse linear combination of dictionary atoms. In the algorithm, we first construct a dictionary for predefined fingerprint image patches. For a new given fingerprint images, represent its patches according to the dictionary by computing l(0)-minimization and then quantize and encode the representation. In this paper, we consider the effect of various factors on compression results. Three groups of fingerprint images are tested. The experiments demonstrate that our algorithm is efficient compared with several competing compression techniques (JPEG, JPEG 2000, and WSQ), especially at high compression ratios. The experiments also illustrate that the proposed algorithm is robust to extract minutiae.

  4. Tracking the sparseness of the underlying support in shallow water acoustic communications

    NASA Astrophysics Data System (ADS)

    Sen Gupta, Ananya; Preisig, James

    2012-06-01

    Tracking the shallow water acoustic channel in real time poses an open challenge towards improving the data rate in high-speed underwater communications. Multipath arrivals due to reflection from the moving ocean surface and the sea bottom, along with surface wave focusing events, lead to a rapidly fluctuating complex-valued channel impulse response and associated Delay-Doppler spread function that follow heavy-tailed distributions. The sparse channel or Delay-Doppler spread function components are difficult to track in real time using popular sparse sensing techniques due to the coherent and dynamic nature of the optimization problem as well as the timevarying and potentially non-stationary sparseness of the underlying support. We build on related work using non-convex optimization to track the shallow water acoustic channel in real time at high precision and tracking speed to develop strategies to estimate the non-stationary sparseness of the underlying support. Specifically, we employ non-convex manifold navigational techniques to estimate the support sparseness to balance the weighting between the L1 norm of the tracked coefficients and the L2 norm of the estimation error. We explore the efficacy of our methods against experimental field data collected at 200 meters range, 15 meters depth and varying wind conditions.

  5. Computational modeling of epidural cortical stimulation

    NASA Astrophysics Data System (ADS)

    Wongsarnpigoon, Amorn; Grill, Warren M.

    2008-12-01

    Epidural cortical stimulation (ECS) is a developing therapy to treat neurological disorders. However, it is not clear how the cortical anatomy or the polarity and position of the electrode affects current flow and neural activation in the cortex. We developed a 3D computational model simulating ECS over the precentral gyrus. With the electrode placed directly above the gyrus, about half of the stimulus current flowed through the crown of the gyrus while current density was low along the banks deep in the sulci. Beneath the electrode, neurons oriented perpendicular to the cortical surface were depolarized by anodic stimulation, and neurons oriented parallel to the boundary were depolarized by cathodic stimulation. Activation was localized to the crown of the gyrus, and neurons on the banks deep in the sulci were not polarized. During regulated voltage stimulation, the magnitude of the activating function was inversely proportional to the thickness of the CSF and dura. During regulated current stimulation, the activating function was not sensitive to the thickness of the dura but was slightly more sensitive than during regulated voltage stimulation to the thickness of the CSF. Varying the width of the gyrus and the position of the electrode altered the distribution of the activating function due to changes in the orientation of the neurons beneath the electrode. Bipolar stimulation, although often used in clinical practice, reduced spatial selectivity as well as selectivity for neuron orientation.

  6. Inpainting with sparse linear combinations of exemplars

    SciTech Connect

    Wohlberg, Brendt

    2008-01-01

    We introduce a new exemplar-based inpainting algorithm based on representing the region to be inpainted as a sparse linear combination of blocks extracted from similar parts of the image being inpainted. This method is conceptually simple, being computed by functional minimization, and avoids the complexity of correctly ordering the filling in of missing regions of other exemplar-based methods. Initial performance comparisons on small inpainting regions indicate that this method provides similar or better performance than other recent methods.

  7. Sparse image reconstruction for molecular imaging.

    PubMed

    Ting, Michael; Raich, Raviv; Hero, Alfred O

    2009-06-01

    The application that motivates this paper is molecular imaging at the atomic level. When discretized at subatomic distances, the volume is inherently sparse. Noiseless measurements from an imaging technology can be modeled by convolution of the image with the system point spread function (psf). Such is the case with magnetic resonance force microscopy (MRFM), an emerging technology where imaging of an individual tobacco mosaic virus was recently demonstrated with nanometer resolution. We also consider additive white Gaussian noise (AWGN) in the measurements. Many prior works of sparse estimators have focused on the case when H has low coherence; however, the system matrix H in our application is the convolution matrix for the system psf. A typical convolution matrix has high coherence. This paper, therefore, does not assume a low coherence H. A discrete-continuous form of the Laplacian and atom at zero (LAZE) p.d.f. used by Johnstone and Silverman is formulated, and two sparse estimators derived by maximizing the joint p.d.f. of the observation and image conditioned on the hyperparameters. A thresholding rule that generalizes the hard and soft thresholding rule appears in the course of the derivation. This so-called hybrid thresholding rule, when used in the iterative thresholding framework, gives rise to the hybrid estimator, a generalization of the lasso. Estimates of the hyperparameters for the lasso and hybrid estimator are obtained via Stein's unbiased risk estimate (SURE). A numerical study with a Gaussian psf and two sparse images shows that the hybrid estimator outperforms the lasso.

  8. Modified sparse regularization for electrical impedance tomography.

    PubMed

    Fan, Wenru; Wang, Huaxiang; Xue, Qian; Cui, Ziqiang; Sun, Benyuan; Wang, Qi

    2016-03-01

    Electrical impedance tomography (EIT) aims to estimate the electrical properties at the interior of an object from current-voltage measurements on its boundary. It has been widely investigated due to its advantages of low cost, non-radiation, non-invasiveness, and high speed. Image reconstruction of EIT is a nonlinear and ill-posed inverse problem. Therefore, regularization techniques like Tikhonov regularization are used to solve the inverse problem. A sparse regularization based on L1 norm exhibits superiority in preserving boundary information at sharp changes or discontinuous areas in the image. However, the limitation of sparse regularization lies in the time consumption for solving the problem. In order to further improve the calculation speed of sparse regularization, a modified method based on separable approximation algorithm is proposed by using adaptive step-size and preconditioning technique. Both simulation and experimental results show the effectiveness of the proposed method in improving the image quality and real-time performance in the presence of different noise intensities and conductivity contrasts. PMID:27036798

  9. Modified sparse regularization for electrical impedance tomography.

    PubMed

    Fan, Wenru; Wang, Huaxiang; Xue, Qian; Cui, Ziqiang; Sun, Benyuan; Wang, Qi

    2016-03-01

    Electrical impedance tomography (EIT) aims to estimate the electrical properties at the interior of an object from current-voltage measurements on its boundary. It has been widely investigated due to its advantages of low cost, non-radiation, non-invasiveness, and high speed. Image reconstruction of EIT is a nonlinear and ill-posed inverse problem. Therefore, regularization techniques like Tikhonov regularization are used to solve the inverse problem. A sparse regularization based on L1 norm exhibits superiority in preserving boundary information at sharp changes or discontinuous areas in the image. However, the limitation of sparse regularization lies in the time consumption for solving the problem. In order to further improve the calculation speed of sparse regularization, a modified method based on separable approximation algorithm is proposed by using adaptive step-size and preconditioning technique. Both simulation and experimental results show the effectiveness of the proposed method in improving the image quality and real-time performance in the presence of different noise intensities and conductivity contrasts.

  10. Aerial Scene Recognition using Efficient Sparse Representation

    SciTech Connect

    Cheriyadat, Anil M

    2012-01-01

    Advanced scene recognition systems for processing large volumes of high-resolution aerial image data are in great demand today. However, automated scene recognition remains a challenging problem. Efficient encoding and representation of spatial and structural patterns in the imagery are key in developing automated scene recognition algorithms. We describe an image representation approach that uses simple and computationally efficient sparse code computation to generate accurate features capable of producing excellent classification performance using linear SVM kernels. Our method exploits unlabeled low-level image feature measurements to learn a set of basis vectors. We project the low-level features onto the basis vectors and use simple soft threshold activation function to derive the sparse features. The proposed technique generates sparse features at a significantly lower computational cost than other methods~\\cite{Yang10, newsam11}, yet it produces comparable or better classification accuracy. We apply our technique to high-resolution aerial image datasets to quantify the aerial scene classification performance. We demonstrate that the dense feature extraction and representation methods are highly effective for automatic large-facility detection on wide area high-resolution aerial imagery.

  11. SAR Image despeckling via sparse representation

    NASA Astrophysics Data System (ADS)

    Wang, Zhongmei; Yang, Xiaomei; Zheng, Liang

    2014-11-01

    SAR image despeckling is an active research area in image processing due to its importance in improving the quality of image for object detection and classification.In this paper, a new approach is proposed for multiplicative noise in SAR image removal based on nonlocal sparse representation by dictionary learning and collaborative filtering. First, a image is divided into many patches, and then a cluster is formed by clustering log-similar image patches using Fuzzy C-means (FCM). For each cluster, an over-complete dictionary is computed using the K-SVD method that iteratively updates the dictionary and the sparse coefficients. The patches belonging to the same cluster are then reconstructed by a sparse combination of the corresponding dictionary atoms. The reconstructed patches are finally collaboratively aggregated to build the denoised image. The experimental results show that the proposed method achieves much better results than many state-of-the-art algorithms in terms of both objective evaluation index (PSNR and ENL) and subjective visual perception.

  12. New shape models of asteroids reconstructed from sparse-in-time photometry

    NASA Astrophysics Data System (ADS)

    Durech, Josef; Hanus, Josef; Vanco, Radim; Oszkiewicz, Dagmara Anna

    2015-08-01

    Asteroid physical parameters - the shape, the sidereal rotation period, and the spin axis orientation - can be reconstructed from the disk-integrated photometry either dense (classical lightcurves) or sparse in time by the lightcurve inversion method. We will review our recent progress in asteroid shape reconstruction from sparse photometry. The problem of finding a unique solution of the inverse problem is time consuming because the sidereal rotation period has to be found by scanning a wide interval of possible periods. This can be efficiently solved by splitting the period parameter space into small parts that are sent to computers of volunteers and processed in parallel. We will show how this approach of distributed computing works with currently available sparse photometry processed in the framework of project Asteroids@home. In particular, we will show the results based on the Lowell Photometric Database. The method produce reliable asteroid models with very low rate of false solutions and the pipelines and codes can be directly used also to other sources of sparse photometry - Gaia data, for example. We will present the distribution of spin axis of hundreds of asteroids, discuss the dependence of the spin obliquity on the size of an asteroid,and show examples of spin-axis distribution in asteroid families that confirm the Yarkovsky/YORP evolution scenario.

  13. Cortical subnetwork dynamics during human language tasks.

    PubMed

    Collard, Maxwell J; Fifer, Matthew S; Benz, Heather L; McMullen, David P; Wang, Yujing; Milsap, Griffin W; Korzeniewska, Anna; Crone, Nathan E

    2016-07-15

    results demonstrate that subnetwork decomposition of event-related cortical interactions is a powerful paradigm for interpreting the rich dynamics of large-scale, distributed cortical networks during human cognitive tasks. PMID:27046113

  14. Efficient visual tracking via low-complexity sparse representation

    NASA Astrophysics Data System (ADS)

    Lu, Weizhi; Zhang, Jinglin; Kpalma, Kidiyo; Ronsin, Joseph

    2015-12-01

    Thanks to its good performance on object recognition, sparse representation has recently been widely studied in the area of visual object tracking. Up to now, little attention has been paid to the complexity of sparse representation, while most works are focused on the performance improvement. By reducing the computation load related to sparse representation hundreds of times, this paper proposes by far the most computationally efficient tracking approach based on sparse representation. The proposal simply consists of two stages of sparse representation, one is for object detection and the other for object validation. Experimentally, it achieves better performance than some state-of-the-art methods in both accuracy and speed.

  15. Identification of aerospace acoustic sources using sparse distributed associative memory

    NASA Technical Reports Server (NTRS)

    Scott, E. A.; Fuller, C. R.; O'Brien, W. F.

    1990-01-01

    A pattern recognition system has been developed to classify five different aerospace acoustic sources. In this paper the performance of two new classifiers, an associative memory classifier and a neural network classifier, is compared to the performance of a previously designed system. Sources are classified using features calculated from the time and frequency domain. Each classifier undergoes a training period where it learns to classify sources correctly based on a set of known sources. After training the classifier is tested with unknown sources. Results show that over 96 percent of sources were identified correctly with the new associative memory classifier. The neural network classifier identified over 81 percent of the sources correctly.

  16. The statistics of repeating patterns of cortical activity can be reproduced by a model network of stochastic binary neurons.

    PubMed

    Roxin, Alex; Hakim, Vincent; Brunel, Nicolas

    2008-10-15

    Calcium imaging of the spontaneous activity in cortical slices has revealed repeating spatiotemporal patterns of transitions between so-called down states and up states (Ikegaya et al., 2004). Here we fit a model network of stochastic binary neurons to data from these experiments, and in doing so reproduce the distributions of such patterns. We use two versions of this model: (1) an unconnected network in which neurons are activated as independent Poisson processes; and (2) a network with an interaction matrix, estimated from the data, representing effective interactions between the neurons. The unconnected model (model 1) is sufficient to account for the statistics of repeating patterns in 11 of the 15 datasets studied. Model 2, with interactions between neurons, is required to account for pattern statistics of the remaining four. Three of these four datasets are the ones that contain the largest number of transitions, suggesting that long datasets are in general necessary to render interactions statistically visible. We then study the topology of the matrix of interactions estimated for these four datasets. For three of the four datasets, we find sparse matrices with long-tailed degree distributions and an overrepresentation of certain network motifs. The remaining dataset exhibits a strongly interconnected, spatially localized subgroup of neurons. In all cases, we find that interactions between neurons facilitate the generation of long patterns that do not repeat exactly.

  17. Analysis of Cortical Flow Models In Vivo

    PubMed Central

    Benink, Hélène A.; Mandato, Craig A.; Bement, William M.

    2000-01-01

    Cortical flow, the directed movement of cortical F-actin and cortical organelles, is a basic cellular motility process. Microtubules are thought to somehow direct cortical flow, but whether they do so by stimulating or inhibiting contraction of the cortical actin cytoskeleton is the subject of debate. Treatment of Xenopus oocytes with phorbol 12-myristate 13-acetate (PMA) triggers cortical flow toward the animal pole of the oocyte; this flow is suppressed by microtubules. To determine how this suppression occurs and whether it can control the direction of cortical flow, oocytes were subjected to localized manipulation of either the contractile stimulus (PMA) or microtubules. Localized PMA application resulted in redirection of cortical flow toward the site of application, as judged by movement of cortical pigment granules, cortical F-actin, and cortical myosin-2A. Such redirected flow was accelerated by microtubule depolymerization, showing that the suppression of cortical flow by microtubules is independent of the direction of flow. Direct observation of cortical F-actin by time-lapse confocal analysis in combination with photobleaching showed that cortical flow is driven by contraction of the cortical F-actin network and that microtubules suppress this contraction. The oocyte germinal vesicle serves as a microtubule organizing center in Xenopus oocytes; experimental displacement of the germinal vesicle toward the animal pole resulted in localized flow away from the animal pole. The results show that 1) cortical flow is directed toward areas of localized contraction of the cortical F-actin cytoskeleton; 2) microtubules suppress cortical flow by inhibiting contraction of the cortical F-actin cytoskeleton; and 3) localized, microtubule-dependent suppression of actomyosin-based contraction can control the direction of cortical flow. We discuss these findings in light of current models of cortical flow. PMID:10930453

  18. Cable energy function of cortical axons.

    PubMed

    Ju, Huiwen; Hines, Michael L; Yu, Yuguo

    2016-01-01

    Accurate estimation of action potential (AP)-related metabolic cost is essential for understanding energetic constraints on brain connections and signaling processes. Most previous energy estimates of the AP were obtained using the Na(+)-counting method, which seriously limits accurate assessment of metabolic cost of ionic currents that underlie AP conduction along the axon. Here, we first derive a full cable energy function for cortical axons based on classic Hodgkin-Huxley (HH) neuronal equations and then apply the cable energy function to precisely estimate the energy consumption of AP conduction along axons with different geometric shapes. Our analytical approach predicts an inhomogeneous distribution of metabolic cost along an axon with either uniformly or nonuniformly distributed ion channels. The results show that the Na(+)-counting method severely underestimates energy cost in the cable model by 20-70%. AP propagation along axons that differ in length may require over 15% more energy per unit of axon area than that required by a point model. However, actual energy cost can vary greatly depending on axonal branching complexity, ion channel density distributions, and AP conduction states. We also infer that the metabolic rate (i.e. energy consumption rate) of cortical axonal branches as a function of spatial volume exhibits a 3/4 power law relationship.

  19. Cable energy function of cortical axons

    PubMed Central

    Ju, Huiwen; Hines, Michael L.; Yu, Yuguo

    2016-01-01

    Accurate estimation of action potential (AP)-related metabolic cost is essential for understanding energetic constraints on brain connections and signaling processes. Most previous energy estimates of the AP were obtained using the Na+-counting method, which seriously limits accurate assessment of metabolic cost of ionic currents that underlie AP conduction along the axon. Here, we first derive a full cable energy function for cortical axons based on classic Hodgkin-Huxley (HH) neuronal equations and then apply the cable energy function to precisely estimate the energy consumption of AP conduction along axons with different geometric shapes. Our analytical approach predicts an inhomogeneous distribution of metabolic cost along an axon with either uniformly or nonuniformly distributed ion channels. The results show that the Na+-counting method severely underestimates energy cost in the cable model by 20–70%. AP propagation along axons that differ in length may require over 15% more energy per unit of axon area than that required by a point model. However, actual energy cost can vary greatly depending on axonal branching complexity, ion channel density distributions, and AP conduction states. We also infer that the metabolic rate (i.e. energy consumption rate) of cortical axonal branches as a function of spatial volume exhibits a 3/4 power law relationship. PMID:27439954

  20. Cable energy function of cortical axons.

    PubMed

    Ju, Huiwen; Hines, Michael L; Yu, Yuguo

    2016-01-01

    Accurate estimation of action potential (AP)-related metabolic cost is essential for understanding energetic constraints on brain connections and signaling processes. Most previous energy estimates of the AP were obtained using the Na(+)-counting method, which seriously limits accurate assessment of metabolic cost of ionic currents that underlie AP conduction along the axon. Here, we first derive a full cable energy function for cortical axons based on classic Hodgkin-Huxley (HH) neuronal equations and then apply the cable energy function to precisely estimate the energy consumption of AP conduction along axons with different geometric shapes. Our analytical approach predicts an inhomogeneous distribution of metabolic cost along an axon with either uniformly or nonuniformly distributed ion channels. The results show that the Na(+)-counting method severely underestimates energy cost in the cable model by 20-70%. AP propagation along axons that differ in length may require over 15% more energy per unit of axon area than that required by a point model. However, actual energy cost can vary greatly depending on axonal branching complexity, ion channel density distributions, and AP conduction states. We also infer that the metabolic rate (i.e. energy consumption rate) of cortical axonal branches as a function of spatial volume exhibits a 3/4 power law relationship. PMID:27439954

  1. SMI-32 parcellates the visual cortical areas of the marmoset.

    PubMed

    Baldauf, Zsolt B

    The distribution pattern of SMI-32-immunoreactivity (SMI-32-ir) of neuronal elements was examined in the visual cortical areas of marmoset monkey. Layer IV of the primary visual cortex (V1) and layers III and V of the extrastriate areas showed the most abundant SMI-32-ir. The different areal and laminar distribution of SMI-32-ir allowed the distinction between various extrastriate areas and determined their exact anatomical boundaries in the New World monkey, Callithrix penicillata. It is shown here that the parcellating nature of SMI-32 described earlier in the visual cortical areas of other mammals - including Old World monkeys - is also present in the marmoset. Furthermore, a comparison became possible between the chemoanatomical organization of New World and Old World primates' visual cortical areas.

  2. A gradient in cortical pathology in multiple sclerosis by in vivo quantitative 7 T imaging.

    PubMed

    Mainero, Caterina; Louapre, Céline; Govindarajan, Sindhuja T; Giannì, Costanza; Nielsen, A Scott; Cohen-Adad, Julien; Sloane, Jacob; Kinkel, Revere P

    2015-04-01

    We used a surface-based analysis of T2* relaxation rates at 7 T magnetic resonance imaging, which allows sampling quantitative T2* throughout the cortical width, to map in vivo the spatial distribution of intracortical pathology in multiple sclerosis. Ultra-high resolution quantitative T2* maps were obtained in 10 subjects with clinically isolated syndrome/early multiple sclerosis (≤ 3 years disease duration), 18 subjects with relapsing-remitting multiple sclerosis (≥ 4 years disease duration), 13 subjects with secondary progressive multiple sclerosis, and in 17 age-matched healthy controls. Quantitative T2* maps were registered to anatomical cortical surfaces for sampling T2* at 25%, 50% and 75% depth from the pial surface. Differences in laminar quantitative T2* between each patient group and controls were assessed using general linear model (P < 0.05 corrected for multiple comparisons). In all 41 multiple sclerosis cases, we tested for associations between laminar quantitative T2*, neurological disability, Multiple Sclerosis Severity Score, cortical thickness, and white matter lesions. In patients, we measured, T2* in intracortical lesions and in the intracortical portion of leukocortical lesions visually detected on 7 T scans. Cortical lesional T2* was compared with patients' normal-appearing cortical grey matter T2* (paired t-test) and with mean cortical T2* in controls (linear regression using age as nuisance factor). Subjects with multiple sclerosis exhibited relative to controls, independent from cortical thickness, significantly increased T2*, consistent with cortical myelin and iron loss. In early disease, T2* changes were focal and mainly confined at 25% depth, and in cortical sulci. In later disease stages T2* changes involved deeper cortical laminae, multiple cortical areas and gyri. In patients, T2* in intracortical and leukocortical lesions was increased compared with normal-appearing cortical grey matter (P < 10(-10) and P < 10(-7)), and mean

  3. Human Adult Cortical Reorganization and Consequent Visual Distortion

    PubMed Central

    Dilks, Daniel D.; Serences, John T.; Rosenau, Benjamin J.; Yantis, Steven; McCloskey, Michael

    2009-01-01

    Neural and behavioral evidence for cortical reorganization in the adult somatosensory system after loss of sensory input (e.g., amputation) has been well documented. In contrast, evidence for reorganization in the adult visual system is far less clear: neural evidence is the subject of controversy, behavioral evidence is sparse, and studies combining neural and behavioral evidence have not previously been reported. Here, we report converging behavioral and neuroimaging evidence from a stroke patient (B.L.) in support of cortical reorganization in the adult human visual system. B.L.’s stroke spared the primary visual cortex (V1), but destroyed fibers that normally provide input to V1 from the upper left visual field (LVF). As a consequence, B.L. is blind in the upper LVF, and exhibits distorted perception in the lower LVF: stimuli appear vertically elongated, toward and into the blind upper LVF. For example, a square presented in the lower LVF is perceived as a rectangle extending upward. We hypothesized that the perceptual distortion was a consequence of cortical reorganization in V1. Extensive behavioral testing supported our hypothesis, and functional magnetic resonance imaging (fMRI) confirmed V1 reorganization. Together, the behavioral and fMRI data show that loss of input to V1 after a stroke leads to cortical reorganization in the adult human visual system, and provide the first evidence that reorganization of the adult visual system affects visual perception. These findings contribute to our understanding of the human adult brain’s capacity to change and has implications for topics ranging from learning to recovery from brain damage. PMID:17804619

  4. Cortical thickness reduction in individuals at ultra-high-risk for psychosis.

    PubMed

    Jung, Wi Hoon; Kim, June Sic; Jang, Joon Hwan; Choi, Jung-Seok; Jung, Myung Hun; Park, Ji-Young; Han, Ji Yeon; Choi, Chi-Hoon; Kang, Do-Hyung; Chung, Chun Kee; Kwon, Jun Soo

    2011-07-01

    Although schizophrenia is characterized by gray matter (GM) abnormalities, particularly in the prefrontal and temporal cortices, it is unclear whether cerebral cortical GM is abnormal in individuals at ultra-high-risk (UHR) for psychosis. We addressed this issue by studying cortical thickness in this group with magnetic resonance imaging (MRI). We measured cortical thickness of 29 individuals with no family history of psychosis at UHR, 31 patients with schizophrenia, and 29 healthy matched control subjects using automated surface-based analysis of structural MRI data. Hemispheric mean and regional cortical thickness were significantly different according to the stage of the disease. Significant cortical differences across these 3 groups were found in the distributed area of cerebral cortices. UHR group showed significant cortical thinning in the prefrontal cortex, anterior cingulate cortex, inferior parietal cortex, parahippocampal cortex, and superior temporal gyrus compared with healthy control subjects. Significant cortical thinning in schizophrenia group relative to UHR group was found in all the regions described above in addition with posterior cingulate cortex, insular cortex, and precentral cortex. These changes were more pronounced in the schizophrenia group compared with the control subjects. These findings suggest that UHR is associated with cortical thinning in regions that correspond to the structural abnormalities found in schizophrenia. These structural abnormalities might reflect functional decline at the prodromal stage of schizophrenia, and there may be progressive thinning of GM cortex over time. PMID:20026559

  5. Branching angles of pyramidal cell dendrites follow common geometrical design principles in different cortical areas.

    PubMed

    Bielza, Concha; Benavides-Piccione, Ruth; López-Cruz, Pedro; Larrañaga, Pedro; DeFelipe, Javier

    2014-08-01

    Unraveling pyramidal cell structure is crucial to understanding cortical circuit computations. Although it is well known that pyramidal cell branching structure differs in the various cortical areas, the principles that determine the geometric shapes of these cells are not fully understood. Here we analyzed and modeled with a von Mises distribution the branching angles in 3D reconstructed basal dendritic arbors of hundreds of intracellularly injected cortical pyramidal cells in seven different cortical regions of the frontal, parietal, and occipital cortex of the mouse. We found that, despite the differences in the structure of the pyramidal cells in these distinct functional and cytoarchitectonic cortical areas, there are common design principles that govern the geometry of dendritic branching angles of pyramidal cells in all cortical areas.

  6. Branching angles of pyramidal cell dendrites follow common geometrical design principles in different cortical areas.

    PubMed

    Bielza, Concha; Benavides-Piccione, Ruth; López-Cruz, Pedro; Larrañaga, Pedro; DeFelipe, Javier

    2014-01-01

    Unraveling pyramidal cell structure is crucial to understanding cortical circuit computations. Although it is well known that pyramidal cell branching structure differs in the various cortical areas, the principles that determine the geometric shapes of these cells are not fully understood. Here we analyzed and modeled with a von Mises distribution the branching angles in 3D reconstructed basal dendritic arbors of hundreds of intracellularly injected cortical pyramidal cells in seven different cortical regions of the frontal, parietal, and occipital cortex of the mouse. We found that, despite the differences in the structure of the pyramidal cells in these distinct functional and cytoarchitectonic cortical areas, there are common design principles that govern the geometry of dendritic branching angles of pyramidal cells in all cortical areas. PMID:25081193

  7. Branching angles of pyramidal cell dendrites follow common geometrical design principles in different cortical areas

    PubMed Central

    Bielza, Concha; Benavides-Piccione, Ruth; López-Cruz, Pedro; Larrañaga, Pedro; DeFelipe, Javier

    2014-01-01

    Unraveling pyramidal cell structure is crucial to understanding cortical circuit computations. Although it is well known that pyramidal cell branching structure differs in the various cortical areas, the principles that determine the geometric shapes of these cells are not fully understood. Here we analyzed and modeled with a von Mises distribution the branching angles in 3D reconstructed basal dendritic arbors of hundreds of intracellularly injected cortical pyramidal cells in seven different cortical regions of the frontal, parietal, and occipital cortex of the mouse. We found that, despite the differences in the structure of the pyramidal cells in these distinct functional and cytoarchitectonic cortical areas, there are common design principles that govern the geometry of dendritic branching angles of pyramidal cells in all cortical areas. PMID:25081193

  8. SAMBA: Sparse Approximation of Moment-Based Arbitrary Polynomial Chaos

    NASA Astrophysics Data System (ADS)

    Ahlfeld, R.; Belkouchi, B.; Montomoli, F.

    2016-09-01

    A new arbitrary Polynomial Chaos (aPC) method is presented for moderately high-dimensional problems characterised by limited input data availability. The proposed methodology improves the algorithm of aPC and extends the method, that was previously only introduced as tensor product expansion, to moderately high-dimensional stochastic problems. The fundamental idea of aPC is to use the statistical moments of the input random variables to develop the polynomial chaos expansion. This approach provides the possibility to propagate continuous or discrete probability density functions and also histograms (data sets) as long as their moments exist, are finite and the determinant of the moment matrix is strictly positive. For cases with limited data availability, this approach avoids bias and fitting errors caused by wrong assumptions. In this work, an alternative way to calculate the aPC is suggested, which provides the optimal polynomials, Gaussian quadrature collocation points and weights from the moments using only a handful of matrix operations on the Hankel matrix of moments. It can therefore be implemented without requiring prior knowledge about statistical data analysis or a detailed understanding of the mathematics of polynomial chaos expansions. The extension to more input variables suggested in this work, is an anisotropic and adaptive version of Smolyak's algorithm that is solely based on the moments of the input probability distributions. It is referred to as SAMBA (PC), which is short for Sparse Approximation of Moment-Based Arbitrary Polynomial Chaos. It is illustrated that for moderately high-dimensional problems (up to 20 different input variables or histograms) SAMBA can significantly simplify the calculation of sparse Gaussian quadrature rules. SAMBA's efficiency for multivariate functions with regard to data availability is further demonstrated by analysing higher order convergence and accuracy for a set of nonlinear test functions with 2, 5 and 10

  9. Guided wavefield reconstruction from sparse measurements

    NASA Astrophysics Data System (ADS)

    Mesnil, Olivier; Ruzzene, Massimo

    2016-02-01

    Guided wave measurements are at the basis of several Non-Destructive Evaluation (NDE) techniques. Although sparse measurements of guided wave obtained using piezoelectric sensors can efficiently detect and locate defects, extensive informa-tion on the shape and subsurface location of defects can be extracted from full-field measurements acquired by Laser Doppler Vibrometers (LDV). Wavefield acquisition from LDVs is generally a slow operation due to the fact that the wave propagation to record must be repeated for each point measurement and the initial conditions must be reached between each measurement. In this research, a Sparse Wavefield Reconstruction (SWR) process using Compressed Sensing is developed. The goal of this technique is to reduce the number of point measurements needed to apply NDE techniques by at least one order of magnitude by extrapolating the knowledge of a few randomly chosen measured pixels over an over-sampled grid. To achieve this, the Lamb wave propagation equation is used to formulate a basis of shape functions in which the wavefield has a sparse representation, in order to comply with the Compressed Sensing requirements and use l1-minimization solvers. The main assumption of this reconstruction process is that every material point of the studied area is a potential source. The Compressed Sensing matrix is defined as being the contribution that would have been received at a measurement location from each possible source, using the dispersion relations of the specimen computed using a Semi-Analytical Finite Element technique. The measurements are then processed through an l1-minimizer to find a minimum corresponding to the set of active sources and their corresponding excitation functions. This minimum represents the best combination of the parameters of the model matching the sparse measurements. Wavefields are then reconstructed using the propagation equation. The set of active sources found by minimization contains all the wave

  10. Effective dimension reduction for sparse functional data

    PubMed Central

    YAO, F.; LEI, E.; WU, Y.

    2015-01-01

    Summary We propose a method of effective dimension reduction for functional data, emphasizing the sparse design where one observes only a few noisy and irregular measurements for some or all of the subjects. The proposed method borrows strength across the entire sample and provides a way to characterize the effective dimension reduction space, via functional cumulative slicing. Our theoretical study reveals a bias-variance trade-off associated with the regularizing truncation and decaying structures of the predictor process and the effective dimension reduction space. A simulation study and an application illustrate the superior finite-sample performance of the method. PMID:26566293

  11. Sparse dynamics for partial differential equations

    PubMed Central

    Schaeffer, Hayden; Caflisch, Russel; Hauck, Cory D.; Osher, Stanley

    2013-01-01

    We investigate the approximate dynamics of several differential equations when the solutions are restricted to a sparse subset of a given basis. The restriction is enforced at every time step by simply applying soft thresholding to the coefficients of the basis approximation. By reducing or compressing the information needed to represent the solution at every step, only the essential dynamics are represented. In many cases, there are natural bases derived from the differential equations, which promote sparsity. We find that our method successfully reduces the dynamics of convection equations, diffusion equations, weak shocks, and vorticity equations with high-frequency source terms. PMID:23533273

  12. Parallel preconditioning techniques for sparse CG solvers

    SciTech Connect

    Basermann, A.; Reichel, B.; Schelthoff, C.

    1996-12-31

    Conjugate gradient (CG) methods to solve sparse systems of linear equations play an important role in numerical methods for solving discretized partial differential equations. The large size and the condition of many technical or physical applications in this area result in the need for efficient parallelization and preconditioning techniques of the CG method. In particular for very ill-conditioned matrices, sophisticated preconditioner are necessary to obtain both acceptable convergence and accuracy of CG. Here, we investigate variants of polynomial and incomplete Cholesky preconditioners that markedly reduce the iterations of the simply diagonally scaled CG and are shown to be well suited for massively parallel machines.

  13. A circuit for motor cortical modulation of auditory cortical activity.

    PubMed

    Nelson, Anders; Schneider, David M; Takatoh, Jun; Sakurai, Katsuyasu; Wang, Fan; Mooney, Richard

    2013-09-01

    Normal hearing depends on the ability to distinguish self-generated sounds from other sounds, and this ability is thought to involve neural circuits that convey copies of motor command signals to various levels of the auditory system. Although such interactions at the cortical level are believed to facilitate auditory comprehension during movements and drive auditory hallucinations in pathological states, the synaptic organization and function of circuitry linking the motor and auditory cortices remain unclear. Here we describe experiments in the mouse that characterize circuitry well suited to transmit motor-related signals to the auditory cortex. Using retrograde viral tracing, we established that neurons in superficial and deep layers of the medial agranular motor cortex (M2) project directly to the auditory cortex and that the axons of some of these deep-layer cells also target brainstem motor regions. Using in vitro whole-cell physiology, optogenetics, and pharmacology, we determined that M2 axons make excitatory synapses in the auditory cortex but exert a primarily suppressive effect on auditory cortical neuron activity mediated in part by feedforward inhibition involving parvalbumin-positive interneurons. Using in vivo intracellular physiology, optogenetics, and sound playback, we also found that directly activating M2 axon terminals in the auditory cortex suppresses spontaneous and stimulus-evoked synaptic activity in auditory cortical neurons and that this effect depends on the relative timing of motor cortical activity and auditory stimulation. These experiments delineate the structural and functional properties of a corticocortical circuit that could enable movement-related suppression of auditory cortical activity. PMID:24005287

  14. Cortical and cancellous bone in the human femoral neck: evaluation of an interactive image analysis system.

    PubMed

    Bell, K L; Garrahan, N; Kneissel, M; Loveridge, N; Grau, E; Stanton, M; Reeve, J

    1996-11-01

    An interactive image analysis package was developed to examine whole cross-sections from the femoral neck. The package quantifies cortical width (Ct.Wi), cortical porosity (Ct.Po), and proportions of cortical, cancellous bone as a percentage of bone plus marrow area. Segmental analysis was used to quantify circumferential variations in bone distribution within the femoral cross-section. To evaluate reproducibility of data four independent operators analyzed previously prepared femoral neck sections from a 2000 BC population. Differences in total and circumferential distributions of cortical and cancellous bone with respect to gender and age of samples were demonstrated. Reproducibility was assessed using coefficients of variation (CV). Analysis of sections using a variable magnification, giving largest possible image size, rather than a set magnification reduced variation between operators for all measurements. Use of a calculated threshold significantly decreased variation between operators for the proportions of cortical and cancellous bone (p < or = 0.026). Dividing the image into 8 rather than 16 segments also improved reproducibility. There was little agreement between operators in the determination of cortical porosity. The mean CV for the other quantitative indices such as cortical width and proportions of cortical and cancellous bone ranged from 4.87% to 13.52%. The genders showed similar patterns in circumferential distribution of bone. Cortical width was significantly greater in the inferior region compared to the other areas, whereas percent cortical bone was lowest at the superior region. The center of mass (COM) for the younger age group was located anteriorly, whereas in the older samples the COM was located posteriorly of the center of area (p = 0.041). Basic data relating to cortical and cancellous bone of acceptable reproducibility in comparison with current standards in iliac histomorphometry can now be provided at modest cost in operator time and

  15. A density functional for sparse matter

    NASA Astrophysics Data System (ADS)

    Langreth, D. C.; Lundqvist, B. I.; Chakarova-Käck, S. D.; Cooper, V. R.; Dion, M.; Hyldgaard, P.; Kelkkanen, A.; Kleis, J.; Kong, Lingzhu; Li, Shen; Moses, P. G.; Murray, E.; Puzder, A.; Rydberg, H.; Schröder, E.; Thonhauser, T.

    2009-02-01

    Sparse matter is abundant and has both strong local bonds and weak nonbonding forces, in particular nonlocal van der Waals (vdW) forces between atoms separated by empty space. It encompasses a broad spectrum of systems, like soft matter, adsorption systems and biostructures. Density-functional theory (DFT), long since proven successful for dense matter, seems now to have come to a point, where useful extensions to sparse matter are available. In particular, a functional form, vdW-DF (Dion et al 2004 Phys. Rev. Lett. 92 246401; Thonhauser et al 2007 Phys. Rev. B 76 125112), has been proposed for the nonlocal correlations between electrons and applied to various relevant molecules and materials, including to those layered systems like graphite, boron nitride and molybdenum sulfide, to dimers of benzene, polycyclic aromatic hydrocarbons (PAHs), doped benzene, cytosine and DNA base pairs, to nonbonding forces in molecules, to adsorbed molecules, like benzene, naphthalene, phenol and adenine on graphite, alumina and metals, to polymer and carbon nanotube (CNT) crystals, and hydrogen storage in graphite and metal-organic frameworks (MOFs), and to the structure of DNA and of DNA with intercalators. Comparison with results from wavefunction calculations for the smaller systems and with experimental data for the extended ones show the vdW-DF path to be promising. This could have great ramifications.

  16. Fast Sparse Level Sets on Graphics Hardware.

    PubMed

    Jalba, Andrei C; van der Laan, Wladimir J; Roerdink, Jos B T M

    2013-01-01

    The level-set method is one of the most popular techniques for capturing and tracking deformable interfaces. Although level sets have demonstrated great potential in visualization and computer graphics applications, such as surface editing and physically based modeling, their use for interactive simulations has been limited due to the high computational demands involved. In this paper, we address this computational challenge by leveraging the increased computing power of graphics processors, to achieve fast simulations based on level sets. Our efficient, sparse GPU level-set method is substantially faster than other state-of-the-art, parallel approaches on both CPU and GPU hardware. We further investigate its performance through a method for surface reconstruction, based on GPU level sets. Our novel multiresolution method for surface reconstruction from unorganized point clouds compares favorably with recent, existing techniques and other parallel implementations. Finally, we point out that both level-set computations and rendering of level-set surfaces can be performed at interactive rates, even on large volumetric grids. Therefore, many applications based on level sets can benefit from our sparse level-set method.

  17. Topological sparse learning of dynamic form patterns.

    PubMed

    Guthier, T; Willert, V; Eggert, J

    2015-01-01

    Motion is a crucial source of information for a variety of tasks in social interactions. The process of how humans recognize complex articulated movements such as gestures or face expressions remains largely unclear. There is an ongoing discussion if and how explicit low-level motion information, such as optical flow, is involved in the recognition process. Motivated by this discussion, we introduce a computational model that classifies the spatial configuration of gradient and optical flow patterns. The patterns are learned with an unsupervised learning algorithm based on translation-invariant nonnegative sparse coding called VNMF that extracts prototypical optical flow patterns shaped, for example, as moving heads or limb parts. A key element of the proposed system is a lateral inhibition term that suppresses activations of competing patterns in the learning process, leading to a low number of dominant and topological sparse activations. We analyze the classification performance of the gradient and optical flow patterns on three real-world human action recognition and one face expression recognition data set. The results indicate that the recognition of human actions can be achieved by gradient patterns alone, but adding optical flow patterns increases the classification performance. The combined patterns outperform other biological-inspired models and are competitive with current computer vision approaches. PMID:25248088

  18. Inferring sparse networks for noisy transient processes.

    PubMed

    Tran, Hoang M; Bukkapatnam, Satish T S

    2016-01-01

    Inferring causal structures of real world complex networks from measured time series signals remains an open issue. The current approaches are inadequate to discern between direct versus indirect influences (i.e., the presence or absence of a directed arc connecting two nodes) in the presence of noise, sparse interactions, as well as nonlinear and transient dynamics of real world processes. We report a sparse regression (referred to as the l1-min) approach with theoretical bounds on the constraints on the allowable perturbation to recover the network structure that guarantees sparsity and robustness to noise. We also introduce averaging and perturbation procedures to further enhance prediction scores (i.e., reduce inference errors), and the numerical stability of l1-min approach. Extensive investigations have been conducted with multiple benchmark simulated genetic regulatory network and Michaelis-Menten dynamics, as well as real world data sets from DREAM5 challenge. These investigations suggest that our approach can significantly improve, oftentimes by 5 orders of magnitude over the methods reported previously for inferring the structure of dynamic networks, such as Bayesian network, network deconvolution, silencing and modular response analysis methods based on optimizing for sparsity, transients, noise and high dimensionality issues. PMID:26916813

  19. Inferring sparse networks for noisy transient processes

    NASA Astrophysics Data System (ADS)

    Tran, Hoang M.; Bukkapatnam, Satish T. S.

    2016-02-01

    Inferring causal structures of real world complex networks from measured time series signals remains an open issue. The current approaches are inadequate to discern between direct versus indirect influences (i.e., the presence or absence of a directed arc connecting two nodes) in the presence of noise, sparse interactions, as well as nonlinear and transient dynamics of real world processes. We report a sparse regression (referred to as the -min) approach with theoretical bounds on the constraints on the allowable perturbation to recover the network structure that guarantees sparsity and robustness to noise. We also introduce averaging and perturbation procedures to further enhance prediction scores (i.e., reduce inference errors), and the numerical stability of -min approach. Extensive investigations have been conducted with multiple benchmark simulated genetic regulatory network and Michaelis-Menten dynamics, as well as real world data sets from DREAM5 challenge. These investigations suggest that our approach can significantly improve, oftentimes by 5 orders of magnitude over the methods reported previously for inferring the structure of dynamic networks, such as Bayesian network, network deconvolution, silencing and modular response analysis methods based on optimizing for sparsity, transients, noise and high dimensionality issues.

  20. Sparse aperture mask wavefront sensor testbed results

    NASA Astrophysics Data System (ADS)

    Subedi, Hari; Zimmerman, Neil T.; Kasdin, N. Jeremy; Riggs, A. J. E.

    2016-07-01

    Coronagraphic exoplanet detection at very high contrast requires the estimation and control of low-order wave- front aberrations. At Princeton High Contrast Imaging Lab (PHCIL), we are working on a new technique that integrates a sparse-aperture mask (SAM) with a shaped pupil coronagraph (SPC) to make precise estimates of these low-order aberrations. We collect the starlight rejected from the coronagraphic image plane and interfere it using a sparse aperture mask (SAM) at the relay pupil to estimate the low-order aberrations. In our previous work we numerically demonstrated the efficacy of the technique, and proposed a method to sense and control these differential aberrations in broadband light. We also presented early testbed results in which the SAM was used to sense pointing errors. In this paper, we will briefly overview the SAM wavefront sensor technique, explain the design of the completed testbed, and report the experimental estimation results of the dominant low-order aberrations such as tip/tit, astigmatism and focus.

  1. OSKI: A Library of Automatically Tuned Sparse Matrix Kernels

    SciTech Connect

    Vuduc, R; Demmel, J W; Yelick, K A

    2005-07-19

    The Optimized Sparse Kernel Interface (OSKI) is a collection of low-level primitives that provide automatically tuned computational kernels on sparse matrices, for use by solver libraries and applications. These kernels include sparse matrix-vector multiply and sparse triangular solve, among others. The primary aim of this interface is to hide the complex decision-making process needed to tune the performance of a kernel implementation for a particular user's sparse matrix and machine, while also exposing the steps and potentially non-trivial costs of tuning at run-time. This paper provides an overview of OSKI, which is based on our research on automatically tuned sparse kernels for modern cache-based superscalar machines.

  2. Consistent estimation of complete neuronal connectivity in large neuronal populations using sparse "shotgun" neuronal activity sampling.

    PubMed

    Mishchenko, Yuriy

    2016-10-01

    We investigate the properties of recently proposed "shotgun" sampling approach for the common inputs problem in the functional estimation of neuronal connectivity. We study the asymptotic correctness, the speed of convergence, and the data size requirements of such an approach. We show that the shotgun approach can be expected to allow the inference of complete connectivity matrix in large neuronal populations under some rather general conditions. However, we find that the posterior error of the shotgun connectivity estimator grows quickly with the size of unobserved neuronal populations, the square of average connectivity strength, and the square of observation sparseness. This implies that the shotgun connectivity estimation will require significantly larger amounts of neuronal activity data whenever the number of neurons in observed neuronal populations remains small. We present a numerical approach for solving the shotgun estimation problem in general settings and use it to demonstrate the shotgun connectivity inference in the examples of simulated synfire and weakly coupled cortical neuronal networks. PMID:27515518

  3. Consistent estimation of complete neuronal connectivity in large neuronal populations using sparse "shotgun" neuronal activity sampling.

    PubMed

    Mishchenko, Yuriy

    2016-10-01

    We investigate the properties of recently proposed "shotgun" sampling approach for the common inputs problem in the functional estimation of neuronal connectivity. We study the asymptotic correctness, the speed of convergence, and the data size requirements of such an approach. We show that the shotgun approach can be expected to allow the inference of complete connectivity matrix in large neuronal populations under some rather general conditions. However, we find that the posterior error of the shotgun connectivity estimator grows quickly with the size of unobserved neuronal populations, the square of average connectivity strength, and the square of observation sparseness. This implies that the shotgun connectivity estimation will require significantly larger amounts of neuronal activity data whenever the number of neurons in observed neuronal populations remains small. We present a numerical approach for solving the shotgun estimation problem in general settings and use it to demonstrate the shotgun connectivity inference in the examples of simulated synfire and weakly coupled cortical neuronal networks.

  4. Sparse regularization techniques provide novel insights into outcome integration processes.

    PubMed

    Mohr, Holger; Wolfensteller, Uta; Frimmel, Steffi; Ruge, Hannes

    2015-01-01

    By exploiting information that is contained in the spatial arrangement of neural activations, multivariate pattern analysis (MVPA) can detect distributed brain activations which are not accessible by standard univariate analysis. Recent methodological advances in MVPA regularization techniques have made it feasible to produce sparse discriminative whole-brain maps with highly specific patterns. Furthermore, the most recent refinement, the Graph Net, explicitly takes the 3D-structure of fMRI data into account. Here, these advanced classification methods were applied to a large fMRI sample (N=70) in order to gain novel insights into the functional localization of outcome integration processes. While the beneficial effect of differential outcomes is well-studied in trial-and-error learning, outcome integration in the context of instruction-based learning has remained largely unexplored. In order to examine neural processes associated with outcome integration in the context of instruction-based learning, two groups of subjects underwent functional imaging while being presented with either differential or ambiguous outcomes following the execution of varying stimulus-response instructions. While no significant univariate group differences were found in the resulting fMRI dataset, L1-regularized (sparse) classifiers performed significantly above chance and also clearly outperformed the standard L2-regularized (dense) Support Vector Machine on this whole-brain between-subject classification task. Moreover, additional L2-regularization via the Elastic Net and spatial regularization by the Graph Net improved interpretability of discriminative weight maps but were accompanied by reduced classification accuracies. Most importantly, classification based on sparse regularization facilitated the identification of highly specific regions differentially engaged under ambiguous and differential outcome conditions, comprising several prefrontal regions previously associated with

  5. Reliable positioning in a sparse GPS network, eastern Ontario

    NASA Astrophysics Data System (ADS)

    Samadi Alinia, H.; Tiampo, K.; Atkinson, G. M.

    2013-12-01

    Canada hosts two regions that are prone to large earthquakes: western British Columbia, and the St. Lawrence River region in eastern Canada. Although eastern Ontario is not as seismically active as other areas of eastern Canada, such as the Charlevoix/Ottawa Valley seismic zone, it experiences ongoing moderate seismicity. In historic times, potentially damaging events have occurred in New York State (Attica, 1929, M=5.7; Plattsburg, 2002, M=5.0), north-central Ontario (Temiskaming, 1935, M=6.2; North Bay, 2000, M=5.0), eastern Ontario (Cornwall, 1944, M=5.8), Georgian Bay (2005, MN=4.3), and western Quebec (Val-Des-Bois,2010, M=5.0, MN=5.8). In eastern Canada, the analysis of detailed, high-precision measurements of surface deformation is a key component in our efforts to better characterize the associated seismic hazard. The data from precise, continuous GPS stations is necessary to adequately characterize surface velocities from which patterns and rates of stress accumulation on faults can be estimated (Mazzotti and Adams, 2005; Mazzotti et al., 2005). Monitoring of these displacements requires employing high accuracy GPS positioning techniques. Detailed strain measurements can determine whether the regional strain everywhere is commensurate with a large event occurring every few hundred years anywhere within this general area or whether large earthquakes are limited to specific areas (Adams and Halchuck, 2003; Mazzotti and Adams, 2005). In many parts of southeastern Ontario and western Québec, GPS stations are distributed quite sparsely, with spacings of approximately 100 km or more. The challenge is to provide accurate solutions for these sparse networks with an approach that is capable of achieving high-accuracy positioning. Here, various reduction techniques are applied to a sparse network installed with the Southern Ontario Seismic Network in eastern Ontario. Recent developments include the implementation of precise point positioning processing on acquired

  6. Feature Selection and Pedestrian Detection Based on Sparse Representation.

    PubMed

    Yao, Shihong; Wang, Tao; Shen, Weiming; Pan, Shaoming; Chong, Yanwen; Ding, Fei

    2015-01-01

    Pedestrian detection have been currently devoted to the extraction of effective pedestrian features, which has become one of the obstacles in pedestrian detection application according to the variety of pedestrian features and their large dimension. Based on the theoretical analysis of six frequently-used features, SIFT, SURF, Haar, HOG, LBP and LSS, and their comparison with experimental results, this paper screens out the sparse feature subsets via sparse representation to investigate whether the sparse subsets have the same description abilities and the most stable features. When any two of the six features are fused, the fusion feature is sparsely represented to obtain its important components. Sparse subsets of the fusion features can be rapidly generated by avoiding calculation of the corresponding index of dimension numbers of these feature descriptors; thus, the calculation speed of the feature dimension reduction is improved and the pedestrian detection time is reduced. Experimental results show that sparse feature subsets are capable of keeping the important components of these six feature descriptors. The sparse features of HOG and LSS possess the same description ability and consume less time compared with their full features. The ratios of the sparse feature subsets of HOG and LSS to their full sets are the highest among the six, and thus these two features can be used to best describe the characteristics of the pedestrian and the sparse feature subsets of the combination of HOG-LSS show better distinguishing ability and parsimony. PMID:26295480

  7. Feature Selection and Pedestrian Detection Based on Sparse Representation

    PubMed Central

    Yao, Shihong; Wang, Tao; Shen, Weiming; Pan, Shaoming; Chong, Yanwen; Ding, Fei

    2015-01-01

    Pedestrian detection have been currently devoted to the extraction of effective pedestrian features, which has become one of the obstacles in pedestrian detection application according to the variety of pedestrian features and their large dimension. Based on the theoretical analysis of six frequently-used features, SIFT, SURF, Haar, HOG, LBP and LSS, and their comparison with experimental results, this paper screens out the sparse feature subsets via sparse representation to investigate whether the sparse subsets have the same description abilities and the most stable features. When any two of the six features are fused, the fusion feature is sparsely represented to obtain its important components. Sparse subsets of the fusion features can be rapidly generated by avoiding calculation of the corresponding index of dimension numbers of these feature descriptors; thus, the calculation speed of the feature dimension reduction is improved and the pedestrian detection time is reduced. Experimental results show that sparse feature subsets are capable of keeping the important components of these six feature descriptors. The sparse features of HOG and LSS possess the same description ability and consume less time compared with their full features. The ratios of the sparse feature subsets of HOG and LSS to their full sets are the highest among the six, and thus these two features can be used to best describe the characteristics of the pedestrian and the sparse feature subsets of the combination of HOG-LSS show better distinguishing ability and parsimony. PMID:26295480

  8. Nonlinear Spike-And-Slab Sparse Coding for Interpretable Image Encoding

    PubMed Central

    Shelton, Jacquelyn A.; Sheikh, Abdul-Saboor; Bornschein, Jörg; Sterne, Philip; Lücke, Jörg

    2015-01-01

    Sparse coding is a popular approach to model natural images but has faced two main challenges: modelling low-level image components (such as edge-like structures and their occlusions) and modelling varying pixel intensities. Traditionally, images are modelled as a sparse linear superposition of dictionary elements, where the probabilistic view of this problem is that the coefficients follow a Laplace or Cauchy prior distribution. We propose a novel model that instead uses a spike-and-slab prior and nonlinear combination of components. With the prior, our model can easily represent exact zeros for e.g. the absence of an image component, such as an edge, and a distribution over non-zero pixel intensities. With the nonlinearity (the nonlinear max combination rule), the idea is to target occlusions; dictionary elements correspond to image components that can occlude each other. There are major consequences of the model assumptions made by both (non)linear approaches, thus the main goal of this paper is to isolate and highlight differences between them. Parameter optimization is analytically and computationally intractable in our model, thus as a main contribution we design an exact Gibbs sampler for efficient inference which we can apply to higher dimensional data using latent variable preselection. Results on natural and artificial occlusion-rich data with controlled forms of sparse structure show that our model can extract a sparse set of edge-like components that closely match the generating process, which we refer to as interpretable components. Furthermore, the sparseness of the solution closely follows the ground-truth number of components/edges in the images. The linear model did not learn such edge-like components with any level of sparsity. This suggests that our model can adaptively well-approximate and characterize the meaningful generation process. PMID:25954947

  9. Imprinting and recalling cortical ensembles.

    PubMed

    Carrillo-Reid, Luis; Yang, Weijian; Bando, Yuki; Peterka, Darcy S; Yuste, Rafael

    2016-08-12

    Neuronal ensembles are coactive groups of neurons that may represent building blocks of cortical circuits. These ensembles could be formed by Hebbian plasticity, whereby synapses between coactive neurons are strengthened. Here we report that repetitive activation with two-photon optogenetics of neuronal populations from ensembles in the visual cortex of awake mice builds neuronal ensembles that recur spontaneously after being imprinted and do not disrupt preexisting ones. Moreover, imprinted ensembles can be recalled by single- cell stimulation and remain coactive on consecutive days. Our results demonstrate the persistent reconfiguration of cortical circuits by two-photon optogenetics into neuronal ensembles that can perform pattern completion. PMID:27516599

  10. Grid cells and cortical representation.

    PubMed

    Moser, Edvard I; Roudi, Yasser; Witter, Menno P; Kentros, Clifford; Bonhoeffer, Tobias; Moser, May-Britt

    2014-07-01

    One of the grand challenges in neuroscience is to comprehend neural computation in the association cortices, the parts of the cortex that have shown the largest expansion and differentiation during mammalian evolution and that are thought to contribute profoundly to the emergence of advanced cognition in humans. In this Review, we use grid cells in the medial entorhinal cortex as a gateway to understand network computation at a stage of cortical processing in which firing patterns are shaped not primarily by incoming sensory signals but to a large extent by the intrinsic properties of the local circuit.

  11. Horizontal integration and cortical dynamics.

    PubMed

    Gilbert, C D

    1992-07-01

    We have discussed several results that lead to a view that cells in the visual system are endowed with dynamic properties, influenced by context, expectation, and long-term modifications of the cortical network. These observations will be important for understanding how neuronal ensembles produce a system that perceives, remembers, and adapts to injury. The advantage to being able to observe changes at early stages in a sensory pathway is that one may be able to understand the way in which neuronal ensembles encode and represent images at the level of their receptive field properties, of cortical topographies, and of the patterns of connections between cells participating in a network.

  12. Broadcasting of cortical activity to the olfactory bulb.

    PubMed

    Boyd, Alison M; Kato, Hiroyuki K; Komiyama, Takaki; Isaacson, Jeffry S

    2015-02-24

    Odor representations are initially formed in the olfactory bulb, which contains a topographic glomerular map of odor molecular features. The bulb transmits sensory information directly to piriform cortex, where it is encoded by distributed ensembles of pyramidal cells without spatial order. Intriguingly, piriform cortex pyramidal cells project back to the bulb, but the information contained in this feedback projection is unknown. Here, we use imaging in awake mice to directly monitor activity in the presynaptic boutons of cortical feedback fibers. We show that the cortex provides the bulb with a rich array of information for any individual odor and that cortical feedback is dependent on brain state. In contrast to the stereotyped, spatial arrangement of olfactory bulb glomeruli, cortical inputs tuned to different odors commingle and indiscriminately target individual glomerular channels. Thus, the cortex modulates early odor representations by broadcasting sensory information diffusely onto spatially ordered bulbar circuits.

  13. Broadcasting of cortical activity to the olfactory bulb.

    PubMed

    Boyd, Alison M; Kato, Hiroyuki K; Komiyama, Takaki; Isaacson, Jeffry S

    2015-02-24

    Odor representations are initially formed in the olfactory bulb, which contains a topographic glomerular map of odor molecular features. The bulb transmits sensory information directly to piriform cortex, where it is encoded by distributed ensembles of pyramidal cells without spatial order. Intriguingly, piriform cortex pyramidal cells project back to the bulb, but the information contained in this feedback projection is unknown. Here, we use imaging in awake mice to directly monitor activity in the presynaptic boutons of cortical feedback fibers. We show that the cortex provides the bulb with a rich array of information for any individual odor and that cortical feedback is dependent on brain state. In contrast to the stereotyped, spatial arrangement of olfactory bulb glomeruli, cortical inputs tuned to different odors commingle and indiscriminately target individual glomerular channels. Thus, the cortex modulates early odor representations by broadcasting sensory information diffusely onto spatially ordered bulbar circuits. PMID:25704808

  14. Critical Fluctuations in Cortical Models Near Instability

    PubMed Central

    Aburn, Matthew J.; Holmes, C. A.; Roberts, James A.; Boonstra, Tjeerd W.; Breakspear, Michael

    2012-01-01

    Computational studies often proceed from the premise that cortical dynamics operate in a linearly stable domain, where fluctuations dissipate quickly and show only short memory. Studies of human electroencephalography (EEG), however, have shown significant autocorrelation at time lags on the scale of minutes, indicating the need to consider regimes where non-linearities influence the dynamics. Statistical properties such as increased autocorrelation length, increased variance, power law scaling, and bistable switching have been suggested as generic indicators of the approach to bifurcation in non-linear dynamical systems. We study temporal fluctuations in a widely-employed computational model (the Jansen–Rit model) of cortical activity, examining the statistical signatures that accompany bifurcations. Approaching supercritical Hopf bifurcations through tuning of the background excitatory input, we find a dramatic increase in the autocorrelation length that depends sensitively on the direction in phase space of the input fluctuations and hence on which neuronal subpopulation is stochastically perturbed. Similar dependence on the input direction is found in the distribution of fluctuation size and duration, which show power law scaling that extends over four orders of magnitude at the Hopf bifurcation. We conjecture that the alignment in phase space between the input noise vector and the center manifold of the Hopf bifurcation is directly linked to these changes. These results are consistent with the possibility of statistical indicators of linear instability being detectable in real EEG time series. However, even in a simple cortical model, we find that these indicators may not necessarily be visible even when bifurcations are present because their expression can depend sensitively on the neuronal pathway of incoming fluctuations. PMID:22952464

  15. Anatomical Abnormalities in Gray and White Matter of the Cortical Surface in Persons with Schizophrenia

    PubMed Central

    Colibazzi, Tiziano; Wexler, Bruce E.; Bansal, Ravi; Hao, Xuejun; Liu, Jun; Sanchez-Peña, Juan; Corcoran, Cheryl; Lieberman, Jeffrey A.; Peterson, Bradley S.

    2013-01-01

    Background Although schizophrenia has been associated with abnormalities in brain anatomy, imaging studies have not fully determined the nature and relative contributions of gray matter (GM) and white matter (WM) disturbances underlying these findings. We sought to determine the pattern and distribution of these GM and WM abnormalities. Furthermore, we aimed to clarify the contribution of abnormalities in cortical thickness and cortical surface area to the reduced GM volumes reported in schizophrenia. Methods We recruited 76 persons with schizophrenia and 57 healthy controls from the community and obtained measures of cortical and WM surface areas, of local volumes along the brain and WM surfaces, and of cortical thickness. Results We detected reduced local volumes in patients along corresponding locations of the brain and WM surfaces in addition to bilateral greater thickness of perisylvian cortices and thinner cortex in the superior frontal and cingulate gyri. Total cortical and WM surface areas were reduced. Patients with worse performance on the serial-position task, a measure of working memory, had a higher burden of WM abnormalities. Conclusions Reduced local volumes along the surface of the brain mirrored the locations of abnormalities along the surface of the underlying WM, rather than of abnormalities of cortical thickness. Moreover, anatomical features of white matter, but not cortical thickness, correlated with measures of working memory. We propose that reductions in WM and smaller total cortical surface area could be central anatomical abnormalities in schizophrenia, driving, at least partially, the reduced regional GM volumes often observed in this illness. PMID:23418459

  16. Elastic-Waveform Inversion with Compressive Sensing for Sparse Seismic Data

    SciTech Connect

    Lin, Youzuo; Huang, Lianjie

    2015-01-26

    Accurate velocity models of compressional- and shear-waves are essential for geothermal reservoir characterization and microseismic imaging. Elastic-waveform inversion of multi-component seismic data can provide high-resolution inversion results of subsurface geophysical properties. However, the method requires seismic data acquired using dense source and receiver arrays. In practice, seismic sources and/or geophones are often sparsely distributed on the surface and/or in a borehole, such as 3D vertical seismic profiling (VSP) surveys. We develop a novel elastic-waveform inversion method with compressive sensing for inversion of sparse seismic data. We employ an alternating-minimization algorithm to solve the optimization problem of our new waveform inversion method. We validate our new method using synthetic VSP data for a geophysical model built using geologic features found at the Raft River enhanced-geothermal-system (EGS) field. We apply our method to synthetic VSP data with a sparse source array and compare the results with those obtained with a dense source array. Our numerical results demonstrate that the velocity mode ls produced with our new method using a sparse source array are almost as accurate as those obtained using a dense source array.

  17. Visual Tracking Based on the Adaptive Color Attention Tuned Sparse Generative Object Model.

    PubMed

    Tian, Chunna; Gao, Xinbo; Wei, Wei; Zheng, Hong

    2015-12-01

    This paper presents a new visual tracking framework based on an adaptive color attention tuned local sparse model. The histograms of sparse coefficients of all patches in an object are pooled together according to their spatial distribution. A particle filter methodology is used as the location model to predict candidates for object verification during tracking. Since color is an important visual clue to distinguish objects from background, we calculate the color similarity between objects in the previous frames and the candidates in current frame, which is adopted as color attention to tune the local sparse representation-based appearance similarity measurement between the object template and candidates. The color similarity can be calculated efficiently with hash coded color names, which helps the tracker find more reliable objects during tracking. We use a flexible local sparse coding of the object to evaluate the degeneration degree of the appearance model, based on which we build a model updating mechanism to alleviate drifting caused by temporal varying multi-factors. Experiments on 76 challenging benchmark color sequences and the evaluation under the object tracking benchmark protocol demonstrate the superiority of the proposed tracker over the state-of-the-art methods in accuracy. PMID:26390460

  18. Subthreshold membrane responses underlying sparse spiking to natural vocal signals in auditory cortex

    PubMed Central

    Perks, Krista Eva; Gentner, Timothy Q.

    2015-01-01

    Natural acoustic communication signals, such as speech, are typically high-dimensional with a wide range of co-varying spectro-temporal features at multiple timescales. The synaptic and network mechanisms for encoding these complex signals are largely unknown. We are investigating these mechanisms in high-level sensory regions of the songbird auditory forebrain, where single neurons show sparse, object-selective spiking responses to conspecific songs. Using whole-cell in-vivo patch clamp techniques in the caudal mesopallium and the caudal nidopallium of starlings, we examine song-driven subthreshold and spiking activity. We find that both the subthreshold and the spiking activity are reliable (i.e., the same song drives a similar response each time it is presented) and specific (i.e. responses to different songs are distinct). Surprisingly, however, the reliability and specificity of the sub-threshold response was uniformly high regardless of when the cell spiked, even for song stimuli that drove no spikes. We conclude that despite a selective and sparse spiking response, high-level auditory cortical neurons are under continuous, non-selective, stimulus-specific synaptic control. To investigate the role of local network inhibition in this synaptic control, we then recorded extracellularly while pharmacologically blocking local GABA-ergic transmission. This manipulation modulated the strength and the reliability of stimulus-driven spiking, consistent with a role for local inhibition in regulating the reliability of network activity and the stimulus specificity of the subthreshold response in single cells. We discuss these results in the context of underlying computations that could generate sparse, stimulus-selective spiking responses, and models for hierarchical pooling. PMID:25728189

  19. Predicting structure in nonsymmetric sparse matrix factorizations

    SciTech Connect

    Gilbert, J.R.; Ng, E.G.

    1992-10-01

    Many computations on sparse matrices have a phase that predicts the nonzero structure of the output, followed by a phase that actually performs the numerical computation. We study structure prediction for computations that involve nonsymmetric row and column permutations and nonsymmetric or non-square matrices. Our tools are bipartite graphs, matchings, and alternating paths. Our main new result concerns LU factorization with partial pivoting. We show that if a square matrix A has the strong Hall property (i.e., is fully indecomposable) then an upper bound due to George and Ng on the nonzero structure of L + U is as tight as possible. To show this, we prove a crucial result about alternating paths in strong Hall graphs. The alternating-paths theorem seems to be of independent interest: it can also be used to prove related results about structure prediction for QR factorization that are due to Coleman, Edenbrandt, Gilbert, Hare, Johnson, Olesky, Pothen, and van den Driessche.

  20. Eigensolver for a Sparse, Large Hermitian Matrix

    NASA Technical Reports Server (NTRS)

    Tisdale, E. Robert; Oyafuso, Fabiano; Klimeck, Gerhard; Brown, R. Chris

    2003-01-01

    A parallel-processing computer program finds a few eigenvalues in a sparse Hermitian matrix that contains as many as 100 million diagonal elements. This program finds the eigenvalues faster, using less memory, than do other, comparable eigensolver programs. This program implements a Lanczos algorithm in the American National Standards Institute/ International Organization for Standardization (ANSI/ISO) C computing language, using the Message Passing Interface (MPI) standard to complement an eigensolver in PARPACK. [PARPACK (Parallel Arnoldi Package) is an extension, to parallel-processing computer architectures, of ARPACK (Arnoldi Package), which is a collection of Fortran 77 subroutines that solve large-scale eigenvalue problems.] The eigensolver runs on Beowulf clusters of computers at the Jet Propulsion Laboratory (JPL).

  1. Compressed Sensing for Reconstructing Sparse Quantum States

    NASA Astrophysics Data System (ADS)

    Rudinger, Kenneth; Joynt, Robert

    2014-03-01

    Compressed sensing techniques have been successfully applied to quantum state tomography, enabling the efficient determination of states that are nearly pure, i.e, of low rank. We show how compressed sensing may be used even when the states to be reconstructed are full rank. Instead, the necessary requirement is that the states be sparse in some known basis (e.g. the Pauli basis). Physical systems at high temperatures in thermal equilibrium are important examples of such states. Using this method, we are able to demonstrate that, like for classical signals, compressed sensing for quantum states exhibits the Donoho-Tanner phase transition. This method will be useful for the determination of the Hamiltonians of artificially constructed quantum systems whose purpose is to simulate condensed-matter models, as it requires many fewer measurements than demanded by standard tomographic procedures. This work was supported in part by ARO, DOD (W911NF-09-1-0439) and NSF (CCR-0635355).

  2. Inverse lithography using sparse mask representations

    NASA Astrophysics Data System (ADS)

    Ionescu, Radu C.; Hurley, Paul; Apostol, Stefan

    2015-03-01

    We present a novel optimisation algorithm for inverse lithography, based on optimization of the mask derivative, a domain inherently sparse, and for rectilinear polygons, invertible. The method is first developed assuming a point light source, and then extended to general incoherent sources. What results is a fast algorithm, producing manufacturable masks (the search space is constrained to rectilinear polygons), and flexible (specific constraints such as minimal line widths can be imposed). One inherent trick is to treat polygons as continuous entities, thus making aerial image calculation extremely fast and accurate. Requirements for mask manufacturability can be integrated in the optimization without too much added complexity. We also explain how to extend the scheme for phase-changing mask optimization.

  3. Blind source separation by sparse decomposition

    NASA Astrophysics Data System (ADS)

    Zibulevsky, Michael; Pearlmutter, Barak A.

    2000-04-01

    The blind source separation problem is to extract the underlying source signals from a set of their linear mixtures, where the mixing matrix is unknown. This situation is common, eg in acoustics, radio, and medical signal processing. We exploit the property of the sources to have a sparse representation in a corresponding signal dictionary. Such a dictionary may consist of wavelets, wavelet packets, etc., or be obtained by learning from a given family of signals. Starting from the maximum a posteriori framework, which is applicable to the case of more sources than mixtures, we derive a few other categories of objective functions, which provide faster and more robust computations, when there are an equal number of sources and mixtures. Our experiments with artificial signals and with musical sounds demonstrate significantly better separation than other known techniques.

  4. Convolutional Sparse Coding for Trajectory Reconstruction.

    PubMed

    Zhu, Yingying; Lucey, Simon

    2015-03-01

    Trajectory basis Non-Rigid Structure from Motion (NRSfM) refers to the process of reconstructing the 3D trajectory of each point of a non-rigid object from just their 2D projected trajectories. Reconstruction relies on two factors: (i) the condition of the composed camera & trajectory basis matrix, and (ii) whether the trajectory basis has enough degrees of freedom to model the 3D point trajectory. These two factors are inherently conflicting. Employing a trajectory basis with small capacity has the positive characteristic of reducing the likelihood of an ill-conditioned system (when composed with the camera) during reconstruction. However, this has the negative characteristic of increasing the likelihood that the basis will not be able to fully model the object's "true" 3D point trajectories. In this paper we draw upon a well known result centering around the Reduced Isometry Property (RIP) condition for sparse signal reconstruction. RIP allow us to relax the requirement that the full trajectory basis composed with the camera matrix must be well conditioned. Further, we propose a strategy for learning an over-complete basis using convolutional sparse coding from naturally occurring point trajectory corpora to increase the likelihood that the RIP condition holds for a broad class of point trajectories and camera motions. Finally, we propose an l1 inspired objective for trajectory reconstruction that is able to "adaptively" select the smallest sub-matrix from an over-complete trajectory basis that balances (i) and (ii). We present more practical 3D reconstruction results compared to current state of the art in trajectory basis NRSfM.

  5. Biomechanics of Single Cortical Neurons

    PubMed Central

    Bernick, Kristin B.; Prevost, Thibault P.; Suresh, Subra; Socrate, Simona

    2011-01-01

    This study presents experimental results and computational analysis of the large strain dynamic behavior of single neurons in vitro with the objective of formulating a novel quantitative framework for the biomechanics of cortical neurons. Relying on the atomic force microscopy (AFM) technique, novel testing protocols are developed to enable the characterization of neural soma deformability over a range of indentation rates spanning three orders of magnitude – 10, 1, and 0.1 μm/s. Modified spherical AFM probes were utilized to compress the cell bodies of neonatal rat cortical neurons in load, unload, reload and relaxation conditions. The cell response showed marked hysteretic features, strong non-linearities, and substantial time/rate dependencies. The rheological data were complemented with geometrical measurements of cell body morphology, i.e. cross-diameter and height estimates. A constitutive model, validated by the present experiments, is proposed to quantify the mechanical behavior of cortical neurons. The model aimed to correlate empirical findings with measurable degrees of (hyper-) elastic resilience and viscosity at the cell level. The proposed formulation, predicated upon previous constitutive model developments undertaken at the cortical tissue level, was implemented into a three-dimensional finite element framework. The simulated cell response was calibrated to the experimental measurements under the selected test conditions, providing a novel single cell model that could form the basis for further refinements. PMID:20971217

  6. MR image super-resolution reconstruction using sparse representation, nonlocal similarity and sparse derivative prior.

    PubMed

    Zhang, Di; He, Jiazhong; Zhao, Yun; Du, Minghui

    2015-03-01

    In magnetic resonance (MR) imaging, image spatial resolution is determined by various instrumental limitations and physical considerations. This paper presents a new algorithm for producing a high-resolution version of a low-resolution MR image. The proposed method consists of two consecutive steps: (1) reconstructs a high-resolution MR image from a given low-resolution observation via solving a joint sparse representation and nonlocal similarity L1-norm minimization problem; and (2) applies a sparse derivative prior based post-processing to suppress blurring effects. Extensive experiments on simulated brain MR images and two real clinical MR image datasets validate that the proposed method achieves much better results than many state-of-the-art algorithms in terms of both quantitative measures and visual perception.

  7. Sparse source configurations in radio tomography of asteroids

    NASA Astrophysics Data System (ADS)

    Pursiainen, S.; Kaasalainen, M.

    2014-07-01

    Our research targets at progress in non-invasive imaging of asteroids to support future planetary research and extra-terrestrial mining activities. This presentation concerns principally radio tomography in which the permittivity distribution inside an asteroid is to be recovered based on the radio frequency signal transmitted from the asteroid's surface and gathered by an orbiter. The focus will be on a sparse distribution (Pursiainen and Kaasalainen, 2013) of signal sources that can be necessary in the challenging in situ environment and within tight payload limits. The general goal in our recent research has been to approximate the minimal number of source positions needed for robust localization of anomalies caused, for example, by an internal void. Characteristic to the localization problem are the large relative changes in signal speed caused by the high permittivity of typical asteroid minerals (e.g. basalt), meaning that a signal path can include strong refractions and reflections. This presentation introduces results of a laboratory experiment in which real travel time data was inverted using a hierarchical Bayesian approach combined with the iterative alternating sequential (IAS) posterior exploration algorithm. Special interest was paid to robustness of the inverse results regarding changes of the prior model and source positioning. According to our results, strongly refractive anomalies can be detected with three or four sources independently of their positioning.

  8. Group-based sparse representation for image restoration.

    PubMed

    Zhang, Jian; Zhao, Debin; Gao, Wen

    2014-08-01

    Traditional patch-based sparse representation modeling of natural images usually suffer from two problems. First, it has to solve a large-scale optimization problem with high computational complexity in dictionary learning. Second, each patch is considered independently in dictionary learning and sparse coding, which ignores the relationship among patches, resulting in inaccurate sparse coding coefficients. In this paper, instead of using patch as the basic unit of sparse representation, we exploit the concept of group as the basic unit of sparse representation, which is composed of nonlocal patches with similar structures, and establish a novel sparse representation modeling of natural images, called group-based sparse representation (GSR). The proposed GSR is able to sparsely represent natural images in the domain of group, which enforces the intrinsic local sparsity and nonlocal self-similarity of images simultaneously in a unified framework. In addition, an effective self-adaptive dictionary learning method for each group with low complexity is designed, rather than dictionary learning from natural images. To make GSR tractable and robust, a split Bregman-based technique is developed to solve the proposed GSR-driven ℓ0 minimization problem for image restoration efficiently. Extensive experiments on image inpainting, image deblurring and image compressive sensing recovery manifest that the proposed GSR modeling outperforms many current state-of-the-art schemes in both peak signal-to-noise ratio and visual perception.

  9. Alterations in cortical thickness development in preterm-born individuals: Implications for high-order cognitive functions

    PubMed Central

    Nam, Kie Woo; Castellanos, Nazareth; Simmons, Andrew; Froudist-Walsh, Seán; Allin, Matthew P.; Walshe, Muriel; Murray, Robin M.; Evans, Alan; Muehlboeck, J-Sebastian; Nosarti, Chiara

    2015-01-01

    Very preterm birth (gestational age < 33 weeks) is associated with alterations in cortical thickness and with neuropsychological/behavioural impairments. Here we studied cortical thickness in very preterm born individuals and controls in mid-adolescence (mean age 15 years) and beginning of adulthood (mean age 20 years), as well as longitudinal changes between the two time points. Using univariate approaches, we showed both increases and decreases in cortical thickness in very preterm born individuals compared to controls. Specifically (1) very preterm born adolescents displayed extensive areas of greater cortical thickness, especially in occipitotemporal and prefrontal cortices, differences which decreased substantially by early adulthood; (2) at both time points, very preterm-born participants showed smaller cortical thickness, especially in parahippocampal and insular regions. We then employed a multivariate approach (support vector machine) to study spatially discriminating features between the two groups, which achieved a mean accuracy of 86.5%. The spatially distributed regions in which cortical thickness best discriminated between the groups (top 5%) included temporal, occipitotemporal, parietal and prefrontal cortices. Within these spatially distributed regions (top 1%), longitudinal changes in cortical thickness in left temporal pole, right occipitotemporal gyrus and left superior parietal lobe were significantly associated with scores on language-based tests of executive function. These results describe alterations in cortical thickness development in preterm-born individuals in their second decade of life, with implications for high-order cognitive processing. PMID:25871628

  10. Alterations in cortical thickness development in preterm-born individuals: Implications for high-order cognitive functions.

    PubMed

    Nam, Kie Woo; Castellanos, Nazareth; Simmons, Andrew; Froudist-Walsh, Seán; Allin, Matthew P; Walshe, Muriel; Murray, Robin M; Evans, Alan; Muehlboeck, J-Sebastian; Nosarti, Chiara

    2015-07-15

    Very preterm birth (gestational age <33 weeks) is associated with alterations in cortical thickness and with neuropsychological/behavioural impairments. Here we studied cortical thickness in very preterm born individuals and controls in mid-adolescence (mean age 15 years) and beginning of adulthood (mean age 20 years), as well as longitudinal changes between the two time points. Using univariate approaches, we showed both increases and decreases in cortical thickness in very preterm born individuals compared to controls. Specifically (1) very preterm born adolescents displayed extensive areas of greater cortical thickness, especially in occipitotemporal and prefrontal cortices, differences which decreased substantially by early adulthood; (2) at both time points, very preterm-born participants showed smaller cortical thickness, especially in parahippocampal and insular regions. We then employed a multivariate approach (support vector machine) to study spatially discriminating features between the two groups, which achieved a mean accuracy of 86.5%. The spatially distributed regions in which cortical thickness best discriminated between the groups (top 5%) included temporal, occipitotemporal, parietal and prefrontal cortices. Within these spatially distributed regions (top 1%), longitudinal changes in cortical thickness in left temporal pole, right occipitotemporal gyrus and left superior parietal lobe were significantly associated with scores on language-based tests of executive function. These results describe alterations in cortical thickness development in preterm-born individuals in their second decade of life, with implications for high-order cognitive processing. PMID:25871628

  11. Cervigram image segmentation based on reconstructive sparse representations

    NASA Astrophysics Data System (ADS)

    Zhang, Shaoting; Huang, Junzhou; Wang, Wei; Huang, Xiaolei; Metaxas, Dimitris

    2010-03-01

    We proposed an approach based on reconstructive sparse representations to segment tissues in optical images of the uterine cervix. Because of large variations in image appearance caused by the changing of the illumination and specular reflection, the color and texture features in optical images often overlap with each other and are not linearly separable. By leveraging sparse representations the data can be transformed to higher dimensions with sparse constraints and become more separated. K-SVD algorithm is employed to find sparse representations and corresponding dictionaries. The data can be reconstructed from its sparse representations and positive and/or negative dictionaries. Classification can be achieved based on comparing the reconstructive errors. In the experiments we applied our method to automatically segment the biomarker AcetoWhite (AW) regions in an archive of 60,000 images of the uterine cervix. Compared with other general methods, our approach showed lower space and time complexity and higher sensitivity.

  12. Sparse Coding on Symmetric Positive Definite Manifolds Using Bregman Divergences.

    PubMed

    Harandi, Mehrtash T; Hartley, Richard; Lovell, Brian; Sanderson, Conrad

    2016-06-01

    This paper introduces sparse coding and dictionary learning for symmetric positive definite (SPD) matrices, which are often used in machine learning, computer vision, and related areas. Unlike traditional sparse coding schemes that work in vector spaces, in this paper, we discuss how SPD matrices can be described by sparse combination of dictionary atoms, where the atoms are also SPD matrices. We propose to seek sparse coding by embedding the space of SPD matrices into the Hilbert spaces through two types of the Bregman matrix divergences. This not only leads to an efficient way of performing sparse coding but also an online and iterative scheme for dictionary learning. We apply the proposed methods to several computer vision tasks where images are represented by region covariance matrices. Our proposed algorithms outperform state-of-the-art methods on a wide range of classification tasks, including face recognition, action recognition, material classification, and texture categorization. PMID:25643414

  13. Actin kinetics shapes cortical network structure and mechanics

    PubMed Central

    Fritzsche, Marco; Erlenkämper, Christoph; Moeendarbary, Emad; Charras, Guillaume; Kruse, Karsten

    2016-01-01

    The actin cortex of animal cells is the main determinant of cellular mechanics. The continuous turnover of cortical actin filaments enables cells to quickly respond to stimuli. Recent work has shown that most of the cortical actin is generated by only two actin nucleators, the Arp2/3 complex and the formin Diaph1. However, our understanding of their interplay, their kinetics, and the length distribution of the filaments that they nucleate within living cells is poor. Such knowledge is necessary for a thorough comprehension of cellular processes and cell mechanics from basic polymer physics principles. We determined cortical assembly rates in living cells by using single-molecule fluorescence imaging in combination with stochastic simulations. We find that formin-nucleated filaments are, on average, 10 times longer than Arp2/3-nucleated filaments. Although formin-generated filaments represent less than 10% of all actin filaments, mechanical measurements indicate that they are important determinants of cortical elasticity. Tuning the activity of actin nucleators to alter filament length distribution may thus be a mechanism allowing cells to adjust their macroscopic mechanical properties to their physiological needs. PMID:27152338

  14. Phasing software for a free flyer space-based sparse mirror array not requiring laser interferometry

    NASA Astrophysics Data System (ADS)

    Maker, David J.

    2004-10-01

    This paper presents new software (and simulations) that would phase a space based free flyer sparse array telescope. This particular sparse array method uses mirrors that are far enough away for sensors at the focal point module to detect tip tilt by simply using the deflection of the beam from each mirror. Also the large distance allows these circle six array mirrors to be actuated flats. For piston the secondary actuated mirrors (one for each large mirror segment of these widely spaced sparse array mirrors distributed on a parabola) are moved in real time to maximize the Strehle ratio using the light from the star the planet is revolving around since that star usually has an extremely high SNR (Signal to Noise Ratio). There is then no need for a 6DOF spider web of laser interferometric beams and deep dish mirrors (as in the competing Darwin and JPL methods) to accomplish this. Also the distance between the six 3 meter aperture mirrors could be large (kilometer range) guaranteeing a high resolution and also substantial light gathering power (with these 6 large mirrors) for imaging the details on the surface of extrasolar terrestrial type planets. In any case such a multisatellite free flyer concept would then be no more complex than the European cluster which is now operational. This is a viable concept and a compelling way to image surface detail on extra solar earthlike planets. It is the ideal engineering solution to the problem of space based large baseline sparse arrays. Significant details of the software requirements have been recently developed. In this paper the Fortran code needed to both simulate and operate the actuators in the secondary mirror for this type of sparse array is discussed.

  15. Extracting sparse signals from high-dimensional data: A statistical mechanics approach

    NASA Astrophysics Data System (ADS)

    Ramezanali, Mohammad

    Sparse reconstruction algorithms aim to retrieve high-dimensional sparse signals from a limited amount of measurements under suitable conditions. As the number of variables go to infinity, these algorithms exhibit sharp phase transition boundaries where the sparse retrieval breaks down. Several sparse reconstruction algorithms are formulated as optimization problems. Few of the prominent ones among these have been analyzed in the literature by statistical mechanical methods. The function to be optimized plays the role of energy. The treatment involves finite temperature replica mean-field theory followed by the zero temperature limit. Although this approach has been successful in reproducing the algorithmic phase transition boundaries, the replica trick and the non-trivial zero temperature limit obscure the underlying reasons for the failure of the algorithms. In this thesis, we employ the "cavity method" to give an alternative derivation of the phase transition boundaries, working directly in the zero-temperature limit. This approach provides insight into the origin of the different terms in the mean field self-consistency equations. The cavity method naturally generates a local susceptibility which leads to an identity that clearly indicates the existence of two phases. The identity also gives us a novel route to the known parametric expressions for the phase boundary of the Basis Pursuit algorithm and to the new ones for the Elastic Net. These transitions being continuous (second order), we explore the scaling laws and critical exponents that are uniquely determined by the nature of the distribution of the density of the nonzero components of the sparse signal. Not only is the phase boundary of the Elastic Net different from that of the Basis Pursuit, we show that the critical behavior of the two algorithms are from different universality classes.

  16. Deep sparse multi-task learning for feature selection in Alzheimer’s disease diagnosis

    PubMed Central

    Suk, Heung-Il; Lee, Seong-Whan; Shen, Dinggang

    2016-01-01

    Recently, neuroimaging-based Alzheimer’s disease (AD) or mild cognitive impairment (MCI) diagnosis has attracted researchers in the field, due to the increasing prevalence of the diseases. Unfortunately, the unfavorable high-dimensional nature of neuroimaging data, but a limited small number of samples available, makes it challenging to build a robust computer-aided diagnosis system. Machine learning techniques have been considered as a useful tool in this respect and, among various methods, sparse regression has shown its validity in the literature. However, to our best knowledge, the existing sparse regression methods mostly try to select features based on the optimal regression coefficients in one step. We argue that since the training feature vectors are composed of both informative and uninformative or less informative features, the resulting optimal regression coefficients are inevidently affected by the uninformative or less informative features. To this end, we first propose a novel deep architecture to recursively discard uninformative features by performing sparse multi-task learning in a hierarchical fashion. We further hypothesize that the optimal regression coefficients reflect the relative importance of features in representing the target response variables. In this regard, we use the optimal regression co-efficients learned in one hierarchy as feature weighting factors in the following hierarchy, and formulate a weighted sparse multi-task learning method. Lastly, we also take into account the distributional characteristics of samples per class and use clustering-induced subclass label vectors as target response values in our sparse regression model. In our experiments on the ADNI cohort, we performed both binary and multi-class classification tasks in AD/MCI diagnosis and showed the superiority of the proposed method by comparing with the state-of-the-art methods. PMID:25993900

  17. Deep sparse multi-task learning for feature selection in Alzheimer's disease diagnosis.

    PubMed

    Suk, Heung-Il; Lee, Seong-Whan; Shen, Dinggang

    2016-06-01

    Recently, neuroimaging-based Alzheimer's disease (AD) or mild cognitive impairment (MCI) diagnosis has attracted researchers in the field, due to the increasing prevalence of the diseases. Unfortunately, the unfavorable high-dimensional nature of neuroimaging data, but a limited small number of samples available, makes it challenging to build a robust computer-aided diagnosis system. Machine learning techniques have been considered as a useful tool in this respect and, among various methods, sparse regression has shown its validity in the literature. However, to our best knowledge, the existing sparse regression methods mostly try to select features based on the optimal regression coefficients in one step. We argue that since the training feature vectors are composed of both informative and uninformative or less informative features, the resulting optimal regression coefficients are inevidently affected by the uninformative or less informative features. To this end, we first propose a novel deep architecture to recursively discard uninformative features by performing sparse multi-task learning in a hierarchical fashion. We further hypothesize that the optimal regression coefficients reflect the relative importance of features in representing the target response variables. In this regard, we use the optimal regression coefficients learned in one hierarchy as feature weighting factors in the following hierarchy, and formulate a weighted sparse multi-task learning method. Lastly, we also take into account the distributional characteristics of samples per class and use clustering-induced subclass label vectors as target response values in our sparse regression model. In our experiments on the ADNI cohort, we performed both binary and multi-class classification tasks in AD/MCI diagnosis and showed the superiority of the proposed method by comparing with the state-of-the-art methods.

  18. Institute for the Study of Sparsely Populated Areas. A Centre for Interdisciplinary Research into Sparsely Populated and Peripheral Regions.

    ERIC Educational Resources Information Center

    Sadler, Peter G.

    The Institute for the Study of Sparsely Populated Areas is a multidisciplinary research unit which acts to coordinate, further, and initiate studies of the economic and social conditions of sparsely populated areas. Short summaries of the eight studies completed in the session of 1977-78 indicate work in such areas as the study of political life…

  19. Auditory experience-dependent cortical circuit shaping for memory formation in bird song learning

    PubMed Central

    Yanagihara, Shin; Yazaki-Sugiyama, Yoko

    2016-01-01

    As in human speech acquisition, songbird vocal learning depends on early auditory experience. During development, juvenile songbirds listen to and form auditory memories of adult tutor songs, which they use to shape their own vocalizations in later sensorimotor learning. The higher-level auditory cortex, called the caudomedial nidopallium (NCM), is a potential storage site for tutor song memory, but no direct electrophysiological evidence of tutor song memory has been found. Here, we identify the neuronal substrate for tutor song memory by recording single-neuron activity in the NCM of behaving juvenile zebra finches. After tutor song experience, a small subset of NCM neurons exhibit highly selective auditory responses to the tutor song. Moreover, blockade of GABAergic inhibition, and sleep decrease their selectivity. Taken together, these results suggest that experience-dependent recruitment of GABA-mediated inhibition shapes auditory cortical circuits, leading to sparse representation of tutor song memory in auditory cortical neurons. PMID:27327620

  20. Auditory experience-dependent cortical circuit shaping for memory formation in bird song learning.

    PubMed

    Yanagihara, Shin; Yazaki-Sugiyama, Yoko

    2016-01-01

    As in human speech acquisition, songbird vocal learning depends on early auditory experience. During development, juvenile songbirds listen to and form auditory memories of adult tutor songs, which they use to shape their own vocalizations in later sensorimotor learning. The higher-level auditory cortex, called the caudomedial nidopallium (NCM), is a potential storage site for tutor song memory, but no direct electrophysiological evidence of tutor song memory has been found. Here, we identify the neuronal substrate for tutor song memory by recording single-neuron activity in the NCM of behaving juvenile zebra finches. After tutor song experience, a small subset of NCM neurons exhibit highly selective auditory responses to the tutor song. Moreover, blockade of GABAergic inhibition, and sleep decrease their selectivity. Taken together, these results suggest that experience-dependent recruitment of GABA-mediated inhibition shapes auditory cortical circuits, leading to sparse representation of tutor song memory in auditory cortical neurons. PMID:27327620

  1. Development of cortical orientation selectivity in the absence of visual experience with contour

    PubMed Central

    Hussain, Shaista; Weliky, Michael

    2011-01-01

    Visual cortical neurons are selective for the orientation of lines, and the full development of this selectivity requires natural visual experience after eye opening. Here we examined whether this selectivity develops without seeing lines and contours. Juvenile ferrets were reared in a dark room and visually trained by being shown a movie of flickering, sparse spots. We found that despite the lack of contour visual experience, the cortical neurons of these ferrets developed strong orientation selectivity and exhibited simple-cell receptive fields. This finding suggests that overt contour visual experience is unnecessary for the maturation of orientation selectivity and is inconsistent with the computational models that crucially require the visual inputs of lines and contours for the development of orientation selectivity. We propose that a correlation-based model supplemented with a constraint on synaptic strength dynamics is able to account for our experimental result. PMID:21753023

  2. The Influence of Synaptic Weight Distribution on Neuronal Population Dynamics

    PubMed Central

    Buice, Michael; Koch, Christof; Mihalas, Stefan

    2013-01-01

    The manner in which different distributions of synaptic weights onto cortical neurons shape their spiking activity remains open. To characterize a homogeneous neuronal population, we use the master equation for generalized leaky integrate-and-fire neurons with shot-noise synapses. We develop fast semi-analytic numerical methods to solve this equation for either current or conductance synapses, with and without synaptic depression. We show that its solutions match simulations of equivalent neuronal networks better than those of the Fokker-Planck equation and we compute bounds on the network response to non-instantaneous synapses. We apply these methods to study different synaptic weight distributions in feed-forward networks. We characterize the synaptic amplitude distributions using a set of measures, called tail weight numbers, designed to quantify the preponderance of very strong synapses. Even if synaptic amplitude distributions are equated for both the total current and average synaptic weight, distributions with sparse but strong synapses produce higher responses for small inputs, leading to a larger operating range. Furthermore, despite their small number, such synapses enable the network to respond faster and with more stability in the face of external fluctuations. PMID:24204219

  3. Cortical and cytoplasmic flow polarity in early embryonic cells of Caenorhabditis elegans

    PubMed Central

    1993-01-01

    We have examined the cortex of Caenorhabditis elegans eggs during pseudocleavage (PC), a period of the first cell cycle which is important for the generation of asymmetry at first cleavage (Strome, S. 1989. Int. Rev. Cytol. 114: 81-123). We have found that directed, actin dependent, cytoplasmic, and cortical flow occurs during this period coincident with a rearrangement of the cortical actin cytoskeleton (Strome, S. 1986. J. Cell Biol. 103: 2241-2252). The flow velocity (4-7 microns/min) is similar to previously determined particle movements driven by cortical actin flows in motile cells. We show that directed flows occur in one of the daughters of the first division that itself divides asymmetrically, but not in its sister that divides symmetrically. The cortical and cytoplasmic events of PC can be mimicked in other cells during cytokinesis by displacing the mitotic apparatus with the microtubule polymerization inhibitor nocodazole. In all cases, the polarity of the resulting cortical and cytoplasmic flows correlates with the position of the attenuated mitotic spindle formed. These cortical flows are also accompanied by a change in the distribution of the cortical actin network. The polarity of this redistribution is similarly correlated with the location of the attenuated spindle. These observations suggest a mechanism for generating polarized flows of cytoplasmic and cortical material during embryonic cleavages. We present a model for the events of PC and suggest how the poles of the mitotic spindle mediate the formation of the contractile ring during cytokinesis in C. elegans. PMID:8509454

  4. Zic deficiency in the cortical marginal zone and meninges results in cortical lamination defects resembling those in type II lissencephaly.

    PubMed

    Inoue, Takashi; Ogawa, Masaharu; Mikoshiba, Katsuhiko; Aruga, Jun

    2008-04-30

    The formation of the highly organized cortical structure depends on the production and correct placement of the appropriate number and types of neurons. The Zic family of zinc-finger transcription factors plays essential roles in regulating the proliferation and differentiation of neuronal progenitors in the medial forebrain and the cerebellum. Examination of the expression of Zic genes demonstrated that Zic1, Zic2, and Zic3 were expressed by the progenitor cells in the septum and cortical hem, the sites of generation of the Cajal-Retzius (CR) cells. Immunohistochemical studies have revealed that Zic proteins were abundantly expressed in the meningeal cells and that the majority of the CR cells distributed in the medial and dorsal cortex also expressed Zic proteins in the mid-late embryonic and postnatal cortical marginal zones. During embryonic cortical development, Zic1/Zic3 double-mutant and hypomorphic Zic2 mutant mice showed a reduction in the number of CR cells in the rostral cortex, whereas the cell number remained unaffected in the caudal cortex. These mutants also showed mislocalization of the CR cells and cortical lamination defects, resembling the changes noted in type II (cobblestone) lissencephaly, throughout the brain. In the Zic1/3 mutant, reduced proliferation of the meningeal cells was observed before the thinner and disrupted organization of the pial basement membrane (BM) with reduced expression of the BM components and the meningeal cell-derived secretory factor. These defects correlated with the changes in the end feet morphology of the radial glial cells. These findings indicate that the Zic genes play critical roles in cortical development through regulating the proliferation of meningeal cells and the pial BM assembly.

  5. Approximation and compression with sparse orthonormal transforms.

    PubMed

    Sezer, Osman Gokhan; Guleryuz, Onur G; Altunbasak, Yucel

    2015-08-01

    We propose a new transform design method that targets the generation of compression-optimized transforms for next-generation multimedia applications. The fundamental idea behind transform compression is to exploit regularity within signals such that redundancy is minimized subject to a fidelity cost. Multimedia signals, in particular images and video, are well known to contain a diverse set of localized structures, leading to many different types of regularity and to nonstationary signal statistics. The proposed method designs sparse orthonormal transforms (SOTs) that automatically exploit regularity over different signal structures and provides an adaptation method that determines the best representation over localized regions. Unlike earlier work that is motivated by linear approximation constructs and model-based designs that are limited to specific types of signal regularity, our work uses general nonlinear approximation ideas and a data-driven setup to significantly broaden its reach. We show that our SOT designs provide a safe and principled extension of the Karhunen-Loeve transform (KLT) by reducing to the KLT on Gaussian processes and by automatically exploiting non-Gaussian statistics to significantly improve over the KLT on more general processes. We provide an algebraic optimization framework that generates optimized designs for any desired transform structure (multiresolution, block, lapped, and so on) with significantly better n -term approximation performance. For each structure, we propose a new prototype codec and test over a database of images. Simulation results show consistent increase in compression and approximation performance compared with conventional methods. PMID:25823033

  6. Sparse alignment for robust tensor learning.

    PubMed

    Lai, Zhihui; Wong, Wai Keung; Xu, Yong; Zhao, Cairong; Sun, Mingming

    2014-10-01

    Multilinear/tensor extensions of manifold learning based algorithms have been widely used in computer vision and pattern recognition. This paper first provides a systematic analysis of the multilinear extensions for the most popular methods by using alignment techniques, thereby obtaining a general tensor alignment framework. From this framework, it is easy to show that the manifold learning based tensor learning methods are intrinsically different from the alignment techniques. Based on the alignment framework, a robust tensor learning method called sparse tensor alignment (STA) is then proposed for unsupervised tensor feature extraction. Different from the existing tensor learning methods, L1- and L2-norms are introduced to enhance the robustness in the alignment step of the STA. The advantage of the proposed technique is that the difficulty in selecting the size of the local neighborhood can be avoided in the manifold learning based tensor feature extraction algorithms. Although STA is an unsupervised learning method, the sparsity encodes the discriminative information in the alignment step and provides the robustness of STA. Extensive experiments on the well-known image databases as well as action and hand gesture databases by encoding object images as tensors demonstrate that the proposed STA algorithm gives the most competitive performance when compared with the tensor-based unsupervised learning methods. PMID:25291733

  7. Optimal parallel solution of sparse triangular systems

    NASA Technical Reports Server (NTRS)

    Alvarado, Fernando L.; Schreiber, Robert

    1990-01-01

    A method for the parallel solution of triangular sets of equations is described that is appropriate when there are many right-handed sides. By preprocessing, the method can reduce the number of parallel steps required to solve Lx = b compared to parallel forward or backsolve. Applications are to iterative solvers with triangular preconditioners, to structural analysis, or to power systems applications, where there may be many right-handed sides (not all available a priori). The inverse of L is represented as a product of sparse triangular factors. The problem is to find a factored representation of this inverse of L with the smallest number of factors (or partitions), subject to the requirement that no new nonzero elements be created in the formation of these inverse factors. A method from an earlier reference is shown to solve this problem. This method is improved upon by constructing a permutation of the rows and columns of L that preserves triangularity and allow for the best possible such partition. A number of practical examples and algorithmic details are presented. The parallelism attainable is illustrated by means of elimination trees and clique trees.

  8. Visual Exploration of Sparse Traffic Trajectory Data.

    PubMed

    Wang, Zuchao; Ye, Tangzhi; Lu, Min; Yuan, Xiaoru; Qu, Huamin; Yuan, Jacky; Wu, Qianliang

    2014-12-01

    In this paper, we present a visual analysis system to explore sparse traffic trajectory data recorded by transportation cells. Such data contains the movements of nearly all moving vehicles on the major roads of a city. Therefore it is very suitable for macro-traffic analysis. However, the vehicle movements are recorded only when they pass through the cells. The exact tracks between two consecutive cells are unknown. To deal with such uncertainties, we first design a local animation, showing the vehicle movements only in the vicinity of cells. Besides, we ignore the micro-behaviors of individual vehicles, and focus on the macro-traffic patterns. We apply existing trajectory aggregation techniques to the dataset, studying cell status pattern and inter-cell flow pattern. Beyond that, we propose to study the correlation between these two patterns with dynamic graph visualization techniques. It allows us to check how traffic congestion on one cell is correlated with traffic flows on neighbouring links, and with route selection in its neighbourhood. Case studies show the effectiveness of our system. PMID:26356895

  9. Sparse coding for layered neural networks

    NASA Astrophysics Data System (ADS)

    Katayama, Katsuki; Sakata, Yasuo; Horiguchi, Tsuyoshi

    2002-07-01

    We investigate storage capacity of two types of fully connected layered neural networks with sparse coding when binary patterns are embedded into the networks by a Hebbian learning rule. One of them is a layered network, in which a transfer function of even layers is different from that of odd layers. The other is a layered network with intra-layer connections, in which the transfer function of inter-layer is different from that of intra-layer, and inter-layered neurons and intra-layered neurons are updated alternately. We derive recursion relations for order parameters by means of the signal-to-noise ratio method, and then apply the self-control threshold method proposed by Dominguez and Bollé to both layered networks with monotonic transfer functions. We find that a critical value αC of storage capacity is about 0.11|a ln a| -1 ( a≪1) for both layered networks, where a is a neuronal activity. It turns out that the basin of attraction is larger for both layered networks when the self-control threshold method is applied.

  10. Partitioning sparse matrices with eigenvectors of graphs

    NASA Technical Reports Server (NTRS)

    Pothen, Alex; Simon, Horst D.; Liou, Kang-Pu

    1990-01-01

    The problem of computing a small vertex separator in a graph arises in the context of computing a good ordering for the parallel factorization of sparse, symmetric matrices. An algebraic approach for computing vertex separators is considered in this paper. It is shown that lower bounds on separator sizes can be obtained in terms of the eigenvalues of the Laplacian matrix associated with a graph. The Laplacian eigenvectors of grid graphs can be computed from Kronecker products involving the eigenvectors of path graphs, and these eigenvectors can be used to compute good separators in grid graphs. A heuristic algorithm is designed to compute a vertex separator in a general graph by first computing an edge separator in the graph from an eigenvector of the Laplacian matrix, and then using a maximum matching in a subgraph to compute the vertex separator. Results on the quality of the separators computed by the spectral algorithm are presented, and these are compared with separators obtained from other algorithms for computing separators. Finally, the time required to compute the Laplacian eigenvector is reported, and the accuracy with which the eigenvector must be computed to obtain good separators is considered. The spectral algorithm has the advantage that it can be implemented on a medium-size multiprocessor in a straightforward manner.

  11. Transformer fault diagnosis using continuous sparse autoencoder.

    PubMed

    Wang, Lukun; Zhao, Xiaoying; Pei, Jiangnan; Tang, Gongyou

    2016-01-01

    This paper proposes a novel continuous sparse autoencoder (CSAE) which can be used in unsupervised feature learning. The CSAE adds Gaussian stochastic unit into activation function to extract features of nonlinear data. In this paper, CSAE is applied to solve the problem of transformer fault recognition. Firstly, based on dissolved gas analysis method, IEC three ratios are calculated by the concentrations of dissolved gases. Then IEC three ratios data is normalized to reduce data singularity and improve training speed. Secondly, deep belief network is established by two layers of CSAE and one layer of back propagation (BP) network. Thirdly, CSAE is adopted to unsupervised training and getting features. Then BP network is used for supervised training and getting transformer fault. Finally, the experimental data from IEC TC 10 dataset aims to illustrate the effectiveness of the presented approach. Comparative experiments clearly show that CSAE can extract features from the original data, and achieve a superior correct differentiation rate on transformer fault diagnosis.

  12. Index statistical properties of sparse random graphs

    NASA Astrophysics Data System (ADS)

    Metz, F. L.; Stariolo, Daniel A.

    2015-10-01

    Using the replica method, we develop an analytical approach to compute the characteristic function for the probability PN(K ,λ ) that a large N ×N adjacency matrix of sparse random graphs has K eigenvalues below a threshold λ . The method allows to determine, in principle, all moments of PN(K ,λ ) , from which the typical sample-to-sample fluctuations can be fully characterized. For random graph models with localized eigenvectors, we show that the index variance scales linearly with N ≫1 for |λ |>0 , with a model-dependent prefactor that can be exactly calculated. Explicit results are discussed for Erdös-Rényi and regular random graphs, both exhibiting a prefactor with a nonmonotonic behavior as a function of λ . These results contrast with rotationally invariant random matrices, where the index variance scales only as lnN , with an universal prefactor that is independent of λ . Numerical diagonalization results confirm the exactness of our approach and, in addition, strongly support the Gaussian nature of the index fluctuations.

  13. High-efficiency imaging through scattering media in noisy environments via sparse image reconstruction

    NASA Astrophysics Data System (ADS)

    Wu, Tengfei; Shao, Xiaopeng; Gong, Changmei; Li, Huijuan; Liu, Jietao

    2015-11-01

    High-efficiency imaging through highly scattering media is urgently desired for various applications. Imaging speed and imaging quality, which determine the imaging efficiency, are two inevitable indices for any optical imaging area. Based on random walk analysis in statistical optics, the elements in a transmission matrix (TM) actually obey Gaussian distribution. Instead of dealing with large amounts of data contained in TM and speckle pattern, imaging can be achieved with only a small number of the data via sparse representation. We make a detailed mathematical analysis of the elements-distribution of the TM of a scattering imaging system and study the imaging method of sparse image reconstruction (SIR). More specifically, we focus on analyzing the optimum sampling rates for the imaging of different structures of targets, which significantly influences both imaging speed and imaging quality. Results show that the optimum sampling rate exists in any noise-level environment if a target can be sparsely represented, and by searching for the optimum sampling rate, it can effectively balance the imaging quality and the imaging speed, which can maximize the imaging efficiency. This work is helpful for practical applications of imaging through highly scattering media with the SIR method.

  14. Reconstitution of cortical Dynein function.

    PubMed

    Roth, Sophie; Laan, Liedewij; Dogterom, Marileen

    2014-01-01

    Cytoplasmic dynein is a major microtubule (MT)-associated motor in nearly all eukaryotic cells. A subpopulation of dyneins associates with the cell cortex and the interaction of this cortical dynein with MTs helps to drive processes such as nuclear migration, mitotic spindle orientation, and cytoskeletal reorientation during wound healing. In this chapter, we describe three types of assays in which interactions between cortical dynein and MTs are reconstituted in vitro at increasing levels of complexity. In the first 1D assay, MTs, nucleated from a centrosome attached to a surface, grow against dynein-coated gold barriers. In this assay configuration, the interactions between MTs and dynein attached to a barrier can be studied in great detail. In the second and third assays, a freely moving dynamic aster is placed in either a 2D microfabricated chamber or a 3D water-in-oil emulsion droplet, with dynein-coated boundaries. These assays can be used to study how cortical dynein positions centrosomes. Finally, we discuss future possibilities for increasing the complexity of these reconstituted systems.

  15. Cortical Control of Affective Networks

    PubMed Central

    Kumar, Sunil; Black, Sherilynn J.; Hultman, Rainbo; Szabo, Steven T.; DeMaio, Kristine D.; Du, Jeanette; Katz, Brittany M.; Feng, Guoping; Covington, Herbert E.; Dzirasa, Kafui

    2013-01-01

    Transcranial magnetic stimulation and deep brain stimulation have emerged as therapeutic modalities for treatment refractory depression; however, little remains known regarding the circuitry that mediates the therapeutic effect of these approaches. Here we show that direct optogenetic stimulation of prefrontal cortex (PFC) descending projection neurons in mice engineered to express Chr2 in layer V pyramidal neurons (Thy1–Chr2 mice) models an antidepressant-like effect in mice subjected to a forced-swim test. Furthermore, we show that this PFC stimulation induces a long-lasting suppression of anxiety-like behavior (but not conditioned social avoidance) in socially stressed Thy1–Chr2 mice: an effect that is observed >10 d after the last stimulation. Finally, we use optogenetic stimulation and multicircuit recording techniques concurrently in Thy1–Chr2 mice to demonstrate that activation of cortical projection neurons entrains neural oscillatory activity and drives synchrony across limbic brain areas that regulate affect. Importantly, these neural oscillatory changes directly correlate with the temporally precise activation and suppression of limbic unit activity. Together, our findings show that the direct activation of cortical projection systems is sufficient to modulate activity across networks underlying affective regulation. They also suggest that optogenetic stimulation of cortical projection systems may serve as a viable therapeutic strategy for treating affective disorders. PMID:23325249

  16. Optimized design and analysis of sparse-sampling FMRI experiments.

    PubMed

    Perrachione, Tyler K; Ghosh, Satrajit S

    2013-01-01

    Sparse-sampling is an important methodological advance in functional magnetic resonance imaging (fMRI), in which silent delays are introduced between MR volume acquisitions, allowing for the presentation of auditory stimuli without contamination by acoustic scanner noise and for overt vocal responses without motion-induced artifacts in the functional time series. As such, the sparse-sampling technique has become a mainstay of principled fMRI research into the cognitive and systems neuroscience of speech, language, hearing, and music. Despite being in use for over a decade, there has been little systematic investigation of the acquisition parameters, experimental design considerations, and statistical analysis approaches that bear on the results and interpretation of sparse-sampling fMRI experiments. In this report, we examined how design and analysis choices related to the duration of repetition time (TR) delay (an acquisition parameter), stimulation rate (an experimental design parameter), and model basis function (an analysis parameter) act independently and interactively to affect the neural activation profiles observed in fMRI. First, we conducted a series of computational simulations to explore the parameter space of sparse design and analysis with respect to these variables; second, we validated the results of these simulations in a series of sparse-sampling fMRI experiments. Overall, these experiments suggest the employment of three methodological approaches that can, in many situations, substantially improve the detection of neurophysiological response in sparse fMRI: (1) Sparse analyses should utilize a physiologically informed model that incorporates hemodynamic response convolution to reduce model error. (2) The design of sparse fMRI experiments should maintain a high rate of stimulus presentation to maximize effect size. (3) TR delays of short to intermediate length can be used between acquisitions of sparse-sampled functional image volumes to increase

  17. Iterative solution of general sparse linear systems on clusters of workstations

    SciTech Connect

    Lo, Gen-Ching; Saad, Y.

    1996-12-31

    Solving sparse irregularly structured linear systems on parallel platforms poses several challenges. First, sparsity makes it difficult to exploit data locality, whether in a distributed or shared memory environment. A second, perhaps more serious challenge, is to find efficient ways to precondition the system. Preconditioning techniques which have a large degree of parallelism, such as multicolor SSOR, often have a slower rate of convergence than their sequential counterparts. Finally, a number of other computational kernels such as inner products could ruin any gains gained from parallel speed-ups, and this is especially true on workstation clusters where start-up times may be high. In this paper we discuss these issues and report on our experience with PSPARSLIB, an on-going project for building a library of parallel iterative sparse matrix solvers.

  18. Large Deformation Multiresolution Diffeomorphic Metric Mapping for Multiresolution Cortical Surfaces: A Coarse-to-Fine Approach.

    PubMed

    Tan, Mingzhen; Qiu, Anqi

    2016-09-01

    Brain surface registration is an important tool for characterizing cortical anatomical variations and understanding their roles in normal cortical development and psychiatric diseases. However, surface registration remains challenging due to complicated cortical anatomy and its large differences across individuals. In this paper, we propose a fast coarse-to-fine algorithm for surface registration by adapting the large diffeomorphic deformation metric mapping (LDDMM) framework for surface mapping and show improvements in speed and accuracy via a multiresolution analysis of surface meshes and the construction of multiresolution diffeomorphic transformations. The proposed method constructs a family of multiresolution meshes that are used as natural sparse priors of the cortical morphology. At varying resolutions, these meshes act as anchor points where the parameterization of multiresolution deformation vector fields can be supported, allowing the construction of a bundle of multiresolution deformation fields, each originating from a different resolution. Using a coarse-to-fine approach, we show a potential reduction in computation cost along with improvements in sulcal alignment when compared with LDDMM surface mapping. PMID:27254865

  19. Detecting a Cortical Fingerprint of Parkinson's Disease for Closed-Loop Neuromodulation

    PubMed Central

    Kern, Kevin; Naros, Georgios; Braun, Christoph; Weiss, Daniel; Gharabaghi, Alireza

    2016-01-01

    Recent evidence suggests that deep brain stimulation (DBS) of the subthalamic nucleus (STN) in Parkinson's disease (PD) mediates its clinical effects by modulating cortical oscillatory activity, presumably via a direct cortico-subthalamic connection. This observation might pave the way for novel closed-loop approaches comprising a cortical sensor. Enhanced beta oscillations (13-35 Hz) have been linked to the pathophysiology of PD and may serve as such a candidate marker to localize a cortical area reliably modulated by DBS. However, beta-oscillations are widely distributed over the cortical surface, necessitating an additional signal source for spotting the cortical area linked to the pathologically synchronized cortico-subcortical motor network. In this context, both cortico-subthalamic coherence and cortico-muscular coherence (CMC) have been studied in PD patients. Whereas, the former requires invasive recordings, the latter allows for non-invasive detection, but displays a rather distributed cortical synchronization pattern in motor tasks. This distributed cortical representation may conflict with the goal of detecting a cortical localization with robust biomarker properties which is detectable on a single subject basis. We propose that this limitation could be overcome when recording CMC at rest. We hypothesized that—unlike healthy subjects—PD would show CMC at rest owing to the enhanced beta oscillations observed in PD. By performing source space analysis of beta CMC recorded during resting-state magnetoencephalography, we provide preliminary evidence in one patient for a cortical hot spot that is modulated most strongly by subthalamic DBS. Such a spot would provide a prominent target region either for direct neuromodulation or for placing a potential sensor in closed-loop DBS approaches, a proposal that requires investigation in a larger cohort of PD patients. PMID:27065781

  20. New Asteroid Models Based on Combined Dense and Sparse Photometry

    NASA Astrophysics Data System (ADS)

    Hanuš, Josef; Durech, J.

    2010-10-01

    For thousands of asteroids we investigated several ten thousands of sparse photometric data from astrometric projects. These data are available on AstDyS server (Asteroids -- Dynamic Site, http://hamilton.dm.unipi.it). We picked 7 astrometric surveys and used their calibrated photometry in lightcurve inversion method for determination of asteroid's convex shapes and rotational states. We present nearly 100 new asteroid models derived from combined dense and sparse data sets, where sparse photometry is taken from AstDyS server and dense lightcurves are from the Uppsala Asteroid Photometric Catalogue (UAPC) and from several individual observers.

  1. Electromagnetic Formation Flight (EMFF) for Sparse Aperture Arrays

    NASA Technical Reports Server (NTRS)

    Kwon, Daniel W.; Miller, David W.; Sedwick, Raymond J.

    2004-01-01

    Traditional methods of actuating spacecraft in sparse aperture arrays use propellant as a reaction mass. For formation flying systems, propellant becomes a critical consumable which can be quickly exhausted while maintaining relative orientation. Additional problems posed by propellant include optical contamination, plume impingement, thermal emission, and vibration excitation. For these missions where control of relative degrees of freedom is important, we consider using a system of electromagnets, in concert with reaction wheels, to replace the consumables. Electromagnetic Formation Flight sparse apertures, powered by solar energy, are designed differently from traditional propulsion systems, which are based on V. This paper investigates the design of sparse apertures both inside and outside the Earth's gravity field.

  2. SPARSKIT: A basic tool kit for sparse matrix computations

    NASA Technical Reports Server (NTRS)

    Saad, Youcef

    1990-01-01

    Presented here are the main features of a tool package for manipulating and working with sparse matrices. One of the goals of the package is to provide basic tools to facilitate the exchange of software and data between researchers in sparse matrix computations. The starting point is the Harwell/Boeing collection of matrices for which the authors provide a number of tools. Among other things, the package provides programs for converting data structures, printing simple statistics on a matrix, plotting a matrix profile, and performing linear algebra operations with sparse matrices.

  3. Accelerating Dynamic Cardiac MR Imaging Using Structured Sparse Representation

    PubMed Central

    Cai, Nian; Wang, Shengru; Zhu, Shasha

    2013-01-01

    Compressed sensing (CS) has produced promising results on dynamic cardiac MR imaging by exploiting the sparsity in image series. In this paper, we propose a new method to improve the CS reconstruction for dynamic cardiac MRI based on the theory of structured sparse representation. The proposed method user the PCA subdictionaries for adaptive sparse representation and suppresses the sparse coding noise to obtain good reconstructions. An accelerated iterative shrinkage algorithm is used to solve the optimization problem and achieve a fast convergence rate. Experimental results demonstrate that the proposed method improves the reconstruction quality of dynamic cardiac cine MRI over the state-of-the-art CS method. PMID:24454528

  4. Stacked Predictive Sparse Decomposition for Classification of Histology Sections

    PubMed Central

    Zhou, Yin; Borowsky, Alexander; Barner, Kenneth; Spellman, Paul

    2016-01-01

    Image-based classification of histology sections, in terms of distinct components (e.g., tumor, stroma, normal), provides a series of indices for histology composition (e.g., the percentage of each distinct components in histology sections), and enables the study of nuclear properties within each component. Furthermore, the study of these indices, constructed from each whole slide image in a large cohort, has the potential to provide predictive models of clinical outcome. For example, correlations can be established between the constructed indices and the patients’ survival information at cohort level, which is a fundamental step towards personalized medicine. However, performance of the existing techniques is hindered as a result of large technical variations (e.g., variations of color/textures in tissue images due to non-standard experimental protocols) and biological heterogeneities (e.g., cell type, cell state) that are always present in a large cohort. We propose a system that automatically learns a series of dictionary elements for representing the underlying spatial distribution using stacked predictive sparse decomposition. The learned representation is then fed into the spatial pyramid matching framework with a linear support vector machine classifier. The system has been evaluated for classification of distinct histological components for two cohorts of tumor types. Throughput has been increased by using of graphical processing unit (GPU), and evaluation indicates a superior performance results, compared with previous research.

  5. Design and evaluation of sparse quantization index modulation watermarking schemes

    NASA Astrophysics Data System (ADS)

    Cornelis, Bruno; Barbarien, Joeri; Dooms, Ann; Munteanu, Adrian; Cornelis, Jan; Schelkens, Peter

    2008-08-01

    In the past decade the use of digital data has increased significantly. The advantages of digital data are, amongst others, easy editing, fast, cheap and cross-platform distribution and compact storage. The most crucial disadvantages are the unauthorized copying and copyright issues, by which authors and license holders can suffer considerable financial losses. Many inexpensive methods are readily available for editing digital data and, unlike analog information, the reproduction in the digital case is simple and robust. Hence, there is great interest in developing technology that helps to protect the integrity of a digital work and the copyrights of its owners. Watermarking, which is the embedding of a signal (known as the watermark) into the original digital data, is one method that has been proposed for the protection of digital media elements such as audio, video and images. In this article, we examine watermarking schemes for still images, based on selective quantization of the coefficients of a wavelet transformed image, i.e. sparse quantization-index modulation (QIM) watermarking. Different grouping schemes for the wavelet coefficients are evaluated and experimentally verified for robustness against several attacks. Wavelet tree-based grouping schemes yield a slightly improved performance over block-based grouping schemes. Additionally, the impact of the deployment of error correction codes on the most promising configurations is examined. The utilization of BCH-codes (Bose, Ray-Chaudhuri, Hocquenghem) results in an improved robustness as long as the capacity of the error codes is not exceeded (cliff-effect).

  6. A Bayesian semiparametric model for bivariate sparse longitudinal data.

    PubMed

    Das, Kiranmoy; Li, Runze; Sengupta, Subhajit; Wu, Rongling

    2013-09-30

    Mixed-effects models have recently become popular for analyzing sparse longitudinal data that arise naturally in biological, agricultural and biomedical studies. Traditional approaches assume independent residuals over time and explain the longitudinal dependence by random effects. However, when bivariate or multivariate traits are measured longitudinally, this fundamental assumption is likely to be violated because of intertrait dependence over time. We provide a more general framework where the dependence of the observations from the same subject over time is not assumed to be explained completely by the random effects of the model. We propose a novel, mixed model-based approach and estimate the error-covariance structure nonparametrically under a generalized linear model framework. We use penalized splines to model the general effect of time, and we consider a Dirichlet process mixture of normal prior for the random-effects distribution. We analyze blood pressure data from the Framingham Heart Study where body mass index, gender and time are treated as covariates. We compare our method with traditional methods including parametric modeling of the random effects and independent residual errors over time. We conduct extensive simulation studies to investigate the practical usefulness of the proposed method. The current approach is very helpful in analyzing bivariate irregular longitudinal traits. PMID:23553747

  7. Sparse Spatio-temporal Inference of Electromagnetic Brain Sources

    NASA Astrophysics Data System (ADS)

    Stahlhut, Carsten; Attias, Hagai T.; Wipf, David; Hansen, Lars K.; Nagarajan, Srikantan S.

    The electromagnetic brain activity measured via MEG (or EEG) can be interpreted as arising from a collection of current dipoles or sources located throughout the cortex. Because the number of candidate locations for these sources is much larger than the number of sensors, source reconstruction involves solving an inverse problem that is severely underdetermined. Bayesian graphical models provide a powerful means of incorporating prior assumptions that narrow the solution space and lead to tractable posterior distributions over the unknown sources given the observed data. In particular, this paper develops a hierarchical, spatio-temporal Bayesian model that accommodates the principled computation of sparse spatial and smooth temporal M/EEG source reconstructions consistent with neurophysiological assumptions in a variety of event-related imaging paradigms. The underlying methodology relies on the notion of automatic relevance determination (ARD) to express the unknown sources via a small collection of spatio-temporal basis functions. Experiments with several data sets provide evidence that the proposed model leads to improved source estimates. The underlying methodology is also well-suited for estimation problems that arise from other brain imaging modalities such as functional or diffusion weighted MRI.

  8. Sparse Sampling of Water Density Fluctuations in Interfacial Environments.

    PubMed

    Xi, Erte; Remsing, Richard C; Patel, Amish J

    2016-02-01

    The free energetics of water density fluctuations near a surface, and the rare low-density fluctuations in particular, serve as reliable indicators of surface hydrophobicity; the easier it is to displace the interfacial waters, the more hydrophobic the underlying surface is. However, characterizing the free energetics of such rare fluctuations requires computationally expensive, non-Boltzmann sampling methods like umbrella sampling. This inherent computational expense associated with umbrella sampling makes it challenging to investigate the role of polarizability or electronic structure effects in influencing interfacial fluctuations. Importantly, it also limits the size of the volume, which can be used to probe interfacial fluctuations. The latter can be particularly important in characterizing the hydrophobicity of large surfaces with molecular-level heterogeneities, such as those presented by proteins. To overcome these challenges, here we present a method for the sparse sampling of water density fluctuations, which is roughly 2 orders of magnitude more efficient than umbrella sampling. We employ thermodynamic integration to estimate the free energy differences between biased ensembles, thereby circumventing the umbrella sampling requirement of overlap between adjacent biased distributions. Further, a judicious choice of the biasing potential allows such free energy differences to be estimated using short simulations, so that the free energetics of water density fluctuations are obtained using only a few, short simulations. Leveraging the efficiency of the method, we characterize water density fluctuations in the entire hydration shell of the protein, ubiquitin, a large volume containing an average of more than 600 waters.

  9. Method and apparatus for distinguishing actual sparse events from sparse event false alarms

    DOEpatents

    Spalding, Richard E.; Grotbeck, Carter L.

    2000-01-01

    Remote sensing method and apparatus wherein sparse optical events are distinguished from false events. "Ghost" images of actual optical phenomena are generated using an optical beam splitter and optics configured to direct split beams to a single sensor or segmented sensor. True optical signals are distinguished from false signals or noise based on whether the ghost image is presence or absent. The invention obviates the need for dual sensor systems to effect a false target detection capability, thus significantly reducing system complexity and cost.

  10. Sparse aperture 3D passive image sensing and recognition

    NASA Astrophysics Data System (ADS)

    Daneshpanah, Mehdi

    The way we perceive, capture, store, communicate and visualize the world has greatly changed in the past century Novel three dimensional (3D) imaging and display systems are being pursued both in academic and industrial settings. In many cases, these systems have revolutionized traditional approaches and/or enabled new technologies in other disciplines including medical imaging and diagnostics, industrial metrology, entertainment, robotics as well as defense and security. In this dissertation, we focus on novel aspects of sparse aperture multi-view imaging systems and their application in quantum-limited object recognition in two separate parts. In the first part, two concepts are proposed. First a solution is presented that involves a generalized framework for 3D imaging using randomly distributed sparse apertures. Second, a method is suggested to extract the profile of objects in the scene through statistical properties of the reconstructed light field. In both cases, experimental results are presented that demonstrate the feasibility of the techniques. In the second part, the application of 3D imaging systems in sensing and recognition of objects is addressed. In particular, we focus on the scenario in which only 10s of photons reach the sensor from the object of interest, as opposed to hundreds of billions of photons in normal imaging conditions. At this level, the quantum limited behavior of light will dominate and traditional object recognition practices may fail. We suggest a likelihood based object recognition framework that incorporates the physics of sensing at quantum-limited conditions. Sensor dark noise has been modeled and taken into account. This framework is applied to 3D sensing of thermal objects using visible spectrum detectors. Thermal objects as cold as 250K are shown to provide enough signature photons to be sensed and recognized within background and dark noise with mature, visible band, image forming optics and detector arrays. The results

  11. Histomorphometric Assessment of Cancellous and Cortical Bone Material Distribution in the Proximal Humerus of Normal and Osteoporotic Individuals: Significantly Reduced Bone Stock in the Metaphyseal and Subcapital Regions of Osteoporotic Individuals.

    PubMed

    Sprecher, Christoph M; Schmidutz, Florian; Helfen, Tobias; Richards, R Geoff; Blauth, Michael; Milz, Stefan

    2015-12-01

    Osteoporosis is a systemic disorder predominantly affecting postmenopausal women but also men at an advanced age. Both genders may suffer from low-energy fractures of, for example, the proximal humerus when reduction of the bone stock or/and quality has occurred.The aim of the current study was to compare the amount of bone in typical fracture zones of the proximal humerus in osteoporotic and non-osteoporotic individuals.The amount of bone in the proximal humerus was determined histomorphometrically in frontal plane sections. The donor bones were allocated to normal and osteoporotic groups using the T-score from distal radius DXA measurements of the same extremities. The T-score evaluation was done according to WHO criteria. Regional thickness of the subchondral plate and the metaphyseal cortical bone were measured using interactive image analysis.At all measured locations the amount of cancellous bone was significantly lower in individuals from the osteoporotic group compared to the non-osteoporotic one. The osteoporotic group showed more significant differences between regions of the same bone than the non-osteoporotic group. In both groups the subchondral cancellous bone and the subchondral plate were least affected by bone loss. In contrast, the medial metaphyseal region in the osteoporotic group exhibited higher bone loss in comparison to the lateral side.This observation may explain prevailing fracture patterns, which frequently involve compression fractures and certainly has an influence on the stability of implants placed in this medial region. It should be considered when planning the anchoring of osteosynthesis materials in osteoporotic patients with fractures of the proximal humerus.

  12. Cortical network architecture for context processing in primate brain

    PubMed Central

    Chao, Zenas C; Nagasaka, Yasuo; Fujii, Naotaka

    2015-01-01

    Context is information linked to a situation that can guide behavior. In the brain, context is encoded by sensory processing and can later be retrieved from memory. How context is communicated within the cortical network in sensory and mnemonic forms is unknown due to the lack of methods for high-resolution, brain-wide neuronal recording and analysis. Here, we report the comprehensive architecture of a cortical network for context processing. Using hemisphere-wide, high-density electrocorticography, we measured large-scale neuronal activity from monkeys observing videos of agents interacting in situations with different contexts. We extracted five context-related network structures including a bottom-up network during encoding and, seconds later, cue-dependent retrieval of the same network with the opposite top-down connectivity. These findings show that context is represented in the cortical network as distributed communication structures with dynamic information flows. This study provides a general methodology for recording and analyzing cortical network neuronal communication during cognition. DOI: http://dx.doi.org/10.7554/eLife.06121.001 PMID:26416139

  13. Functional Doppler optical coherence tomography for cortical blood flow imaging

    NASA Astrophysics Data System (ADS)

    Yu, Lingfeng; Liu, Gangjun; Nguyen, Elaine; Choi, Bernard; Chen, Zhongping

    2010-02-01

    Optical methods have been widely used in basic neuroscience research to study the cerebral blood flow dynamics in order to overcome the low spatial resolution associated with magnetic resonance imaging and positron emission tomography. Although laser Doppler imaging and laser speckle imaging can map out en face cortical hemodynamics and columns, depth resolution is not available. Two-photon microscopy has been used for mapping cortical activity. However, flow measurement requires fluorescent dye injection, which can be problematic. The noninvasive and high resolution tomographic capabilities of optical coherence tomography make it a promising technique for mapping depth resolved cortical blood flow. Here, we present a functional Doppler optical coherence tomography (OCT) imaging modality for quantitative evaluation of cortical blood flow in a mouse model. Fast, repeated, Doppler OCT scans across a vessel of interest were performed to record flow dynamic information with a high temporal resolution of the cardiac cycles. Spectral Doppler analysis of continuous Doppler images demonstrates how the velocity components and longitudinally projected flow-volume-rate change over time, thereby providing complementary temporal flow information to the spatially distributed flow information of Doppler OCT. The proposed functional Doppler OCT imaging modality can be used to diagnose vessel stenosis/blockage or monitor blood flow changes due to pharmacological agents/neuronal activities. Non-invasive in-vivo mice experiments were performed to verify the capabilities of function Doppler OCT.

  14. Finding One Community in a Sparse Graph

    NASA Astrophysics Data System (ADS)

    Montanari, Andrea

    2015-10-01

    We consider a random sparse graph with bounded average degree, in which a subset of vertices has higher connectivity than the background. In particular, the average degree inside this subset of vertices is larger than outside (but still bounded). Given a realization of such graph, we aim at identifying the hidden subset of vertices. This can be regarded as a model for the problem of finding a tightly knitted community in a social network, or a cluster in a relational dataset. In this paper we present two sets of contributions: ( i) We use the cavity method from spin glass theory to derive an exact phase diagram for the reconstruction problem. In particular, as the difference in edge probability increases, the problem undergoes two phase transitions, a static phase transition and a dynamic one. ( ii) We establish rigorous bounds on the dynamic phase transition and prove that, above a certain threshold, a local algorithm (belief propagation) correctly identify most of the hidden set. Below the same threshold no local algorithm can achieve this goal. However, in this regime the subset can be identified by exhaustive search. For small hidden sets and large average degree, the phase transition for local algorithms takes an intriguingly simple form. Local algorithms succeed with high probability for deg _in - deg _out > √{deg _out/e} and fail for deg _in - deg _out < √{deg _out/e} (with deg _in, deg _out the average degrees inside and outside the community). We argue that spectral algorithms are also ineffective in the latter regime. It is an open problem whether any polynomial time algorithms might succeed for deg _in - deg _out < √{deg _out/e}.

  15. Transplantation of tectal tissue in rats. I. Organization of transplants and pattern of distribution of host afferents within them

    SciTech Connect

    Lund, R.D.; Harvey, A.R.

    1981-01-01

    We have examined the maturation of tectal tissue transplanted from fetal rats to the midbrain of newborns and have characterized the distribution of host retinal and cortical afferents within the transplants. The transplants develop characteristic internal order and connections which distinguish them from either embryonic cortex or retina placed in the same region. Host retinal afferents project to clearly circumscribed regions, where they synapse mainly on small dendrites or dendritic spines, and only rarely on vesicle-containing profiles. The retinorecipient areas contain few stained axons in neurofibrillar preparations and are almost always located at the surface of the transplant. There is very little overlap in the input from the two eyes into a single transplant even though the projections from each eye may lie adjacent to one another. Cortical afferents spread more broadly in the transplants, but are largely absent from areas of optic termination and from other more deeply located regions with sparse fiber staining properties. The observations suggest that when placed close to its normal location, tectal tissue can develop a number of features characteristic of normal superior colliculus. Appreciation of the internal order of the transplants makes it possible to investigate the cortical and retinal afferent pathways using physiological techniques.

  16. Multiple kernel learning for sparse representation-based classification.

    PubMed

    Shrivastava, Ashish; Patel, Vishal M; Chellappa, Rama

    2014-07-01

    In this paper, we propose a multiple kernel learning (MKL) algorithm that is based on the sparse representation-based classification (SRC) method. Taking advantage of the nonlinear kernel SRC in efficiently representing the nonlinearities in the high-dimensional feature space, we propose an MKL method based on the kernel alignment criteria. Our method uses a two step training method to learn the kernel weights and sparse codes. At each iteration, the sparse codes are updated first while fixing the kernel mixing coefficients, and then the kernel mixing coefficients are updated while fixing the sparse codes. These two steps are repeated until a stopping criteria is met. The effectiveness of the proposed method is demonstrated using several publicly available image classification databases and it is shown that this method can perform significantly better than many competitive image classification algorithms. PMID:24835226

  17. Ensemble polarimetric SAR image classification based on contextual sparse representation

    NASA Astrophysics Data System (ADS)

    Zhang, Lamei; Wang, Xiao; Zou, Bin; Qiao, Zhijun

    2016-05-01

    Polarimetric SAR image interpretation has become one of the most interesting topics, in which the construction of the reasonable and effective technique of image classification is of key importance. Sparse representation represents the data using the most succinct sparse atoms of the over-complete dictionary and the advantages of sparse representation also have been confirmed in the field of PolSAR classification. However, it is not perfect, like the ordinary classifier, at different aspects. So ensemble learning is introduced to improve the issue, which makes a plurality of different learners training and obtained the integrated results by combining the individual learner to get more accurate and ideal learning results. Therefore, this paper presents a polarimetric SAR image classification method based on the ensemble learning of sparse representation to achieve the optimal classification.

  18. STIS Sparse Field CTE test-internal {Cycle 12}

    NASA Astrophysics Data System (ADS)

    Goudfrooij, Paul

    2003-07-01

    CTE measurements are made using the "internal sparse field test", along the parallel axis. The "POS=" optional parameter, introduced during cycle 11, is used to provide off-center MSM positionings of some slits. All exposures are internals.

  19. STIS Sparse Field CTE test-internal {Cycle 11}

    NASA Astrophysics Data System (ADS)

    Goudfrooij, Paul

    2002-07-01

    CTE measurements are made using the "internal sparse field test", along the parallel axis. The new "POS=" optional parameter is used to provide off-center MSM positionings of some slits. All exposures are internals.

  20. Sparse source approaches to radio tomography of asteroid

    NASA Astrophysics Data System (ADS)

    Pursiainen, Sampsa

    Currently, there is a growing interest towards non-invasive imaging of asteroids to support future planetary research and extra-terrestrial mining activities. This presentation concentrates on our recent developments regarding radio tomography in which the signal velocity (refractive index) distribution inside an asteroid is to be recovered from radio frequency data gathered by an orbiter. The tomography approach in question is closely related to that of the CONSERT experiment aiming at recovery of a comet nucleus structure as a part of the ROSETTA mission. The focus will be on a sparse distribution of signal sources that can be necessary in the challenging in situ environment and within tight payload limits. The general goal in our recent research has been to approximate the minimal number of source positions needed for robust localization of anomalies caused, for example, by an internal void. Characteristic to the localization problem are the large relative changes in signal speed caused by the high refractive index of typical asteroid minerals (e.g. basalt), meaning that a signal path can include strong refractions and reflections. The inversion strategy applied combines a hierarchical Bayesian inverse model and the iterative alternating sequential (IAS) posterior exploration algorithm. Methods relying on ray tracing and finite-difference time-domain (FDTD) forward simulation have been utilized in forward (data) simulation. Both simulated and real experimental data have been utilized. Special interest has been paid to robustness of the inverse results regarding changes of the prior model and source positioning. The results have been encouraging: strongly refractive anomalies can be detected already with two sources independently of their positioning, and the robustness has been observed to increase rapidly along with the number of sources.

  1. Testing of Error-Correcting Sparse Permutation Channel Codes

    NASA Technical Reports Server (NTRS)

    Shcheglov, Kirill, V.; Orlov, Sergei S.

    2008-01-01

    A computer program performs Monte Carlo direct numerical simulations for testing sparse permutation channel codes, which offer strong error-correction capabilities at high code rates and are considered especially suitable for storage of digital data in holographic and volume memories. A word in a code of this type is characterized by, among other things, a sparseness parameter (M) and a fixed number (K) of 1 or "on" bits in a channel block length of N.

  2. Out-of-Core Solutions of Complex Sparse Linear Equations

    NASA Technical Reports Server (NTRS)

    Yip, E. L.

    1982-01-01

    ETCLIB is library of subroutines for obtaining out-of-core solutions of complex sparse linear equations. Routines apply to dense and sparse matrices too large to be stored in core. Useful for solving any set of linear equations, but particularly useful in cases where coefficient matrix has no special properties that guarantee convergence with any of interative processes. The only assumption made is that coefficient matrix is not singular.

  3. The cortical structure of consolidated memory: a hypothesis on the role of the cingulate-entorhinal cortical connection.

    PubMed

    Insel, Nathan; Takehara-Nishiuchi, Kaori

    2013-11-01

    Daily experiences are represented by networks of neurons distributed across the neocortex, bound together for rapid storage and later retrieval by the hippocampus. While the hippocampus is necessary for retrieving recent episode-based memory associations, over time, consolidation processes take place that enable many of these associations to be expressed independent of the hippocampus. It is generally thought that mechanisms of consolidation involve synaptic weight changes between cortical regions; or, in other words, the formation of "horizontal" cortico-cortical connections. Here, we review anatomical, behavioral, and physiological data which suggest that the connections in and between the entorhinal and cingulate cortices may be uniquely important for the long-term storage of memories that initially depend on the hippocampus. We propose that current theories of consolidation that divide memory into dual systems of hippocampus and neocortex might be improved by introducing a third, middle layer of entorhinal and cingulate allocortex, the synaptic weights within which are necessary and potentially sufficient for maintaining initially hippocampus-dependent associations over long time periods. This hypothesis makes a number of still untested predictions, and future experiments designed to address these will help to fill gaps in the current understanding of the cortical structure of consolidated memory.

  4. Cortical microtubule rearrangements and cell wall patterning

    PubMed Central

    Oda, Yoshihisa

    2015-01-01

    Plant cortical microtubules, which form a highly ordered array beneath the plasma membrane, play essential roles in determining cell shape and function by directing the arrangement of cellulosic and non-cellulosic compounds on the cell surface. Interphase transverse arrays of cortical microtubules self-organize through their dynamic instability and inter-microtubule interactions, and by branch-form microtubule nucleation and severing. Recent studies revealed that distinct spatial signals including ROP GTPase, cellular geometry, and mechanical stress regulate the behavior of cortical microtubules at the subcellular and supercellular levels, giving rise to dramatic rearrangements in the cortical microtubule array in response to internal and external cues. Increasing evidence indicates that negative regulators of microtubules also contribute to the rearrangement of the cortical microtubule array. In this review, I summarize recent insights into how the rearrangement of the cortical microtubule array leads to proper, flexible cell wall patterning. PMID:25904930

  5. Circadian regulation of human cortical excitability

    PubMed Central

    Ly, Julien Q. M.; Gaggioni, Giulia; Chellappa, Sarah L.; Papachilleos, Soterios; Brzozowski, Alexandre; Borsu, Chloé; Rosanova, Mario; Sarasso, Simone; Middleton, Benita; Luxen, André; Archer, Simon N.; Phillips, Christophe; Dijk, Derk-Jan; Maquet, Pierre; Massimini, Marcello; Vandewalle, Gilles

    2016-01-01

    Prolonged wakefulness alters cortical excitability, which is essential for proper brain function and cognition. However, besides prior wakefulness, brain function and cognition are also affected by circadian rhythmicity. Whether the regulation of cognition involves a circadian impact on cortical excitability is unknown. Here, we assessed cortical excitability from scalp electroencephalography (EEG) responses to transcranial magnetic stimulation in 22 participants during 29 h of wakefulness under constant conditions. Data reveal robust circadian dynamics of cortical excitability that are strongest in those individuals with highest endocrine markers of circadian amplitude. In addition, the time course of cortical excitability correlates with changes in EEG synchronization and cognitive performance. These results demonstrate that the crucial factor for cortical excitability, and basic brain function in general, is the balance between circadian rhythmicity and sleep need, rather than sleep homoeostasis alone. These findings have implications for clinical applications such as non-invasive brain stimulation in neurorehabilitation. PMID:27339884

  6. Inhibitory Circuits in Cortical Layer 5

    PubMed Central

    Naka, Alexander; Adesnik, Hillel

    2016-01-01

    Inhibitory neurons play a fundamental role in cortical computation and behavior. Recent technological advances, such as two photon imaging, targeted in vivo recording, and molecular profiling, have improved our understanding of the function and diversity of cortical interneurons, but for technical reasons most work has been directed towards inhibitory neurons in the superficial cortical layers. Here we review current knowledge specifically on layer 5 (L5) inhibitory microcircuits, which play a critical role in controlling cortical output. We focus on recent work from the well-studied rodent barrel cortex, but also draw on evidence from studies in primary visual cortex and other cortical areas. The diversity of both deep inhibitory neurons and their pyramidal cell targets make this a challenging but essential area of study in cortical computation and sensory processing. PMID:27199675

  7. Hamilton-Jacobi skeleton on cortical surfaces.

    PubMed

    Shi, Y; Thompson, P M; Dinov, I; Toga, A W

    2008-05-01

    In this paper, we propose a new method to construct graphical representations of cortical folding patterns by computing skeletons on triangulated cortical surfaces. In our approach, a cortical surface is first partitioned into sulcal and gyral regions via the solution of a variational problem using graph cuts, which can guarantee global optimality. After that, we extend the method of Hamilton-Jacobi skeleton [1] to subsets of triangulated surfaces, together with a geometrically intuitive pruning process that can trade off between skeleton complexity and the completeness of representing folding patterns. Compared with previous work that uses skeletons of 3-D volumes to represent sulcal patterns, the skeletons on cortical surfaces can be easily decomposed into branches and provide a simpler way to construct graphical representations of cortical morphometry. In our experiments, we demonstrate our method on two different cortical surface models, its ability of capturing major sulcal patterns and its application to compute skeletons of gyral regions. PMID:18450539

  8. Circadian regulation of human cortical excitability.

    PubMed

    Ly, Julien Q M; Gaggioni, Giulia; Chellappa, Sarah L; Papachilleos, Soterios; Brzozowski, Alexandre; Borsu, Chloé; Rosanova, Mario; Sarasso, Simone; Middleton, Benita; Luxen, André; Archer, Simon N; Phillips, Christophe; Dijk, Derk-Jan; Maquet, Pierre; Massimini, Marcello; Vandewalle, Gilles

    2016-06-24

    Prolonged wakefulness alters cortical excitability, which is essential for proper brain function and cognition. However, besides prior wakefulness, brain function and cognition are also affected by circadian rhythmicity. Whether the regulation of cognition involves a circadian impact on cortical excitability is unknown. Here, we assessed cortical excitability from scalp electroencephalography (EEG) responses to transcranial magnetic stimulation in 22 participants during 29 h of wakefulness under constant conditions. Data reveal robust circadian dynamics of cortical excitability that are strongest in those individuals with highest endocrine markers of circadian amplitude. In addition, the time course of cortical excitability correlates with changes in EEG synchronization and cognitive performance. These results demonstrate that the crucial factor for cortical excitability, and basic brain function in general, is the balance between circadian rhythmicity and sleep need, rather than sleep homoeostasis alone. These findings have implications for clinical applications such as non-invasive brain stimulation in neurorehabilitation.

  9. Saliency Detection Using Sparse and Nonlinear Feature Representation

    PubMed Central

    Zhao, Qingjie; Manzoor, Muhammad Farhan; Ishaq Khan, Saqib

    2014-01-01

    An important aspect of visual saliency detection is how features that form an input image are represented. A popular theory supports sparse feature representation, an image being represented with a basis dictionary having sparse weighting coefficient. Another method uses a nonlinear combination of image features for representation. In our work, we combine the two methods and propose a scheme that takes advantage of both sparse and nonlinear feature representation. To this end, we use independent component analysis (ICA) and covariant matrices, respectively. To compute saliency, we use a biologically plausible center surround difference (CSD) mechanism. Our sparse features are adaptive in nature; the ICA basis function are learnt at every image representation, rather than being fixed. We show that Adaptive Sparse Features when used with a CSD mechanism yield better results compared to fixed sparse representations. We also show that covariant matrices consisting of nonlinear integration of color information alone are sufficient to efficiently estimate saliency from an image. The proposed dual representation scheme is then evaluated against human eye fixation prediction, response to psychological patterns, and salient object detection on well-known datasets. We conclude that having two forms of representation compliments one another and results in better saliency detection. PMID:24895644

  10. Vector sparse representation of color image using quaternion matrix analysis.

    PubMed

    Xu, Yi; Yu, Licheng; Xu, Hongteng; Zhang, Hao; Nguyen, Truong

    2015-04-01

    Traditional sparse image models treat color image pixel as a scalar, which represents color channels separately or concatenate color channels as a monochrome image. In this paper, we propose a vector sparse representation model for color images using quaternion matrix analysis. As a new tool for color image representation, its potential applications in several image-processing tasks are presented, including color image reconstruction, denoising, inpainting, and super-resolution. The proposed model represents the color image as a quaternion matrix, where a quaternion-based dictionary learning algorithm is presented using the K-quaternion singular value decomposition (QSVD) (generalized K-means clustering for QSVD) method. It conducts the sparse basis selection in quaternion space, which uniformly transforms the channel images to an orthogonal color space. In this new color space, it is significant that the inherent color structures can be completely preserved during vector reconstruction. Moreover, the proposed sparse model is more efficient comparing with the current sparse models for image restoration tasks due to lower redundancy between the atoms of different color channels. The experimental results demonstrate that the proposed sparse image model avoids the hue bias issue successfully and shows its potential as a general and powerful tool in color image analysis and processing domain. PMID:25643407

  11. Visual tracking based on extreme learning machine and sparse representation.

    PubMed

    Wang, Baoxian; Tang, Linbo; Yang, Jinglin; Zhao, Baojun; Wang, Shuigen

    2015-01-01

    The existing sparse representation-based visual trackers mostly suffer from both being time consuming and having poor robustness problems. To address these issues, a novel tracking method is presented via combining sparse representation and an emerging learning technique, namely extreme learning machine (ELM). Specifically, visual tracking can be divided into two consecutive processes. Firstly, ELM is utilized to find the optimal separate hyperplane between the target observations and background ones. Thus, the trained ELM classification function is able to remove most of the candidate samples related to background contents efficiently, thereby reducing the total computational cost of the following sparse representation. Secondly, to further combine ELM and sparse representation, the resultant confidence values (i.e., probabilities to be a target) of samples on the ELM classification function are used to construct a new manifold learning constraint term of the sparse representation framework, which tends to achieve robuster results. Moreover, the accelerated proximal gradient method is used for deriving the optimal solution (in matrix form) of the constrained sparse tracking model. Additionally, the matrix form solution allows the candidate samples to be calculated in parallel, thereby leading to a higher efficiency. Experiments demonstrate the effectiveness of the proposed tracker. PMID:26506359

  12. Visual Tracking Based on Extreme Learning Machine and Sparse Representation

    PubMed Central

    Wang, Baoxian; Tang, Linbo; Yang, Jinglin; Zhao, Baojun; Wang, Shuigen

    2015-01-01

    The existing sparse representation-based visual trackers mostly suffer from both being time consuming and having poor robustness problems. To address these issues, a novel tracking method is presented via combining sparse representation and an emerging learning technique, namely extreme learning machine (ELM). Specifically, visual tracking can be divided into two consecutive processes. Firstly, ELM is utilized to find the optimal separate hyperplane between the target observations and background ones. Thus, the trained ELM classification function is able to remove most of the candidate samples related to background contents efficiently, thereby reducing the total computational cost of the following sparse representation. Secondly, to further combine ELM and sparse representation, the resultant confidence values (i.e., probabilities to be a target) of samples on the ELM classification function are used to construct a new manifold learning constraint term of the sparse representation framework, which tends to achieve robuster results. Moreover, the accelerated proximal gradient method is used for deriving the optimal solution (in matrix form) of the constrained sparse tracking model. Additionally, the matrix form solution allows the candidate samples to be calculated in parallel, thereby leading to a higher efficiency. Experiments demonstrate the effectiveness of the proposed tracker. PMID:26506359

  13. Automatic target recognition using group-structured sparse representation

    NASA Astrophysics Data System (ADS)

    Sun, Bo; Wu, Xuewen; He, Jun; Zhu, Xiaoming; Chen, Chao

    2014-06-01

    Sparse representation classification method has been increasingly used in the fields of computer vision and pattern analysis, due to its high recognition rate, little dependence on the features, robustness to corruption and occlusion, and etc. However, most of these existing methods aim to find the sparsest representations of the test sample y in an overcomplete dictionary, which do not particularly consider the relevant structure between the atoms in the dictionary. Moreover, sufficient training samples are always required by the sparse representation method for effective recognition. In this paper we formulate the classification as a group-structured sparse representation problem using a sparsity-inducing norm minimization optimization and propose a novel sparse representation-based automatic target recognition (ATR) framework for the practical applications in which the training samples are drawn from the simulation models of real targets. The experimental results show that the proposed approach improves the recognition rate of standard sparse models, and our system can effectively and efficiently recognize targets under real environments, especially, where the good characteristics of the sparse representation based classification method are kept.

  14. A Rare Hydrocephalus Complication: Cortical Blindness.

    PubMed

    Ünal, Emre; Göçmen, Rahşan; Işıkay, Ayşe İlksen; Tekşam, Özlem

    2015-01-01

    Cortical blindness related to bilateral occipital lobe infarction is an extremely rare complication of hydrocephalus. Compression of the posterior cerebral artery, secondary to tentorial herniation, is the cause of occipital infarction. Particularly in children and mentally ill patients, cortical blindness may be missed. Therefore, early diagnosis and treatment of hydrocephalus is important. We present herein a child of ventricular shunt malfunction complicated by cortical blindness. PMID:27411424

  15. Communication and wiring in the cortical connectome

    PubMed Central

    Budd, Julian M. L.; Kisvárday, Zoltán F.

    2012-01-01

    In cerebral cortex, the huge mass of axonal wiring that carries information between near and distant neurons is thought to provide the neural substrate for cognitive and perceptual function. The goal of mapping the connectivity of cortical axons at different spatial scales, the cortical connectome, is to trace the paths of information flow in cerebral cortex. To appreciate the relationship between the connectome and cortical function, we need to discover the nature and purpose of the wiring principles underlying cortical connectivity. A popular explanation has been that axonal length is strictly minimized both within and between cortical regions. In contrast, we have hypothesized the existence of a multi-scale principle of cortical wiring where to optimize communication there is a trade-off between spatial (construction) and temporal (routing) costs. Here, using recent evidence concerning cortical spatial networks we critically evaluate this hypothesis at neuron, local circuit, and pathway scales. We report three main conclusions. First, the axonal and dendritic arbor morphology of single neocortical neurons may be governed by a similar wiring principle, one that balances the conservation of cellular material and conduction delay. Second, the same principle may be observed for fiber tracts connecting cortical regions. Third, the absence of sufficient local circuit data currently prohibits any meaningful assessment of the hypothesis at this scale of cortical organization. To avoid neglecting neuron and microcircuit levels of cortical organization, the connectome framework should incorporate more morphological description. In addition, structural analyses of temporal cost for cortical circuits should take account of both axonal conduction and neuronal integration delays, which appear mostly of the same order of magnitude. We conclude the hypothesized trade-off between spatial and temporal costs may potentially offer a powerful explanation for cortical wiring patterns

  16. Cortical Tremor (CT) with coincident orthostatic movements.

    PubMed

    Termsarasab, Pichet; Frucht, Steven J

    2015-01-01

    Cortical tremor (CT) is a form of cortical reflex myoclonus that can mimic essential tremor (ET). Clinical features that are helpful in distinguishing CT from ET are the irregular and jerky appearance of the movements. We report two patients with CT with coexisting orthostatic movements, either orthostatic tremor (OT) or myoclonus, who experienced functional improvement in both cortical myoclonus and orthostatic movements when treated with levetiracetam. PMID:26788343

  17. A Rare Hydrocephalus Complication: Cortical Blindness.

    PubMed

    Ünal, Emre; Göçmen, Rahşan; Işıkay, Ayşe İlksen; Tekşam, Özlem

    2015-01-01

    Cortical blindness related to bilateral occipital lobe infarction is an extremely rare complication of hydrocephalus. Compression of the posterior cerebral artery, secondary to tentorial herniation, is the cause of occipital infarction. Particularly in children and mentally ill patients, cortical blindness may be missed. Therefore, early diagnosis and treatment of hydrocephalus is important. We present herein a child of ventricular shunt malfunction complicated by cortical blindness.

  18. Associations between cortical thickness and general intelligence in children, adolescents and young adults

    PubMed Central

    Menary, Kyle; Collins, Paul F.; Porter, James N.; Muetzel, Ryan; Olson, Elizabeth A.; Kumar, Vipin; Steinbach, Michael; Lim, Kelvin O.; Luciana, Monica

    2013-01-01

    Neuroimaging research indicates that human intellectual ability is related to brain structure including the thickness of the cerebral cortex. Most studies indicate that general intelligence is positively associated with cortical thickness in areas of association cortex distributed throughout both brain hemispheres. In this study, we performed a cortical thickness mapping analysis on data from 182 healthy typically developing males and females ages 9 to 24 years to identify correlates of general intelligence (g) scores. To determine if these correlates also mediate associations of specific cognitive abilities with cortical thickness, we regressed specific cognitive test scores on g scores and analyzed the residuals with respect to cortical thickness. The effect of age on the association between cortical thickness and intelligence was examined. We found a widely distributed pattern of positive associations between cortical thickness and g scores, as derived from the first unrotated principal factor of a factor analysis of Wechsler Abbreviated Scale of Intelligence (WASI) subtest scores. After WASI specific cognitive subtest scores were regressed on g factor scores, the residual score variances did not correlate significantly with cortical thickness in the full sample with age covaried. When participants were grouped at the age median, significant positive associations of cortical thickness were obtained in the older group for g-residualized scores on Block Design (a measure of visual-motor integrative processing) while significant negative associations of cortical thickness were observed in the younger group for g-residualized Vocabulary scores. These results regarding correlates of general intelligence are concordant with the existing literature, while the findings from younger versus older subgroups have implications for future research on brain structural correlates of specific cognitive abilities, as well as the cognitive domain specificity of behavioral

  19. Cortical auditory disorders: clinical and psychoacoustic features.

    PubMed Central

    Mendez, M F; Geehan, G R

    1988-01-01

    The symptoms of two patients with bilateral cortical auditory lesions evolved from cortical deafness to other auditory syndromes: generalised auditory agnosia, amusia and/or pure word deafness, and a residual impairment of temporal sequencing. On investigation, both had dysacusis, absent middle latency evoked responses, acoustic errors in sound recognition and matching, inconsistent auditory behaviours, and similarly disturbed psychoacoustic discrimination tasks. These findings indicate that the different clinical syndromes caused by cortical auditory lesions form a spectrum of related auditory processing disorders. Differences between syndromes may depend on the degree of involvement of a primary cortical processing system, the more diffuse accessory system, and possibly the efferent auditory system. Images PMID:2450968

  20. Imaging through turbid media via sparse representation: imaging quality comparison of three projection matrices

    NASA Astrophysics Data System (ADS)

    Shao, Xiaopeng; Li, Huijuan; Wu, Tengfei; Dai, Weijia; Bi, Xiangli

    2015-05-01

    The incident light will be scattered away due to the inhomogeneity of the refractive index in many materials which will greatly reduce the imaging depth and degrade the imaging quality. Many exciting methods have been presented in recent years for solving this problem and realizing imaging through a highly scattering medium, such as the wavefront modulation technique and reconstruction technique. The imaging method based on compressed sensing (CS) theory can decrease the computational complexity because it doesn't require the whole speckle pattern to realize reconstruction. One of the key premises of this method is that the object is sparse or can be sparse representation. However, choosing a proper projection matrix is very important to the imaging quality. In this paper, we analyzed that the transmission matrix (TM) of a scattering medium obeys circular Gaussian distribution, which makes it possible that a scattering medium can be used as the measurement matrix in the CS theory. In order to verify the performance of this method, a whole optical system is simulated. Various projection matrices are introduced to make the object sparse, including the fast Fourier transform (FFT) basis, the discrete cosine transform (DCT) basis and the discrete wavelet transform (DWT) basis, the imaging performances of each of which are compared comprehensively. Simulation results show that for most targets, applying the discrete wavelet transform basis will obtain an image in good quality. This work can be applied to biomedical imaging and used to develop real-time imaging through highly scattering media.

  1. Blind spectral unmixing based on sparse component analysis for hyperspectral remote sensing imagery

    NASA Astrophysics Data System (ADS)

    Zhong, Yanfei; Wang, Xinyu; Zhao, Lin; Feng, Ruyi; Zhang, Liangpei; Xu, Yanyan

    2016-09-01

    Recently, many blind source separation (BSS)-based techniques have been applied to hyperspectral unmixing. In this paper, a new blind spectral unmixing method based on sparse component analysis (BSUSCA) is proposed to solve the problem of highly mixed data. The BSUSCA algorithm consists of an alternative scheme based on two-block alternating optimization, by which we can simultaneously obtain the endmember signatures and their corresponding fractional abundances. According to the spatial distribution of the endmembers, the sparse properties of the fractional abundances are considered in the proposed algorithm. A sparse component analysis (SCA)-based mixing matrix estimation method is applied to update the endmember signatures, and the abundance estimation problem is solved by the alternating direction method of multipliers (ADMM). SCA is utilized for the unmixing due to its various advantages, including the unique solution and robust modeling assumption. The robustness of the proposed algorithm is verified through simulated experimental study. The experimental results using both simulated data and real hyperspectral remote sensing images confirm the high efficiency and precision of the proposed algorithm.

  2. MAP Support Detection for Greedy Sparse Signal Recovery Algorithms in Compressive Sensing

    NASA Astrophysics Data System (ADS)

    Lee, Namyoon

    2016-10-01

    A reliable support detection is essential for a greedy algorithm to reconstruct a sparse signal accurately from compressed and noisy measurements. This paper proposes a novel support detection method for greedy algorithms, which is referred to as "\\textit{maximum a posteriori (MAP) support detection}". Unlike existing support detection methods that identify support indices with the largest correlation value in magnitude per iteration, the proposed method selects them with the largest likelihood ratios computed under the true and null support hypotheses by simultaneously exploiting the distributions of sensing matrix, sparse signal, and noise. Leveraging this technique, MAP-Matching Pursuit (MAP-MP) is first presented to show the advantages of exploiting the proposed support detection method, and a sufficient condition for perfect signal recovery is derived for the case when the sparse signal is binary. Subsequently, a set of iterative greedy algorithms, called MAP-generalized Orthogonal Matching Pursuit (MAP-gOMP), MAP-Compressive Sampling Matching Pursuit (MAP-CoSaMP), and MAP-Subspace Pursuit (MAP-SP) are presented to demonstrate the applicability of the proposed support detection method to existing greedy algorithms. From empirical results, it is shown that the proposed greedy algorithms with highly reliable support detection can be better, faster, and easier to implement than basis pursuit via linear programming.

  3. Cortical Specializations Underlying Fast Computations

    PubMed Central

    Volgushev, Maxim

    2016-01-01

    The time course of behaviorally relevant environmental events sets temporal constraints on neuronal processing. How does the mammalian brain make use of the increasingly complex networks of the neocortex, while making decisions and executing behavioral reactions within a reasonable time? The key parameter determining the speed of computations in neuronal networks is a time interval that neuronal ensembles need to process changes at their input and communicate results of this processing to downstream neurons. Theoretical analysis identified basic requirements for fast processing: use of neuronal populations for encoding, background activity, and fast onset dynamics of action potentials in neurons. Experimental evidence shows that populations of neocortical neurons fulfil these requirements. Indeed, they can change firing rate in response to input perturbations very quickly, within 1 to 3 ms, and encode high-frequency components of the input by phase-locking their spiking to frequencies up to 300 to 1000 Hz. This implies that time unit of computations by cortical ensembles is only few, 1 to 3 ms, which is considerably faster than the membrane time constant of individual neurons. The ability of cortical neuronal ensembles to communicate on a millisecond time scale allows for complex, multiple-step processing and precise coordination of neuronal activity in parallel processing streams, while keeping the speed of behavioral reactions within environmentally set temporal constraints. PMID:25689988

  4. Gyrification from constrained cortical expansion

    PubMed Central

    Tallinen, Tuomas; Chung, Jun Young; Biggins, John S.; Mahadevan, L.

    2014-01-01

    The exterior of the mammalian brain—the cerebral cortex—has a conserved layered structure whose thickness varies little across species. However, selection pressures over evolutionary time scales have led to cortices that have a large surface area to volume ratio in some organisms, with the result that the brain is strongly convoluted into sulci and gyri. Here we show that the gyrification can arise as a nonlinear consequence of a simple mechanical instability driven by tangential expansion of the gray matter constrained by the white matter. A physical mimic of the process using a layered swelling gel captures the essence of the mechanism, and numerical simulations of the brain treated as a soft solid lead to the formation of cusped sulci and smooth gyri similar to those in the brain. The resulting gyrification patterns are a function of relative cortical expansion and relative thickness (compared with brain size), and are consistent with observations of a wide range of brains, ranging from smooth to highly convoluted. Furthermore, this dependence on two simple geometric parameters that characterize the brain also allows us to qualitatively explain how variations in these parameters lead to anatomical anomalies in such situations as polymicrogyria, pachygyria, and lissencephalia. PMID:25136099

  5. Sleep and olfactory cortical plasticity

    PubMed Central

    Barnes, Dylan C.; Wilson, Donald A.

    2014-01-01

    In many systems, sleep plays a vital role in memory consolidation and synaptic homeostasis. These processes together help store information of biological significance and reset synaptic circuits to facilitate acquisition of information in the future. In this review, we describe recent evidence of sleep-dependent changes in olfactory system structure and function which contribute to odor memory and perception. During slow-wave sleep, the piriform cortex becomes hypo-responsive to odor stimulation and instead displays sharp-wave activity similar to that observed within the hippocampal formation. Furthermore, the functional connectivity between the piriform cortex and other cortical and limbic regions is enhanced during slow-wave sleep compared to waking. This combination of conditions may allow odor memory consolidation to occur during a state of reduced external interference and facilitate association of odor memories with stored hedonic and contextual cues. Evidence consistent with sleep-dependent odor replay within olfactory cortical circuits is presented. These data suggest that both the strength and precision of odor memories is sleep-dependent. The work further emphasizes the critical role of synaptic plasticity and memory in not only odor memory but also basic odor perception. The work also suggests a possible link between sleep disturbances that are frequently co-morbid with a wide range of pathologies including Alzheimer’s disease, schizophrenia and depression and the known olfactory impairments associated with those disorders. PMID:24795585

  6. Sensory-evoked perturbations of locomotor activity by sparse sensory input: a computational study.

    PubMed

    Bui, Tuan V; Brownstone, Robert M

    2015-04-01

    Sensory inputs from muscle, cutaneous, and joint afferents project to the spinal cord, where they are able to affect ongoing locomotor activity. Activation of sensory input can initiate or prolong bouts of locomotor activity depending on the identity of the sensory afferent activated and the timing of the activation within the locomotor cycle. However, the mechanisms by which afferent activity modifies locomotor rhythm and the distribution of sensory afferents to the spinal locomotor networks have not been determined. Considering the many sources of sensory inputs to the spinal cord, determining this distribution would provide insights into how sensory inputs are integrated to adjust ongoing locomotor activity. We asked whether a sparsely distributed set of sensory inputs could modify ongoing locomotor activity. To address this question, several computational models of locomotor central pattern generators (CPGs) that were mechanistically diverse and generated locomotor-like rhythmic activity were developed. We show that sensory inputs restricted to a small subset of the network neurons can perturb locomotor activity in the same manner as seen experimentally. Furthermore, we show that an architecture with sparse sensory input improves the capacity to gate sensory information by selectively modulating sensory channels. These data demonstrate that sensory input to rhythm-generating networks need not be extensively distributed. PMID:25673740

  7. The Relation of Focal Lesions to Cortical Thickness in Pediatric Traumatic Brain Injury.

    PubMed

    Bigler, Erin D; Zielinski, Brandon A; Goodrich-Hunsaker, Naomi; Black, Garrett M; Huff, B S Trevor; Christiansen, Zachary; Wood, Dawn-Marie; Abildskov, Tracy J; Dennis, Maureen; Taylor, H Gerry; Rubin, Kenneth; Vannatta, Kathryn; Gerhardt, Cynthia A; Stancin, Terry; Yeates, Keith Owen

    2016-10-01

    In a sample of children with traumatic brain injury, this magnetic resonance imaging (MRI)-based investigation examined whether presence of a focal lesion uniquely influenced cortical thickness in any brain region. Specifically, the study explored the relation of cortical thickness to injury severity as measured by Glasgow Coma Scale score and length of stay, along with presence of encephalomalacia, focal white matter lesions or presence of hemosiderin deposition as a marker of shear injury. For comparison, a group of children without head injury but with orthopedic injury of similar age and sex were also examined. Both traumatic brain injury and orthopedic injury children had normally reduced cortical thickness with age, assumed to reflect neuronal pruning. However, the reductions observed within the traumatic brain injury sample were similar to those in the orthopedic injury group, suggesting that in this sample traumatic brain injury, per se, did not uniquely alter cortical thickness in any brain region at the group level. Injury severity in terms of Glasgow Coma Scale or longer length of stay was associated with greater reductions in frontal and occipitoparietal cortical thickness. However, presence of focal lesions were not related to unique changes in cortical thickness despite having a prominent distribution of lesions within frontotemporal regions among children with traumatic brain injury. Because focal lesions were highly heterogeneous, their association with cortical thickness and development appeared to be idiosyncratic, and not associated with group level effects.

  8. A research of 3D gravity inversion based on the recovery of sparse underdetermined linear equations

    NASA Astrophysics Data System (ADS)

    Zhaohai, M.

    2014-12-01

    Because of the properties of gravity data, it is made difficult to solve the problem of multiple solutions. There are two main types of 3D gravity inversion methods:One of two methods is based on the improvement of the instability of the sensitive matrix, solving the problem of multiple solutions and instability in 3D gravity inversion. Another is to join weight function into the 3D gravity inversion iteration. Through constant iteration, it can renewal density values and weight function to achieve the purpose to solve the multiple solutions and instability of the 3D gravity data inversion. Thanks to the sparse nature of the solutions of 3D gravity data inversions, we can transform it into a sparse equation. Then, through solving the sparse equations, we can get perfect 3D gravity inversion results. The main principle is based on zero norm of sparse matrix solution of the equation. Zero norm is mainly to solve the nonzero solution of the sparse matrix. However, the method of this article adopted is same as the principle of zero norm. But the method is the opposite of zero norm to obtain zero value solution. Through the form of a Gaussian fitting solution of the zero norm, we can find the solution by using regularization principle. Moreover, this method has been proved that it had a certain resistance to random noise in the mathematics, and it was more suitable than zero norm for the solution of the geophysical data. 3D gravity which is adopted in this article can well identify abnormal body density distribution characteristics, and it can also recognize the space position of abnormal distribution very well. We can take advantage of the density of the upper and lower limit penalty function to make each rectangular residual density within a reasonable range. Finally, this 3D gravity inversion is applied to a variety of combination model test, such as a single straight three-dimensional model, the adjacent straight three-dimensional model and Y three

  9. A Tool for Alignment and Averaging of Sparse Fluorescence Signals in Rod-Shaped Bacteria.

    PubMed

    Goudsmits, Joris M H; van Oijen, Antoine M; Robinson, Andrew

    2016-04-26

    Fluorescence microscopy studies have shown that many proteins localize to highly specific subregions within bacterial cells. Analyzing the spatial distribution of low-abundance proteins within cells is highly challenging because information obtained from multiple cells needs to be combined to provide well-defined maps of protein locations. We present (to our knowledge) a novel tool for fast, automated, and user-impartial analysis of fluorescent protein distribution across the short axis of rod-shaped bacteria. To demonstrate the strength of our approach in extracting spatial distributions and visualizing dynamic intracellular processes, we analyzed sparse fluorescence signals from single-molecule time-lapse images of individual Escherichia coli cells. In principle, our tool can be used to provide information on the distribution of signal intensity across the short axis of any rod-shaped object. PMID:27119631

  10. Assessment criteria for MEG/EEG cortical patch tests

    NASA Astrophysics Data System (ADS)

    Im, Chang-Hwan; An, Kwang-Ok; Jung, Hyun-Kyo; Kwon, Hyukchan; Lee, Yong-Ho

    2003-08-01

    To validate newly developed methods or implemented software for magnetoencephalography/electroencephalography (MEG/EEG) source localization problems, many researchers have used human skull phantom experiments or artificially constructed forward data sets. Between the two methods, the use of an artificial data set constructed with forward calculation attains superiority over the use of a human skull phantom in that it is simple to implement, adjust and control various conditions. Nowadays, for the forward calculation, especially for the cortically distributed source models, generating artificial activation patches on a brain cortical surface has been popularized instead of activating some point dipole sources. However, no well-established assessment criterion to validate the reconstructed results quantitatively has yet been introduced. In this paper, we suggest some assessment criteria to compare and validate the various MEG/EEG source localization techniques or implemented software applied to the cortically distributed source model. Four different criteria can be used to measure accuracy, degrees of focalization, noise-robustness, existence of spurious sources and so on. To verify the usefulness of the proposed criteria, four different results from two different noise conditions and two different reconstruction techniques were compared for several patches. The simulated results show that the new criteria can provide us with a reliable index to validate the MEG/EEG source localization techniques.

  11. Assessment criteria for MEG/EEG cortical patch tests.

    PubMed

    Im, Chang-Hwan; An, Kwang-Ok; Jung, Hyun-Kyo; Kwon, Hyukchan; Lee, Yong-Ho

    2003-08-01

    To validate newly developed methods or implemented software for magnetoencephalography/electroencephalography (MEG/EEG) source localization problems, many researchers have used human skull phantom experiments or artificially constructed forward data sets. Between the two methods, the use of an artificial data set constructed with forward calculation attains superiority over the use of a human skull phantom in that it is simple to implement, adjust and control various conditions. Nowadays, for the forward calculation, especially for the cortically distributed source models, generating artificial activation patches on a brain cortical surface has been popularized instead of activating some point dipole sources. However, no well-established assessment criterion to validate the reconstructed results quantitatively has yet been introduced. In this paper, we suggest some assessment criteria to compare and validate the various MEG/EEG source localization techniques or implemented software applied to the cortically distributed source model. Four different criteria can be used to measure accuracy, degrees of focalization, noise-robustness, existence of spurious sources and so on. To verify the usefulness of the proposed criteria, four different results from two different noise conditions and two different reconstruction techniques were compared for several patches. The simulated results show that the new criteria can provide us with a reliable index to validate the MEG/EEG source localization techniques.

  12. Cortical idiosyncrasies predict the perception of object size

    PubMed Central

    Moutsiana, Christina; de Haas, Benjamin; Papageorgiou, Andriani; van Dijk, Jelle A.; Balraj, Annika; Greenwood, John A.; Schwarzkopf, D. Samuel

    2016-01-01

    Perception is subjective. Even basic judgments, like those of visual object size, vary substantially between observers and also across the visual field within the same observer. The way in which the visual system determines the size of objects remains unclear, however. We hypothesize that object size is inferred from neuronal population activity in V1 and predict that idiosyncrasies in cortical functional architecture should therefore explain individual differences in size judgments. Here we show results from novel behavioural methods and functional magnetic resonance imaging (fMRI) demonstrating that biases in size perception are correlated with the spatial tuning of neuronal populations in healthy volunteers. To explain this relationship, we formulate a population read-out model that directly links the spatial distribution of V1 representations to our perceptual experience of visual size. Taken together, our results suggest that the individual perception of simple stimuli is warped by idiosyncrasies in visual cortical organization. PMID:27357864

  13. Statistics of single unit responses in the human medial temporal lobe: A sparse and overdispersed code

    NASA Astrophysics Data System (ADS)

    Magyar, Andrew

    The recent discovery of cells that respond to purely conceptual features of the environment (particular people, landmarks, objects, etc) in the human medial temporal lobe (MTL), has raised many questions about the nature of the neural code in humans. The goal of this dissertation is to develop a novel statistical method based upon maximum likelihood regression which will then be applied to these experiments in order to produce a quantitative description of the coding properties of the human MTL. In general, the method is applicable to any experiments in which a sequence of stimuli are presented to an organism while the binary responses of a large number of cells are recorded in parallel. The central concept underlying the approach is the total probability that a neuron responds to a random stimulus, called the neuronal sparsity. The model then estimates the distribution of response probabilities across the population of cells. Applying the method to single-unit recordings from the human medial temporal lobe, estimates of the sparsity distributions are acquired in four regions: the hippocampus, the entorhinal cortex, the amygdala, and the parahippocampal cortex. The resulting distributions are found to be sparse (large fraction of cells with a low response probability) and highly non-uniform, with a large proportion of ultra-sparse neurons that possess a very low response probability, and a smaller population of cells which respond much more frequently. Rammifications of the results are discussed in relation to the sparse coding hypothesis, and comparisons are made between the statistics of the human medial temporal lobe cells and place cells observed in the rodent hippocampus.

  14. Cortical thickness gradients in structural hierarchies

    PubMed Central

    Wagstyl, Konrad; Ronan, Lisa; Goodyer, Ian M.; Fletcher, Paul C.

    2015-01-01

    MRI, enabling in vivo analysis of cortical morphology, offers a powerful tool in the assessment of brain development and pathology. One of the most ubiquitous measures used—the thickness of the cortex—shows abnormalities in a number of diseases and conditions, but the functional and biological correlates of such alterations are unclear. If the functional connotations of structural MRI measures are to be understood, we must strive to clarify the relationship between measures such as cortical thickness and their cytoarchitectural determinants. We therefore sought to determine whether patterns of cortical thickness mirror a key motif of the cortex, specifically its structural hierarchical organisation. We delineated three sensory hierarchies (visual, somatosensory and auditory) in two species—macaque and human—and explored whether cortical thickness was correlated with specific cytoarchitectural characteristics. Importantly, we controlled for cortical folding which impacts upon thickness and may obscure regional differences. Our results suggest that an easily measurable macroscopic brain parameter, namely, cortical thickness, is systematically related to cytoarchitecture and to the structural hierarchical organisation of the cortex. We argue that the measurement of cortical thickness gradients may become an important way to develop our understanding of brain structure–function relationships. The identification of alterations in such gradients may complement the observation of regionally localised cortical thickness changes in our understanding of normal development and neuropsychiatric illnesses. PMID:25725468

  15. Cortical Correspondence with Probabilistic Fiber Connectivity

    PubMed Central

    Oguz, Ipek; Niethammer, Marc; Cates, Josh; Whitaker, Ross; Fletcher, Thomas; Vachet, Clement; Styner, Martin

    2009-01-01

    This paper presents a novel method of optimizing point-based correspondence among populations of human cortical surfaces by combining structural cues with probabilistic connectivity maps. The proposed method establishes a tradeoff between an even sampling of the cortical surfaces (a low surface entropy) and the similarity of corresponding points across the population (a low ensemble entropy). The similarity metric, however, isn’t constrained to be just spatial proximity, but uses local sulcal depth measurements as well as probabilistic connectivity maps, computed from DWI scans via a stochastic tractography algorithm, to enhance the correspondence definition. We propose a novel method for projecting this fiber connectivity information on the cortical surface, using a surface evolution technique. Our cortical correspondence method does not require a spherical parameterization. Experimental results are presented, showing improved correspondence quality demonstrated by a cortical thickness analysis, as compared to correspondence methods using spatial metrics as the sole correspondence criterion. PMID:19694301

  16. Online Hierarchical Sparse Representation of Multifeature for Robust Object Tracking

    PubMed Central

    Qu, Shiru

    2016-01-01

    Object tracking based on sparse representation has given promising tracking results in recent years. However, the trackers under the framework of sparse representation always overemphasize the sparse representation and ignore the correlation of visual information. In addition, the sparse coding methods only encode the local region independently and ignore the spatial neighborhood information of the image. In this paper, we propose a robust tracking algorithm. Firstly, multiple complementary features are used to describe the object appearance; the appearance model of the tracked target is modeled by instantaneous and stable appearance features simultaneously. A two-stage sparse-coded method which takes the spatial neighborhood information of the image patch and the computation burden into consideration is used to compute the reconstructed object appearance. Then, the reliability of each tracker is measured by the tracking likelihood function of transient and reconstructed appearance models. Finally, the most reliable tracker is obtained by a well established particle filter framework; the training set and the template library are incrementally updated based on the current tracking results. Experiment results on different challenging video sequences show that the proposed algorithm performs well with superior tracking accuracy and robustness. PMID:27630710

  17. FPGA implementation of sparse matrix algorithm for information retrieval

    NASA Astrophysics Data System (ADS)

    Bojanic, Slobodan; Jevtic, Ruzica; Nieto-Taladriz, Octavio

    2005-06-01

    Information text data retrieval requires a tremendous amount of processing time because of the size of the data and the complexity of information retrieval algorithms. In this paper the solution to this problem is proposed via hardware supported information retrieval algorithms. Reconfigurable computing may adopt frequent hardware modifications through its tailorable hardware and exploits parallelism for a given application through reconfigurable and flexible hardware units. The degree of the parallelism can be tuned for data. In this work we implemented standard BLAS (basic linear algebra subprogram) sparse matrix algorithm named Compressed Sparse Row (CSR) that is showed to be more efficient in terms of storage space requirement and query-processing timing over the other sparse matrix algorithms for information retrieval application. Although inverted index algorithm is treated as the de facto standard for information retrieval for years, an alternative approach to store the index of text collection in a sparse matrix structure gains more attention. This approach performs query processing using sparse matrix-vector multiplication and due to parallelization achieves a substantial efficiency over the sequential inverted index. The parallel implementations of information retrieval kernel are presented in this work targeting the Virtex II Field Programmable Gate Arrays (FPGAs) board from Xilinx. A recent development in scientific applications is the use of FPGA to achieve high performance results. Computational results are compared to implementations on other platforms. The design achieves a high level of parallelism for the overall function while retaining highly optimised hardware within processing unit.

  18. X-ray computed tomography using curvelet sparse regularization

    SciTech Connect

    Wieczorek, Matthias Vogel, Jakob; Lasser, Tobias; Frikel, Jürgen; Demaret, Laurent; Eggl, Elena; Pfeiffer, Franz; Kopp, Felix; Noël, Peter B.

    2015-04-15

    Purpose: Reconstruction of x-ray computed tomography (CT) data remains a mathematically challenging problem in medical imaging. Complementing the standard analytical reconstruction methods, sparse regularization is growing in importance, as it allows inclusion of prior knowledge. The paper presents a method for sparse regularization based on the curvelet frame for the application to iterative reconstruction in x-ray computed tomography. Methods: In this work, the authors present an iterative reconstruction approach based on the alternating direction method of multipliers using curvelet sparse regularization. Results: Evaluation of the method is performed on a specifically crafted numerical phantom dataset to highlight the method’s strengths. Additional evaluation is performed on two real datasets from commercial scanners with different noise characteristics, a clinical bone sample acquired in a micro-CT and a human abdomen scanned in a diagnostic CT. The results clearly illustrate that curvelet sparse regularization has characteristic strengths. In particular, it improves the restoration and resolution of highly directional, high contrast features with smooth contrast variations. The authors also compare this approach to the popular technique of total variation and to traditional filtered backprojection. Conclusions: The authors conclude that curvelet sparse regularization is able to improve reconstruction quality by reducing noise while preserving highly directional features.

  19. Online Hierarchical Sparse Representation of Multifeature for Robust Object Tracking

    PubMed Central

    Qu, Shiru

    2016-01-01

    Object tracking based on sparse representation has given promising tracking results in recent years. However, the trackers under the framework of sparse representation always overemphasize the sparse representation and ignore the correlation of visual information. In addition, the sparse coding methods only encode the local region independently and ignore the spatial neighborhood information of the image. In this paper, we propose a robust tracking algorithm. Firstly, multiple complementary features are used to describe the object appearance; the appearance model of the tracked target is modeled by instantaneous and stable appearance features simultaneously. A two-stage sparse-coded method which takes the spatial neighborhood information of the image patch and the computation burden into consideration is used to compute the reconstructed object appearance. Then, the reliability of each tracker is measured by the tracking likelihood function of transient and reconstructed appearance models. Finally, the most reliable tracker is obtained by a well established particle filter framework; the training set and the template library are incrementally updated based on the current tracking results. Experiment results on different challenging video sequences show that the proposed algorithm performs well with superior tracking accuracy and robustness.

  20. Robust visual multitask tracking via composite sparse model

    NASA Astrophysics Data System (ADS)

    Jin, Bo; Jing, Zhongliang; Wang, Meng; Pan, Han

    2014-11-01

    Recently, multitask learning was applied to visual tracking by learning sparse particle representations in a joint task, which led to the so-called multitask tracking algorithm (MTT). Although MTT shows impressive tracking performances by mining the interdependencies between particles, the individual feature of each particle is underestimated. The utilized L1,q norm regularization assumes all features are shared between all particles and results in nearly identical representation coefficients in nonsparse rows. We propose a composite sparse multitask tracking algorithm (CSMTT). We develop a composite sparse model to formulate the object appearance as a combination of the shared feature component, the individual feature component, and the outlier component. The composite sparsity is achieved via the L and L1,1 norm minimization, and is optimized by the alternating direction method of multipliers, which provides a favorable reconstruction performance and an impressive computational efficiency. Moreover, a dynamical dictionary updating scheme is proposed to capture appearance changes. CSMTT is tested on real-world video sequences under various challenges, and experimental results show that the composite sparse model achieves noticeable lower reconstruction errors and higher computational speeds than traditional sparse models, and CSMTT has consistently better tracking performances against seven state-of-the-art trackers.

  1. Image fusion via nonlocal sparse K-SVD dictionary learning.

    PubMed

    Li, Ying; Li, Fangyi; Bai, Bendu; Shen, Qiang

    2016-03-01

    Image fusion aims to merge two or more images captured via various sensors of the same scene to construct a more informative image by integrating their details. Generally, such integration is achieved through the manipulation of the representations of the images concerned. Sparse representation plays an important role in the effective description of images, offering a great potential in a variety of image processing tasks, including image fusion. Supported by sparse representation, in this paper, an approach for image fusion by the use of a novel dictionary learning scheme is proposed. The nonlocal self-similarity property of the images is exploited, not only at the stage of learning the underlying description dictionary but during the process of image fusion. In particular, the property of nonlocal self-similarity is combined with the traditional sparse dictionary. This results in an improved learned dictionary, hereafter referred to as the nonlocal sparse K-SVD dictionary (where K-SVD stands for the K times singular value decomposition that is commonly used in the literature), and abbreviated to NL_SK_SVD. The performance of the NL_SK_SVD dictionary is applied for image fusion using simultaneous orthogonal matching pursuit. The proposed approach is evaluated with different types of images, and compared with a number of alternative image fusion techniques. The resultant superior fused images using the present approach demonstrates the efficacy of the NL_SK_SVD dictionary in sparse image representation.

  2. Online Hierarchical Sparse Representation of Multifeature for Robust Object Tracking.

    PubMed

    Yang, Honghong; Qu, Shiru

    2016-01-01

    Object tracking based on sparse representation has given promising tracking results in recent years. However, the trackers under the framework of sparse representation always overemphasize the sparse representation and ignore the correlation of visual information. In addition, the sparse coding methods only encode the local region independently and ignore the spatial neighborhood information of the image. In this paper, we propose a robust tracking algorithm. Firstly, multiple complementary features are used to describe the object appearance; the appearance model of the tracked target is modeled by instantaneous and stable appearance features simultaneously. A two-stage sparse-coded method which takes the spatial neighborhood information of the image patch and the computation burden into consideration is used to compute the reconstructed object appearance. Then, the reliability of each tracker is measured by the tracking likelihood function of transient and reconstructed appearance models. Finally, the most reliable tracker is obtained by a well established particle filter framework; the training set and the template library are incrementally updated based on the current tracking results. Experiment results on different challenging video sequences show that the proposed algorithm performs well with superior tracking accuracy and robustness. PMID:27630710

  3. Estimation of Cortical Connectivity From EEG Using State-Space Models

    PubMed Central

    Cheung, Bing Leung Patrick; Riedner, Brady; Tononi, Giulio; Van Veen, Barry D.

    2010-01-01

    A state-space formulation is introduced for estimating multivariate autoregressive (MVAR) models of cortical connectivity from noisy, scalp recorded EEG. A state equation represents the MVAR model of cortical dynamics while an observation equation describes the physics relating the cortical signals to the measured EEG and the presence of spatially correlated noise. We assume the cortical signals originate from known regions of cortex, but that the spatial distribution of activity within each region is unknown. An expectation maximization algorithm is developed to directly estimate the MVAR model parameters, the spatial activity distribution components, and the spatial covariance matrix of the noise from the measured EEG. Simulation and analysis demonstrate that this integrated approach is less sensitive to noise than two-stage approaches in which the cortical signals are first estimated from EEG measurements, and next an MVAR model is fit to the estimated cortical signals. The method is further demonstrated by estimating conditional Granger causality using EEG data collected while subjects passively watch a movie. PMID:20501341

  4. Cortical Cartography and Caret Software

    PubMed Central

    Van Essen, David C.

    2011-01-01

    Caret software is widely used for analyzing and visualizing many types of fMRI data, often in conjunction with experimental data from other modalities. This article places Caret’s development in a historical context that spans three decades of brain mapping – from the early days of manually generated flat maps to the nascent field of human connectomics. It also highlights some of Caret’s distinctive capabilities. This includes the ease of visualizing data on surfaces and/or volumes and on atlases as well as individual subjects. Caret can display many types of experimental data using various combinations of overlays (e.g., fMRI activation maps, cortical parcellations, areal boundaries), and it has other features that facilitate the analysis and visualization of complex neuroimaging datasets. PMID:22062192

  5. Gyrification from constrained cortical expansion

    NASA Astrophysics Data System (ADS)

    Tallinen, Tuomas

    The convolutions of the human brain are a symbol of its functional complexity. But how does the outer surface of the brain, the layered cortex of neuronal gray matter get its folds? In this talk, we ask to which extent folding of the brain can be explained as a purely mechanical consequence of unpatterned growth of the cortical layer relative to the sublayers. Modeling the growing brain as a soft layered solid leads to elastic instabilities and the formation of cusped sulci and smooth gyri consistent with observations across species in both normal and pathological situations. Furthermore, we apply initial geometries obtained from fetal brain MRI to address the question of how the brain geometry and folding patterns may be coupled via mechanics.

  6. Cortical cartography and Caret software.

    PubMed

    Van Essen, David C

    2012-08-15

    Caret software is widely used for analyzing and visualizing many types of fMRI data, often in conjunction with experimental data from other modalities. This article places Caret's development in a historical context that spans three decades of brain mapping--from the early days of manually generated flat maps to the nascent field of human connectomics. It also highlights some of Caret's distinctive capabilities. This includes the ease of visualizing data on surfaces and/or volumes and on atlases as well as individual subjects. Caret can display many types of experimental data using various combinations of overlays (e.g., fMRI activation maps, cortical parcellations, areal boundaries), and it has other features that facilitate the analysis and visualization of complex neuroimaging datasets.

  7. Nicotinic modulation of cortical circuits

    PubMed Central

    Arroyo, Sergio; Bennett, Corbett; Hestrin, Shaul

    2014-01-01

    The ascending cholinergic neuromodulatory system sends projections throughout cortex and has been shown to play an important role in a number of cognitive functions including arousal, working memory, and attention. However, despite a wealth of behavioral and anatomical data, understanding how cholinergic synapses modulate cortical function has been limited by the inability to selectively activate cholinergic axons. Now, with the development of optogenetic tools and cell-type specific Cre-driver mouse lines, it has become possible to stimulate cholinergic axons from the basal forebrain (BF) and probe cholinergic synapses in the cortex for the first time. Here we review recent work studying the cell-type specificity of nicotinic signaling in the cortex, synaptic mechanisms mediating cholinergic transmission, and the potential functional role of nicotinic modulation. PMID:24734005

  8. Unsupervised fetal cortical surface parcellation

    NASA Astrophysics Data System (ADS)

    Dahdouh, Sonia; Limperopoulos, Catherine

    2016-03-01

    At the core of many neuro-imaging studies, atlas-based brain parcellations are used for example to study normal brain evolution across the lifespan. These atlases rely on the assumption that the same anatomical features are present on all subjects to be studied and that these features are stable enough to allow meaningful comparisons between different brain surfaces and structures These methods, however, often fail when applied to fetal MRI data, due to the lack of consistent anatomical features present across gestation. This paper presents a novel surface-based fetal cortical parcellation framework which attempts to circumvent the lack of consistent anatomical features by proposing a brain parcellation scheme that is based solely on learned geometrical features. A mesh signature incorporating both extrinsic and intrinsic geometrical features is proposed and used in a clustering scheme to define a parcellation of the fetal brain. This parcellation is then learned using a Random Forest (RF) based learning approach and then further refined in an alpha-expansion graph-cut scheme. Based on the votes obtained by the RF inference procedure, a probability map is computed and used as a data term in the graph-cut procedure. The smoothness term is defined by learning a transition matrix based on the dihedral angles of the faces. Qualitative and quantitative results on a cohort of both healthy and high-risk fetuses are presented. Both visual and quantitative assessments show good results demonstrating a reliable method for fetal brain data and the possibility of obtaining a parcellation of the fetal cortical surfaces using only geometrical features.

  9. Cortical spreading depression: An enigma

    NASA Astrophysics Data System (ADS)

    Miura, R. M.; Huang, H.; Wylie, J. J.

    2007-08-01

    The brain is a complex organ with active components composed largely of neurons, glial cells, and blood vessels. There exists an enormous experimental and theoretical literature on the mechanisms involved in the functioning of the brain, but we still do not have a good understanding of how it works on a gross mechanistic level. In general, the brain maintains a homeostatic state with relatively small ion concentration changes, the major ions being sodium, potassium, and chloride. Calcium ions are present in smaller quantities but still play an important role in many phenomena. Cortical spreading depression (CSD for short) was discovered over 60 years ago by A.A.P. Leão, a Brazilian physiologist doing his doctoral research on epilepsy at Harvard University, “Spreading depression of activity in the cerebral cortex," J. Neurophysiol., 7 (1944), pp. 359-390. Cortical spreading depression is characterized by massive changes in ionic concentrations and slow nonlinear chemical waves, with speeds on the order of mm/min, in the cortex of different brain structures in various experimental animals. In humans, CSD is associated with migraine with aura, where a light scintillation in the visual field propagates, then disappears, and is followed by a sustained headache. To date, CSD remains an enigma, and further detailed experimental and theoretical investigations are needed to develop a comprehensive picture of the diverse mechanisms involved in producing CSD. A number of mechanisms have been hypothesized to be important for CSD wave propagation. In this paper, we briefly describe several characteristics of CSD wave propagation, and examine some of the mechanisms that are believed to be important, including ion diffusion, membrane ionic currents, osmotic effects, spatial buffering, neurotransmitter substances, gap junctions, metabolic pumps, and synaptic connections. Continuum models of CSD, consisting of coupled nonlinear diffusion equations for the ion concentrations, and

  10. Population spikes in cortical networks during different functional states

    PubMed Central

    Mark, Shirley; Tsodyks, Misha

    2012-01-01

    Brain computational challenges vary between behavioral states. Engaged animals react according to incoming sensory information, while in relaxed and sleeping states consolidation of the learned information is believed to take place. Different states are characterized by different forms of cortical activity. We study a possible neuronal mechanism for generating these diverse dynamics and suggest their possible functional significance. Previous studies demonstrated that brief synchronized increase in a neural firing [Population Spikes (PS)] can be generated in homogenous recurrent neural networks with short-term synaptic depression (STD). Here we consider more realistic networks with clustered architecture. We show that the level of synchronization in neural activity can be controlled smoothly by network parameters. The network shifts from asynchronous activity to a regime in which clusters synchronized separately, then, the synchronization between the clusters increases gradually to fully synchronized state. We examine the effects of different synchrony levels on the transmission of information by the network. We find that the regime of intermediate synchronization is preferential for the flow of information between sparsely connected areas. Based on these results, we suggest that the regime of intermediate synchronization corresponds to engaged behavioral state of the animal, while global synchronization is exhibited during relaxed and sleeping states. PMID:22811663

  11. Sparse representation based face recognition using weighted regions

    NASA Astrophysics Data System (ADS)

    Bilgazyev, Emil; Yeniaras, E.; Uyanik, I.; Unan, Mahmut; Leiss, E. L.

    2013-12-01

    Face recognition is a challenging research topic, especially when the training (gallery) and recognition (probe) images are acquired using different cameras under varying conditions. Even a small noise or occlusion in the images can compromise the accuracy of recognition. Lately, sparse encoding based classification algorithms gave promising results for such uncontrollable scenarios. In this paper, we introduce a novel methodology by modeling the sparse encoding with weighted patches to increase the robustness of face recognition even further. In the training phase, we define a mask (i.e., weight matrix) using a sparse representation selecting the facial regions, and in the recognition phase, we perform comparison on selected facial regions. The algorithm was evaluated both quantitatively and qualitatively using two comprehensive surveillance facial image databases, i.e., SCfaceandMFPV, with the results clearly superior to common state-of-the-art methodologies in different scenarios.

  12. Uncovering Transcriptional Regulatory Networks by Sparse Bayesian Factor Model

    NASA Astrophysics Data System (ADS)

    Meng, Jia; Zhang, Jianqiu(Michelle); Qi, Yuan(Alan); Chen, Yidong; Huang, Yufei

    2010-12-01

    The problem of uncovering transcriptional regulation by transcription factors (TFs) based on microarray data is considered. A novel Bayesian sparse correlated rectified factor model (BSCRFM) is proposed that models the unknown TF protein level activity, the correlated regulations between TFs, and the sparse nature of TF-regulated genes. The model admits prior knowledge from existing database regarding TF-regulated target genes based on a sparse prior and through a developed Gibbs sampling algorithm, a context-specific transcriptional regulatory network specific to the experimental condition of the microarray data can be obtained. The proposed model and the Gibbs sampling algorithm were evaluated on the simulated systems, and results demonstrated the validity and effectiveness of the proposed approach. The proposed model was then applied to the breast cancer microarray data of patients with Estrogen Receptor positive ([InlineEquation not available: see fulltext.]) status and Estrogen Receptor negative ([InlineEquation not available: see fulltext.]) status, respectively.

  13. Joint sparse representation for robust multimodal biometrics recognition.

    PubMed

    Shekhar, Sumit; Patel, Vishal M; Nasrabadi, Nasser M; Chellappa, Rama

    2014-01-01

    Traditional biometric recognition systems rely on a single biometric signature for authentication. While the advantage of using multiple sources of information for establishing the identity has been widely recognized, computational models for multimodal biometrics recognition have only recently received attention. We propose a multimodal sparse representation method, which represents the test data by a sparse linear combination of training data, while constraining the observations from different modalities of the test subject to share their sparse representations. Thus, we simultaneously take into account correlations as well as coupling information among biometric modalities. A multimodal quality measure is also proposed to weigh each modality as it gets fused. Furthermore, we also kernelize the algorithm to handle nonlinearity in data. The optimization problem is solved using an efficient alternative direction method. Various experiments show that the proposed method compares favorably with competing fusion-based methods.

  14. Sparse nonnegative matrix factorization with ℓ0-constraints

    PubMed Central

    Peharz, Robert; Pernkopf, Franz

    2012-01-01

    Although nonnegative matrix factorization (NMF) favors a sparse and part-based representation of nonnegative data, there is no guarantee for this behavior. Several authors proposed NMF methods which enforce sparseness by constraining or penalizing the ℓ1-norm of the factor matrices. On the other hand, little work has been done using a more natural sparseness measure, the ℓ0-pseudo-norm. In this paper, we propose a framework for approximate NMF which constrains the ℓ0-norm of the basis matrix, or the coefficient matrix, respectively. For this purpose, techniques for unconstrained NMF can be easily incorporated, such as multiplicative update rules, or the alternating nonnegative least-squares scheme. In experiments we demonstrate the benefits of our methods, which compare to, or outperform existing approaches. PMID:22505792

  15. Sparse representation-based image restoration via nonlocal supervised coding

    NASA Astrophysics Data System (ADS)

    Li, Ao; Chen, Deyun; Sun, Guanglu; Lin, Kezheng

    2016-09-01

    Sparse representation (SR) and nonlocal technique (NLT) have shown great potential in low-level image processing. However, due to the degradation of the observed image, SR and NLT may not be accurate enough to obtain a faithful restoration results when they are used independently. To improve the performance, in this paper, a nonlocal supervised coding strategy-based NLT for image restoration is proposed. The novel method has three main contributions. First, to exploit the useful nonlocal patches, a nonnegative sparse representation is introduced, whose coefficients can be utilized as the supervised weights among patches. Second, a novel objective function is proposed, which integrated the supervised weights learning and the nonlocal sparse coding to guarantee a more promising solution. Finally, to make the minimization tractable and convergence, a numerical scheme based on iterative shrinkage thresholding is developed to solve the above underdetermined inverse problem. The extensive experiments validate the effectiveness of the proposed method.

  16. Sparse representation-based image restoration via nonlocal supervised coding

    NASA Astrophysics Data System (ADS)

    Li, Ao; Chen, Deyun; Sun, Guanglu; Lin, Kezheng

    2016-10-01

    Sparse representation (SR) and nonlocal technique (NLT) have shown great potential in low-level image processing. However, due to the degradation of the observed image, SR and NLT may not be accurate enough to obtain a faithful restoration results when they are used independently. To improve the performance, in this paper, a nonlocal supervised coding strategy-based NLT for image restoration is proposed. The novel method has three main contributions. First, to exploit the useful nonlocal patches, a nonnegative sparse representation is introduced, whose coefficients can be utilized as the supervised weights among patches. Second, a novel objective function is proposed, which integrated the supervised weights learning and the nonlocal sparse coding to guarantee a more promising solution. Finally, to make the minimization tractable and convergence, a numerical scheme based on iterative shrinkage thresholding is developed to solve the above underdetermined inverse problem. The extensive experiments validate the effectiveness of the proposed method.

  17. Sparse Partial Equilibrium Tables in Chemically Resolved Reactive Flow

    NASA Astrophysics Data System (ADS)

    Vitello, Peter; Fried, Laurence E.; Pudliner, Brian; McAbee, Tom

    2004-07-01

    The detonation of an energetic material is the result of a complex interaction between kinetic chemical reactions and hydrodynamics. Unfortunately, little is known concerning the detailed chemical kinetics of detonations in energetic materials. CHEETAH uses rate laws to treat species with the slowest chemical reactions, while assuming other chemical species are in equilibrium. CHEETAH supports a wide range of elements and condensed detonation products and can also be applied to gas detonations. A sparse hash table of equation of state values is used in CHEETAH to enhance the efficiency of kinetic reaction calculations. For large-scale parallel hydrodynamic calculations, CHEETAH uses parallel communication to updates to the cache. We present here details of the sparse caching model used in the CHEETAH coupled to an ALE hydrocode. To demonstrate the efficiency of modeling using a sparse cache model we consider detonations in energetic materials.

  18. SAR target classification based on multiscale sparse representation

    NASA Astrophysics Data System (ADS)

    Ruan, Huaiyu; Zhang, Rong; Li, Jingge; Zhan, Yibing

    2016-03-01

    We propose a novel multiscale sparse representation approach for SAR target classification. It firstly extracts the dense SIFT descriptors on multiple scales, then trains a global multiscale dictionary by sparse coding algorithm. After obtaining the sparse representation, the method applies spatial pyramid matching (SPM) and max pooling to summarize the features for each image. The proposed method can provide more information and descriptive ability than single-scale ones. Moreover, it costs less extra computation than existing multiscale methods which compute a dictionary for each scale. The MSTAR database and ship database collected from TerraSAR-X images are used in classification setup. Results show that the best overall classification rate of the proposed approach can achieve 98.83% on the MSTAR database and 92.67% on the TerraSAR-X ship database.

  19. A Multiobjective Sparse Feature Learning Model for Deep Neural Networks.

    PubMed

    Gong, Maoguo; Liu, Jia; Li, Hao; Cai, Qing; Su, Linzhi

    2015-12-01

    Hierarchical deep neural networks are currently popular learning models for imitating the hierarchical architecture of human brain. Single-layer feature extractors are the bricks to build deep networks. Sparse feature learning models are popular models that can learn useful representations. But most of those models need a user-defined constant to control the sparsity of representations. In this paper, we propose a multiobjective sparse feature learning model based on the autoencoder. The parameters of the model are learnt by optimizing two objectives, reconstruction error and the sparsity of hidden units simultaneously to find a reasonable compromise between them automatically. We design a multiobjective induced learning procedure for this model based on a multiobjective evolutionary algorithm. In the experiments, we demonstrate that the learning procedure is effective, and the proposed multiobjective model can learn useful sparse features.

  20. Automatic landslide and mudflow detection method via multichannel sparse representation

    NASA Astrophysics Data System (ADS)

    Chao, Chen; Zhou, Jianjun; Hao, Zhuo; Sun, Bo; He, Jun; Ge, Fengxiang

    2015-10-01

    Landslide and mudflow detection is an important application of aerial images and high resolution remote sensing images, which is crucial for national security and disaster relief. Since the high resolution images are often large in size, it's necessary to develop an efficient algorithm for landslide and mudflow detection. Based on the theory of sparse representation and, we propose a novel automatic landslide and mudflow detection method in this paper, which combines multi-channel sparse representation and eight neighbor judgment methods. The whole process of the detection is totally automatic. We make the experiment on a high resolution image of ZhouQu district of Gansu province in China on August, 2010 and get a promising result which proved the effective of using sparse representation on landslide and mudflow detection.

  1. Sparse Partial Equilibrium Tables in Chemically Resolved Reactive Flow

    SciTech Connect

    Vitello, P; Fried, L E; Pudliner, B; McAbee, T

    2003-07-14

    The detonation of an energetic material is the result of a complex interaction between kinetic chemical reactions and hydrodynamics. Unfortunately, little is known concerning the detailed chemical kinetics of detonations in energetic materials. CHEETAH uses rate laws to treat species with the slowest chemical reactions, while assuming other chemical species are in equilibrium. CHEETAH supports a wide range of elements and condensed detonation products and can also be applied to gas detonations. A sparse hash table of equation of state values, called the ''cache'' is used in CHEETAH to enhance the efficiency of kinetic reaction calculations. For large-scale parallel hydrodynamic calculations, CHEETAH uses MPI communication to updates to the cache. We present here details of the sparse caching model used in the CHEETAH. To demonstrate the efficiency of modeling using a sparse cache model we consider detonations in energetic materials.

  2. Joint sparse representation for robust multimodal biometrics recognition.

    PubMed

    Shekhar, Sumit; Patel, Vishal M; Nasrabadi, Nasser M; Chellappa, Rama

    2014-01-01

    Traditional biometric recognition systems rely on a single biometric signature for authentication. While the advantage of using multiple sources of information for establishing the identity has been widely recognized, computational models for multimodal biometrics recognition have only recently received attention. We propose a multimodal sparse representation method, which represents the test data by a sparse linear combination of training data, while constraining the observations from different modalities of the test subject to share their sparse representations. Thus, we simultaneously take into account correlations as well as coupling information among biometric modalities. A multimodal quality measure is also proposed to weigh each modality as it gets fused. Furthermore, we also kernelize the algorithm to handle nonlinearity in data. The optimization problem is solved using an efficient alternative direction method. Various experiments show that the proposed method compares favorably with competing fusion-based methods. PMID:24231870

  3. Sparse Solution of High-Dimensional Model Calibration Inverse Problems under Uncertainty in Prior Structural Connectivity

    NASA Astrophysics Data System (ADS)

    Mohammad khaninezhad, M.; Jafarpour, B.

    2012-12-01

    Data limitation and heterogeneity of the geologic formations introduce significant uncertainty in predicting the related flow and transport processes in these environments. Fluid flow and displacement behavior in subsurface systems is mainly controlled by the structural connectivity models that create preferential flow pathways (or barriers). The connectivity of extreme geologic features strongly constrains the evolution of the related flow and transport processes in subsurface formations. Therefore, characterization of the geologic continuity and facies connectivity is critical for reliable prediction of the flow and transport behavior. The goal of this study is to develop a robust and geologically consistent framework for solving large-scale nonlinear subsurface characterization inverse problems under uncertainty about geologic continuity and structural connectivity. We formulate a novel inverse modeling approach by adopting a sparse reconstruction perspective, which involves two major components: 1) sparse description of hydraulic property distribution under significant uncertainty in structural connectivity and 2) formulation of an effective sparsity-promoting inversion method that is robust against prior model uncertainty. To account for the significant variability in the structural connectivity, we use, as prior, multiple distinct connectivity models. For sparse/compact representation of high-dimensional hydraulic property maps, we investigate two methods. In one approach, we apply the principle component analysis (PCA) to each prior connectivity model individually and combine the resulting leading components from each model to form a diverse geologic dictionary. Alternatively, we combine many realizations of the hydraulic properties from different prior connectivity models and use them to generate a diverse training dataset. We use the training dataset with a sparsifying transform, such as K-SVD, to construct a sparse geologic dictionary that is robust to

  4. Source term identification in atmospheric modelling via sparse optimization

    NASA Astrophysics Data System (ADS)

    Adam, Lukas; Branda, Martin; Hamburger, Thomas

    2015-04-01

    Inverse modelling plays an important role in identifying the amount of harmful substances released into atmosphere during major incidents such as power plant accidents or volcano eruptions. Another possible application of inverse modelling lies in the monitoring the CO2 emission limits where only observations at certain places are available and the task is to estimate the total releases at given locations. This gives rise to minimizing the discrepancy between the observations and the model predictions. There are two standard ways of solving such problems. In the first one, this discrepancy is regularized by adding additional terms. Such terms may include Tikhonov regularization, distance from a priori information or a smoothing term. The resulting, usually quadratic, problem is then solved via standard optimization solvers. The second approach assumes that the error term has a (normal) distribution and makes use of Bayesian modelling to identify the source term. Instead of following the above-mentioned approaches, we utilize techniques from the field of compressive sensing. Such techniques look for a sparsest solution (solution with the smallest number of nonzeros) of a linear system, where a maximal allowed error term may be added to this system. Even though this field is a developed one with many possible solution techniques, most of them do not consider even the simplest constraints which are naturally present in atmospheric modelling. One of such examples is the nonnegativity of release amounts. We believe that the concept of a sparse solution is natural in both problems of identification of the source location and of the time process of the source release. In the first case, it is usually assumed that there are only few release points and the task is to find them. In the second case, the time window is usually much longer than the duration of the actual release. In both cases, the optimal solution should contain a large amount of zeros, giving rise to the

  5. The MUSIC algorithm for sparse objects: a compressed sensing analysis

    NASA Astrophysics Data System (ADS)

    Fannjiang, Albert C.

    2011-03-01

    The multiple signal classification (MUSIC) algorithm, and its extension for imaging sparse extended objects, with noisy data is analyzed by compressed sensing (CS) techniques. A thresholding rule is developed to augment the standard MUSIC algorithm. The notion of restricted isometry property (RIP) and an upper bound on the restricted isometry constant (RIC) are employed to establish sufficient conditions for the exact localization by MUSIC with or without noise. In the noiseless case, the sufficient condition gives an upper bound on the numbers of random sampling and incident directions necessary for exact localization. In the noisy case, the sufficient condition assumes additionally an upper bound for the noise-to-object ratio in terms of the RIC and the dynamic range of objects. This bound points to the super-resolution capability of the MUSIC algorithm. Rigorous comparison of performance between MUSIC and the CS minimization principle, basis pursuit denoising (BPDN), is given. In general, the MUSIC algorithm guarantees to recover, with high probability, s scatterers with n= {O}(s^2) random sampling and incident directions and sufficiently high frequency. For the favorable imaging geometry where the scatterers are distributed on a transverse plane MUSIC guarantees to recover, with high probability, s scatterers with a median frequency and n= {O}(s) random sampling/incident directions. Moreover, for the problems of spectral estimation and source localizations both BPDN and MUSIC guarantee, with high probability, to identify exactly the frequencies of random signals with the number n= {O}(s) of sampling times. However, in the absence of abundant realizations of signals, BPDN is the preferred method for spectral estimation. Indeed, BPDN can identify the frequencies approximately with just one realization of signals with the recovery error at worst linearly proportional to the noise level. Numerical results confirm that BPDN outperforms MUSIC in the well

  6. Content addressable systolic array for sparse matrix computation

    SciTech Connect

    Wing, O.

    1983-01-01

    A systolic array is proposed which is specifically designed to solve a system of sparse linear equations. The array consists of a number of processing elements connected in a ring. Each processing element has its own content addressable memory where the nonzero elements of the sparse matrix are stored. Matrix elements to which elementary operations are applied are extracted from the memory by content addressing. The system of equations is solved in a systolic fashion and the solution is obtained in nz+5n-2 steps where nz is the number of nonzero elements along and below the diagonal and n is the number of equations. 13 references.

  7. Towards an Accurate Performance Modeling of Parallel SparseFactorization

    SciTech Connect

    Grigori, Laura; Li, Xiaoye S.

    2006-05-26

    We present a performance model to analyze a parallel sparseLU factorization algorithm on modern cached-based, high-end parallelarchitectures. Our model characterizes the algorithmic behavior bytakingaccount the underlying processor speed, memory system performance, aswell as the interconnect speed. The model is validated using theSuperLU_DIST linear system solver, the sparse matrices from realapplications, and an IBM POWER3 parallel machine. Our modelingmethodology can be easily adapted to study performance of other types ofsparse factorizations, such as Cholesky or QR.

  8. D Super-Resolution Approach for Sparse Laser Scanner Data

    NASA Astrophysics Data System (ADS)

    Hosseinyalamdary, S.; Yilmaz, A.

    2015-08-01

    Laser scanner point cloud has been emerging in Photogrammetry and computer vision to achieve high level tasks such as object tracking, object recognition and scene understanding. However, low cost laser scanners are noisy, sparse and prone to systematic errors. This paper proposes a novel 3D super resolution approach to reconstruct surface of the objects in the scene. This method works on sparse, unorganized point clouds and has superior performance over other surface recovery approaches. Since the proposed approach uses anisotropic diffusion equation, it does not deteriorate the object boundaries and it preserves topology of the object.

  9. Sparse Matrix for ECG Identification with Two-Lead Features

    PubMed Central

    Tseng, Kuo-Kun; Luo, Jiao; Wang, Wenmin; Haiting, Dong

    2015-01-01

    Electrocardiograph (ECG) human identification has the potential to improve biometric security. However, improvements in ECG identification and feature extraction are required. Previous work has focused on single lead ECG signals. Our work proposes a new algorithm for human identification by mapping two-lead ECG signals onto a two-dimensional matrix then employing a sparse matrix method to process the matrix. And that is the first application of sparse matrix techniques for ECG identification. Moreover, the results of our experiments demonstrate the benefits of our approach over existing methods. PMID:25961074

  10. A LONE code for the sparse control of quantum systems

    NASA Astrophysics Data System (ADS)

    Ciaramella, G.; Borzì, A.

    2016-03-01

    In many applications with quantum spin systems, control functions with a sparse and pulse-shaped structure are often required. These controls can be obtained by solving quantum optimal control problems with L1-penalized cost functionals. In this paper, the MATLAB package LONE is presented aimed to solving L1-penalized optimal control problems governed by unitary-operator quantum spin models. This package implements a new strategy that includes a globalized semi-smooth Krylov-Newton scheme and a continuation procedure. Results of numerical experiments demonstrate the ability of the LONE code in computing accurate sparse optimal control solutions.

  11. Robust head pose estimation using locality-constrained sparse coding

    NASA Astrophysics Data System (ADS)

    Kim, Hyunduk; Lee, Sang-Heon; Sohn, Myoung-Kyu

    2015-12-01

    Sparse coding (SC) method has been shown to deliver successful result in a variety of computer vision applications. However, it does not consider the underlying structure of the data in the feature space. On the other hand, locality constrained linear coding (LLC) utilizes locality constraint to project each input data into its local-coordinate system. Based on the recent success of LLC, we propose a novel locality-constrained sparse coding (LSC) method to overcome the limitation of the SC. In experiments, the proposed algorithms were applied to head pose estimation applications. Experimental results demonstrated that the LSC method is better than state-of-the-art methods.

  12. Reconstruction Techniques for Sparse Multistatic Linear Array Microwave Imaging

    SciTech Connect

    Sheen, David M.; Hall, Thomas E.

    2014-06-09

    Sequentially-switched linear arrays are an enabling technology for a number of near-field microwave imaging applications. Electronically sequencing along the array axis followed by mechanical scanning along an orthogonal axis allows dense sampling of a two-dimensional aperture in near real-time. In this paper, a sparse multi-static array technique will be described along with associated Fourier-Transform-based and back-projection-based image reconstruction algorithms. Simulated and measured imaging results are presented that show the effectiveness of the sparse array technique along with the merits and weaknesses of each image reconstruction approach.

  13. Moving target detection for frequency agility radar by sparse reconstruction

    NASA Astrophysics Data System (ADS)

    Quan, Yinghui; Li, YaChao; Wu, Yaojun; Ran, Lei; Xing, Mengdao; Liu, Mengqi

    2016-09-01

    Frequency agility radar, with randomly varied carrier frequency from pulse to pulse, exhibits superior performance compared to the conventional fixed carrier frequency pulse-Doppler radar against the electromagnetic interference. A novel moving target detection (MTD) method is proposed for the estimation of the target's velocity of frequency agility radar based on pulses within a coherent processing interval by using sparse reconstruction. Hardware implementation of orthogonal matching pursuit algorithm is executed on Xilinx Virtex-7 Field Programmable Gata Array (FPGA) to perform sparse optimization. Finally, a series of experiments are performed to evaluate the performance of proposed MTD method for frequency agility radar systems.

  14. Local cortical dynamics of burst suppression in the anaesthetized brain.

    PubMed

    Lewis, Laura D; Ching, Shinung; Weiner, Veronica S; Peterfreund, Robert A; Eskandar, Emad N; Cash, Sydney S; Brown, Emery N; Purdon, Patrick L

    2013-09-01

    Burst suppression is an electroencephalogram pattern that consists of a quasi-periodic alternation between isoelectric 'suppressions' lasting seconds or minutes, and high-voltage 'bursts'. It is characteristic of a profoundly inactivated brain, occurring in conditions including hypothermia, deep general anaesthesia, infant encephalopathy and coma. It is also used in neurology as an electrophysiological endpoint in pharmacologically induced coma for brain protection after traumatic injury and during status epilepticus. Classically, burst suppression has been regarded as a 'global' state with synchronous activity throughout cortex. This assumption has influenced the clinical use of burst suppression as a way to broadly reduce neural activity. However, the extent of spatial homogeneity has not been fully explored due to the challenges in recording from multiple cortical sites simultaneously. The neurophysiological dynamics of large-scale cortical circuits during burst suppression are therefore not well understood. To address this question, we recorded intracranial electrocorticograms from patients who entered burst suppression while receiving propofol general anaesthesia. The electrodes were broadly distributed across cortex, enabling us to examine both the dynamics of burst suppression within local cortical regions and larger-scale network interactions. We found that in contrast to previous characterizations, bursts could be substantially asynchronous across the cortex. Furthermore, the state of burst suppression itself could occur in a limited cortical region while other areas exhibited ongoing continuous activity. In addition, we found a complex temporal structure within bursts, which recapitulated the spectral dynamics of the state preceding burst suppression, and evolved throughout the course of a single burst. Our observations imply that local cortical dynamics are not homogeneous, even during significant brain inactivation. Instead, cortical and, implicitly

  15. Spatiotemporal SERT expression in cortical map development.

    PubMed

    Chen, Xiaoning; Petit, Emilie I; Dobrenis, Kostantin; Sze, Ji Ying

    2016-09-01

    The cerebral cortex is organized into morphologically distinct areas that provide biological frameworks underlying perception, cognition, and behavior. Profiling mouse and human cortical transcriptomes have revealed temporal-specific differential gene expression modules in distinct neocortical areas during cortical map establishment. However, the biological roles of spatiotemporal gene expression in cortical patterning and how cortical topographic gene expression is regulated are largely unknown. Here, we characterize temporal- and spatial-defined expression of serotonin (5-HT) transporter (SERT) in glutamatergic neurons during sensory map development in mice. SERT is transiently expressed in glutamatergic thalamic neurons projecting to sensory cortices and in pyramidal neurons in the prefrontal cortex (PFC) and hippocampus (HPC) during the period that lays down the basic functional neural circuits. We previously identified that knockout of SERT in the thalamic neurons blocks 5-HT uptake by their thalamocortical axons, resulting in excessive 5-HT signaling that impairs sensory map architecture. In contrast, here we show that selective SERT knockout in the PFC and HPC neurons does not perturb sensory map patterning. These data suggest that transient SERT expression in specific glutamatergic neurons provides area-specific instructions for cortical map patterning. Hence, genetic and pharmacological manipulations of this SERT function could illuminate the fundamental genetic programming of cortex-specific maps and biological roles of temporal-specific cortical topographic gene expression in normal development and mental disorders. PMID:27282696

  16. A Turing Reaction-Diffusion Model for Human Cortical Folding Patterns and Cortical Pattern Malformations

    NASA Astrophysics Data System (ADS)

    Hurdal, Monica K.; Striegel, Deborah A.

    2011-11-01

    Modeling and understanding cortical folding pattern formation is important for quantifying cortical development. We present a biomathematical model for cortical folding pattern formation in the human brain and apply this model to study diseases involving cortical pattern malformations associated with neural migration disorders. Polymicrogyria is a cortical malformation disease resulting in an excessive number of small gyri. Our mathematical model uses a Turing reaction-diffusion system to model cortical folding. The lateral ventricle (LV) and ventricular zone (VZ) of the brain are critical components in the formation of cortical patterning. In early cortical development the shape of the LV can be modeled with a prolate spheroid and the VZ with a prolate spheroid surface. We use our model to study how global cortex characteristics, such as size and shape of the LV, affect cortical pattern formation. We demonstrate increasing domain scale can increase the number of gyri and sulci formed. Changes in LV shape can account for sulcus directionality. By incorporating LV size and shape, our model is able to elucidate which parameters can lead to excessive cortical folding.

  17. Cortical astrocytes rewire somatosensory cortical circuits for peripheral neuropathic pain.

    PubMed

    Kim, Sun Kwang; Hayashi, Hideaki; Ishikawa, Tatsuya; Shibata, Keisuke; Shigetomi, Eiji; Shinozaki, Youichi; Inada, Hiroyuki; Roh, Seung Eon; Kim, Sang Jeong; Lee, Gihyun; Bae, Hyunsu; Moorhouse, Andrew J; Mikoshiba, Katsuhiko; Fukazawa, Yugo; Koizumi, Schuichi; Nabekura, Junichi

    2016-05-01

    Long-term treatments to ameliorate peripheral neuropathic pain that includes mechanical allodynia are limited. While glial activation and altered nociceptive transmission within the spinal cord are associated with the pathogenesis of mechanical allodynia, changes in cortical circuits also accompany peripheral nerve injury and may represent additional therapeutic targets. Dendritic spine plasticity in the S1 cortex appears within days following nerve injury; however, the underlying cellular mechanisms of this plasticity and whether it has a causal relationship to allodynia remain unsolved. Furthermore, it is not known whether glial activation occurs within the S1 cortex following injury or whether it contributes to this S1 synaptic plasticity. Using in vivo 2-photon imaging with genetic and pharmacological manipulations of murine models, we have shown that sciatic nerve ligation induces a re-emergence of immature metabotropic glutamate receptor 5 (mGluR5) signaling in S1 astroglia, which elicits spontaneous somatic Ca2+ transients, synaptogenic thrombospondin 1 (TSP-1) release, and synapse formation. This S1 astrocyte reactivation was evident only during the first week after injury and correlated with the temporal changes in S1 extracellular glutamate levels and dendritic spine turnover. Blocking the astrocytic mGluR5-signaling pathway suppressed mechanical allodynia, while activating this pathway in the absence of any peripheral injury induced long-lasting (>1 month) allodynia. We conclude that reawakened astrocytes are a key trigger for S1 circuit rewiring and that this contributes to neuropathic mechanical allodynia. PMID:27064281

  18. Cortical astrocytes rewire somatosensory cortical circuits for peripheral neuropathic pain

    PubMed Central

    Hayashi, Hideaki; Ishikawa, Tatsuya; Shibata, Keisuke; Inada, Hiroyuki; Roh, Seung Eon; Kim, Sang Jeong; Moorhouse, Andrew J.

    2016-01-01

    Long-term treatments to ameliorate peripheral neuropathic pain that includes mechanical allodynia are limited. While glial activation and altered nociceptive transmission within the spinal cord are associated with the pathogenesis of mechanical allodynia, changes in cortical circuits also accompany peripheral nerve injury and may represent additional therapeutic targets. Dendritic spine plasticity in the S1 cortex appears within days following nerve injury; however, the underlying cellular mechanisms of this plasticity and whether it has a causal relationship to allodynia remain unsolved. Furthermore, it is not known whether glial activation occurs within the S1 cortex following injury or whether it contributes to this S1 synaptic plasticity. Using in vivo 2-photon imaging with genetic and pharmacological manipulations of murine models, we have shown that sciatic nerve ligation induces a re-emergence of immature metabotropic glutamate receptor 5 (mGluR5) signaling in S1 astroglia, which elicits spontaneous somatic Ca2+ transients, synaptogenic thrombospondin 1 (TSP-1) release, and synapse formation. This S1 astrocyte reactivation was evident only during the first week after injury and correlated with the temporal changes in S1 extracellular glutamate levels and dendritic spine turnover. Blocking the astrocytic mGluR5-signaling pathway suppressed mechanical allodynia, while activating this pathway in the absence of any peripheral injury induced long-lasting (>1 month) allodynia. We conclude that reawakened astrocytes are a key trigger for S1 circuit rewiring and that this contributes to neuropathic mechanical allodynia. PMID:27064281

  19. Adsorption in sparse networks. 2: Silica aerogels

    SciTech Connect

    Scherer, G.W.; Calas, S.; Sempere, R.

    1998-06-15

    The model developed in Part 1 is applied to nitrogen adsorption isotherms obtained for a series of silica aerogels whose densities are varied by partial sintering. The isotherms are adequately described by a cubic network model, with all of the pores falling in the mesopore range; the adsorption and desorption branches are fit by the same pore size distribution. For the least dense gels, a substantial portion of the pore volume is not detected by condensation. The model attributes this effect to the shape of the adsorbate/adsorptive interface, which can adopt zero curvature even in mesopores, because of the shape of the network.

  20. Cortical representation of ipsilateral arm movements in monkey and man

    PubMed Central

    Ganguly, Karunesh; Secundo, Lavi; Ranade, Gireeja; Orsborn, Amy; Chang, Edward F.; Dimitrov, Dragan F.; Wallis, Jonathan D.; Barbaro, Nicholas M.; Knight, Robert T.; Carmena, Jose M.

    2009-01-01

    A fundamental organizational principle of the primate motor system is cortical control of contralateral limb movements. Motor areas also appear to play a role in the control of ipsilateral limb movements. Several studies in monkeys have shown that individual neurons in primary motor cortex (M1) may represent, on average, the direction of movements of the ipsilateral arm. Given the increasing body of evidence demonstrating that neural ensembles can reliably represent information with a high temporal resolution, here we characterize the distributed neural representation of ipsilateral upper limb kinematics in both monkey and man. In two macaque monkeys trained to perform center-out reaching movements, we found that the ensemble spiking activity in M1 could continuously represent ipsilateral limb position. Interestingly, this representation was more correlated with joint angles than hand position. Using bilateral EMG recordings, we excluded the possibility that postural or mirror movements could exclusively account for these findings. In addition, linear methods could decode limb position from cortical field potentials in both monkeys. We also found that M1 spiking activity could control a biomimetic brain-machine interface reflecting ipsilateral kinematics. Finally, we recorded cortical field potentials from three human subjects and also consistently found evidence of a neural representation for ipsilateral movement parameters. Together, our results demonstrate the presence of a high-fidelity neural representation for ipsilateral movement and illustrates that it can be successfully incorporated into a brain-machine interface. PMID:19828809

  1. Characterizing Thalamo-Cortical Disturbances in Schizophrenia and Bipolar Illness

    PubMed Central

    Anticevic, Alan; Cole, Michael W.; Repovs, Grega; Murray, John D.; Brumbaugh, Margaret S.; Winkler, Anderson M.; Savic, Aleksandar; Krystal, John H.; Pearlson, Godfrey D.; Glahn, David C.

    2014-01-01

    Schizophrenia is a devastating neuropsychiatric syndrome associated with distributed brain dysconnectivity that may involve large-scale thalamo-cortical systems. Incomplete characterization of thalamic connectivity in schizophrenia limits our understanding of its relationship to symptoms and to diagnoses with shared clinical presentation, such as bipolar illness, which may exist on a spectrum. Using resting-state functional magnetic resonance imaging, we characterized thalamic connectivity in 90 schizophrenia patients versus 90 matched controls via: (1) Subject-specific anatomically defined thalamic seeds; (2) anatomical and data-driven clustering to assay within-thalamus dysconnectivity; and (3) machine learning to classify diagnostic membership via thalamic connectivity for schizophrenia and for 47 bipolar patients and 47 matched controls. Schizophrenia analyses revealed functionally related disturbances: Thalamic over-connectivity with bilateral sensory–motor cortices, which predicted symptoms, but thalamic under-connectivity with prefrontal–striatal–cerebellar regions relative to controls, possibly reflective of sensory gating and top-down control disturbances. Clustering revealed that this dysconnectivity was prominent for thalamic nuclei densely connected with the prefrontal cortex. Classification and cross-diagnostic results suggest that thalamic dysconnectivity may be a neural marker for disturbances across diagnoses. Present findings, using one of the largest schizophrenia and bipolar neuroimaging samples to date, inform basic understanding of large-scale thalamo-cortical systems and provide vital clues about the complex nature of its disturbances in severe mental illness. PMID:23825317

  2. Prostaglandin E2 Prevents Disuse-Induced Cortical Bone Loss

    NASA Technical Reports Server (NTRS)

    Jee, Webster S. S.; Akamine, T.; Ke, Hua Zhu; Li, Xiao Jian; Tang, L. Y.; Zeng, Q. Q.

    1992-01-01

    The object of this study was to determine whether prostaglandin E2 (PGE2) can prevent disuse (underloaded)-induced cortical bone loss as well as add extra bone to underloaded bones. Thirteen-month-old retired female Sprague-Dawley breeders served as controls or were subjected to simultaneous right hindlimb immobilization by bandaging and daily subcutaneous doses of 0, 1, 3, or 6 mg PGE2/kg/d for two and six weeks. Histomorphometric analyses were performed on double-fluorescent labeled undecalcified tibial shaft sections (proximal to the tibiofibular junction). Disuse-induced cortical bone loss occurred by enlarging the marrow cavity and increasing intracortical porosity. PGE2 treatment of disuse shafts further increased intracortical porosity above that in disuse alone controls. This bone loss was counteracted by enhancement of periosteal and corticoendosteal bone formation. Stimulation of periosteal and corticoendosteal bone formation slightly enlarged the total tissue (cross-sectional) area and inhibited marrow cavity enlargement. These PGE2-induced activities netted the same percentage of cortical bone with a different distribution than the beginning and age related controls. These findings indicate the PGE2-induced increase in bone formation compensated for the disuse and PGE2-induced bone loss, and thus prevented immobilization induced bone loss.

  3. Active Chemical Thermodynamics promoted by activity of cortical actin

    NASA Astrophysics Data System (ADS)

    Bhattacharya, Bhaswati; Chaudhuri, Abhishek; Gowrishankar, Kripa; Rao, Madan

    2011-03-01

    The spatial distribution and dynamics of formation and breakup of the nanoclusters of cell surface proteins is controlled by the active remodeling dynamics of the underlying cortical actin. To explain these observations, we have proposed a novel mechanism of nanoclustering, involving the transient binding to and advection along constitutively occuring ``asters'' of cortical actin. We study the consequences of such active actin-based clustering, in the context of chemical reactions involving conformational changes of cell surface proteins. We find that the active remodeling of cortical actin, can give rise to a dramatic increase in efficiency and extent of conformational spread, even at low levels of expression at the cell surface. We define a activity temperature (τa) arising due to actin activities which can be used to describe chemical thermodynamics of the system. We plot TTT (time-temparature-transformation) curves and compute the Arrhenius factors which depend on τa . With this, the active asters can be treated as enzymes whose enzymatic reaction rate can be related to the activity.

  4. Cortical and cap sedimentation in gravitropic Equisetum roots

    NASA Technical Reports Server (NTRS)

    Ridge, R. W.; Sack, F. D.

    1992-01-01

    Although the rootcap is required for gravitropic sensing, various classical and contemporary data raise the question of whether additional sensing occurs away from the cap in roots. Roots of Equisetum hyemale L. (horsetail) were examined by light and electron microscopy to determine which cell components were distributed with respect to gravity both in and away from the rootcap. Adventitious roots from stem cuttings were gravitropic in a vertical orientation or if reoriented to the horizontal. Obvious amyloplast sedimentation was found in vertical and in reoriented roots 1) in cells in the center of the rootcap and 2) in young, elongating cortical cells located in two to three layers outside the endodermis. These cortical amyloplasts were smaller than cap amyloplasts and, unlike central cap amyloplasts, were occasionally found in the top of the cell. The nucleus was also sedimented on top of the amyloplasts in both cell types, both in vertical and in reoriented roots. Sedimentation of both organelles ceased as cortical cells elongated further or as cap cells became peripheral in location. In both cell types with sedimentation, endoplasmic reticulum was located in the cell periphery, but showed no obvious enrichment near the lower part of the cell in vertical roots. This is the first modern report of sedimentation away from the cap in roots, and it provides structural evidence that gravitropic sensing may not be confined to the cap in all roots.

  5. Global Neuromagnetic Cortical Fields Have Non-Zero Velocity

    PubMed Central

    Alexander, David M.; Nikolaev, Andrey R.; Jurica, Peter; Zvyagintsev, Mikhail; Mathiak, Klaus; van Leeuwen, Cees

    2016-01-01

    Globally coherent patterns of phase can be obscured by analysis techniques that aggregate brain activity measures across-trials, whether prior to source localization or for estimating inter-areal coherence. We analyzed, at single-trial level, whole head MEG recorded during an observer-triggered apparent motion task. Episodes of globally coherent activity occurred in the delta, theta, alpha and beta bands of the signal in the form of large-scale waves, which propagated with a variety of velocities. Their mean speed at each frequency band was proportional to temporal frequency, giving a range of 0.06 to 4.0 m/s, from delta to beta. The wave peaks moved over the entire measurement array, during both ongoing activity and task-relevant intervals; direction of motion was more predictable during the latter. A large proportion of the cortical signal, measurable at the scalp, exists as large-scale coherent motion. We argue that the distribution of observable phase velocities in MEG is dominated by spatial filtering considerations in combination with group velocity of cortical activity. Traveling waves may index processes involved in global coordination of cortical activity. PMID:26953886

  6. Linking cortical network synchrony and excitability

    PubMed Central

    Meisel, Christian

    2016-01-01

    ABSTRACT Theoretical approaches based on dynamical systems theory can provide useful frameworks to guide experiments and analysis techniques when investigating cortical network activity. The notion of phase transitions between qualitatively different kinds of network dynamics has been such a framework inspiring novel approaches to neurophysiological data analysis over the recent years. One particular intriguing hypothesis has been that cortical networks reside in the vicinity of a phase transition. Although the final verdict on this hypothesis is still out, trying to understand cortex dynamics from this viewpoint has recently led to interesting insights on cortical network function with relevance for clinical practice. PMID:27065159

  7. Focal Cortical Dysplasia in Childhood Epilepsy.

    PubMed

    Shaker, Tarek; Bernier, Anne; Carmant, Lionel

    2016-05-01

    Focal cortical dysplasia is a common cause of medication resistant epilepsy. A better understanding of its presentation, pathophysiology and consequences have helped us improved its treatment and outcome. This paper reviews the most recent classification, pathophysiology and imaging findings in clinical research as well as the knowledge gained from studying genetic and lesional animal models of focal cortical dysplasia. This review of this recently gained knowledge will most likely help develop new research models and new therapeutic targets for patients with epilepsy associated with focal cortical dysplasia. PMID:27544467

  8. Representation of memories in the cortical-hippocampal system: Results from the application of population similarity analyses.

    PubMed

    McKenzie, Sam; Keene, Christopher S; Farovik, Anja; Bladon, John; Place, Ryan; Komorowski, Robert; Eichenbaum, Howard

    2016-10-01

    Here we consider the value of neural population analysis as an approach to understanding how information is represented in the hippocampus and cortical areas and how these areas might interact as a brain system to support memory. We argue that models based on sparse coding of different individual features by single neurons in these areas (e.g., place cells, grid cells) are inadequate to capture the complexity of experience represented within this system. By contrast, population analyses of neurons with denser coding and mixed selectivity reveal new and important insights into the organization of memories. Furthermore, comparisons of the organization of information in interconnected areas suggest a model of hippocampal-cortical interactions that mediates the fundamental features of memory.

  9. Representation of memories in the cortical-hippocampal system: Results from the application of population similarity analyses.

    PubMed

    McKenzie, Sam; Keene, Christopher S; Farovik, Anja; Bladon, John; Place, Ryan; Komorowski, Robert; Eichenbaum, Howard

    2016-10-01

    Here we consider the value of neural population analysis as an approach to understanding how information is represented in the hippocampus and cortical areas and how these areas might interact as a brain system to support memory. We argue that models based on sparse coding of different individual features by single neurons in these areas (e.g., place cells, grid cells) are inadequate to capture the complexity of experience represented within this system. By contrast, population analyses of neurons with denser coding and mixed selectivity reveal new and important insights into the organization of memories. Furthermore, comparisons of the organization of information in interconnected areas suggest a model of hippocampal-cortical interactions that mediates the fundamental features of memory. PMID:26748022

  10. Brain Plasticity in Blind Subjects Centralizes Beyond the Modal Cortices

    PubMed Central

    Ortiz-Terán, Laura; Ortiz, Tomás; Perez, David L.; Aragón, Jose Ignacio; Diez, Ibai; Pascual-Leone, Alvaro; Sepulcre, Jorge

    2016-01-01

    It is well established that the human brain reorganizes following sensory deprivations. In blind individuals, visual processing regions including the lateral occipital cortex (LOC) are activated by auditory and tactile stimuli as demonstrated by neurophysiological and neuroimaging investigations. The mechanisms for such plasticity remain unclear, but shifts in connectivity across existing neural networks appear to play a critical role. The majority of research efforts to date have focused on neuroplastic changes within visual unimodal regions, however we hypothesized that neuroplastic alterations may also occur in brain networks beyond the visual cortices including involvement of multimodal integration regions and heteromodal cortices. In this study, two recently developed graph-theory based functional connectivity analyses, interconnector analyses and local and distant connectivity, were applied to investigate functional reorganization in regional and distributed neural-systems in late-onset blind (LB) and congenitally blind (CB) cohorts each compared to their own group of sighted controls. While functional network alterations as measured by the degree of differential links (DDL) occurred in sensory cortices, neuroplastic changes were most prominent within multimodal and association cortices. Subjects with LB showed enhanced multimodal integration connections in the parieto-opercular, temporoparietal junction (TPJ) and ventral premotor (vPM) regions, while CB individuals exhibited increased superior parietal cortex (SPC) connections. This study reveals the critical role of recipient multi-sensory integration areas in network reorganization and cross-modal plasticity in blind individuals. These findings suggest that aspects of cross-modal neuroplasticity and adaptive sensory-motor and auditory functions may potentially occur through reorganization in multimodal integration regions. PMID:27458350

  11. Brain Plasticity in Blind Subjects Centralizes Beyond the Modal Cortices.

    PubMed

    Ortiz-Terán, Laura; Ortiz, Tomás; Perez, David L; Aragón, Jose Ignacio; Diez, Ibai; Pascual-Leone, Alvaro; Sepulcre, Jorge

    2016-01-01

    It is well established that the human brain reorganizes following sensory deprivations. In blind individuals, visual processing regions including the lateral occipital cortex (LOC) are activated by auditory and tactile stimuli as demonstrated by neurophysiological and neuroimaging investigations. The mechanisms for such plasticity remain unclear, but shifts in connectivity across existing neural networks appear to play a critical role. The majority of research efforts to date have focused on neuroplastic changes within visual unimodal regions, however we hypothesized that neuroplastic alterations may also occur in brain networks beyond the visual cortices including involvement of multimodal integration regions and heteromodal cortices. In this study, two recently developed graph-theory based functional connectivity analyses, interconnector analyses and local and distant connectivity, were applied to investigate functional reorganization in regional and distributed neural-systems in late-onset blind (LB) and congenitally blind (CB) cohorts each compared to their own group of sighted controls. While functional network alterations as measured by the degree of differential links (DDL) occurred in sensory cortices, neuroplastic changes were most prominent within multimodal and association cortices. Subjects with LB showed enhanced multimodal integration connections in the parieto-opercular, temporoparietal junction (TPJ) and ventral premotor (vPM) regions, while CB individuals exhibited increased superior parietal cortex (SPC) connections. This study reveals the critical role of recipient multi-sensory integration areas in network reorganization and cross-modal plasticity in blind individuals. These findings suggest that aspects of cross-modal neuroplasticity and adaptive sensory-motor and auditory functions may potentially occur through reorganization in multimodal integration regions. PMID:27458350

  12. Nonlinear random response of large-scale sparse finite element plate bending problems

    NASA Astrophysics Data System (ADS)

    Chokshi, Swati

    Acoustic fatigue is one of the major design considerations for skin panels exposed to high levels of random pressure at subsonic/supersonic/hypersonic speeds. The nonlinear large deflection random response of the single-bay panels aerospace structures subjected to random excitations at various sound pressure levels (SPLs) is investigated. The nonlinear responses of plate analyses are limited to determine the root-mean-square displacement under uniformly distributed pressure random loads. Efficient computational technologies like sparse storage schemes and parallel computation are proposed and incorporated to solve large-scale, nonlinear large deflection random vibration problems for both types of loading cases: (1) synchronized in time and (2) unsynchronized and statistically uncorrelated in time. For the first time, large scale plate bending problems subjected to unsynchronized load are solved using parallel computing capabilities to account for computational burden due to the simulation of the unsynchronized random pressure fluctuations. The main focus of the research work is placed upon computational issues involved in the nonlinear modal methodologies. A nonlinear FEM method in time domain is incorporated with the Monte Carlo simulation and sparse computational technologies, including the efficient sparse Subspace Eigen-solutions are presented and applied to accurately determine the random response with a refined, large finite element mesh for the first time. Sparse equation solver and sparse matrix operations embedded inside the subspace Eigen-solution algorithms are also exploited. The approach uses the von-Karman nonlinear strain-displacement relations and the classical plate theory. In the proposed methodologies, the solution for a small number (say less than 100) of lowest linear, sparse Eigen-pairs need to be solved for only once, in order to transform nonlinear large displacements from the conventional structural degree-of-freedom (dof) into the modal

  13. Sparse covariance estimation in heterogeneous samples*

    PubMed Central

    Rodríguez, Abel; Lenkoski, Alex; Dobra, Adrian

    2015-01-01

    Standard Gaussian graphical models implicitly assume that the conditional independence among variables is common to all observations in the sample. However, in practice, observations are usually collected from heterogeneous populations where such an assumption is not satisfied, leading in turn to nonlinear relationships among variables. To address such situations we explore mixtures of Gaussian graphical models; in particular, we consider both infinite mixtures and infinite hidden Markov models where the emission distributions correspond to Gaussian graphical models. Such models allow us to divide a heterogeneous population into homogenous groups, with each cluster having its own conditional independence structure. As an illustration, we study the trends in foreign exchange rate fluctuations in the pre-Euro era. PMID:26925189

  14. Rich-Club Organization in Effective Connectivity among Cortical Neurons.

    PubMed

    Nigam, Sunny; Shimono, Masanori; Ito, Shinya; Yeh, Fang-Chin; Timme, Nicholas; Myroshnychenko, Maxym; Lapish, Christopher C; Tosi, Zachary; Hottowy, Pawel; Smith, Wesley C; Masmanidis, Sotiris C; Litke, Alan M; Sporns, Olaf; Beggs, John M

    2016-01-20

    The performance of complex networks, like the brain, depends on how effectively their elements communicate. Despite the importance of communication, it is virtually unknown how information is transferred in local cortical networks, consisting of hundreds of closely spaced neurons. To address this, it is important to record simultaneously from hundreds of neurons at a spacing that matches typical axonal connection distances, and at a temporal resolution that matches synaptic delays. We used a 512-electrode array (60 μm spacing) to record spontaneous activity at 20 kHz from up to 500 neurons simultaneously in slice cultures of mouse somatosensory cortex for 1 h at a time. We applied a previously validated version of transfer entropy to quantify information transfer. Similar to in vivo reports, we found an approximately lognormal distribution of firing rates. Pairwise information transfer strengths also were nearly lognormally distributed, similar to reports of synaptic strengths. Some neurons transferred and received much more information than others, which is consistent with previous predictions. Neurons with the highest outgoing and incoming information transfer were more strongly connected to each other than chance, thus forming a "rich club." We found similar results in networks recorded in vivo from rodent cortex, suggesting the generality of these findings. A rich-club structure has been found previously in large-scale human brain networks and is thought to facilitate communication between cortical regions. The discovery of a small, but information-rich, subset of neurons within cortical regions suggests that this population will play a vital role in communication, learning, and memory. Significance statement: Many studies have focused on communication networks between cortical brain regions. In contrast, very few studies have examined communication networks within a cortical region. This is the first study to combine such a large number of neurons (several

  15. Rich-Club Organization in Effective Connectivity among Cortical Neurons

    PubMed Central

    Shimono, Masanori; Ito, Shinya; Yeh, Fang-Chin; Timme, Nicholas; Myroshnychenko, Maxym; Lapish, Christopher C.; Tosi, Zachary; Hottowy, Pawel; Smith, Wesley C.; Masmanidis, Sotiris C.; Litke, Alan M.; Sporns, Olaf; Beggs, John M.

    2016-01-01

    The performance of complex networks, like the brain, depends on how effectively their elements communicate. Despite the importance of communication, it is virtually unknown how information is transferred in local cortical networks, consisting of hundreds of closely spaced neurons. To address this, it is important to record simultaneously from hundreds of neurons at a spacing that matches typical axonal connection distances, and at a temporal resolution that matches synaptic delays. We used a 512-electrode array (60 μm spacing) to record spontaneous activity at 20 kHz from up to 500 neurons simultaneously in slice cultures of mouse somatosensory cortex for 1 h at a time. We applied a previously validated version of transfer entropy to quantify information transfer. Similar to in vivo reports, we found an approximately lognormal distribution of firing rates. Pairwise information transfer strengths also were nearly lognormally distributed, similar to reports of synaptic strengths. Some neurons transferred and received much more information than others, which is consistent with previous predictions. Neurons with the highest outgoing and incoming information transfer were more strongly connected to each other than chance, thus forming a “rich club.” We found similar results in networks recorded in vivo from rodent cortex, suggesting the generality of these findings. A rich-club structure has been found previously in large-scale human brain networks and is thought to facilitate communication between cortical regions. The discovery of a small, but information-rich, subset of neurons within cortical regions suggests that this population will play a vital role in communication, learning, and memory. SIGNIFICANCE STATEMENT Many studies have focused on communication networks between cortical brain regions. In contrast, very few studies have examined communication networks within a cortical region. This is the first study to combine such a large number of neurons (several

  16. MR image reconstruction algorithms for sparse k-space data: a Java-based integration.

    PubMed

    de Beer, R; Coron, A; Graveron-Demilly, D; Lethmate, R; Nastase, S; van Ormondt, D; Wajer, F T A W

    2002-11-01

    We have worked on multi-dimensional magnetic resonance imaging (MRI) data acquisition and related image reconstruction methods that aim at reducing the MRI scan time. To achieve this scan-time reduction we have combined the approach of 'increasing the speed' of k-space acquisition with that of 'deliberately omitting' acquisition of k-space trajectories (sparse sampling). Today we have a whole range of (sparse) sampling distributions and related reconstruction methods. In the context of a European Union Training and Mobility of Researchers project we have decided to integrate all methods into one coordinating software system. This system meets the requirements that it is highly structured in an object-oriented manner using the Unified Modeling Language and the Java programming environment, that it uses the client-server approach, that it allows multi-client communication sessions with facilities for sharing data and that it is a true distributed computing system with guaranteed reliability using core activities of the Java Jini package. PMID:12413561

  17. Inference of the sparse kinetic Ising model using the decimation method.

    PubMed

    Decelle, Aurélien; Zhang, Pan

    2015-05-01

    In this paper we study the inference of the kinetic Ising model on sparse graphs by the decimation method. The decimation method, which was first proposed in Decelle and Ricci-Tersenghi [Phys. Rev. Lett. 112, 070603 (2014)] for the static inverse Ising problem, tries to recover the topology of the inferred system by setting the weakest couplings to zero iteratively. During the decimation process the likelihood function is maximized over the remaining couplings. Unlike the ℓ(1)-optimization-based methods, the decimation method does not use the Laplace distribution as a heuristic choice of prior to select a sparse solution. In our case, the whole process can be done auto-matically without fixing any parameters by hand. We show that in the dynamical inference problem, where the task is to reconstruct the couplings of an Ising model given the data, the decimation process can be applied naturally into a maximum-likelihood optimization algorithm, as opposed to the static case where pseudolikelihood method needs to be adopted. We also use extensive numerical studies to validate the accuracy of our methods in dynamical inference problems. Our results illustrate that, on various topologies and with different distribution of couplings, the decimation method outperforms the widely used ℓ(1)-optimization-based methods. PMID:26066148

  18. Geometry Shapes Propagation: Assessing the Presence and Absence of Cortical Symmetries through a Computational Model of Cortical Spreading Depression

    PubMed Central

    Kroos, Julia M.; Diez, Ibai; Cortes, Jesus M.; Stramaglia, Sebastiano; Gerardo-Giorda, Luca

    2016-01-01

    Cortical spreading depression (CSD), a depolarization wave which originates in the visual cortex and travels toward the frontal lobe, has been suggested to be one neural correlate of aura migraine. To the date, little is known about the mechanisms which can trigger or stop aura migraine. Here, to shed some light on this problem and, under the hypothesis that CSD might mediate aura migraine, we aim to study different aspects favoring or disfavoring the propagation of CSD. In particular, by using a computational neuronal model distributed throughout a realistic cortical mesh, we study the role that the geometry has in shaping CSD. Our results are two-fold: first, we found significant differences in the propagation traveling patterns of CSD, both intra and inter-hemispherically, revealing important asymmetries in the propagation profile. Second, we developed methods able to identify brain regions featuring a peculiar behavior during CSD propagation. Our study reveals dynamical aspects of CSD, which, if applied to subject-specific cortical geometry, might shed some light on how to differentiate between healthy subjects and those suffering migraine. PMID:26869913

  19. Cortical circuits for perceptual inference.

    PubMed

    Friston, Karl; Kiebel, Stefan

    2009-10-01

    This paper assumes that cortical circuits have evolved to enable inference about the causes of sensory input received by the brain. This provides a principled specification of what neural circuits have to achieve. Here, we attempt to address how the brain makes inferences by casting inference as an optimisation problem. We look at how the ensuing recognition dynamics could be supported by directed connections and message-passing among neuronal populations, given our knowledge of intrinsic and extrinsic neuronal connections. We assume that the brain models the world as a dynamic system, which imposes causal structure on the sensorium. Perception is equated with the optimisation or inversion of this internal model, to explain sensory input. Given a model of how sensory data are generated, we use a generic variational approach to model inversion to furnish equations that prescribe recognition; i.e., the dynamics of neuronal activity that represents the causes of sensory input. Here, we focus on a model whose hierarchical and dynamical structure enables simulated brains to recognise and predict sequences of sensory states. We first review these models and their inversion under a variational free-energy formulation. We then show that the brain has the necessary infrastructure to implement this inversion and present stimulations using synthetic birds that generate and recognise birdsongs.

  20. Cortical circuits for perceptual inference.

    PubMed

    Friston, Karl; Kiebel, Stefan

    2009-10-01

    This paper assumes that cortical circuits have evolved to enable inference about the causes of sensory input received by the brain. This provides a principled specification of what neural circuits have to achieve. Here, we attempt to address how the brain makes inferences by casting inference as an optimisation problem. We look at how the ensuing recognition dynamics could be supported by directed connections and message-passing among neuronal populations, given our knowledge of intrinsic and extrinsic neuronal connections. We assume that the brain models the world as a dynamic system, which imposes causal structure on the sensorium. Perception is equated with the optimisation or inversion of this internal model, to explain sensory input. Given a model of how sensory data are generated, we use a generic variational approach to model inversion to furnish equations that prescribe recognition; i.e., the dynamics of neuronal activity that represents the causes of sensory input. Here, we focus on a model whose hierarchical and dynamical structure enables simulated brains to recognise and predict sequences of sensory states. We first review these models and their inversion under a variational free-energy formulation. We then show that the brain has the necessary infrastructure to implement this inversion and present stimulations using synthetic birds that generate and recognise birdsongs. PMID:19635656