Encoding Cortical Dynamics in Sparse Features
Khan, Sheraz; Lefèvre, Julien; Baillet, Sylvain; Michmizos, Konstantinos P.; Ganesan, Santosh; Kitzbichler, Manfred G.; Zetino, Manuel; Hämäläinen, Matti S.; Papadelis, Christos; Kenet, Tal
2014-01-01
Distributed cortical solutions of magnetoencephalography (MEG) and electroencephalography (EEG) exhibit complex spatial and temporal dynamics. The extraction of patterns of interest and dynamic features from these cortical signals has so far relied on the expertise of investigators. There is a definite need in both clinical and neuroscience research for a method that will extract critical features from high-dimensional neuroimaging data in an automatic fashion. We have previously demonstrated the use of optical flow techniques for evaluating the kinematic properties of motion field projected on non-flat manifolds like in a cortical surface. We have further extended this framework to automatically detect features in the optical flow vector field by using the modified and extended 2-Riemannian Helmholtz–Hodge decomposition (HHD). Here, we applied these mathematical models on simulation and MEG data recorded from a healthy individual during a somatosensory experiment and an epilepsy pediatric patient during sleep. We tested whether our technique can automatically extract salient dynamical features of cortical activity. Simulation results indicated that we can precisely reproduce the simulated cortical dynamics with HHD; encode them in sparse features and represent the propagation of brain activity between distinct cortical areas. Using HHD, we decoded the somatosensory N20 component into two HHD features and represented the dynamics of brain activity as a traveling source between two primary somatosensory regions. In the epilepsy patient, we displayed the propagation of the epileptic activity around the margins of a brain lesion. Our findings indicate that HHD measures computed from cortical dynamics can: (i) quantitatively access the cortical dynamics in both healthy and disease brain in terms of sparse features and dynamic brain activity propagation between distinct cortical areas, and (ii) facilitate a reproducible, automated analysis of experimental and clinical
Encoding cortical dynamics in sparse features.
Khan, Sheraz; Lefèvre, Julien; Baillet, Sylvain; Michmizos, Konstantinos P; Ganesan, Santosh; Kitzbichler, Manfred G; Zetino, Manuel; Hämäläinen, Matti S; Papadelis, Christos; Kenet, Tal
2014-01-01
Distributed cortical solutions of magnetoencephalography (MEG) and electroencephalography (EEG) exhibit complex spatial and temporal dynamics. The extraction of patterns of interest and dynamic features from these cortical signals has so far relied on the expertise of investigators. There is a definite need in both clinical and neuroscience research for a method that will extract critical features from high-dimensional neuroimaging data in an automatic fashion. We have previously demonstrated the use of optical flow techniques for evaluating the kinematic properties of motion field projected on non-flat manifolds like in a cortical surface. We have further extended this framework to automatically detect features in the optical flow vector field by using the modified and extended 2-Riemannian Helmholtz-Hodge decomposition (HHD). Here, we applied these mathematical models on simulation and MEG data recorded from a healthy individual during a somatosensory experiment and an epilepsy pediatric patient during sleep. We tested whether our technique can automatically extract salient dynamical features of cortical activity. Simulation results indicated that we can precisely reproduce the simulated cortical dynamics with HHD; encode them in sparse features and represent the propagation of brain activity between distinct cortical areas. Using HHD, we decoded the somatosensory N20 component into two HHD features and represented the dynamics of brain activity as a traveling source between two primary somatosensory regions. In the epilepsy patient, we displayed the propagation of the epileptic activity around the margins of a brain lesion. Our findings indicate that HHD measures computed from cortical dynamics can: (i) quantitatively access the cortical dynamics in both healthy and disease brain in terms of sparse features and dynamic brain activity propagation between distinct cortical areas, and (ii) facilitate a reproducible, automated analysis of experimental and clinical
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.
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.
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.
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.
Sparse asynchronous cortical generators can produce measurable scalp EEG signals.
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
Sparse cortical source localization using spatio-temporal atoms.
Korats, Gundars; Ranta, Radu; Le Cam, Steven; Louis-Dorr, Valérie
2015-08-01
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
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.
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.
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.
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.
Integer sparse distributed memory: analysis and results.
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
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.
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.
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.
Sparsey™: event recognition via deep hierarchical sparse distributed codes
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
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.
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.
Investigation of wall-bounded turbulence over sparsely distributed roughness
NASA Astrophysics Data System (ADS)
Placidi, Marco; Ganapathisubramani, Bharath
2011-11-01
The effects of sparsely distributed roughness elements on the structure of a turbulent boundary layer are examined by performing a series of Particle Image Velocimetry (PIV) experiments in a wind tunnel. From the literature, the best way to characterise a rough wall, especially one where the density of roughness elements is sparse, is unclear. In this study, rough surfaces consisting of sparsely and uniformly distributed LEGO® blocks are used. Five different patterns are adopted in order to examine the effects of frontal solidity (λf, frontal area of the roughness elements per unit wall-parallel area), plan solidity (λp, plan area of roughness elements per unit wall-parallel area) and the geometry of the roughness element (square and cylindrical elements), on the turbulence structure. The Karman number, Reτ , has been matched, at the value of approximately 2300, in order to compare across the different cases. In the talk, we will present detailed analysis of mean and rms velocity profiles, Reynolds stresses and quadrant decomposition.
EPR Oximetry in Three Spatial Dimensions using Sparse Spin Distribution
Som, Subhojit; Potter, Lee C.; Ahmad, Rizwan; Vikram, Deepti S.; Kuppusamy, Periannan
2008-01-01
A method is presented to use continuous wave electron paramagnetic resonance imaging for rapid measurement of oxygen partial pressure in three spatial dimensions. A particulate paramagnetic probe is employed to create a sparse distribution of spins in a volume of interest. Information encoding location and spectral linewidth is collected by varying the spatial orientation and strength of an applied magnetic gradient field. Data processing exploits the spatial sparseness of spins to detect voxels with nonzero spin and to estimate the spectral linewidth for those voxels. The parsimonious representation of spin locations and linewidths permits an order of magnitude reduction in data acquisition time, compared to four-dimensional tomographic reconstruction using traditional spectral-spatial imaging. The proposed oximetry method is experimentally demonstrated for a lithium octa-n-butoxy naphthalocyanine (LiNc-BuO) probe using an L-band EPR spectrometer. PMID:18538600
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.
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
Multiple peaks of species abundance distributions induced by sparse interactions.
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
Improved load distribution in parallel sparse Cholesky factorization
NASA Technical Reports Server (NTRS)
Rothberg, Edward; Schreiber, Robert
1994-01-01
Compared to the customary column-oriented approaches, block-oriented, distributed-memory sparse Cholesky factorization benefits from an asymptotic reduction in interprocessor communication volume and an asymptotic increase in the amount of concurrency that is exposed in the problem. Unfortunately, block-oriented approaches (specifically, the block fan-out method) have suffered from poor balance of the computational load. As a result, achieved performance can be quite low. This paper investigates the reasons for this load imbalance and proposes simple block mapping heuristics that dramatically improve it. The result is a roughly 20% increase in realized parallel factorization performance, as demonstrated by performance results from an Intel Paragon system. We have achieved performance of nearly 3.2 billion floating point operations per second with this technique on a 196-node Paragon system.
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.
In-Memory Computing Architectures for Sparse Distributed Memory.
Kang, Mingu; Shanbhag, Naresh R
2016-08-01
This paper presents an energy-efficient and high-throughput architecture for Sparse Distributed Memory (SDM)-a computational model of the human brain [1]. The proposed SDM architecture is based on the recently proposed in-memory computing kernel for machine learning applications called Compute Memory (CM) [2], [3]. CM achieves energy and throughput efficiencies by deeply embedding computation into the memory array. SDM-specific techniques such as hierarchical binary decision (HBD) are employed to reduce the delay and energy further. The CM-based SDM (CM-SDM) is a mixed-signal circuit, and hence circuit-aware behavioral, energy, and delay models in a 65 nm CMOS process are developed in order to predict system performance of SDM architectures in the auto- and hetero-associative modes. The delay and energy models indicate that CM-SDM, in general, can achieve up to 25 × and 12 × delay and energy reduction, respectively, over conventional SDM. When classifying 16 × 16 binary images with high noise levels (input bad pixel ratios: 15%-25%) into nine classes, all SDM architectures are able to generate output bad pixel ratios (Bo) ≤ 2%. The CM-SDM exhibits negligible loss in accuracy, i.e., its Bo degradation is within 0.4% as compared to that of the conventional SDM. PMID:27305686
Two-dimensional shape recognition using sparse distributed memory
NASA Technical Reports Server (NTRS)
Kanerva, Pentti; Olshausen, Bruno
1990-01-01
Researchers propose a method for recognizing two-dimensional shapes (hand-drawn characters, for example) with an associative memory. The method consists of two stages: first, the image is preprocessed to extract tangents to the contour of the shape; second, the set of tangents is converted to a long bit string for recognition with sparse distributed memory (SDM). SDM provides a simple, massively parallel architecture for an associative memory. Long bit vectors (256 to 1000 bits, for example) serve as both data and addresses to the memory, and patterns are grouped or classified according to similarity in Hamming distance. At the moment, tangents are extracted in a simple manner by progressively blurring the image and then using a Canny-type edge detector (Canny, 1986) to find edges at each stage of blurring. This results in a grid of tangents. While the technique used for obtaining the tangents is at present rather ad hoc, researchers plan to adopt an existing framework for extracting edge orientation information over a variety of resolutions, such as suggested by Watson (1987, 1983), Marr and Hildreth (1980), or Canny (1986).
Sparse Solution of Fiber Orientation Distribution Function by Diffusion Decomposition
Yeh, Fang-Cheng; Tseng, Wen-Yih Isaac
2013-01-01
Fiber orientation is the key information in diffusion tractography. Several deconvolution methods have been proposed to obtain fiber orientations by estimating a fiber orientation distribution function (ODF). However, the L2 regularization used in deconvolution often leads to false fibers that compromise the specificity of the results. To address this problem, we propose a method called diffusion decomposition, which obtains a sparse solution of fiber ODF by decomposing the diffusion ODF obtained from q-ball imaging (QBI), diffusion spectrum imaging (DSI), or generalized q-sampling imaging (GQI). A simulation study, a phantom study, and an in-vivo study were conducted to examine the performance of diffusion decomposition. The simulation study showed that diffusion decomposition was more accurate than both constrained spherical deconvolution and ball-and-sticks model. The phantom study showed that the angular error of diffusion decomposition was significantly lower than those of constrained spherical deconvolution at 30° crossing and ball-and-sticks model at 60° crossing. The in-vivo study showed that diffusion decomposition can be applied to QBI, DSI, or GQI, and the resolved fiber orientations were consistent regardless of the diffusion sampling schemes and diffusion reconstruction methods. The performance of diffusion decomposition was further demonstrated by resolving crossing fibers on a 30-direction QBI dataset and a 40-direction DSI dataset. In conclusion, diffusion decomposition can improve angular resolution and resolve crossing fibers in datasets with low SNR and substantially reduced number of diffusion encoding directions. These advantages may be valuable for human connectome studies and clinical research. PMID:24146772
Is cortical distribution of spectral power a stable individual characteristic?
Knyazev, Gennady G
2009-05-01
General understanding in EEG research is that cortical distribution of spectral power varies as a function of time, frequency, state, and experimental condition. There are findings, however, which show that individual-specific patterns of cortical spectral power distribution could be amazingly stable, at least in some experimental conditions. In this study two different experimental datasets were used to analyze stability and variability of individual pattern of cortical spectral power distribution across time, experimental conditions, and frequency bands. First experiment consisted of presentation of pictures of emotional facial expressions. Second experiment was an auditory stop-signal task. In both experiments a number of psychometric measures were obtained from each participant. It has been shown that in spite of high short-term variability, individual-specific patterns of cortical spectral power distribution are remarkably stable across frequency bands, long periods of time, and experimental conditions. These patterns are related to state and trait participant's characteristics. The antero-posterior spectral power gradient emerged as the most prominent feature associated with important personality dimensions. Relatively higher oscillatory activity in the frontal cortical region relates to female gender and Behavioral Inhibition tendencies. Relatively higher activity at posterior sites is associated with Extraversion. Significant differences in event-related spectral perturbations upon presentation of emotionally loaded stimuli were found between high and low antero-posterior gradient participants. These data show that cortical distribution of oscillatory activity may be seen as a relatively stable individual characteristic. Enhanced or diminished oscillatory activity of some cortical regions, such as the prefrontal cortex, may play an important role in organization of human behavior. PMID:19047002
Storing structured sparse memories in a multi-modular cortical network model.
Dubreuil, Alexis M; Brunel, Nicolas
2016-04-01
We study the memory performance of a class of modular attractor neural networks, where modules are potentially fully-connected networks connected to each other via diluted long-range connections. On this anatomical architecture we store memory patterns of activity using a Willshaw-type learning rule. P patterns are split in categories, such that patterns of the same category activate the same set of modules. We first compute the maximal storage capacity of these networks. We then investigate their error-correction properties through an exhaustive exploration of parameter space, and identify regions where the networks behave as an associative memory device. The crucial parameters that control the retrieval abilities of the network are (1) the ratio between the number of synaptic contacts of long- and short-range origins (2) the number of categories in which a module is activated and (3) the amount of local inhibition. We discuss the relationship between our model and networks of cortical patches that have been observed in different cortical areas. PMID:26852335
Cortical bone distribution in the femoral neck of strepsirhine primates.
Demes, B; Jungers, W L; Walker, C
2000-10-01
The thickness of the inferior and superior cortices of the femoral neck was measured on X-rays of 181 strepsirhine primate femora representing 24 species. Neck length, neck depth and neck-shaft angle were also measured. The strength of the femoral neck in frontal bending was estimated by modeling the neck as a hollow cylinder, with neck depth as the outer diameter and cortical thickness representing the superior and inferior shell dimensions. Results indicate that the inferior cortex is always thicker than the superior cortex. The ratio of superior to inferior cortical thickness is highly variable but distinguishes two of the three locomotor groups in the sample. Vertical clingers and leapers have higher ratios (i.e., a more even distribution of cortical bone) than quadrupeds. The slow climbers tend to have the lowest ratios, although they do not differ significantly from the leapers and quadrupeds. These results do not confirm prior theoretical expectations and reported data for anthropoid primates that link greater asymmetry of the cortical shell to more stereotypical hip excursions. The ratio of superior to inferior cortical thickness is unrelated to body mass, femoral neck length, and neck-shaft angle, calling into question whether the short neck of strepsirhine primates acts as a cantilever beam in bending. On the other hand, the estimated section moduli are highly correlated with body mass and neck length, a correlation that is driven primarily by body mass. In conclusion, we believe that an alternative interpretation to the cantilever beam model is needed to explain the asymmetry in bone distribution in the femoral neck, at least in strepsirhine primates (e.g., a thicker inferior cortex is required to reinforce the strongly curved inferior surface). As in prior studies of cross-sectional geometry of long bones, we found slightly positive allometry of cortical dimensions with body mass. PMID:11006046
SuperLU{_}DIST: A scalable distributed-memory sparse direct solver for unsymmetric linear systems
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.
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.
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.
A class of designs for a sparse distributed memory
NASA Technical Reports Server (NTRS)
Jaeckel, Louis A.
1989-01-01
A general class of designs for a space distributed memory (SDM) is described. The author shows that Kanerva's original design and the selected-coordinate design are related, and that there is a series of possible intermediate designs between those two designs. In each such design, the set of addresses that activate a memory location is a sphere in the address space. We can also have hybrid designs, in which the memory locations may be a mixture of those found in the other designs. In some applications, the bits of the read and write addresses that will actually be used might be mostly zeros; that is, the addresses might lie on or near z hyperplane in the address space. The author describes a hyperplane design which is adapted to this situation and compares it to an adaptation of Kanerva's design. To study the performance of these designs, he computes the expected number of memory locations activated by both of two addresses.
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.
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.
Analysis, tuning and comparison of two general sparse solvers for distributed memory computers
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.
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. PMID:1414117
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.
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
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. PMID:21724511
Short-Term Variations in Response Distribution to Cortical Stimulation
ERIC Educational Resources Information Center
Lesser, Ronald P.; Lee, Hyang Woon; Webber, W. R. S.; Prince, Barry; Crone, Nathan E.; Miglioretti, Diana L.
2008-01-01
Patterns of responses in the cerebral cortex can vary, and are influenced by pre-existing cortical function, but it is not known how rapidly these variations can occur in humans. We investigated how rapidly response patterns to electrical stimulation can vary in intact human brain. We also investigated whether the type of functional change…
Sparse distributed memory: understanding the speed and robustness of expert memory.
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
Sparse distributed memory: understanding the speed and robustness of expert memory
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
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.
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.
Bachega, Leonardo R; Hariharan, Srikanth; Bouman, Charles A; Shroff, Ness B
2015-12-01
This paper introduces the vector sparse matrix transform (vector SMT), a new decorrelating transform suitable for performing distributed processing of high-dimensional signals in sensor networks. We assume that each sensor in the network encodes its measurements into vector outputs instead of scalar ones. The proposed transform decorrelates a sequence of pairs of vector outputs, until these vectors are decorrelated. In our experiments, we simulate distributed anomaly detection by a network of cameras, monitoring a spatial region. Each camera records an image of the monitored environment from its particular viewpoint and outputs a vector encoding the image. Our results, with both artificial and real data, show that the proposed vector SMT transform effectively decorrelates image measurements from the multiple cameras in the network while maintaining low overall communication energy consumption. Since it enables joint processing of the multiple vector outputs, our method provides significant improvements to anomaly detection accuracy when compared with the baseline case when the images are processed independently. PMID:26415179
NASA Technical Reports Server (NTRS)
Jaeckel, Louis A.
1990-01-01
Previously, a method was described of representing a class of simple visual images so that they could be used with a Sparse Distributed Memory (SDM). Herein, two possible implementations are described of a SDM, for which these images, suitably encoded, will serve both as addresses to the memory and as data to be stored in the memory. A key feature of both implementations is that a pattern that is represented as an unordered set with a variable number of members can be used as an address to the memory. In the 1st model, an image is encoded as a 9072 bit string to be used as a read or write address; the bit string may also be used as data to be stored in the memory. Another representation, in which an image is encoded as a 256 bit string, may be used with either model as data to be stored in the memory, but not as an address. In the 2nd model, an image is not represented as a vector of fixed length to be used as an address. Instead, a rule is given for determining which memory locations are to be activated in response to an encoded image. This activation rule treats the pieces of an image as an unordered set. With this model, the memory can be simulated, based on a method of computing the approximate result of a read operation.
Parks, N.J.; Jee, W.S.; Dell, R.B.; Miller, G.E.
1986-07-01
The distribution of bone calcium between morphologically identifiable cortical and trabecular bone obtained by dissection and quantitated by neutron activation analysis (NAA) is described. The skeleton of a female beagle dog was dissected into approximately 400 pieces and assayed for /sup 49/Ca produced in the University of California, Irvine TRIGA reactor. For each of the skeletal sections, we give the initial weight of the alcohol-fixed tissue, which includes cortical bone, trabecular bone, marrow, and cartilage, and a final tissue weight after the marrow and trabecular bone have been dissected away; total section and cortical section calcium weights are reported. The level of detail is represented, for example, by the vertebrae, which were divided into three parts (body, spine, and transverse processes) and by the long bones, which were divided into 10-12 parts such that characterization of the epiphysis, metaphysis, and diaphysis was accomplished. The median percentage cortical calcium values for cervical, thoracic, and lumbar vertebrae were 82%, 56%, and 66%, respectively; however, variation within these groups and among individual vertebral sections was about a factor of 2. For long bones, the median percentage cortical calcium varied from 90-100% in the midshaft to below 50% in the proximal and distal sections. The final calculated cortical tissue-to-calcium mass ratio (TCR) varied from about 4.5 for midshafts of the long bones to about 9 for thoracic vertebral bodies and indicated that the mineral fraction of cortical bone is not constant throughout the skeleton. The ratio of cortical to trabecular calcium in the skeleton was 79.6:20.4.
Alix regulates cortical actin and the spatial distribution of endosomes.
Cabezas, Alicia; Bache, Kristi G; Brech, Andreas; Stenmark, Harald
2005-06-15
Alix/AIP1 is a proline-rich protein that has been implicated in apoptosis, endocytic membrane trafficking and viral budding. To further elucidate the functions of Alix, we used RNA interference to specifically suppress its expression. Depletion of Alix caused a striking redistribution of early endosomes from a peripheral to a perinuclear location. The redistribution of endosomes did not affect transferrin recycling or degradation of endocytosed epidermal growth factor receptors, although the uptake of transferrin was mildly reduced when Alix was downregulated. Quantitative immunoelectron microscopy showed that multivesicular endosomes of Alix-depleted cells contained normal amounts of CD63, whereas their levels of lysobisphosphatidic acid were reduced. Alix depletion also caused an accumulation of unusual actin structures that contained clathrin and cortactin, a protein that couples membrane dynamics to the cortical actin cytoskeleton. Our results suggest that Alix functions in the actin-dependent intracellular positioning of endosomes, but that it is not essential for endocytic recycling or for trafficking of membrane proteins between early and late endosomes in non-polarised cells. PMID:15914539
Herculano-Houzel, Suzana; Watson, Charles; Paxinos, George
2013-01-01
How are neurons distributed along the cortical surface and across functional areas? Here we use the isotropic fractionator (Herculano-Houzel and Lent, 2005) to analyze the distribution of neurons across the entire isocortex of the mouse, divided into 18 functional areas defined anatomically. We find that the number of neurons underneath a surface area (the N/A ratio) varies 4.5-fold across functional areas and neuronal density varies 3.2-fold. The face area of S1 contains the most neurons, followed by motor cortex and the primary visual cortex. Remarkably, while the distribution of neurons across functional areas does not accompany the distribution of surface area, it mirrors closely the distribution of cortical volumes—with the exception of the visual areas, which hold more neurons than expected for their volume. Across the non-visual cortex, the volume of individual functional areas is a shared linear function of their number of neurons, while in the visual areas, neuronal densities are much higher than in all other areas. In contrast, the 18 functional areas cluster into three different zones according to the relationship between the N/A ratio and cortical thickness and neuronal density: these three clusters can be called visual, sensory, and, possibly, associative. These findings are remarkably similar to those in the human cerebral cortex (Ribeiro et al., 2013) and suggest that, like the human cerebral cortex, the mouse cerebral cortex comprises two zones that differ in how neurons form the cortical volume, and three zones that differ in how neurons are distributed underneath the cortical surface, possibly in relation to local differences in connectivity through the white matter. Our results suggest that beyond the developmental divide into visual and non-visual cortex, functional areas initially share a common distribution of neurons along the parenchyma that become delimited into functional areas according to the pattern of connectivity established later
Ryynänen, Outi R M; Hyttinen, Jari A K; Laarne, Päivi H; Malmivuo, Jaakko A
2004-09-01
The purpose of the present study was to examine the spatial resolution of electroencephalography (EEG) by means of inverse cortical EEG solution. The main interest was to study how the number of measurement electrodes and the amount of measurement noise affects the spatial resolution. A three-layer spherical head model was used to obtain the source-field relationship of cortical potentials and scalp EEG field. Singular value decomposition was used to evaluate the spatial resolution with various measurement noise estimates. The results suggest that as the measurement noise increases the advantage of dense electrode systems is decreased. With low realistic measurement noise, a more accurate inverse cortical potential distribution can be obtained with an electrode system where the distance between two electrodes is as small as 16 mm, corresponding to as many as 256 measurement electrodes. In clinical measurement environments, it is always beneficial to have at least 64 measurement electrodes. PMID:15376503
Reinsberger, Claus; Tanaka, Naoaki; Cole, Andrew J.; Woo Lee, Jong; Dworetzky, Barbara A.; Bromfield, Edward B.; Hamiwka, Lorie; Bourgeois, Blaise F.; Golby, Alexandra J.; Madsen, Joseph R.; Stufflebeam, Steven M.
2011-01-01
To evaluate cortical architecture in mesial temporal lobe epilepsy (MTLE) with respect to electrophysiology, we analyze both magnetic resonance imaging (MRI) and magnetoencephalography (MEG) in 19 patients with left MTLE. We divide the patients into two groups: 9 patients (Group A) had vertically oriented antero-medial equivalent current dipoles (ECDs). 10 patients (Group B) had ECDs that were diversely oriented and widely distributed. Group analysis of MRI data showed widespread cortical thinning in Group B compared with Group A, in the left hemisphere involving the cingulate, supramarginal, occipito-temporal and parahippocampal gyri, precuneus and parietal lobule, and in the right hemisphere involving the fronto-medial, -central and -basal gyri and the precuneus. These results suggest that regardless of the presence of hippocampal sclerosis, in a subgroup of patients with MTLE a large cortical network is affected. This finding may, in part, explain the unfavorable outcome in some MTLE patients after epilepsy surgery. PMID:20472073
Assessment of water distribution changes in human cortical bone by nuclear magnetic resonance
NASA Astrophysics Data System (ADS)
Ni, Qingwen; Nyman, Jeffry S.; Wang, Xiaodu; DeLos Santos, Armondo; Nicolella, Daniel P.
2007-03-01
A NMR spin-spin (T2) relaxation technique has been described for determining water distribution changes in human cortical bone tissue. The advantages of using NMR T2 relaxation techniques for bone water distribution are illustrated. The CPMG T2 relaxation data can be inverted to T2 relaxation distribution and this distribution then can be transformed to a pore size distribution with the longer relaxation times corresponding to larger pores. The FID T2 relaxation data can be inverted to T2 relaxation distribution and this distribution then can be transformed to bound- and mobile-water distribution with the longest relaxation time corresponding to mobile water and the middle relaxation time corresponding to bound water. The technique is applied to quantify apparent changes in porosity, bound and mobile water in cortical bone. Overall bone porosity is determined using the calibrated NMR fluid volume from the proton relaxation data divided by overall bone volume. The NMR bound and mobile water changes were determined from cortical bone specimens obtained from male and female donors of different ages. Differences in water distribution were found between specimens from male and female donors. Furthermore, the distribution of water within a single specimen was found to be non-homogeneous. Our results show that the ratio of the average bound to mobile water in bone from male donors is higher than in bone from female donors when the bone porosities are similar between male and female groups. We also show that the average bone porosity multiplied by the ratio of bound to mobile water is constant for both male and female bone groups. This parameter may be used as a measure of bone quality describing both porosity and water content, both of which may be important determinants of bone strength and fracture resistance.
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.
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. PMID:26285224
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
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.
Sparse Distributed Representation of Odors in a Large-scale Olfactory Bulb Circuit
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
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.
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
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
NASA Astrophysics Data System (ADS)
George, Jacob
The present study deals with the effects of sparsely distributed three-dimensional elements on two-dimensional (2-D) and three-dimensional (3-D) turbulent boundary layers (TBL) such as those that occur on submarines, ship hulls, etc. This study was achieved in three parts: Part 1 dealt with the cylinders when placed individually in the turbulent boundary layers, thereby considering the effect of a single perturbation on the TBL; Part 2 considered the effects when the same individual elements were placed in a sparse and regular distribution, thus studying the response of the flow to a sequence of perturbations; and in Part 3, the distributions were subjected to 3-D turbulent boundary layers, thus examining the effects of streamwise and spanwise pressure gradients on the same perturbed flows as considered in Part 2. The 3-D turbulent boundary layers were generated by an idealized wing-body junction flow. Detailed 3-velocity-component Laser-Doppler Velocimetry (LDV) and other measurements were carried out to understand and describe the rough-wall flow structure. The measurements include mean velocities, turbulence quantities (Reynolds stresses and triple products), skin friction, surface pressure and oil flow visualizations in 2-D and 3-D rough-wall flows for Reynolds numbers, based on momentum thickness, greater than 7000. Very uniform circular cylindrical roughness elements of 0.38mm, 0.76mm and 1.52mm height (k) were used in square and diagonal patterns, yielding six different roughness geometries of rough-wall surface. For the 2-D rough-wall flows, the roughness Reynolds numbers, k +, based on the element height (k) and the friction velocity (Utau), range from 26 to 131. Results for the 2-D rough-wall flows reveal that the velocity-defect law is similar for both smooth and rough surfaces, and the semi-logarithmic velocity-distribution curve is shifted by an amount DeltaU/U, depending on the height of the roughness element, showing that Delta U/Utau is a function
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.
Three-dimensional distribution of cortical synapses: a replicated point pattern-based analysis.
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
Three-dimensional distribution of cortical synapses: a replicated point pattern-based analysis
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
Roxin, Alex
2011-01-01
Neuronal network models often assume a fixed probability of connection between neurons. This assumption leads to random networks with binomial in-degree and out-degree distributions which are relatively narrow. Here I study the effect of broad degree distributions on network dynamics by interpolating between a binomial and a truncated power-law distribution for the in-degree and out-degree independently. This is done both for an inhibitory network (I network) as well as for the recurrent excitatory connections in a network of excitatory and inhibitory neurons (EI network). In both cases increasing the width of the in-degree distribution affects the global state of the network by driving transitions between asynchronous behavior and oscillations. This effect is reproduced in a simplified rate model which includes the heterogeneity in neuronal input due to the in-degree of cells. On the other hand, broadening the out-degree distribution is shown to increase the fraction of common inputs to pairs of neurons. This leads to increases in the amplitude of the cross-correlation (CC) of synaptic currents. In the case of the I network, despite strong oscillatory CCs in the currents, CCs of the membrane potential are low due to filtering and reset effects, leading to very weak CCs of the spike-count. In the asynchronous regime of the EI network, broadening the out-degree increases the amplitude of CCs in the recurrent excitatory currents, while CC of the total current is essentially unaffected as are pairwise spiking correlations. This is due to a dynamic balance between excitatory and inhibitory synaptic currents. In the oscillatory regime, changes in the out-degree can have a large effect on spiking correlations and even on the qualitative dynamical state of the network. PMID:21556129
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
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.
Inferring learning rules from distributions of firing rates in cortical neurons.
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
Distributed cortical adaptation during learning of a brain–computer interface task
Wander, Jeremiah D.; Blakely, Timothy; Miller, Kai J.; Weaver, Kurt E.; Johnson, Lise A.; Olson, Jared D.; Fetz, Eberhard E.; Rao, Rajesh P. N.; Ojemann, Jeffrey G.
2013-01-01
The majority of subjects who attempt to learn control of a brain–computer interface (BCI) can do so with adequate training. Much like when one learns to type or ride a bicycle, BCI users report transitioning from a deliberate, cognitively focused mindset to near automatic control as training progresses. What are the neural correlates of this process of BCI skill acquisition? Seven subjects were implanted with electrocorticography (ECoG) electrodes and had multiple opportunities to practice a 1D BCI task. As subjects became proficient, strong initial task-related activation was followed by lessening of activation in prefrontal cortex, premotor cortex, and posterior parietal cortex, areas that have previously been implicated in the cognitive phase of motor sequence learning and abstract task learning. These results demonstrate that, although the use of a BCI only requires modulation of a local population of neurons, a distributed network of cortical areas is involved in the acquisition of BCI proficiency. PMID:23754426
Misof, B M; Dempster, D W; Zhou, Hua; Roschger, P; Fratzl-Zelman, N; Fratzl, P; Silverberg, S J; Shane, E; Cohen, A; Stein, E; Nickolas, T L; Recker, R R; Lappe, J; Bilezikian, J P; Klaushofer, K
2014-10-01
Bone mineralization density distribution (BMDD) is an important determinant of bone mechanical properties. The most available skeletal site for access to the BMDD is the iliac crest. Compared to cancellous bone much less information on BMDD is available for cortical bone. Hence, we analyzed complete transiliac crest bone biopsy samples from premenopausal women (n = 73) aged 25-48 years, clinically classified as healthy, by quantitative backscattered electron imaging for cortical (Ct.) and cancellous (Cn.) BMDD. The Ct.BMDD was characterized by the arithmetic mean of the BMDD of the cortical plates. We found correlations between Ct. and Cn. BMDD variables with correlation coefficients r between 0.42 and 0.73 (all p < 0.001). Additionally to this synchronous behavior of cortical and cancellous compartments, we found that the heterogeneity of mineralization densities (Ct.Ca(Width)), as well as the cortical porosity (Ct.Po) was larger for a lower average degree of mineralization (Ct.Ca(Mean)). Moreover, Ct.Po correlated negatively with the percentage of highly mineralized bone areas (Ct.Ca(High)) and positively with the percentage of lowly mineralized bone areas (Ct.Ca(Low)). In conclusion, the correlation of cortical with cancellous BMDD in the iliac crest of the study cohort suggests coordinated regulation of bone turnover between both bone compartments. Only in a few cases, there was a difference in the degree of mineralization of >1wt % between both cortices suggesting a possible modeling situation. This normative dataset of healthy premenopausal women will provide a reference standard by which disease- and treatment-specific effects can be assessed at the level of cortical bone BMDD. PMID:25134800
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
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.
Distribution of cortical granules in bovine oocytes classified by cumulus complex.
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
Distribution of the lingual foramina in mandibular cortical bone in Koreans
Kim, Dae Hyun; Kim, Moon Yong
2013-01-01
Objectives The interforminal region, between the mandibular foramen, is known as a relatively safe area that is free of anatomic structures, such as inferior alveolar nerve, submandibular fossa, and lingual side of the mandible is occasionally neglected for its low clinical importance. Even in the case of a severely constricted alveolus, perforation of the lingual cortical bone had been intended. However, anterior extension of the inferior alveolar canal, important anatomic structure, such as concavity of lingual bone, lingual foramina, and lingual canal, has recently been reported through various studies, and untypical bleeding by perforation of the lingual plate on implantation has also been reported. Therefore, in this study, we performed radiographic and statistical analysis on distribution and appearance frequencies of the lingual foramina that causes perforation of the mandibular lingual cortical bone to prevent complications, such as untypical bleeding, during surgical procedure. Materials and Methods We measured the horizontal length from a midline of the mandible to the lingual foramina, as well as the horizontal length from the alveolar crest to the lingual foramina and from the lingual foramina to the mandibular border by multi-detector computed tomography of 187 patients, who visited Dankook University Dental Hospital for various reasons from January 1, 2008 to August 31, 2012. Results From a total of 187 human mandibles, 110 (58.8%) mandibles had lingual foramina; 39 (20.9%) had bilateral lingual foramen; 34 (18.2%) had the only left lingual foramen; and 37 (19.8%) had the only right lingual foramen. Conclusion When there is consistent bleeding during a surgical procedure, clinicians must consider damages on the branches of the sublingual artery, which penetrate the lingual foramina. Also, when there is a lingual foramina larger than 1 mm in diameter on a pre-implantation computed tomography, clinicians must beware of vessel damage. In order to prevent
Grassmannian sparse representations
NASA Astrophysics Data System (ADS)
Azary, Sherif; Savakis, Andreas
2015-05-01
We present Grassmannian sparse representations (GSR), a sparse representation Grassmann learning framework for efficient classification. Sparse representation classification offers a powerful approach for recognition in a variety of contexts. However, a major drawback of sparse representation methods is their computational performance and memory utilization for high-dimensional data. A Grassmann manifold is a space that promotes smooth surfaces where points represent subspaces and the relationship between points is defined by the mapping of an orthogonal matrix. Grassmann manifolds are well suited for computer vision problems because they promote high between-class discrimination and within-class clustering, while offering computational advantages by mapping each subspace onto a single point. The GSR framework combines Grassmannian kernels and sparse representations, including regularized least squares and least angle regression, to improve high accuracy recognition while overcoming the drawbacks of performance and dependencies on high dimensional data distributions. The effectiveness of GSR is demonstrated on computationally intensive multiview action sequences, three-dimensional action sequences, and face recognition datasets.
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.
A scalable 2-D parallel sparse solver
Kothari, S.C.; Mitra, S.
1995-12-01
Scalability beyond a small number of processors, typically 32 or less, is known to be a problem for existing parallel general sparse (PGS) direct solvers. This paper presents a parallel general sparse PGS direct solver for general sparse linear systems on distributed memory machines. The algorithm is based on the well-known sequential sparse algorithm Y12M. To achieve efficient parallelization, a 2-D scattered decomposition of the sparse matrix is used. The proposed algorithm is more scalable than existing parallel sparse direct solvers. Its scalability is evaluated on a 256 processor nCUBE2s machine using Boeing/Harwell benchmark matrices.
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
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.
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.
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
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
Krieg, Sandro M; Sollmann, Nico; Tanigawa, Noriko; Foerschler, Annette; Meyer, Bernhard; Ringel, Florian
2016-05-01
Navigated transcranial magnetic stimulation (nTMS) gains increasing importance in presurgical language mapping. Although bipolar direct cortical stimulation (DCS) is regarded as the gold standard for intraoperative mapping of language-related areas, it cannot be used to map the healthy human brain due to its invasive character. Therefore, the present study employed a non-invasive virtual-lesion modality to provide a causality-confirmed cortical language map of the healthy human brain by repetitive nTMS (rTMS) with functional specifications beyond language-positive/language-negative distinction. Fifty right-handed healthy volunteers underwent rTMS language mapping of the left hemisphere combined with an object-naming task. The induced errors were categorized and frequency maps were calculated. Moreover, a principal component analysis (PCA) was performed on the basis of language-positive cortical regions for each error category. The left hemisphere was stimulated at 258-789 sites (median: 361.5 sites), and 12-241 naming errors (median: 72.5 errors) were observed. In male subjects, a total number of 2091 language errors were elicited by 9579 stimulation trains, which is equal to an error rate of 21.8 %. Within females, 10,238 stimulation trains elicited 2032 language errors (19.8 %). PCA revealed that the inferior parietal lobe (IPL) and middle frontal gyrus (MFG) were causally involved in object naming as a semantic center and an executive control center. For the first time, this study provides causality-based data and a model that approximates the distribution of language-related cortical areas grouped for different functional aspects of single-word production processes by PCA. PMID:25894631
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. PMID:25458179
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. PMID
Sparse encoding of automatic visual association in hippocampal networks.
Hulme, Oliver J; Skov, Martin; Chadwick, Martin J; Siebner, Hartwig R; Ramsøy, Thomas Z
2014-11-15
Intelligent action entails exploiting predictions about associations between elements of ones environment. The hippocampus and mediotemporal cortex are endowed with the network topology, physiology, and neurochemistry to automatically and sparsely code sensori-cognitive associations that can be reconstructed from single or partial inputs. Whilst acquiring fMRI data and performing an attentional task, participants were incidentally presented with a sequence of cartoon images. By assigning subjects a post-scan free-association task on the same images we assayed the density of associations triggered by these stimuli. Using multivariate Bayesian decoding, we show that human hippocampal and temporal neocortical structures host sparse associative representations that are automatically triggered by visual input. Furthermore, as predicted theoretically, there was a significant increase in sparsity in the Cornu Ammonis subfields, relative to the entorhinal cortex. Remarkably, the sparsity of CA encoding correlated significantly with associative memory performance over subjects; elsewhere within the temporal lobe, entorhinal, parahippocampal, perirhinal and fusiform cortices showed the highest model evidence for the sparse encoding of associative density. In the absence of reportability or attentional confounds, this charts a distribution of visual associative representations within hippocampal populations and their temporal lobe afferent fields, and demonstrates the viability of retrospective associative sampling techniques for assessing the form of reflexive associative encoding. PMID:25038440
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. PMID:26983726
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
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
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…
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
Liewald, Daniel; Miller, Robert; Logothetis, Nikos; Wagner, Hans-Joachim; Schüz, Almut
2014-10-01
The aim of this study was to obtain information on the axonal diameters of cortico-cortical fibres in the human brain, connecting distant regions of the same hemisphere via the white matter. Samples for electron microscopy were taken from the region of the superior longitudinal fascicle and from the transitional white matter between temporal and frontal lobe where the uncinate and inferior occipitofrontal fascicle merge. We measured the inner diameter of cross sections of myelinated axons. For comparison with data from the literature on the human corpus callosum, we also took samples from that region. For comparison with well-fixed material, we also included samples from corresponding regions of a monkey brain (Macaca mulatta). Fibre diameters in human brains ranged from 0.16 to 9 μm. Distributions of diameters were similar in the three systems of cortico-cortical fibres investigated, both in humans and the monkey, with most of the average values below 1 μm diameter and a small population of much thicker fibres. Within individual human brains, the averages were larger in the superior longitudinal fascicle than in the transitional zone between temporal and frontal lobe. An asymmetry between left and right could be found in one of the human brains, as well as in the monkey brain. A correlation was also found between the thickness of the myelin sheath and the inner axon diameter for axons whose calibre was greater than about 0.6 μm. The results are compared to white matter data in other mammals and are discussed with respect to conduction velocity, brain size, cognition, as well as diffusion weighted imaging studies. PMID:25142940
Marzagalli, R; Leggio, G M; Bucolo, C; Pricoco, E; Keay, K A; Cardile, V; Castorina, S; Salomone, S; Drago, F; Castorina, A
2016-03-01
Dopamine D3 receptors (D3Rs) are implicated in several aspects of cognition, but their role in aversive conditioning has only been marginally uncovered. Investigations have reported that blockade of D3Rs enhances the acquisition of fear memories, a phenomenon tightly linked to the neuropeptide pituitary adenylate cyclase-activating peptide (PACAP). However, the impact of D3R ablation on the PACAPergic system in regions critical for the formation of new memories remains unexplored. To address this issue, levels of PACAP and its receptors were compared in the hippocampus and cerebral cortex (CX) of mice devoid of functional D3Rs (D3R(-/-)) and wild-types (WTs) using a series of comparative immunohistochemical and biochemical analyses. Morphometric and stereological data revealed increased hippocampal area and volume in D3R(-/-) mice, and augmented neuronal density in CA1 and CA2/3 subfields. PACAP levels were increased in the hippocampus of D3R(-/-) mice. Expression of PACAP receptors was also heightened in mutant mice. In the CX, PACAP immunoreactivity (IR), was restricted to cortical layer V in WTs, but was distributed throughout layers IV-VI in D3R(-/-) mice, along with increased mRNAs, protein concentration and staining scores. Consistently, PAC1, VPAC1 and VPAC2 IRs were variably redistributed in CX, with a general upregulation in cortical layers II-IV in knockout animals. Our interpretation of these findings is that disturbed dopamine neurotransmission due to genetic D3R blockade may enhance the PACAP/PAC1-VPAC axis, a key endogenous system for the processing of fear memories. This could explain, at least in part, the facilitated acquisition and consolidation of aversive memories in D3R(-/-) mice. PMID:26718601
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
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.
2016-04-01
The rotational state of asteroids is controlled by various physical mechanisms including collisions, internal damping and the Yarkovsky-O'Keefe-Radzievskii-Paddack (YORP) effect. We have analysed the changes in magnitude between consecutive detections of ˜ 60,000 asteroids measured by the 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 toward 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.
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.
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
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
Mestres-Missé, Anna; Trampel, Robert; Turner, Robert; Kotz, Sonja A
2016-04-01
A key aspect of optimal behavior is the ability to predict what will come next. To achieve this, we must have a fairly good idea of the probability of occurrence of possible outcomes. This is based both on prior knowledge about a particular or similar situation and on immediately relevant new information. One question that arises is: when considering converging prior probability and external evidence, is the most probable outcome selected or does the brain represent degrees of uncertainty, even highly improbable ones? Using functional magnetic resonance imaging, the current study explored these possibilities by contrasting words that differ in their probability of occurrence, namely, unbalanced ambiguous words and unambiguous words. Unbalanced ambiguous words have a strong frequency-based bias towards one meaning, while unambiguous words have only one meaning. The current results reveal larger activation in lateral prefrontal and insular cortices in response to dominant ambiguous compared to unambiguous words even when prior and contextual information biases one interpretation only. These results suggest a probability distribution, whereby all outcomes and their associated probabilities of occurrence-even if very low-are represented and maintained. PMID:25523107
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
Sparse Biclustering of Transposable Data
Tan, Kean Ming
2013-01-01
We consider the task of simultaneously clustering the rows and columns of a large transposable data matrix. We assume that the matrix elements are normally distributed with a bicluster-specific mean term and a common variance, and perform biclustering by maximizing the corresponding log likelihood. We apply an ℓ1 penalty to the means of the biclusters in order to obtain sparse and interpretable biclusters. Our proposal amounts to a sparse, symmetrized version of k-means clustering. We show that k-means clustering of the rows and of the columns of a data matrix can be seen as special cases of our proposal, and that a relaxation of our proposal yields the singular value decomposition. In addition, we propose a framework for bi-clustering based on the matrix-variate normal distribution. The performances of our proposals are demonstrated in a simulation study and on a gene expression data set. This article has supplementary material online. PMID:25364221
Sparse Biclustering of Transposable Data.
Tan, Kean Ming; Witten, Daniela M
2014-01-01
We consider the task of simultaneously clustering the rows and columns of a large transposable data matrix. We assume that the matrix elements are normally distributed with a bicluster-specific mean term and a common variance, and perform biclustering by maximizing the corresponding log likelihood. We apply an ℓ1 penalty to the means of the biclusters in order to obtain sparse and interpretable biclusters. Our proposal amounts to a sparse, symmetrized version of k-means clustering. We show that k-means clustering of the rows and of the columns of a data matrix can be seen as special cases of our proposal, and that a relaxation of our proposal yields the singular value decomposition. In addition, we propose a framework for bi-clustering based on the matrix-variate normal distribution. The performances of our proposals are demonstrated in a simulation study and on a gene expression data set. This article has supplementary material online. PMID:25364221
SparsePZ: Sparse Representation of Photometric Redshift PDFs
NASA Astrophysics Data System (ADS)
Carrasco Kind, Matias; Brunner, R. J.
2015-11-01
SparsePZ uses sparse basis representation to fully represent individual photometric redshift probability density functions (PDFs). This approach requires approximately half the parameters for the same multi-Gaussian fitting accuracy, and has the additional advantage that an entire PDF can be stored by using a 4-byte integer per basis function. Only 10-20 points per galaxy are needed to reconstruct both the individual PDFs and the ensemble redshift distribution, N(z), to an accuracy of 99.9 per cent when compared to the one built using the original PDFs computed with a resolution of δz = 0.01, reducing the required storage of 200 original values by a factor of 10-20. This basis representation can be directly extended to a cosmological analysis, thereby increasing computational performance without losing resolution or accuracy.
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.
Estimating sparse precision matrices
NASA Astrophysics Data System (ADS)
Padmanabhan, Nikhil; White, Martin; Zhou, Harrison H.; O'Connell, Ross
2016-05-01
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/√{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/√{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.
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/√{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/√{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.
Sparse representation with kernels.
Gao, Shenghua; Tsang, Ivor Wai-Hung; Chia, Liang-Tien
2013-02-01
Recent research has shown the initial success of sparse coding (Sc) in solving many computer vision tasks. Motivated by the fact that kernel trick can capture the nonlinear similarity of features, which helps in finding a sparse representation of nonlinear features, we propose kernel sparse representation (KSR). Essentially, KSR is a sparse coding technique in a high dimensional feature space mapped by an implicit mapping function. We apply KSR to feature coding in image classification, face recognition, and kernel matrix approximation. More specifically, by incorporating KSR into spatial pyramid matching (SPM), we develop KSRSPM, which achieves a good performance for image classification. Moreover, KSR-based feature coding can be shown as a generalization of efficient match kernel and an extension of Sc-based SPM. We further show that our proposed KSR using a histogram intersection kernel (HIK) can be considered a soft assignment extension of HIK-based feature quantization in the feature coding process. Besides feature coding, comparing with sparse coding, KSR can learn more discriminative sparse codes and achieve higher accuracy for face recognition. Moreover, KSR can also be applied to kernel matrix approximation in large scale learning tasks, and it demonstrates its robustness to kernel matrix approximation, especially when a small fraction of the data is used. Extensive experimental results demonstrate promising results of KSR in image classification, face recognition, and kernel matrix approximation. All these applications prove the effectiveness of KSR in computer vision and machine learning tasks. PMID:23014744
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.
Structured Multifrontal Sparse Solver
Energy Science and Technology Software Center (ESTSC)
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
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. PMID:24139950
Modeling cortical source dynamics and interactions during seizure.
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
Ducommun, Christine Y; Michel, Christoph M; Clarke, Stephanie; Adriani, Michela; Seeck, Margitta; Landis, Theodor; Blanke, Olaf
2004-09-16
The extent to which the auditory system, like the visual system, processes spatial stimulus characteristics such as location and motion in separate specialized neuronal modules or in one homogeneously distributed network is unresolved. Here we present a patient with a selective deficit for the perception and discrimination of auditory motion following resection of the right anterior temporal lobe and the right posterior superior temporal gyrus (STG). Analysis of stimulus identity and location within the auditory scene remained intact. In addition, intracranial auditory evoked potentials, recorded preoperatively, revealed motion-specific responses selectively over the resected right posterior STG, and electrical cortical stimulation of this region was experienced by the patient as incoming moving sounds. Collectively, these data present a patient with cortical motion deafness, providing evidence that cortical processing of auditory motion is performed in a specialized module within the posterior STG. PMID:15363389
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
González-Hernández, J A; Cedeño, I; Pita-Alcorta, C; Galán, L; Aubert, E; Figueredo-Rodríguez, P
2003-04-01
Prefrontal dysfunction has been associated with schizophrenia. Activation during Wisconsin card sorting test (WCST) is a common approach used in functional neuroimaging to address this failure. Equally, current knowledge states that oscillations are basic forms of cells-assembly communications during mental activity. Promising results were revealed in a previous study assessing healthy subjects, WCST and oscillations. However, those previous studies failed to meet the functional integration of the network during the WCST in schizophrenics, based on the induced oscillations and their distributed cortical sources. In this research, we utilized the brain electrical tomography (variable-resolution brain electromagnetic tomography) technique to accomplish this goal. Task specific delta, theta, alpha and beta-2 oscillations were induced and simultaneously synchronized over large extensions of cortex, encompassing prefrontal, temporal and posterior regions as in healthy subjects. Every frequency had a well-defined network involving a variable number of areas and sharing some of them. Oscillations at 11.5, 5.0 and 30 Hz seem to reflect an abnormal increase or decrease, being located at supplementary motor area (SMA), left occipitotemporal region (OT), and right frontotemporal subregions (RFT), respectively. Three cortical areas appeared to be critical, that may lead to difficulties either in coordinating/sequencing the input/output of the prefrontal networks-SMA, and retention of information in memory-RFT, both preceded or paralleled by a deficient visual information processing-OT. PMID:12694897
Sparse subspace clustering: algorithm, theory, and applications.
Elhamifar, Ehsan; Vidal, René
2013-11-01
Many real-world problems deal with collections of high-dimensional data, such as images, videos, text, and web documents, DNA microarray data, and more. Often, such high-dimensional data lie close to low-dimensional structures corresponding to several classes or categories to which the data belong. In this paper, we propose and study an algorithm, called sparse subspace clustering, to cluster data points that lie in a union of low-dimensional subspaces. The key idea is that, among the infinitely many possible representations of a data point in terms of other points, a sparse representation corresponds to selecting a few points from the same subspace. This motivates solving a sparse optimization program whose solution is used in a spectral clustering framework to infer the clustering of the data into subspaces. Since solving the sparse optimization program is in general NP-hard, we consider a convex relaxation and show that, under appropriate conditions on the arrangement of the subspaces and the distribution of the data, the proposed minimization program succeeds in recovering the desired sparse representations. The proposed algorithm is efficient and can handle data points near the intersections of subspaces. Another key advantage of the proposed algorithm with respect to the state of the art is that it can deal directly with data nuisances, such as noise, sparse outlying entries, and missing entries, by incorporating the model of the data into the sparse optimization program. We demonstrate the effectiveness of the proposed algorithm through experiments on synthetic data as well as the two real-world problems of motion segmentation and face clustering. PMID:24051734
Sparse inpainting and isotropy
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.
Sparse matrix test collections
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.
Optical sparse aperture imaging.
Miller, Nicholas J; Dierking, Matthew P; Duncan, Bradley D
2007-08-10
The resolution of a conventional diffraction-limited imaging system is proportional to its pupil diameter. A primary goal of sparse aperture imaging is to enhance resolution while minimizing the total light collection area; the latter being desirable, in part, because of the cost of large, monolithic apertures. Performance metrics are defined and used to evaluate several sparse aperture arrays constructed from multiple, identical, circular subapertures. Subaperture piston and/or tilt effects on image quality are also considered. We selected arrays with compact nonredundant autocorrelations first described by Golay. We vary both the number of subapertures and their relative spacings to arrive at an optimized array. We report the results of an experiment in which we synthesized an image from multiple subaperture pupil fields by masking a large lens with a Golay array. For this experiment we imaged a slant edge feature of an ISO12233 resolution target in order to measure the modulation transfer function. We note the contrast reduction inherent in images formed through sparse aperture arrays and demonstrate the use of a Wiener-Helstrom filter to restore contrast in our experimental images. Finally, we describe a method to synthesize images from multiple subaperture focal plane intensity images using a phase retrieval algorithm to obtain estimates of subaperture pupil fields. Experimental results from synthesizing an image of a point object from multiple subaperture images are presented, and weaknesses of the phase retrieval method for this application are discussed. PMID:17694146
Glennon, Mark; Keane, Michael A; Elliott, Mark A; Sauseng, Paul
2016-05-01
Attentional blink (AB) describes a visuo-perceptual phenomenon in which the second of 2 targets within a rapid serial visual presentation stream is not detected. There are several cognitive models attempting to explain the fundamentals of this information processing bottleneck. Here, we used electroencephalographic recordings and the analysis of interregional phase synchronization of rhythmical brain activity to investigate the neural bases of the AB. By investigating the time course of interregional phase synchronization separately for trials in which participants failed to report the second target correctly (AB trials) and trials in which no AB occurred, and by clustering interregional connections based on their functional similarity, it was possible to define several distinct cortical networks. Analyzing these networks comprising phase synchronization-over a large spectrum of brain frequencies from theta to gamma activity-it was possible to identify neural correlates for cognitive subfunctions involved in the AB, such as the encoding of targets into working memory, tuning of attentional filters, and the recruitment of general cognitive resources. This parallel activation of functionally distinct neural processes substantiates the eligibility of several cognitive models on the AB. PMID:25750255
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
Cerebellar Functional Parcellation Using Sparse Dictionary Learning Clustering.
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
Cerebellar Functional Parcellation Using Sparse Dictionary Learning Clustering
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
Energy Science and Technology Software Center (ESTSC)
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
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.
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.
Energy Science and Technology Software Center (ESTSC)
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
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
Neonatal Atlas Construction Using Sparse Representation
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
Compressed Sampling of Spectrally Sparse Signals Using Sparse Circulant Matrices
NASA Astrophysics Data System (ADS)
Xu, Guangjie; Wang, Huali; Sun, Lei; Zeng, Weijun; Wang, Qingguo
2014-11-01
Circulant measurement matrices constructed by partial cyclically shifts of one generating sequence, are easier to be implemented in hardware than widely used random measurement matrices; however, the diminishment of randomness makes it more sensitive to signal noise. Selecting a deterministic sequence with optimal periodic autocorrelation property (PACP) as generating sequence, would enhance the noise robustness of circulant measurement matrix, but this kind of deterministic circulant matrices only exists in the fixed periodic length. Actually, the selection of generating sequence doesn't affect the compressive performance of circulant measurement matrix but the subspace energy in spectrally sparse signals. Sparse circulant matrices, whose generating sequence is a sparse sequence, could keep the energy balance of subspaces and have similar noise robustness to deterministic circulant matrices. In addition, sparse circulant matrices have no restriction on length and are more suitable for the compressed sampling of spectrally sparse signals at arbitrary dimensionality.
Percolation on Sparse Networks
NASA Astrophysics Data System (ADS)
Karrer, Brian; Newman, M. E. J.; Zdeborová, Lenka
2014-11-01
We study percolation on networks, which is used as a model of the resilience of networked systems such as the Internet to attack or failure and as a simple model of the spread of disease over human contact networks. We reformulate percolation as a message passing process and demonstrate how the resulting equations can be used to calculate, among other things, the size of the percolating cluster and the average cluster size. The calculations are exact for sparse networks when the number of short loops in the network is small, but even on networks with many short loops we find them to be highly accurate when compared with direct numerical simulations. By considering the fixed points of the message passing process, we also show that the percolation threshold on a network with few loops is given by the inverse of the leading eigenvalue of the so-called nonbacktracking matrix.
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.
Reconstructing spatially extended brain sources via enforcing multiple transform sparseness.
Zhu, Min; Zhang, Wenbo; Dickens, Deanna L; Ding, Lei
2014-02-01
Accurate estimation of location and extent of neuronal sources from EEG/MEG remain challenging. In the present study, a new source imaging method, i.e. variation and wavelet based sparse source imaging (VW-SSI), is proposed to better estimate cortical source locations and extents. VW-SSI utilizes the L1-norm regularization method with the enforcement of transform sparseness in both variation and wavelet domains. The performance of the proposed method is assessed by both simulated and experimental MEG data, obtained from a language task and a motor task. Compared to L2-norm regularizations, VW-SSI demonstrates significantly improved capability in reconstructing multiple extended cortical sources with less spatial blurredness and less localization error. With the use of transform sparseness, VW-SSI overcomes the over-focused problem in classic SSI methods. With the use of two transformations, VW-SSI further indicates significantly better performance in estimating MEG source locations and extents than other SSI methods with single transformations. The present experimental results indicate that VW-SSI can successfully estimate neural sources (and their spatial coverage) located in close areas while responsible for different functions, i.e. temporal cortical sources for auditory and language processing, and sources on the pre-bank and post-bank of the central sulcus. Meantime, all other methods investigated in the present study fail to recover these phenomena. Precise estimation of cortical source locations and extents from EEG/MEG is of significance for applications in neuroscience and neurology. PMID:24103850
James, Gareth M.; Sabatti, Chiara; Zhou, Nengfeng; Zhu, Ji
2011-01-01
In many organisms the expression levels of each gene are controlled by the activation levels of known “Transcription Factors” (TF). A problem of considerable interest is that of estimating the “Transcription Regulation Networks” (TRN) relating the TFs and genes. While the expression levels of genes can be observed, the activation levels of the corresponding TFs are usually unknown, greatly increasing the difficulty of the problem. Based on previous experimental work, it is often the case that partial information about the TRN is available. For example, certain TFs may be known to regulate a given gene or in other cases a connection may be predicted with a certain probability. In general, the biology of the problem indicates there will be very few connections between TFs and genes. Several methods have been proposed for estimating TRNs. However, they all suffer from problems such as unrealistic assumptions about prior knowledge of the network structure or computational limitations. We propose a new approach that can directly utilize prior information about the network structure in conjunction with observed gene expression data to estimate the TRN. Our approach uses L1 penalties on the network to ensure a sparse structure. This has the advantage of being computationally efficient as well as making many fewer assumptions about the network structure. We use our methodology to construct the TRN for E. coli and show that the estimate is biologically sensible and compares favorably with previous estimates. PMID:21625366
Completeness for sparse potential scattering
Shen, Zhongwei
2014-01-15
The present paper is devoted to the scattering theory of a class of continuum Schrödinger operators with deterministic sparse potentials. We first establish the limiting absorption principle for both modified free resolvents and modified perturbed resolvents. This actually is a weak form of the classical limiting absorption principle. We then prove the existence and completeness of local wave operators, which, in particular, imply the existence of wave operators. Under additional assumptions on the sparse potential, we prove the completeness of wave operators. In the context of continuum Schrödinger operators with sparse potentials, this paper gives the first proof of the completeness of wave operators.
The sparseness of neuronal responses in ferret primary visual cortex.
Tolhurst, David J; Smyth, Darragh; Thompson, Ian D
2009-02-25
Various arguments suggest that neuronal coding of natural sensory stimuli should be sparse (i.e., individual neurons should respond rarely but should respond reliably). We examined sparseness of visual cortical neurons in anesthetized ferret to flashed natural scenes. Response behavior differed widely between neurons. The median firing rate of 4.1 impulses per second was slightly higher than predicted from consideration of metabolic load. Thirteen percent of neurons (12 of 89) responded to <5% of the images, but one-half responded to >25% of images. Multivariate analysis of the range of sparseness values showed that 67% of the variance was accounted for by differing response patterns to moving gratings. Repeat presentation of images showed that response variance for natural images exaggerated sparseness measures; variance was scaled with mean response, but with a lower Fano factor than for the responses to moving gratings. This response variability and the "soft" sparse responses (Rehn and Sommer, 2007) raise the question of what constitutes a reliable neuronal response and imply parallel signaling by multiple neurons. We investigated whether the temporal structure of responses might be reliable enough to give additional information about natural scenes. Poststimulus time histogram shape was similar for "strong" and "weak" stimuli, with no systematic change in first-spike latency with stimulus strength. The variance of first-spike latency for repeat presentations of the same image was greater than the latency variance between images. In general, responses to flashed natural scenes do not seem compatible with a sparse encoding in which neurons fire rarely but reliably. PMID:19244512
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
Spatiotemporal System Identification With Continuous Spatial Maps and Sparse Estimation.
Aram, Parham; Kadirkamanathan, Visakan; Anderson, Sean R
2015-11-01
We present a framework for the identification of spatiotemporal linear dynamical systems. We use a state-space model representation that has the following attributes: 1) the number of spatial observation locations are decoupled from the model order; 2) the model allows for spatial heterogeneity; 3) the model representation is continuous over space; and 4) the model parameters can be identified in a simple and sparse estimation procedure. The model identification procedure we propose has four steps: 1) decomposition of the continuous spatial field using a finite set of basis functions where spatial frequency analysis is used to determine basis function width and spacing, such that the main spatial frequency contents of the underlying field can be captured; 2) initialization of states in closed form; 3) initialization of state-transition and input matrix model parameters using sparse regression-the least absolute shrinkage and selection operator method; and 4) joint state and parameter estimation using an iterative Kalman-filter/sparse-regression algorithm. To investigate the performance of the proposed algorithm we use data generated by the Kuramoto model of spatiotemporal cortical dynamics. The identification algorithm performs successfully, predicting the spatiotemporal field with high accuracy, whilst the sparse regression leads to a compact model. PMID:25647667
Threaded Operations on Sparse Matrices
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.
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.
Mean-field sparse optimal control
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
NASA Astrophysics Data System (ADS)
Lu, Yiliang; Yan, Yan; Chai, Xinyu; Ren, Qiushi; Chen, Yao; Li, Liming
2013-06-01
Objective. A visual prosthesis based on penetrating electrode stimulation within the optic nerve (ON) is a potential way to restore partial functional vision for blind patients. We investigated the retinotopic organization of ON stimulation and its spatial resolution. Approach. A five-electrode array was inserted perpendicularly into the ON or a single electrode was advanced to different depths within the ON (˜1-2 mm behind the eyeball, 13 cats). A sparse noise method was used to map ON electrode position and the visual cortex. Cortical responses were recorded by a 5 × 6 array. The visuotopic correspondence between the retinotopic position of the ON electrode was compared with the visual evoked cortical map and the electrical evoked potentials elicited in response to ON stimulation. Main results. Electrical stimulation with penetrating ON electrodes elicited cortical responses in visuotopographically corresponding areas of the cortex. Stimulation of the temporal side of the ON elicited cortical responses corresponding to the central visual field. The visual field position shifted from the lower to central visual field as the electrode penetrated through the depth of the ON. A spatial resolution of ˜ 2° to 3° within a limited cortical visuotopic representation could be obtained by this approach. Significance. Visuotopic electrical stimulation with a relatively fine spatial resolution can be accomplished using penetrating electrodes implanted at multiple sites and at different depths within the ON just behind the globe. This study also provides useful experimental data for the design of electrode density and the distribution of penetrating ON electrodes for a visual prosthesis.
Learning Sparse Representations of Depth
NASA Astrophysics Data System (ADS)
Tosic, Ivana; Olshausen, Bruno A.; Culpepper, Benjamin J.
2011-09-01
This paper introduces a new method for learning and inferring sparse representations of depth (disparity) maps. The proposed algorithm relaxes the usual assumption of the stationary noise model in sparse coding. This enables learning from data corrupted with spatially varying noise or uncertainty, typically obtained by laser range scanners or structured light depth cameras. Sparse representations are learned from the Middlebury database disparity maps and then exploited in a two-layer graphical model for inferring depth from stereo, by including a sparsity prior on the learned features. Since they capture higher-order dependencies in the depth structure, these priors can complement smoothness priors commonly used in depth inference based on Markov Random Field (MRF) models. Inference on the proposed graph is achieved using an alternating iterative optimization technique, where the first layer is solved using an existing MRF-based stereo matching algorithm, then held fixed as the second layer is solved using the proposed non-stationary sparse coding algorithm. This leads to a general method for improving solutions of state of the art MRF-based depth estimation algorithms. Our experimental results first show that depth inference using learned representations leads to state of the art denoising of depth maps obtained from laser range scanners and a time of flight camera. Furthermore, we show that adding sparse priors improves the results of two depth estimation methods: the classical graph cut algorithm by Boykov et al. and the more recent algorithm of Woodford et al.
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.
Sparse modeling of spatial environmental variables associated with asthma.
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
Sparse modeling of spatial environmental variables associated with asthma
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
Sparsely-synchronized brain rhythm in a small-world neural network
NASA Astrophysics Data System (ADS)
Kim, Sang-Yoon; Lim, Woochang
2013-07-01
Sparsely-synchronized cortical rhythms, associated with diverse cognitive functions, have been observed in electric recordings of brain activity. At the population level, cortical rhythms exhibit small-amplitude fast oscillations while at the cellular level, individual neurons show stochastic firings sparsely at a much lower rate than the population rate. We study the effect of network architecture on sparse synchronization in an inhibitory population of subthreshold Morris-Lecar neurons (which cannot fire spontaneously without noise). Previously, sparse synchronization was found to occur for cases of both global coupling ( i.e., regular all-to-all coupling) and random coupling. However, a real neural network is known to be non-regular and non-random. Here, we consider sparse Watts-Strogatz small-world networks which interpolate between a regular lattice and a random graph via rewiring. We start from a regular lattice with only short-range connections and then investigate the emergence of sparse synchronization by increasing the rewiring probability p for the short-range connections. For p = 0, the average synaptic path length between pairs of neurons becomes long; hence, only an unsynchronized population state exists because the global efficiency of information transfer is low. However, as p is increased, long-range connections begin to appear, and global effective communication between distant neurons may be available via shorter synaptic paths. Consequently, as p passes a threshold p th (}~ 0.044), sparsely-synchronized population rhythms emerge. However, with increasing p, longer axon wirings become expensive because of their material and energy costs. At an optimal value p* DE (}~ 0.24) of the rewiring probability, the ratio of the synchrony degree to the wiring cost is found to become maximal. In this way, an optimal sparse synchronization is found to occur at a minimal wiring cost in an economic small-world network through trade-off between synchrony and
Sparsely sampling the sky: Regular vs. random sampling
NASA Astrophysics Data System (ADS)
Paykari, P.; Pires, S.; Starck, J.-L.; Jaffe, A. H.
2015-09-01
Aims: The next generation of galaxy surveys, aiming to observe millions of galaxies, are expensive both in time and money. This raises questions regarding the optimal investment of this time and money for future surveys. In a previous work, we have shown that a sparse sampling strategy could be a powerful substitute for the - usually favoured - contiguous observation of the sky. In our previous paper, regular sparse sampling was investigated, where the sparse observed patches were regularly distributed on the sky. The regularity of the mask introduces a periodic pattern in the window function, which induces periodic correlations at specific scales. Methods: In this paper, we use a Bayesian experimental design to investigate a "random" sparse sampling approach, where the observed patches are randomly distributed over the total sparsely sampled area. Results: We find that in this setting, the induced correlation is evenly distributed amongst all scales as there is no preferred scale in the window function. Conclusions: This is desirable when we are interested in any specific scale in the galaxy power spectrum, such as the matter-radiation equality scale. As the figure of merit shows, however, there is no preference between regular and random sampling to constrain the overall galaxy power spectrum and the cosmological parameters.
Galaxy redshift surveys with sparse sampling
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.
Iterative Sparse Approximation of the Gravitational Potential
NASA Astrophysics Data System (ADS)
Telschow, R.
2012-04-01
In recent applications in the approximation of gravitational potential fields, several new challenges arise. We are concerned with a huge quantity of data (e.g. in case of the Earth) or strongly irregularly distributed data points (e.g. in case of the Juno mission to Jupiter), where both of these problems bring the established approximation methods to their limits. Our novel method, which is a matching pursuit, however, iteratively chooses a best basis out of a large redundant family of trial functions to reconstruct the signal. It is independent of the data points which makes it possible to take into account a much higher amount of data and, furthermore, handle irregularly distributed data, since the algorithm is able to combine arbitrary spherical basis functions, i.e., global as well as local trial functions. This additionaly results in a solution, which is sparse in the sense that it features more basis functions where the signal has a higher local detail density. Summarizing, we get a method which reconstructs large quantities of data with a preferably low number of basis functions, combining global as well as several localizing functions to a sparse basis and a solution which is locally adapted to the data density and also to the detail density of the signal.
Amesos2 Templated Direct Sparse Solver Package
Energy Science and Technology Software Center (ESTSC)
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.
Ryynänen, Outi R M; Hyttinen, Jari A K; Malmivuo, Jaakko A
2006-09-01
The purpose of the present theoretical study was to examine the spatial resolution of electroencephalography (EEG) by means of the accuracy of the inverse cortical EEG solution. The study focused on effect of the amount of measurement noise and the number of electrodes on the spatial resolution with different resistivity ratios for the scalp, skull and brain. The results show that if the relative skull resistivity is lower than earlier believed, the spatial resolution of different electrode systems is less sensitive to the measurement noise. Furthermore, there is then also greater advantage to be obtained with high-resolution EEG at realistic noise levels. PMID:16941841
P-SPARSLIB: A parallel sparse iterative solution package
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.
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.
Finding communities in sparse networks
Singh, Abhinav; Humphries, Mark D.
2015-01-01
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. PMID:25742951
Precise Feature Based Time Scales and Frequency Decorrelation Lead to a Sparse Auditory Code
Chen, Chen; Read, Heather L.; Escabí, Monty A.
2012-01-01
Sparse redundancy reducing codes have been proposed as efficient strategies for representing sensory stimuli. A prevailing hypothesis suggests that sensory representations shift from dense redundant codes in the periphery to selective sparse codes in cortex. We propose an alternative framework where sparseness and redundancy depend on sensory integration time scales and demonstrate that the central nucleus of the inferior colliculus (ICC) of cats encodes sound features by precise sparse spike trains. Direct comparisons with auditory cortical neurons demonstrate that ICC responses were sparse and uncorrelated as long as the spike train time scales were matched to the sensory integration time scales relevant to ICC neurons. Intriguingly, correlated spiking in the ICC was substantially lower than predicted by linear or nonlinear models and strictly observed for neurons with best frequencies within a “critical band,” the hallmark of perceptual frequency resolution in mammals. This is consistent with a sparse asynchronous code throughout much of the ICC and a complementary correlation code within a critical band that may allow grouping of perceptually relevant cues. PMID:22723685
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.
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.
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
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
A performance study of sparse Cholesky factorization on INTEL iPSC/860
NASA Technical Reports Server (NTRS)
Zubair, M.; Ghose, M.
1992-01-01
The problem of Cholesky factorization of a sparse matrix has been very well investigated on sequential machines. A number of efficient codes exist for factorizing large unstructured sparse matrices. However, there is a lack of such efficient codes on parallel machines in general, and distributed machines in particular. Some of the issues that are critical to the implementation of sparse Cholesky factorization on a distributed memory parallel machine are ordering, partitioning and mapping, load balancing, and ordering of various tasks within a processor. Here, we focus on the effect of various partitioning schemes on the performance of sparse Cholesky factorization on the Intel iPSC/860. Also, a new partitioning heuristic for structured as well as unstructured sparse matrices is proposed, and its performance is compared with other schemes.
Dose-shaping using targeted sparse optimization
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
Scenario generation for stochastic optimization problems via the sparse grid method
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.
ESTIMATION OF FUNCTIONALS OF SPARSE COVARIANCE MATRICES
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
Fast generation of sparse random kernel graphs
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
Fast generation of sparse random kernel graphs
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.
Fast Generation of Sparse Random Kernel Graphs
2015-01-01
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 𝒪(n(logn)2). As a practical example we show how to generate samples of power-law degree distribution graphs with tunable assortativity. PMID:26356296
Cortical Reorganization following Injury Early in Life
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
Mesoscopic Patterns of Neural Activity Support Songbird Cortical Sequences
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
Mesoscopic patterns of neural activity support songbird cortical sequences.
Markowitz, Jeffrey E; Liberti, William A; Guitchounts, Grigori; Velho, Tarciso; Lois, Carlos; Gardner, Timothy J
2015-06-01
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
Sparse Coding for Alpha Matting
NASA Astrophysics Data System (ADS)
Johnson, Jubin; Varnousfaderani, Ehsan Shahrian; Cholakkal, Hisham; Rajan, Deepu
2016-07-01
Existing color sampling based alpha matting methods use the compositing equation to estimate alpha at a pixel from pairs of foreground (F) and background (B) samples. The quality of the matte depends on the selected (F,B) pairs. In this paper, the matting problem is reinterpreted as a sparse coding of pixel features, wherein the sum of the codes gives the estimate of the alpha matte from a set of unpaired F and B samples. A non-parametric probabilistic segmentation provides a certainty measure on the pixel belonging to foreground or background, based on which a dictionary is formed for use in sparse coding. By removing the restriction to conform to (F,B) pairs, this method allows for better alpha estimation from multiple F and B samples. The same framework is extended to videos, where the requirement of temporal coherence is handled effectively. Here, the dictionary is formed by samples from multiple frames. A multi-frame graph model, as opposed to a single image as for image matting, is proposed that can be solved efficiently in closed form. Quantitative and qualitative evaluations on a benchmark dataset are provided to show that the proposed method outperforms current state-of-the-art in image and video matting.
Bayesian Learning in Sparse Graphical Factor Models via Variational Mean-Field Annealing
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
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.
Image fusion using sparse overcomplete feature dictionaries
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.
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.
Pharmacology of cortical inhibition
Krnjević, K.; Randić, Mirjana; Straughan, D. W.
1966-01-01
1. We have studied the effects of various pharmacological agents on the cortical inhibitory process described in the previous two papers (Krnjević, Randić & Straughan, 1966a, b); the drugs were mostly administered directly by iontophoresis from micropipettes and by systemic injection (I.V.). 2. Strychnine given by iontophoresis or by the application of a strong solution to the cortical surface potentiated excitatory effects, but very large iontophoretic doses also depressed neuronal firing. Subconvulsive and even convulsive systemic doses had little or no effect at the cortical level. There was no evidence, with any method of application, that strychnine directly interferes with the inhibitory process. 3. Tetanus toxin, obtained from two different sources and injected into the cortex 12-48 hr previously, also failed to block cortical inhibition selectively. As with strychnine, there was some evidence of increased responses to excitatory inputs. 4. Other convulsant drugs which failed to block cortical inhibition included picrotoxin, pentamethylene tetrazole, thiosemicarbazide, longchain ω-amino acids and morphine. 5. The inhibition was not obviously affected by cholinomimetic agents or by antagonists of ACh. 6. α- and β-antagonists of adrenergic transmission were also ineffective. 7. Cortical inhibition was fully developed in the presence of several general anaesthetics, including ether, Dial, pentobarbitone, Mg and chloralose. A temporary reduction in inhibition which is sometimes observed after systemic doses of pentobarbitone, is probably secondary to a fall in blood pressure. 8. Several central excitants such as amphetamine, caffeine and lobeline also failed to show any specific antagonistic action on cortical inhibition. 9. In view of the possibility that GABA is the chemical agent mediating cortical inhibition, an attempt was made to find a selective antagonist of its depressant action on cortical neurones. None of the agents listed above, nor any other
Varying Coefficient Models for Sparse Noise-contaminated Longitudinal Data
2014-01-01
Summary In this paper we propose a varying coefficient model for highly sparse longitudinal data that allows for error-prone time-dependent variables and time-invariant covariates. We develop a new estimation procedure, based on covariance representation techniques, that enables effective borrowing of information across all subjects in sparse and irregular longitudinal data observed with measurement error, a challenge in which there is no adequate solution currently. More specifically, sparsity is addressed via a functional analysis approach that considers the observed longitudinal data as noise contaminated realizations of a random process that produces smooth trajectories. This approach allows for estimation based on pooled data, borrowing strength from all subjects, in targeting the mean functions and auto- and cross-covariances to overcome sparse noisy designs. The resulting estimators are shown to be uniformly consistent. Consistent prediction for the response trajectories are also obtained via conditional expectation under Gaussian assumptions. Asymptotic distribution of the predicted response trajectories are derived, allowing for construction of asymptotic pointwise confidence bands. Efficacy of the proposed method is investigated in simulation studies and compared to the commonly used local polynomial smoothing method. The proposed method is illustrated with a sparse longitudinal data set, examining the age-varying relationship between calcium absorption and dietary calcium. Prediction of individual calcium absorption curves as a function of age are also examined. PMID:25589822
Scaled norm-based Euclidean projection for sparse speaker adaptation
NASA Astrophysics Data System (ADS)
Kim, Younggwan; Kim, Myung Jong; Kim, Hoirin
2015-12-01
To reduce data storage for speaker adaptive (SA) models, in our previous work, we proposed a sparse speaker adaptation method which can efficiently reduce the number of adapted parameters by using Euclidean projection onto the L 1-ball (EPL1) while maintaining recognition performance comparable to maximum a posteriori (MAP) adaptation. In the EPL1-based sparse speaker adaptation framework, however, the adapted Gaussian mean vectors are mostly concentrated on dimensions having large variances because of assuming unit variance for all dimensions. To make EPL1 more flexible, in this paper, we propose scaled norm-based Euclidean projection (SNEP) which can consider dimension-specific variances. By using SNEP, we also propose a new sparse speaker adaptation method which can consider the variances of a speaker-independent model. Our experiments show that the adapted components of mean vectors are evenly distributed in all dimensions, and we can obtain sparsely adapted models with no loss of phone recognition performance from the proposed method compared with MAP adaptation.
Sparse representation for vehicle recognition
NASA Astrophysics Data System (ADS)
Monnig, Nathan D.; Sakla, Wesam
2014-06-01
The Sparse Representation for Classification (SRC) algorithm has been demonstrated to be a state-of-the-art algorithm for facial recognition applications. Wright et al. demonstrate that under certain conditions, the SRC algorithm classification performance is agnostic to choice of linear feature space and highly resilient to image corruption. In this work, we examined the SRC algorithm performance on the vehicle recognition application, using images from the semi-synthetic vehicle database generated by the Air Force Research Laboratory. To represent modern operating conditions, vehicle images were corrupted with noise, blurring, and occlusion, with representation of varying pose and lighting conditions. Experiments suggest that linear feature space selection is important, particularly in the cases involving corrupted images. Overall, the SRC algorithm consistently outperforms a standard k nearest neighbor classifier on the vehicle recognition task.
Sparse and stable Markowitz portfolios
Brodie, Joshua; Daubechies, Ingrid; De Mol, Christine; Giannone, Domenico; Loris, Ignace
2009-01-01
We consider the problem of portfolio selection within the classical Markowitz mean-variance framework, reformulated as a constrained least-squares regression problem. We propose to add to the objective function a penalty proportional to the sum of the absolute values of the portfolio weights. This penalty regularizes (stabilizes) the optimization problem, encourages sparse portfolios (i.e., portfolios with only few active positions), and allows accounting for transaction costs. Our approach recovers as special cases the no-short-positions portfolios, but does allow for short positions in limited number. We implement this methodology on two benchmark data sets constructed by Fama and French. Using only a modest amount of training data, we construct portfolios whose out-of-sample performance, as measured by Sharpe ratio, is consistently and significantly better than that of the naïve evenly weighted portfolio. PMID:19617537
Sparsely Sampled Phase-Insensitive Ultrasonic Transducer Arrays
NASA Technical Reports Server (NTRS)
Johnston, Patrick H.
1992-01-01
Three methods of interpretation of outputs from sparsely sampled two-dimensional array of receiving ultrasonic transducers used in transmission experiments investigated. Methods are: description of sampled beam in terms of first few spatial moments of sampled distribution of energy; use of signal-dependent cutoff to limit extent of effective receiver aperture; and use of spatial interpolation to increase apparent density of sampling during computation. Methods reduce errors in computations of shapes of ultrasonic beams.
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.
Approximate Orthogonal Sparse Embedding for Dimensionality Reduction.
Lai, Zhihui; Wong, Wai Keung; Xu, Yong; Yang, Jian; Zhang, David
2016-04-01
Locally linear embedding (LLE) is one of the most well-known manifold learning methods. As the representative linear extension of LLE, orthogonal neighborhood preserving projection (ONPP) has attracted widespread attention in the field of dimensionality reduction. In this paper, a unified sparse learning framework is proposed by introducing the sparsity or L1-norm learning, which further extends the LLE-based methods to sparse cases. Theoretical connections between the ONPP and the proposed sparse linear embedding are discovered. The optimal sparse embeddings derived from the proposed framework can be computed by iterating the modified elastic net and singular value decomposition. We also show that the proposed model can be viewed as a general model for sparse linear and nonlinear (kernel) subspace learning. Based on this general model, sparse kernel embedding is also proposed for nonlinear sparse feature extraction. Extensive experiments on five databases demonstrate that the proposed sparse learning framework performs better than the existing subspace learning algorithm, particularly in the cases of small sample sizes. PMID:25955995
Rawal, Seema; Morisseau, Christophe; Hammock, Bruce D.; Shivachar, Amruthesh C
2013-01-01
The microsomal epoxide hydrolase (mEH) and soluble epoxide hydrolase (sEH) enzymes exist in a variety of cells and tissues, including liver, kidney and testis. However, very little is known about brain epoxide hydrolases. Here we report the expression, localization and subcellular distribution of mEH and sEH in cultured neonatal rat cortical astrocytes by immunocytochemistry, subcellular fractionation, western blotting and radiometric enzyme assays. Our results showed a diffused immunofluorescence pattern for mEH, which co-localized with the astroglial cytoskeletal marker, glial fibrillary acidic protein (GFAP). The GFAP-positive cells also expressed sEH which was mainly localized in the cytoplasm especially in and around the nucleus. Western blot analyses, revealed a distinct protein band with a molecular mass of ~50 kDa, the signal intensity of which increased about 1.5-fold in the microsomal fraction over the whole cell lysate and other subcellular fractions. The polyclonal anti-human sEH rabbit serum recognized a protein band with a molecular mass similar to that of purified sEH protein (~62 kDa), and the signal intensity increased 1.7-fold in the 105,000×g supernatant fraction over the cell lysate. Although the corresponding mEH enzyme activities generally corroborated with the immunocytochemical and western blotting data a low sEH enzyme activity was detected especially in the total cell lysate and in the soluble fractions. These results suggest that rat brain cortical astrocytes differentially co-express mEH and sEH enzymes. The differential subcellular localization of mEH and sEH may play a role in the cerebrovascular functions that are known to be affected by brain-derived vasoactive epoxides. PMID:18711743
Approximate inverse preconditioners for general sparse matrices
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.
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.
Scale-Invariant Sparse PCA on High Dimensional Meta-elliptical Data
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
Towards robust and effective shape modeling: sparse shape composition.
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
Anderson, Lauren G; Meeker, Rick B; Poulton, Winona E; Huang, David Y
2010-09-01
Carboxy terminus of Hsc70-interacting protein (CHIP) is thought to be a cytoprotective protein with protein quality control roles in neurodegenerative diseases and myocardial ischemia. This study describes the localization of CHIP expression in normal rodent brain and the early CHIP response in primary cultures of cortical neurons following ischemic stress models: heat stress (HS) and oxygen-glucose deprivation (OGD). CHIP was highly expressed throughout the brain, predominantly in neurons. The staining pattern was primarily cytoplasmic, although small amounts were seen in the nucleus. More intense nuclear staining was observed in primary cultured neurons which increased with stress. Nuclear accumulation of CHIP occurred within 5-10 min of HS and decreased to baseline levels or lower by 30-60 min. Decrease in nuclear CHIP at 30-60 min of HS was associated with a sharp increase in delayed cell death. While no changes in cytoplasmic CHIP were observed immediately following OGD, nuclear levels of CHIP increased slightly in response to OGD durations of 30 to 240 min. OGD-induced increases in nuclear CHIP decreased slowly during post-ischemic recovery. Nuclear CHIP decreased earlier in recovery following 120 min of OGD (4 h) than 30 min of OGD (12 h). Significant cell death first appeared between 12 and 24 h after OGD, again suggesting that delayed cell death follows closely behind the disappearance of nuclear CHIP. The ability of CHIP to translocate to and accumulate in the nucleus may be a limiting variable that determines how effectively cells respond to external stressors to facilitate cell survival. Using primary neuronal cell cultures, we were able to demonstrate rapid translocation of CHIP to the nucleus within minutes of heat stress and oxygen-glucose deprivation. An inverse relationship between nuclear CHIP and delayed cell death at 24 h suggests that the decrease in nuclear CHIP following extreme stress is linked to delayed cell death. Our findings of acute
Decoding of Covert Vowel Articulation Using Electroencephalography Cortical Currents.
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
Decoding of Covert Vowel Articulation Using Electroencephalography Cortical Currents
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
The cortical and cerebellar representation of the lumbar spine.
Boendermaker, Bart; Meier, Michael L; Luechinger, Roger; Humphreys, B Kim; Hotz-Boendermaker, Sabina
2014-08-01
Eight decades after Penfield's discovery of the homunculus only sparse evidence exists on the cortical representation of the lumbar spine. The aim of our investigation was the description of the lumbar spine's cortical representation in healthy subjects during the application of measured manual pressure. Twenty participants in the prone position were investigated during functional magnetic resonance imaging (fMRI). An experienced manual therapist applied non-painful, posterior-to-anterior (PA) pressure on three lumbar spinous processes (L1, L3, and L5). The pressure (30 N) was monitored and controlled by sensors. The randomized stimulation protocol consisted of 68 pressure stimuli of 5 s duration. Blood oxygenation level dependent (BOLD) responses were analyzed in relation to the lumbar stimulations. The results demonstrate that controlled PA pressure on the lumbar spine induced significant activation patterns. The major new finding was a strong and consistent activation bilaterally in the somatosensory cortices (S1 and S2). In addition, bilateral activation was located medially in the anterior cerebellum. The activation pattern also included other cortical areas probably related to anticipatory postural adjustments. These revealed stable somatosensory maps of the lumbar spine in healthy subjects can subsequently be used as a baseline to investigate cortical and subcortical reorganization in low back pain patients. PMID:24464423
Synaptogenesis in Purified Cortical Subplate Neurons
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
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
Prefrontal cortical minicolumn: from executive control to disrupted cognitive processing
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
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.
Resistant multiple sparse canonical correlation.
Coleman, Jacob; Replogle, Joseph; Chandler, Gabriel; Hardin, Johanna
2016-04-01
Canonical correlation analysis (CCA) is a multivariate technique that takes two datasets and forms the most highly correlated possible pairs of linear combinations between them. Each subsequent pair of linear combinations is orthogonal to the preceding pair, meaning that new information is gleaned from each pair. By looking at the magnitude of coefficient values, we can find out which variables can be grouped together, thus better understanding multiple interactions that are otherwise difficult to compute or grasp intuitively. CCA appears to have quite powerful applications to high-throughput data, as we can use it to discover, for example, relationships between gene expression and gene copy number variation. One of the biggest problems of CCA is that the number of variables (often upwards of 10,000) makes biological interpretation of linear combinations nearly impossible. To limit variable output, we have employed a method known as sparse canonical correlation analysis (SCCA), while adding estimation which is resistant to extreme observations or other types of deviant data. In this paper, we have demonstrated the success of resistant estimation in variable selection using SCCA. Additionally, we have used SCCA to find multiple canonical pairs for extended knowledge about the datasets at hand. Again, using resistant estimators provided more accurate estimates than standard estimators in the multiple canonical correlation setting. R code is available and documented at https://github.com/hardin47/rmscca. PMID:26963062
Sparse Spectrotemporal Coding of Sounds
NASA Astrophysics Data System (ADS)
Klein, David J.; König, Peter; Körding, Konrad P.
2003-12-01
Recent studies of biological auditory processing have revealed that sophisticated spectrotemporal analyses are performed by central auditory systems of various animals. The analysis is typically well matched with the statistics of relevant natural sounds, suggesting that it produces an optimal representation of the animal's acoustic biotope. We address this topic using simulated neurons that learn an optimal representation of a speech corpus. As input, the neurons receive a spectrographic representation of sound produced by a peripheral auditory model. The output representation is deemed optimal when the responses of the neurons are maximally sparse. Following optimization, the simulated neurons are similar to real neurons in many respects. Most notably, a given neuron only analyzes the input over a localized region of time and frequency. In addition, multiple subregions either excite or inhibit the neuron, together producing selectivity to spectral and temporal modulation patterns. This suggests that the brain's solution is particularly well suited for coding natural sound; therefore, it may prove useful in the design of new computational methods for processing speech.
Sparse Bayesian infinite factor models
Bhattacharya, A.; Dunson, D. B.
2011-01-01
We focus on sparse modelling of high-dimensional covariance matrices using Bayesian latent factor models. We propose a multiplicative gamma process shrinkage prior on the factor loadings which allows introduction of infinitely many factors, with the loadings increasingly shrunk towards zero as the column index increases. We use our prior on a parameter-expanded loading matrix to avoid the order dependence typical in factor analysis models and develop an efficient Gibbs sampler that scales well as data dimensionality increases. The gain in efficiency is achieved by the joint conjugacy property of the proposed prior, which allows block updating of the loadings matrix. We propose an adaptive Gibbs sampler for automatically truncating the infinite loading matrix through selection of the number of important factors. Theoretical results are provided on the support of the prior and truncation approximation bounds. A fast algorithm is proposed to produce approximate Bayes estimates. Latent factor regression methods are developed for prediction and variable selection in applications with high-dimensional correlated predictors. Operating characteristics are assessed through simulation studies, and the approach is applied to predict survival times from gene expression data. PMID:23049129
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.
Recent History Functional Linear Models for Sparse Longitudinal Data
Kim, Kion; Şentürk, Damla; Li, Runze
2011-01-01
We consider the recent history functional linear models, relating a longitudinal response to a longitudinal predictor where the predictor process only in a sliding window into the recent past has an effect on the response value at the current time. We propose an estimation procedure for recent history functional linear models that is geared towards sparse longitudinal data, where the observation times across subjects are irregular and total number of measurements per subject is small. The proposed estimation procedure builds upon recent developments in literature for estimation of functional linear models with sparse data and utilizes connections between the recent history functional linear models and varying coefficient models. We establish uniform consistency of the proposed estimators, propose prediction of the response trajectories and derive their asymptotic distribution leading to asymptotic point-wise confidence bands. We include a real data application and simulation studies to demonstrate the efficacy of the proposed methodology. PMID:21691421
Enhancing Scalability of Sparse Direct Methods
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.
Sparse High Dimensional Models in Economics
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
Imaging correlography with sparse collecting apertures
NASA Astrophysics Data System (ADS)
Idell, Paul S.; Fienup, J. R.
1987-01-01
This paper investigates the possibility of implementing an imaging correlography system with sparse arrays of intensity detectors. The theory underlying the image formation process for imaging correlography is reviewed, emphasizing the spatial filtering effects that sparse collecting apertures have on the reconstructed imagery. Image recovery with sparse arrays of intensity detectors through the use of computer experiments in which laser speckle measurements are digitally simulated is then demonstrated. It is shown that the quality of imagery reconstructed using this technique is visibly enhanced when appropriate filtering techniques are applied. A performance tradeoff between collecting array redundancy and the number of speckle pattern measurements is briefly discussed.
Feature selection and multi-kernel learning for sparse representation on a manifold.
Wang, Jim Jing-Yan; Bensmail, Halima; Gao, Xin
2014-03-01
Sparse representation has been widely studied as a part-based data representation method and applied in many scientific and engineering fields, such as bioinformatics and medical imaging. It seeks to represent a data sample as a sparse linear combination of some basic items in a dictionary. Gao et al. (2013) recently proposed Laplacian sparse coding by regularizing the sparse codes with an affinity graph. However, due to the noisy features and nonlinear distribution of the data samples, the affinity graph constructed directly from the original feature space is not necessarily a reliable reflection of the intrinsic manifold of the data samples. To overcome this problem, we integrate feature selection and multiple kernel learning into the sparse coding on the manifold. To this end, unified objectives are defined for feature selection, multiple kernel learning, sparse coding, and graph regularization. By optimizing the objective functions iteratively, we develop novel data representation algorithms with feature selection and multiple kernel learning respectively. Experimental results on two challenging tasks, N-linked glycosylation prediction and mammogram retrieval, demonstrate that the proposed algorithms outperform the traditional sparse coding methods. PMID:24333479
Cortical thinning in psychopathy
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
Cortical control of facial expression.
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
Sparse principal component analysis in cancer research
Hsu, Ying-Lin; Huang, Po-Yu; Chen, Dung-Tsa
2015-01-01
A critical challenging component in analyzing high-dimensional data in cancer research is how to reduce the dimension of data and how to extract relevant features. Sparse principal component analysis (PCA) is a powerful statistical tool that could help reduce data dimension and select important variables simultaneously. In this paper, we review several approaches for sparse PCA, including variance maximization (VM), reconstruction error minimization (REM), singular value decomposition (SVD), and probabilistic modeling (PM) approaches. A simulation study is conducted to compare PCA and the sparse PCAs. An example using a published gene signature in a lung cancer dataset is used to illustrate the potential application of sparse PCAs in cancer research. PMID:26719835
Finding Nonoverlapping Substructures of a Sparse Matrix
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.
Scenario generation for stochastic optimization problems via the sparse grid method
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
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
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.
2014-01-01
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 birefringence 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 48.28±38.78%; 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), decreased non-significantly the semi-homogeneous birefringent osteons (8.36±10.63 vs. 5.41±9.13, p=0.40) and birefringent bright (4.14±8.90 vs. 2.08±3.36, p=0.10) osteons. Further, lamellar thickness significantly increased from 3.78±0.11μm to 4.47±0.14μm (p=0.0002) for bright, and from 3.32±0.12μm to 3.70±0.12μm (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 initial degree of calcification was observed, relative to intermediate-low degree of calcification (57.16±3.08 vs. 32.90±3.69, p=0.04), the 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 point to study the reduction in fracture risk when PTH is used to treat osteoporosis. PMID:22161803
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.
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.
Increased temporolimbic cortical folding complexity in temporal lobe epilepsy
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
Sparse and redundant representations for inverse problems and recognition
NASA Astrophysics Data System (ADS)
Patel, Vishal M.
Sparse and redundant representation of data enables the description of signals as linear combinations of a few atoms from a dictionary. In this dissertation, we study applications of sparse and redundant representations in inverse problems and object recognition. Furthermore, we propose two novel imaging modalities based on the recently introduced theory of Compressed Sensing (CS). This dissertation consists of four major parts. In the first part of the dissertation, we study a new type of deconvolution algorithm that is based on estimating the image from a shearlet decomposition. Shearlets provide a multi-directional and multi-scale decomposition that has been mathematically shown to represent distributed discontinuities such as edges better than traditional wavelets. We develop a deconvolution algorithm that allows for the approximation inversion operator to be controlled on a multi-scale and multi-directional basis. Furthermore, we develop a method for the automatic determination of the threshold values for the noise shrinkage for each scale and direction without explicit knowledge of the noise variance using a generalized cross validation method. In the second part of the dissertation, we study a reconstruction method that recovers highly undersampled images assumed to have a sparse representation in a gradient domain by using partial measurement samples that are collected in the Fourier domain. Our method makes use of a robust generalized Poisson solver that greatly aids in achieving a significantly improved performance over similar proposed methods. We will demonstrate by experiments that this new technique is more flexible to work with either random or restricted sampling scenarios better than its competitors. In the third part of the dissertation, we introduce a novel Synthetic Aperture Radar (SAR) imaging modality which can provide a high resolution map of the spatial distribution of targets and terrain using a significantly reduced number of needed
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.
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
Malformations of cortical development
Pang, Trudy; Atefy, Ramin; Sheen, Volney
2012-01-01
Background Malformations of cortical development (MCD) are increasingly recognized as an important cause of epilepsy and developmental delay. MCD encompass a wide spectrum of disorders with various underlying genetic etiologies and clinical manifestations. High resolution imaging has dramatically improved our recognition of MCD. Review Summary This review will provide a brief overview of the stages of normal cortical development, including neuronal proliferation, neuroblast migration, and neuronal organization. Disruptions at various stages lead to characteristic MCD. Disorders of neurogenesis give rise to microcephaly (small brain) or macrocephaly (large brain). Disorders of early neuroblast migration give rise to periventricular heterotopia (neurons located along the ventricles), whereas abnormalities later in migration lead to lissencephaly (smooth brain) or subcortical band heterotopia (smooth brain with a band of heterotopic neurons under the cortex). Abnormal neuronal migration arrest give rise to over-migration of neurons in cobblestone lissencephaly. Lastly, disorders of neuronal organization cause polymicrogyria (abnormally small gyri and sulci). This review will also discuss the known genetic mutations and potential mechanisms that contribute to these syndromes. Conclusion Identification of various gene mutations has not only given us greater insight into some of the pathophysiologic basis of MCD, but also an understanding of the processes involved in normal cortical development. PMID:18469675
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.
Finding nonoverlapping substructures of a sparse matrix
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.
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.
Cortical Clefts and Cortical Bumps: A Continuous Spectrum
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.
The biology and dynamics of mammalian cortical granules
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
Fast wavelet based sparse approximate inverse preconditioner
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.
A unified approach to sparse signal processing
NASA Astrophysics Data System (ADS)
Marvasti, Farokh; Amini, Arash; Haddadi, Farzan; Soltanolkotabi, Mahdi; Khalaj, Babak Hossein; Aldroubi, Akram; Sanei, Saeid; Chambers, Janathon
2012-12-01
A unified view of the area of sparse signal processing is presented in tutorial form by bringing together various fields in which the property of sparsity has been successfully exploited. For each of these fields, various algorithms and techniques, which have been developed to leverage sparsity, are described succinctly. The common potential benefits of significant reduction in sampling rate and processing manipulations through sparse signal processing are revealed. The key application domains of sparse signal processing are sampling, coding, spectral estimation, array processing, component analysis, and multipath channel estimation. In terms of the sampling process and reconstruction algorithms, linkages are made with random sampling, compressed sensing, and rate of innovation. The redundancy introduced by channel coding in finite and real Galois fields is then related to over-sampling with similar reconstruction algorithms. The error locator polynomial (ELP) and iterative methods are shown to work quite effectively for both sampling and coding applications. The methods of Prony, Pisarenko, and MUltiple SIgnal Classification (MUSIC) are next shown to be targeted at analyzing signals with sparse frequency domain representations. Specifically, the relations of the approach of Prony to an annihilating filter in rate of innovation and ELP in coding are emphasized; the Pisarenko and MUSIC methods are further improvements of the Prony method under noisy environments. The iterative methods developed for sampling and coding applications are shown to be powerful tools in spectral estimation. Such narrowband spectral estimation is then related to multi-source location and direction of arrival estimation in array processing. Sparsity in unobservable source signals is also shown to facilitate source separation in sparse component analysis; the algorithms developed in this area such as linear programming and matching pursuit are also widely used in compressed sensing. Finally
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.
Sparse representation of complex MRI images.
Nandakumar, Hari Prasad; Ji, Jim
2008-01-01
Sparse representation of images acquired from Magnet Resonance Imaging (MRI) has several potential applications. MRI is unique in that the raw images are complex. Complex wavelet transforms (CWT) can be used to produce flexible signal representations when compared to Discrete Wavelet Transform (DWT). In this work, five different schemes using CWT or DWT are tested for sparse representation of MRI images which are in the form of complex values, separate real/imaginary, or separate magnitude/phase. The experimental results on real in-vivo MRI images show that appropriate CWT, e.g., dual-tree CWT (DTCWT), can achieve sparsity better than DWT with similar Mean Square Error. PMID:19162677
Native ultrametricity of sparse random ensembles
NASA Astrophysics Data System (ADS)
Avetisov, V.; Krapivsky, P. L.; Nechaev, S.
2016-01-01
We investigate the eigenvalue density in ensembles of large sparse Bernoulli random matrices. Analyzing in detail the spectral density of ensembles of linear subgraphs, we discuss its ultrametric nature and show that near the spectrum boundary, the tails of the spectral density exhibit a Lifshitz singularity typical for Anderson localization. We pay attention to an intriguing connection of the spectral density to the Dedekind η-function. We conjecture that ultrametricity emerges in rare-event statistics and is inherit to generic complex sparse systems.
Analog system for computing sparse codes
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.
Sparse representation in speech signal processing
NASA Astrophysics Data System (ADS)
Lee, Te-Won; Jang, Gil-Jin; Kwon, Oh-Wook
2003-11-01
We review the sparse representation principle for processing speech signals. A transformation for encoding the speech signals is learned such that the resulting coefficients are as independent as possible. We use independent component analysis with an exponential prior to learn a statistical representation for speech signals. This representation leads to extremely sparse priors that can be used for encoding speech signals for a variety of purposes. We review applications of this method for speech feature extraction, automatic speech recognition and speaker identification. Furthermore, this method is also suited for tackling the difficult problem of separating two sounds given only a single microphone.
Tensor methods for large, sparse unconstrained optimization
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.
Cortical basal ganglionic degeneration.
Scarmeas, N; Chin, S S; Marder, K
2001-10-01
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
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.
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.
Six Principles of Visual Cortical Dynamics
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
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
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.
Second SIAM conference on sparse matrices: Abstracts. Final technical report
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.
Data traffic reduction schemes for sparse Cholesky factorizations
NASA Technical Reports Server (NTRS)
Naik, Vijay K.; Patrick, Merrell L.
1988-01-01
Load distribution schemes are presented which minimize the total data traffic in the Cholesky factorization of dense and sparse, symmetric, positive definite matrices on multiprocessor systems with local and shared memory. The total data traffic in factoring an n x n sparse, symmetric, positive definite matrix representing an n-vertex regular 2-D grid graph using n (sup alpha), alpha is equal to or less than 1, processors are shown to be O(n(sup 1 + alpha/2)). It is O(n(sup 3/2)), when n (sup alpha), alpha is equal to or greater than 1, processors are used. Under the conditions of uniform load distribution, these results are shown to be asymptotically optimal. The schemes allow efficient use of up to O(n) processors before the total data traffic reaches the maximum value of O(n(sup 3/2)). The partitioning employed within the scheme, allows a better utilization of the data accessed from shared memory than those of previously published methods.
Two-Dimensional Pattern-Coupled Sparse Bayesian Learning via Generalized Approximate Message Passing
NASA Astrophysics Data System (ADS)
Fang, Jun; Zhang, Lizao; Li, Hongbin
2016-06-01
We consider the problem of recovering two-dimensional (2-D) block-sparse signals with \\emph{unknown} cluster patterns. Two-dimensional block-sparse patterns arise naturally in many practical applications such as foreground detection and inverse synthetic aperture radar imaging. To exploit the block-sparse structure, we introduce a 2-D pattern-coupled hierarchical Gaussian prior model to characterize the statistical pattern dependencies among neighboring coefficients. Unlike the conventional hierarchical Gaussian prior model where each coefficient is associated independently with a unique hyperparameter, the pattern-coupled prior for each coefficient not only involves its own hyperparameter, but also its immediate neighboring hyperparameters. Thus the sparsity patterns of neighboring coefficients are related to each other and the hierarchical model has the potential to encourage 2-D structured-sparse solutions. An expectation-maximization (EM) strategy is employed to obtain the maximum a posterior (MAP) estimate of the hyperparameters, along with the posterior distribution of the sparse signal. In addition, the generalized approximate message passing (GAMP) algorithm is embedded into the EM framework to efficiently compute an approximation of the posterior distribution of hidden variables, which results in a significant reduction in computational complexity. Numerical results are provided to illustrate the effectiveness of the proposed algorithm.
Multilevel sparse functional principal component analysis.
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
Multilevel sparse functional principal component analysis
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
Structured Sparse Method for Hyperspectral Unmixing
NASA Astrophysics Data System (ADS)
Zhu, Feiyun; Wang, Ying; Xiang, Shiming; Fan, Bin; Pan, Chunhong
2014-02-01
Hyperspectral Unmixing (HU) has received increasing attention in the past decades due to its ability of unveiling information latent in hyperspectral data. Unfortunately, most existing methods fail to take advantage of the spatial information in data. To overcome this limitation, we propose a Structured Sparse regularized Nonnegative Matrix Factorization (SS-NMF) method based on the following two aspects. First, we incorporate a graph Laplacian to encode the manifold structures embedded in the hyperspectral data space. In this way, the highly similar neighboring pixels can be grouped together. Second, the lasso penalty is employed in SS-NMF for the fact that pixels in the same manifold structure are sparsely mixed by a common set of relevant bases. These two factors act as a new structured sparse constraint. With this constraint, our method can learn a compact space, where highly similar pixels are grouped to share correlated sparse representations. Experiments on real hyperspectral data sets with different noise levels demonstrate that our method outperforms the state-of-the-art methods significantly.
A Comparative Study of Sparse Associative Memories
NASA Astrophysics Data System (ADS)
Gripon, Vincent; Heusel, Judith; Löwe, Matthias; Vermet, Franck
2016-05-01
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.
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.
Sparse matrix orderings for factorized inverse preconditioners
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.