Statistical physics of pairwise probability models.

Abstract:

:Statistical models for describing the probability distribution over the states of biological systems are commonly used for dimensional reduction. Among these models, pairwise models are very attractive in part because they can be fit using a reasonable amount of data: knowledge of the mean values and correlations between pairs of elements in the system is sufficient. Not surprisingly, then, using pairwise models for studying neural data has been the focus of many studies in recent years. In this paper, we describe how tools from statistical physics can be employed for studying and using pairwise models. We build on our previous work on the subject and study the relation between different methods for fitting these models and evaluating their quality. In particular, using data from simulated cortical networks we study how the quality of various approximate methods for inferring the parameters in a pairwise model depends on the time bin chosen for binning the data. We also study the effect of the size of the time bin on the model quality itself, again using simulated data. We show that using finer time bins increases the quality of the pairwise model. We offer new ways of deriving the expressions reported in our previous work for assessing the quality of pairwise models.

journal_name

Front Comput Neurosci

authors

Roudi Y,Aurell E,Hertz JA

doi

10.3389/neuro.10.022.2009

subject

Has Abstract

pub_date

2009-11-17 00:00:00

pages

22

issn

1662-5188

journal_volume

3

pub_type

杂志文章
  • The Effects of Capillary Transit Time Heterogeneity (CTH) on the Cerebral Uptake of Glucose and Glucose Analogs: Application to FDG and Comparison to Oxygen Uptake.

    abstract::Glucose is the brain's principal source of ATP, but the extent to which cerebral glucose consumption (CMRglc) is coupled with its oxygen consumption (CMRO2) remains unclear. Measurements of the brain's oxygen-glucose index OGI = CMRO2/CMRglc suggest that its oxygen uptake largely suffices for oxidative phosphorylation...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2016.00103

    authors: Angleys H,Jespersen SN,Østergaard L

    更新日期:2016-10-13 00:00:00

  • Anti-kindling Induced by Two-Stage Coordinated Reset Stimulation with Weak Onset Intensity.

    abstract::Abnormal neuronal synchrony plays an important role in a number of brain diseases. To specifically counteract abnormal neuronal synchrony by desynchronization, Coordinated Reset (CR) stimulation, a spatiotemporally patterned stimulation technique, was designed with computational means. In neuronal networks with spike ...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2016.00044

    authors: Zeitler M,Tass PA

    更新日期:2016-05-17 00:00:00

  • Fast convergence of learning requires plasticity between inferior olive and deep cerebellar nuclei in a manipulation task: a closed-loop robotic simulation.

    abstract::The cerebellum is known to play a critical role in learning relevant patterns of activity for adaptive motor control, but the underlying network mechanisms are only partly understood. The classical long-term synaptic plasticity between parallel fibers (PFs) and Purkinje cells (PCs), which is driven by the inferior oli...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章,评审

    doi:10.3389/fncom.2014.00097

    authors: Luque NR,Garrido JA,Carrillo RR,D'Angelo E,Ros E

    更新日期:2014-08-15 00:00:00

  • A micro-pool model for decision-related signals in visual cortical areas.

    abstract::The study of sensory signaling in the visual cortex has been greatly advanced by the recording of neural activity simultaneously with the performance of a specific psychophysical task. Individual nerve cells may also increase their firing leading up to the particular choice or decision made on a single psychophysical ...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2013.00115

    authors: Parker AJ

    更新日期:2013-08-13 00:00:00

  • Bayesian Inference of Synaptic Quantal Parameters from Correlated Vesicle Release.

    abstract::Synaptic transmission is both history-dependent and stochastic, resulting in varying responses to presentations of the same presynaptic stimulus. This complicates attempts to infer synaptic parameters and has led to the proposal of a number of different strategies for their quantification. Recently Bayesian approaches...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2016.00116

    authors: Bird AD,Wall MJ,Richardson MJ

    更新日期:2016-11-25 00:00:00

  • A Spiking Neural Model of HT3D for Corner Detection.

    abstract::Obtaining good quality image features is of remarkable importance for most computer vision tasks. It has been demonstrated that the first layers of the human visual cortex are devoted to feature detection. The need for these features has made line, segment, and corner detection one of the most studied topics in comput...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2018.00037

    authors: Bachiller-Burgos P,Manso LJ,Bustos P

    更新日期:2018-06-01 00:00:00

  • Synaptic bouton properties are tuned to best fit the prevailing firing pattern.

    abstract::The morphology of presynaptic specializations can vary greatly ranging from classical single-release-site boutons in the central nervous system to boutons of various sizes harboring multiple vesicle release sites. Multi-release-site boutons can be found in several neural contexts, for example at the neuromuscular junc...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2014.00101

    authors: Knodel MM,Geiger R,Ge L,Bucher D,Grillo A,Wittum G,Schuster CM,Queisser G

    更新日期:2014-09-09 00:00:00

  • Learning view invariant recognition with partially occluded objects.

    abstract::This paper investigates how a neural network model of the ventral visual pathway, VisNet, can form separate view invariant representations of a number of objects seen rotating together. In particular, in the current work one of the rotating objects is always partially occluded by the other objects present during train...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2012.00048

    authors: Tromans JM,Higgins I,Stringer SM

    更新日期:2012-07-25 00:00:00

  • Neuronal Degeneration Impairs Rhythms Between Connected Microcircuits.

    abstract::Synchronization of neural activity across brain regions is critical to processes that include perception, learning, and memory. After traumatic brain injury (TBI), neuronal degeneration is one possible effect and can alter communication between neural circuits. Consequently, synchronization between neurons may change ...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2020.00018

    authors: Schumm SN,Gabrieli D,Meaney DF

    更新日期:2020-03-03 00:00:00

  • Density Visualization Pipeline: A Tool for Cellular and Network Density Visualization and Analysis.

    abstract::Neuron classification is an important component in analyzing network structure and quantifying the effect of neuron topology on signal processing. Current quantification and classification approaches rely on morphology projection onto lower-dimensional spaces. In this paper a 3D visualization and quantification tool i...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2020.00042

    authors: Grein S,Qi G,Queisser G

    更新日期:2020-06-26 00:00:00

  • A simple transfer function for nonlinear dendritic integration.

    abstract::Relatively recent advances in patch clamp recordings and iontophoresis have enabled unprecedented study of neuronal post-synaptic integration ("dendritic integration"). Findings support a separate layer of integration in the dendritic branches before potentials reach the cell's soma. While integration between branches...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2015.00098

    authors: Singh MF,Zald DH

    更新日期:2015-08-10 00:00:00

  • Differing effects of attention in single-units and populations are well predicted by heterogeneous tuning and the normalization model of attention.

    abstract::Single-unit measurements have reported many different effects of attention on contrast-response (e.g., contrast-gain, response-gain, additive-offset dependent on visibility), while functional imaging measurements have more uniformly reported increases in response across all contrasts (additive-offset). The normalizati...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2014.00012

    authors: Hara Y,Pestilli F,Gardner JL

    更新日期:2014-02-19 00:00:00

  • Enabling functional neural circuit simulations with distributed computing of neuromodulated plasticity.

    abstract::A major puzzle in the field of computational neuroscience is how to relate system-level learning in higher organisms to synaptic plasticity. Recently, plasticity rules depending not only on pre- and post-synaptic activity but also on a third, non-local neuromodulatory signal have emerged as key candidates to bridge th...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2010.00141

    authors: Potjans W,Morrison A,Diesmann M

    更新日期:2010-11-23 00:00:00

  • A single theoretical framework for circular features processing in humans: orientation and direction of motion compared.

    abstract::Common computational principles underlie processing of various visual features in the cortex. They are considered to create similar patterns of contextual modulations in behavioral studies for different features as orientation and direction of motion. Here, I studied the possibility that a single theoretical framework...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2012.00028

    authors: Tzvetanov T

    更新日期:2012-05-22 00:00:00

  • Signal enhancement in the output stage of the basal ganglia by synaptic short-term plasticity in the direct, indirect, and hyperdirect pathways.

    abstract::Many of the synapses in the basal ganglia display short-term plasticity. Still, computational models have not yet been used to investigate how this affects signaling. Here we use a model of the basal ganglia network, constrained by available data, to quantitatively investigate how synaptic short-term plasticity affect...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2013.00076

    authors: Lindahl M,Kamali Sarvestani I,Ekeberg O,Kotaleski JH

    更新日期:2013-06-19 00:00:00

  • Structure learning and the Occam's razor principle: a new view of human function acquisition.

    abstract::We often encounter pairs of variables in the world whose mutual relationship can be described by a function. After training, human responses closely correspond to these functional relationships. Here we study how humans predict unobserved segments of a function that they have been trained on and we compare how human p...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2014.00121

    authors: Narain D,Smeets JB,Mamassian P,Brenner E,van Beers RJ

    更新日期:2014-09-30 00:00:00

  • Simultaneous stability and sensitivity in model cortical networks is achieved through anti-correlations between the in- and out-degree of connectivity.

    abstract::Neuronal networks in rodent barrel cortex are characterized by stable low baseline firing rates. However, they are sensitive to the action potentials of single neurons as suggested by recent single-cell stimulation experiments that reported quantifiable behavioral responses in response to short spike trains elicited i...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2013.00156

    authors: Vasquez JC,Houweling AR,Tiesinga P

    更新日期:2013-11-07 00:00:00

  • Hyperpolarization-Activated Current Induces Period-Doubling Cascades and Chaos in a Cold Thermoreceptor Model.

    abstract::In this article, we describe and analyze the chaotic behavior of a conductance-based neuronal bursting model. This is a model with a reduced number of variables, yet it retains biophysical plausibility. Inspired by the activity of cold thermoreceptors, the model contains a persistent Sodium current, a Calcium-activate...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2017.00012

    authors: Xu K,Maidana JP,Caviedes M,Quero D,Aguirre P,Orio P

    更新日期:2017-03-10 00:00:00

  • Visual motion integration is mediated by directional ambiguities in local motion signals.

    abstract::The output of primary visual cortex (V1) is a piecemeal representation of the visual scene and the response of any one cell cannot unambiguously guide sensorimotor behavior. It remains unsolved how subsequent stages of cortical processing combine ("pool") these early visual signals into a coherent representation. We (...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2013.00167

    authors: Rocchi F,Ledgeway T,Webb BS

    更新日期:2013-11-18 00:00:00

  • Stability constraints on large-scale structural brain networks.

    abstract::Stability is an important dynamical property of complex systems and underpins a broad range of coherent self-organized behavior. Based on evidence that some neurological disorders correspond to linear instabilities, we hypothesize that stability constrains the brain's electrical activity and influences its structure a...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2013.00031

    authors: Gray RT,Robinson PA

    更新日期:2013-04-12 00:00:00

  • On the dynamics of cortical development: synchrony and synaptic self-organization.

    abstract::We describe a model for cortical development that resolves long-standing difficulties of earlier models. It is proposed that, during embryonic development, synchronous firing of neurons and their competition for limited metabolic resources leads to selection of an array of neurons with ultra-small-world characteristic...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2013.00004

    authors: Wright JJ,Bourke PD

    更新日期:2013-02-15 00:00:00

  • Alterations of Muscle Synergies During Voluntary Arm Reaching Movement in Subacute Stroke Survivors at Different Levels of Impairment.

    abstract::Motor system uses muscle synergies as a modular organization to simplify the control of movements. Motor cortical impairments, such as stroke and spinal cord injuries, disrupt the orchestration of the muscle synergies and result in abnormal movements. In this paper, the alterations of muscle synergies in subacute stro...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2018.00069

    authors: Pan B,Sun Y,Xie B,Huang Z,Wu J,Hou J,Liu Y,Huang Z,Zhang Z

    更新日期:2018-08-21 00:00:00

  • Computational Neural Modeling of Auditory Cortical Receptive Fields.

    abstract::Previous studies have shown that the auditory cortex can enhance the perception of behaviorally important sounds in the presence of background noise, but the mechanisms by which it does this are not yet elucidated. Rapid plasticity of spectrotemporal receptive fields (STRFs) in the primary (A1) cortical neurons is obs...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2019.00028

    authors: Chambers JD,Elgueda D,Fritz JB,Shamma SA,Burkitt AN,Grayden DB

    更新日期:2019-05-24 00:00:00

  • A network that performs brute-force conversion of a temporal sequence to a spatial pattern: relevance to odor recognition.

    abstract::A classic problem in neuroscience is how temporal sequences (TSs) can be recognized. This problem is exemplified in the olfactory system, where an odor is defined by the TS of olfactory bulb (OB) output that occurs during a sniff. This sequence is discrete because the output is subdivided by gamma frequency oscillatio...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2014.00108

    authors: Sanders H,Kolterman BE,Shusterman R,Rinberg D,Koulakov A,Lisman J

    更新日期:2014-09-17 00:00:00

  • Conscious Multisensory Integration: Introducing a Universal Contextual Field in Biological and Deep Artificial Neural Networks.

    abstract::Conscious awareness plays a major role in human cognition and adaptive behavior, though its function in multisensory integration is not yet fully understood, hence, questions remain: How does the brain integrate the incoming multisensory signals with respect to different external environments? How are the roles of the...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2020.00015

    authors: Adeel A

    更新日期:2020-05-19 00:00:00

  • Unsupervised Few-Shot Feature Learning via Self-Supervised Training.

    abstract::Learning from limited exemplars (few-shot learning) is a fundamental, unsolved problem that has been laboriously explored in the machine learning community. However, current few-shot learners are mostly supervised and rely heavily on a large amount of labeled examples. Unsupervised learning is a more natural procedure...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2020.00083

    authors: Ji Z,Zou X,Huang T,Wu S

    更新日期:2020-10-14 00:00:00

  • Neural circuits for peristaltic wave propagation in crawling Drosophila larvae: analysis and modeling.

    abstract::Drosophila larvae crawl by peristaltic waves of muscle contractions, which propagate along the animal body and involve the simultaneous contraction of the left and right side of each segment. Coordinated propagation of contraction does not require sensory input, suggesting that movement is generated by a central patte...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2013.00024

    authors: Gjorgjieva J,Berni J,Evers JF,Eglen SJ

    更新日期:2013-04-04 00:00:00

  • A Computational Model of Interactions Between Neuronal and Astrocytic Networks: The Role of Astrocytes in the Stability of the Neuronal Firing Rate.

    abstract::Recent research in neuroscience indicates the importance of tripartite synapses and gliotransmission mediated by astrocytes in neuronal system modulation. Although the astrocyte and neuronal network functions are interrelated, they are fundamentally different in their signaling patterns and, possibly, the time scales ...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2019.00092

    authors: Lenk K,Satuvuori E,Lallouette J,Ladrón-de-Guevara A,Berry H,Hyttinen JAK

    更新日期:2020-01-22 00:00:00

  • Unsupervised Domain Adaptation With Optimal Transport in Multi-Site Segmentation of Multiple Sclerosis Lesions From MRI Data.

    abstract::Automatic segmentation of Multiple Sclerosis (MS) lesions from Magnetic Resonance Imaging (MRI) images is essential for clinical assessment and treatment planning of MS. Recent years have seen an increasing use of Convolutional Neural Networks (CNNs) for this task. Although these methods provide accurate segmentation,...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2020.00019

    authors: Ackaouy A,Courty N,Vallée E,Commowick O,Barillot C,Galassi F

    更新日期:2020-03-09 00:00:00

  • Analog Signaling With the "Digital" Molecular Switch CaMKII.

    abstract::Molecular switches, such as the protein kinase CaMKII, play a fundamental role in cell signaling by decoding inputs into either high or low states of activity; because the high activation state can be turned on and persist after the input ceases, these switches have earned a reputation as "digital." Although this on/o...

    journal_title:Frontiers in computational neuroscience

    pub_type: 杂志文章

    doi:10.3389/fncom.2018.00092

    authors: Clarke SE

    更新日期:2018-11-22 00:00:00