Quantitative Biology - Neurons and Cognition Publications (50)

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Quantitative Biology - Neurons and Cognition Publications

We address the problem of designing artificial agents capable of reproducing human behavior in a competitive game involving dynamic control. Given data consisting of multiple realizations of inputs generated by pairs of interacting players, we model each agent's actions as governed by a time-varying latent goal state coupled to a control model. These goals, in turn, are described as stochastic processes evolving according to player-specific value functions depending on the current state of the game. Read More


This article is written in response to a Progressions article by Kanwisher in the Journal of Neuroscience, The Quest for the FFA and Where It Led (Kanwisher, 2017). I reflect on the extensive research program dedicated to the study of how and why perceptual expertise explains the many ways that faces are special, a research program which both predates and follows the Kanwisher (1997) landmark article where the fusiform face area (FFA) is named. The expertise accounts suggests that the FFA is an area recruited by expertise individuating objects that are perceptually similar because they share a configuration of parts. Read More


Neural codes are collections of binary strings motivated by patterns of neural activity. In this paper, we study algorithmic and enumerative aspects of convex neural codes in dimension 1 (i.e. Read More


Neurons in the dorsal subregion of the medial superior temporal (MSTd) area respond to large, complex patterns of retinal flow, implying a role in the analysis of self-motion. Some neurons are selective for the expanding radial motion that occurs as an observer moves through the environment ("heading"), and computational models can account for this finding. However, ample evidence suggests that MSTd neurons may exhibit a continuum of visual response selectivity to large-field motion stimuli, but the underlying computational principles by which these response properties are derived remain poorly understood. Read More


Mathematical modeling has broad applications in neuroscience whether modeling the dynamics of a single synapse or an entire network of neurons. In Part I, we model vesicle replenishment and release at the photoreceptor synapse to better understand how visual information is processed. In Part II, we explore a simple model of neural networks with the goal of discovering how network structure shapes the behavior of the network. Read More


Line attractors in neural networks have been suggested to be the basis of many brain functions, such as working memory, oculomotor control, head direction, locomotion, and sensory processing. In recent work, we incorporated pulse gating into feedforward neural networks and showed that the transmission of graded information can be viewed as a line attractor in the firing rate of transiently synchronous populations. While this was revealed in an analysis using rate models, graded information transfer persisted in spiking neural networks and was robust to intrinsic and extrinsic noise. Read More


Brains need to predict how our muscles and body react to motor commands. How networks of spiking neurons can learn to reproduce these non-linear dynamics, using local, online and stable learning rules, is an important, open question. Here, we present a supervised learning scheme for the feedforward and recurrent connections in a network of heterogeneous spiking neurons. Read More


We present here a browser-based application for visualizing patterns of connectivity in 3D stacked data matrices with large numbers of pairwise relations. Visualizing a connectivity matrix, looking for trends and patterns, and dynamically manipulating these values is a challenge for scientists from diverse fields, including neuroscience and genomics. In particular, high-dimensional neural data include those acquired via electroencephalography (EEG), electrocorticography (ECoG), magnetoencephalography (MEG), and functional MRI. Read More


Our century has unprecedented new challenges, which need creative solutions and deep thinking. Contemplative, deep thinking became an "endangered species" in our rushing world of Tweets, elevator pitches and fast decisions. Here we describe that important aspects of both creativity and deep thinking can be understood as network phenomena of conceptual and social networks. Read More


Identification of intended movement type and movement phase of hand grasp shaping are critical features for the control of volitional neuroprosthetics. We demonstrate that neural dynamics during visually-guided imagined grasp shaping can encode intended movement. We apply Procrustes analysis and LASSO regression to achieve 72% accuracy (chance = 25%) in distinguishing between visually-guided imagined grasp trajectories. Read More


Polychronous neural groups are effective structures for the recognition of precise spike-timing patterns but the detection method is an inefficient multi-stage brute force process that works off-line on pre-recorded simulation data. This work presents a new model of polychronous patterns that can capture precise sequences of spikes directly in the neural simulation. In this scheme, each neuron is assigned a randomized code that is used to tag the post-synaptic neurons whenever a spike is transmitted. Read More


To provide an explanation of the evolution of scientific knowledge, I start from the assumption that knowledge is based on concepts, and propose that each concept about reality is affected by vagueness. This entails a paradox, which I term Knowledge Paradox (KP): i.e. Read More


Based on a set of subjects and a collection of descriptors obtained from the Alzheimer's Disease Neuroimaging Initiative database, we use redescription mining to find rules revealing associations between these determinants which provides insights about the Alzheimer's disease (AD). We applied a four-step redescription mining algorithm (CLUS-RM), which has been extended to engender constraint-based redescription mining (CBRM) and enables several modes of targeted exploration of specific, user-defined associations. To a large extent we confirmed known findings, previously reported in the literature. Read More


In the present work we analyzed the pupil size behavior of forty subjects while they read well defined sentences with different contextual predictability (i.e., regular sentences and proverbs). Read More


Recently, several experiments have demonstrated the existence of fractional diffusion in the neuronal transmission occurring in the Purkinje cells, whose malfunctioning is known to be related to the lack of voluntary coordination and the appearance of tremors. Also, a classical mathematical feature is that (fractional) parabolic equations possess smoothing effects, in contrast with the case of hyperbolic equations, which typically exhibit shocks and discontinuities. In this paper, we show how a simple toy-model of a highly ramified structure, somehow inspired by that of the Purkinje cells, may produce a fractional diffusion via the superposition of travelling waves that solve a hyperbolic equation. Read More


Background: Measures of spike train synchrony are widely used in both experimental and computational neuroscience. Time-scale independent and parameter-free measures, such as the ISI-distance, the SPIKE-distance and SPIKE-synchronization, are preferable to time-scale parametric measures, since by adapting to the local firing rate they take into account all the time-scales of a given dataset. New Method: In data containing multiple time-scales (e. Read More


We propose an extension of the cable equation by introducing a Caputo time fractional derivative. The fundamental solutions of the most common boundary problems are derived analitically via Laplace Transform, and result be written in terms of known special functions. This generalization could be useful to describe anomalous diffusion phenomena with leakage as signal conduction in spiny dendrites. Read More


The cable model is widely used in several fields of science to describe the propagation of signals. A relevant medical and biological example is the anomalous subdiffusion in spiny neuronal dendrites observed in several studies of the last decade. Anomalous subdiffusion can be modelled in several ways introducing some fractional component into the classical cable model. Read More


The temporal and spatial development of Parkinson's disease has been characterised as the progressive formation of {\alpha}-synuclein aggregations through susceptible neuronal pathways. This article describes a new model for this progression mechanism in which Parkinsonian damage moves over time through the nervous system by the combined effect of the reaction kinetics of pathogenesis and molecular diffusion. In the reaction-diffusion model, the change from a healthy state to the disease state advances through the nervous system as a wave front of Parkinsonian damage, marking its path by accumulations of damaged {\alpha}-synuclein and neurotoxic levels of oxidative species. Read More


A number of popular measures of dependence between pairs of band-limited signals rely on analytic phase. A common misconception is that the dependence revealed by these measures must be specific to the spectral range of the filtered input signals. Implicitly or explicitly, obtaining analytic phase involves normalizing the signal by its own envelope, which is a nonlinear operation that introduces broad spectral leakage. Read More


There is mounting evidence of a link between the properties of electroencephalograms (EEGs) of depressive patients and the outcome of pharmacotherapy. The goal of this study was to develop an EEG biomarker of antidepressant treatment response which would require only a single EEG measurement. We recorded resting, 21-channel EEG in 17 inpatients suffering from bipolar depression in eyes closed and eyes open conditions. Read More


Real-time fMRI neurofeedback (rtfMRI-nf) with simultaneous EEG allows volitional modulation of BOLD activity of target brain regions and investigation of related electrophysiological activity. We applied this approach to study correlations between thalamic BOLD activity and alpha EEG rhythm. Healthy volunteers in the experimental group (EG, n=15) learned to upregulate BOLD activity of the target region consisting of the mediodorsal (MD) and anterior (AN) thalamic nuclei using the rtfMRI-nf during retrieval of happy autobiographical memories. Read More


Finding the origin of slow and infra-slow oscillations could reveal or explain brain mechanisms in health and disease. Here, we present a biophysically constrained computational model of a neural network where the inclusion of astrocytes introduced slow and infra-slow-oscillations, through two distinct mechanisms. Specifically, we show how astrocytes can modulate the fast network activity through their slow inter-cellular calcium wave speed and amplitude and possibly cause the oscillatory imbalances observed in diseases commonly known for such abnormalities, namely Alzheimer's disease, Parkinson's disease, epilepsy, depression and ischemic stroke. Read More


We consider a new model of individual neuron of Integrate-and-Fire (IF) type with fractional noise. The correlations of its spike trains are studied and proved to have long memory, unlike classical IF models. To measure correctly long-range dependence, it is often necessary to know if the data are stationary. Read More


Neuro-electronic hybrid promises to bring up a model architecture for computing. Such computing architecture could help to bring the power of biological connection and electronic circuits together for better computing paradigm. Such paradigms for solving real world tasks with higher accuracy is on demand now. Read More


Determining how synaptic coupling within and between regions is modulated during sensory processing is an important topic in neuroscience. Electrophysiological recordings provide detailed spiking information about neurons but have traditionally been confined to a particular region or layer of cortex. Here, we develop a novel theoretical framework that relies on efficiently calculating the first and second order statistics in a multi-population firing rate model. Read More


We propose that the brain performs approximate probabilistic inference using nonlinear recurrent processing in redundant population codes. Different overlapping patterns of neural population activity encode the brain's estimates and uncertainties about latent variables that could explain its sense data. Nonlinear processing implicitly passes messages about these variables along a graph that determines which latent variables interact according to an internal model of the world. Read More


Rapid experimental advances now enable simultaneous electrophysiological recording of neural activity at single-cell resolution across large regions of the nervous system. Models of this neural network activity will necessarily increase in size and complexity, thus increasing the computational cost of simulating them and new challenges in analyzing them. Here we present a novel approximation method to approximate the activity and firing statistics of a general firing rate network model (of Wilson-Cowan type) subject to noisy correlated background inputs. Read More


The distribution of the geometric distances of connected neurons is a practical factor underlying neural networks in the brain. It can affect the brain\'s dynamic properties at the ground level. Karbowski derived a power-law decay distribution that has not yet been verified by experiment. Read More


In the presented study Parent/Teacher Disruptive Behavior Disorder (DBD) rating scale based on the Diagnostic and Statistical Manual of Mental Disorders (DSM-IV-TR [APA, 2000]) which was developed by Pelham and his colleagues (Pelham et al., 1992) was translated and adopted for assessment of childhood behavioral abnormalities, especially ADHD, ODD and CD in Georgian children and adolescents. The DBD rating scale was translated into Georgian language using back translation technique by English language philologists and checked and corrected by qualified psychologists and psychiatrist of Georgia. Read More


Exactly solvable neural network models with asymmetric weights are rare, and exact solutions are available only in some mean-field approaches. In this article we find exact analytical solutions of an asymmetric spin-glass-like model of arbitrary size and we perform a complete study of its dynamical and statistical properties. The network has discrete-time evolution equations, binary firing rates and can be driven by noise with any distribution. Read More


The brain's functional diversity is reflected in the meso-scale architecture of its connectome, i.e. its division into clusters and communities of topologically-related brain regions. Read More


Experimental records of active bundle motility are used to demonstrate the presence of a low-dimensional chaotic attractor in hair cell dynamics. Dimensionality tests from dynamic systems theory are applied to estimate the number of independent variables sufficient for modeling the hair cell response. Poincare maps are constructed to observe a quasiperiodic transition from chaos to order with increasing amplitudes of mechanical forcing. Read More


Neuroscientists are actively pursuing high-precision maps, or graphs, consisting of networks of neurons and connecting synapses in mammalian and non-mammalian brains. Such graphs, when coupled with physiological and behavioral data, are likely to facilitate greater understanding of how circuits in these networks give rise to complex information processing capabilities. Given that the automated or semi-automated methods required to achieve the acquisition of these graphs are still evolving, we develop a metric for measuring the performance of such methods by comparing their output with those generated by human annotators ("ground truth" data). Read More


Uncertainty, spatial or temporal errors, variability, are classic themes in the study of human and animal behaviors. Several theoretical approaches1 and concepts have been adopted to tackle those issues, often considering the CNS as an observer, using Shannon information and entropy, signal to noise ratio, and recently a Bayesian approach, and free energy minimization. In the coordination dynamics framework, addressing pattern formation processes underlying cognitive functions, and goal directed human movement among others, the tools employed originate from the statistical physics of Brownian motion and stochastic processes. Read More


Natural images follow statistics inherited by the structure of our physical (visual) environment. In particular, a prominent facet of this structure is that images can be described by a relatively sparse number of features. We designed a sparse coding algorithm biologically-inspired by the architecture of the primary visual cortex. Read More


Researchers in many disciplines have previously used a variety of mathematical techniques for analyzing group interactions. Here we use a new metric for this purpose, called 'integrated information' or 'phi.' Phi was originally developed by neuroscientists as a measure of consciousness in brains, but it captures, in a single mathematical quantity, two properties that are important in many other kinds of groups as well: differentiated information and integration. Read More


The study of electroencephalographic (EEG) bursts in preterm infants provides valuable information about maturation or prognostication after perinatal asphyxia. Over the last two decades, a number of works proposed algorithms to automatically detect EEG bursts in preterm infants, but they were designed for populations under 35 weeks of post menstrual age (PMA). However, as the brain activity evolves rapidly during postnatal life, these solutions might be under-performing with increasing PMA. Read More


A central challenge in neuroscience is to understand neural computations and circuit mechanisms that underlie the encoding of ethologically relevant, natural stimuli. In multilayered neural circuits, nonlinear processes such as synaptic transmission and spiking dynamics present a significant obstacle to the creation of accurate computational models of responses to natural stimuli. Here we demonstrate that deep convolutional neural networks (CNNs) capture retinal responses to natural scenes nearly to within the variability of a cell's response, and are markedly more accurate than linear-nonlinear (LN) models and Generalized Linear Models (GLMs). Read More


Obtaining meaningful quantitative descriptions of the statistical dependence within multivariate systems is a difficult open problem. Recently, the Partial Information Decomposition (PID) was proposed to decompose mutual information (MI) about a target variable into components which are redundant, unique and synergistic within different subsets of predictor variables. Here, we propose to apply the elegant formalism of the PID to multivariate entropy, resulting in a Partial Entropy Decomposition (PED). Read More


The correlated variability in the responses of a neural population to the repeated presentation of a sensory stimulus is a universally observed phenomenon. Such correlations have been studied in much detail, both with respect to their mechanistic origin and to their influence on stimulus discrimination and on the performance of population codes. In particular, recurrent neural network models have been used to understand the origin (or lack) of correlations in neural activity. Read More


Inverse problems in statistical physics are motivated by the challenges of `big data' in different fields, in particular high-throughput experiments in biology. In inverse problems, the usual procedure of statistical physics needs to be reversed: Instead of calculating observables on the basis of model parameters, we seek to infer parameters of a model based on observations. In this review, we focus on the inverse Ising problem and closely related problems, namely how to infer the interactions between spins given observed spin correlations, magnetisations, or other data. Read More


One of the most important challenges in mathematical neuroscience is to properly illustrate the stochastic nature of neurons. Among different approaches, the noisy leaky integrate-and-fire and the escape rate models are probably the most popular. These two models are usually chosen to express different noise action over the neural cell. Read More


The graph theoretic properties of the clustering coefficient, characteristic (or average) path length, global and local efficiency, provide valuable information regarding the structure of a graph. These four properties have applications to biological and social networks and have dominated much of the the literature in these fields. While much work has done in applied settings, there has yet to be a mathematical comparison of these metrics from a theoretical standpoint. Read More


A major obstacle to understanding neural coding and computation is the fact that experimental recordings typically sample only a small fraction of the neurons in a circuit. Measured neural properties are skewed by interactions between recorded neurons and the "hidden" portion of the network. To properly interpret neural data, we thus need a better understanding of the relationships between measured effective neural properties and the true underlying physiological properties. Read More


In the present work, we develop a deep-learning approach for differentiating the eye-movement behavior of people with neurodegenerative diseases over healthy control subjects during reading well-defined sentences. We define an information compaction of the eye-tracking data of subjects without and with probable Alzheimer's disease when reading a set of well-defined, previously validated, sentences including high-, low-predictable sentences, and proverbs. Using this information we train a set of denoising sparse-autoencoders and build a deep neural network with these and a softmax classifier. Read More


We investigate scaling properties of human brain functional networks in the resting-state. Analyzing network degree distributions, we statistically test whether their tails scale as power-law or not. Initial studies, based on least-squares fitting, were shown to be inadequate for precise estimation of power-law distributions. Read More


We study heterogeneous distribution of gains in neural fields using techniques of quantum mechanics by exploiting a relationship of our model and the time-independent Schr\"{o}dinger equation. We show that specific relationships between the connectivity kernel and the gain of the population can explain the behavior of the neural field in simulations. In particular, we show this relationships for the gating of activity between two regions (step potential), the propagation of activity throughout another region (barrier) and, most importantly, the existence of bumps in gain-contained regions (gain well). Read More


Many biological and cognitive systems do not operate deep into one or other regime of activity. Instead, they exploit critical surfaces poised at transitions in their parameter space. The pervasiveness of criticality in natural systems suggests that there may be general principles inducing this behaviour. Read More


We present a database for research on affect, personality traits and mood by means of neuro-physiological signals. Different to other databases, we elicited affect using both short and long videos in two settings, one with individual viewers and one with groups of viewers. The database allows the multimodal study of the affective responses of individuals in relation to their personality and mood, and the analysis of how these responses are affected by (i) the individual/group setting, and (ii) the duration of the videos (short vs long). Read More