Quantitative Biology - Neurons and Cognition Publications (50)

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Quantitative Biology - Neurons and Cognition Publications

Synapses in real neural circuits can take discrete values, including zero (silent or potential) synapses. The computational role of zero synapses in unsupervised feature learning of unlabeled noisy data is still unclear, yet important to understand how the sparseness of synaptic activity is shaped during learning and its relationship with receptive field formation. Here, we formulate this kind of sparse feature learning by statistical mechanics approach. Read More


A promising approach towards understanding neural networks is to view them as implementations of online algorithms optimizing principled objectives. Existing neural algorithms capturing both neural activity dynamics and synaptic weight updates implement the same operation, either minimization or maximization of the objective, with respect to each variable. Here, we derive neural networks from principled min-max objectives: by minimizing with respect to neural activity and feedforward synaptic weights, and maximizing with respect to lateral synaptic weights. Read More


When we encounter a new person or place, we may easily encode it into our memories, or we may quickly forget it. Recent work finds that this likelihood of encoding a given entity - memorability - is highly consistent across viewers and intrinsic to an image; people tend to remember and forget the same images. However, several forces influence our memories beyond the memorability of the stimulus itself - for example, how attention-grabbing the stimulus is, how much attentional resources we dedicate to the task, or how primed we are for that stimulus. Read More


In a seminal paper by von Stein and Sarnthein (200), it was hypothesized that "bottom-up" information processing of "content" elicits local, high frequency (beta-gamma) oscillations, whereas "top-down" processing is "contextual", characterized by large scale integration spanning distant cortical regions, and implemented by slower frequency (theta-alpha) oscillations. This corresponds to a mechanism of cortical information transactions, where synchronization of beta-gamma oscillations between distant cortical regions is mediated by widespread theta-alpha oscillations. It is the aim of this paper to express this hypothesis quantitatively, in terms of a model that will allow testing this type of information transaction mechanism. Read More


The working memory capacity (WMC) of 400 Russian college students was measured using the Tarnow Unchunkable Test [2] which tests WMC alone without requiring explicit working memory operations. We found small-sized WMC differences by gender and the possibility that the male/female ratio increases for low and high WMC creating a u-shaped curve. The gender proportion in each academic fields was a strong determinant of the average WMC (r2=0. Read More


In the past few years, new technologies in the field of neuroscience have made it possible to simultaneously image activity in large populations of neurons at cellular resolution in behaving animals. In mid-2016, a huge repository of this so-called "calcium imaging" data was made publicly-available. The availability of this large-scale data resource opens the door to a host of scientific questions, for which new statistical methods must be developed. Read More


2017Mar
Affiliations: 1Charite, FU, HU, BIH, BCCN, BCAN, Neurocure, Berlin, 2University Medical Center Hamburg-Eppendorf, 3Charite, FU, HU, BIH, BCCN, BCAN, Neurocure, Berlin, 4Charite, FU, HU, BIH, BCCN, BCAN, Neurocure, Berlin

Standard neuroimaging data analysis based on traditional principles of experimental design, modelling, and statistical inference is increasingly complemented by novel analysis methods, driven e.g. by machine learning methods. Read More


The term gestalt has been widely used in the field of psychology which defined the perception of human mind to group any object not in part but as a unified whole. Music in general is polytonic i.e. Read More


We investigate a recently proposed model for cortical computation which performs relational inference. It consists of several interconnected, structurally equivalent populations of leaky integrate-and-fire (LIF) neurons, which are trained in a self-organized fashion with spike-timing dependent plasticity (STDP). Despite its robust learning dynamics, the model is susceptible to a problem typical for recurrent networks which use a correlation based (Hebbian) learning rule: if trained with high learning rates, the recurrent connections can cause strong feedback loops in the network dynamics, which lead to the emergence of attractor states. Read More


We introduce SIM-CE, an advanced, user-friendly modeling and simulation environment in Simulink for performing multi-scale behavioral analysis of the nervous system of Caenorhabditis elegans (C. elegans). SIM-CE contains an implementation of the mathematical models of C. Read More


Caenorhabditis elegans (C. elegans) illustrated remarkable behavioral plasticities including complex non-associative and associative learning representations. Understanding the principles of such mechanisms presumably leads to constructive inspirations for the design of efficient learning algorithms. Read More


We explore how to study dynamical interactions between brain regions using functional multilayer networks whose layers represent the different frequency bands at which a brain operates. Specifically, we investigate the consequences of considering the brain as a multilayer network in which all brain regions can interact with each other at different frequency bands, instead of as a multiplex network, in which interactions between different frequency bands are only allowed within each brain region and not between them. We study the second smallest eigenvalue of the combinatorial supra-Laplacian matrix of the multilayer network in detail, and we thereby show that the heterogeneity of interlayer edges and, especially, the fraction of missing edges crucially modify the spectral properties of the multilayer network. Read More


Despite being originally inspired by the central nervous system, artificial neural networks have diverged from their biological archetypes as they have been remodeled to fit particular tasks. In this paper, we review several possibilites to reverse map these architectures to biologically more realistic spiking networks with the aim of emulating them on fast, low-power neuromorphic hardware. Since many of these devices employ analog components, which cannot be perfectly controlled, finding ways to compensate for the resulting effects represents a key challenge. Read More


It has been proposed that cultural evolution was made possible by a cognitive transition brought about by onset of the capacity for self-triggered recall and rehearsal. Here we develop a novel idea that models of collectively autocatalytic networks, developed for understanding the origin and organization of life, may also help explain the origin of the kind of cognitive structure that makes cultural evolution possible. In our setting, mental representations (for example, memories, concepts, ideas) play the role of 'molecules', and 'reactions' involve the evoking of one representation by another through remindings, associations, and stimuli. Read More


We demonstrate that behavioral probabilities of human decision makers share many common features with quantum probabilities. This does not imply that humans are some quantum objects, but just shows that the mathematics of quantum theory is applicable to the description of human decision making. The applicability of quantum rules for describing decision making is connected with the nontrivial process of making decisions in the case of composite prospects under uncertainty. Read More


We propose a model of an adaptive network of spiking neurons that gives rise to a hypernetwork of its dynamic states at the upper level of description. Left to itself, the network exhibits a sequence of transient clustering which relates to a traffic in the hypernetwork in the form of a random walk. Receiving inputs the system is able to generate reproducible sequences corresponding to stimulus-specific paths in the hypernetwork. Read More


Obsessive-compulsive disorder (OCD) is a common psychiatric disorder with a lifetime prevalence of 2-3 percent. Recently, brain activity in the resting state is gathering attention as a new means of exploring altered functional connectivity in psychiatric disorders. Although previous resting-state functional magnetic resonance imaging studies investigated neurobiological abnormalities of patients with OCD, there are concerns that should be addressed. Read More


Neural data analysis has increasingly incorporated causal information to study circuit connectivity. Dimensional reduction forms the basis of most analyses of large multivariate time series. Here, we present a new, multitaper-based decomposition for stochastic, multivariate time series that acts on the covariance of the time series at all lags, $C(\tau)$, as opposed to standard methods that decompose the time series, $\mathbf{X}(t)$, using only information at zero-lag. Read More


Recent evidence suggests that neural information is encoded in packets and may be flexibly routed from region to region. We have hypothesized that neural circuits are split into sub-circuits where one sub-circuit controls information propagation via pulse gating and a second sub-circuit processes graded information under the control of the first sub-circuit. Using an explicit pulse-gating mechanism, we have been able to show how information may be processed by such pulse-controlled circuits and also how, by allowing the information processing circuit to interact with the gating circuit, decisions can be made. Read More


Psychiatric illnesses are often associated with multiple symptoms, whose severity must be graded for accurate diagnosis and treatment. This grading is usually done by trained clinicians based on human observations and judgments made within doctor-patient sessions. Current research provides sufficient reason to expect that the human voice may carry biomarkers or signatures of many, if not all, these symptoms. Read More


The evident robustness of neural computation is hypothesized to arise from some degree of local stability around dynamically-generated sequences of local-circuit activity states involving many neurons. Recently, it was discovered that even randomly-connected cortical circuit models exhibit dynamics in which their phase-space partitions into a multitude of attractor basins enclosing complex network state trajectories. We provide the first theory of the random geometry of this disordered phase space. Read More


Avalanches of electrochemical activity in brain networks have been empirically reported to obey scale-invariant behavior --characterized by power-law distributions up to some upper cut-off-- both in vitro and in vivo. Elucidating whether such scaling laws stem from the underlying neural dynamics operating at the edge of a phase transition is a fascinating possibility, as systems poised at criticality have been argued to exhibit a number of important functional advantages. Here we employ a well-known model for neural dynamics with synaptic plasticity, to elucidate an alternative scenario in which neuronal avalanches can coexist, overlapping in time, but still remaining scale-free. Read More


This paper proposes that cognitive humor can be modeled using the mathematical framework of quantum theory. We begin with brief overviews of both research on humor, and the generalized quantum framework. We show how the bisociation of incongruous frames or word meanings in jokes can be modeled as a linear superposition of a set of basis states, or possible interpretations, in a complex Hilbert space. Read More


Neurons in the intact brain receive a continuous and irregular synaptic bombardment from excitatory and inhibitory pre-synaptic neurons, which determines the firing activity of the stimulated neuron. In order to investigate the influence of inhibitory stimulation on the firing time statistics, we consider Leaky Integrate-and-Fire neurons subject to inhibitory instantaneous post-synaptic potentials. In particular, we report exact results for the firing rate, the coefficient of variation and the spike train spectrum for various synaptic weight distributions. Read More


Deep learning has led to remarkable advances when applied to problems where the data distribution does not change over the course of learning. In stark contrast, biological neural networks continually adapt to changing domains, and solve a diversity of tasks simultaneously. Furthermore, synapses in biological neurons are not simply real-valued scalars, but possess complex molecular machinery enabling non-trivial learning dynamics. Read More


We study the problem of optimal oculomotor control during the execution of visual search tasks. We introduce a computational model of human eye movements, which takes into account various constraints of the human visual and oculomotor systems. In the model, the choice of the subsequent fixation location is posed as a problem of stochastic optimal control, which relies on reinforcement learning methods. Read More


Spontaneous, synchronous bursting of neural population is a widely observed phenomenon in nervous networks, which is considered important for functions and dysfunctions of the brain. However, how the global synchrony across a large number of neurons emerges from an initially non-bursting network state is not fully understood. In this study, we develop a new state-space reconstruction method combined with high-resolution recordings of cultured neurons. Read More


How spiking networks are able to perform probabilistic inference is an intriguing question, not only for understanding information processing in the brain, but also for transferring these computational principles to neuromorphic silicon circuits. A number of computationally powerful spiking network models have been proposed, but most of them have only been tested, under ideal conditions, in software simulations. Any implementation in an analog, physical system, be it in vivo or in silico, will generally lead to distorted dynamics due to the physical properties of the underlying substrate. Read More


A stochastic model of excitatory and inhibitory interactions which bears universality traits is introduced and studied. The endogenous component of noise, stemming from finite size corrections, drives robust inter-nodes correlations, that persist at large large distances. Anti-phase synchrony at small frequencies is resolved on adjacent nodes and found to promote the spontaneous generation of long-ranged stochastic patterns, that invade the network as a whole. Read More


In recent years, there has been strong interest in neuroscience studies to investigate brain organization through networks of brain regions that demonstrate strong functional connectivity (FC). These networks are extracted from observed fMRI using data-driven analytic methods such as independent component analysis (ICA). A notable limitation of these FC methods is that they do not provide any information on the underlying structural connectivity (SC), which is believed to serve as the basis for interregional interactions in brain activity. Read More


A key question in neuroscience is at which level functional meaning emerges from biophysical phenomena. In most vertebrate systems, precise functions are assigned at the level of neural populations, while single-neurons are deemed unreliable and redundant. Here we challenge this view and show that many single-neuron quantities, including voltages, firing thresholds, excitation, inhibition, and spikes, acquire precise functional meaning whenever a network learns to transmit information parsimoniously and precisely to the next layer. Read More


Neuronal firing activities have attracted a lot of attention since a large population of spatiotemporal patterns in the brain is the basis for adaptive behavior and can also reveal the signs for various neurological disorders including Alzheimer's, schizophrenia, epilepsy and others. Here, we study the dynamics of a simple neuronal network using different sets of settings on a neuromorphic chip. We observed three different types of collective neuronal firing activities, which agree with the clinical data taken from the brain. Read More


Anticipated synchronization (AS) is a counter intuitive behavior that has been observed in several systems. When AS establishes in a sender-receiver configuration, the latter can predict the future dynamics of the former for certain parameter values. In particular, in neuroscience AS was proposed to explain the apparent discrepancy between information flow and time lag in the cortical activity recorded in monkeys. Read More


Regularization occurs when the output a learner produces is less variable than the linguistic data they observed. In an artificial language learning experiment, we show that there exist at least two independent sources of regularization bias in cognition: a domain-general source based on cognitive load and a domain-specific source triggered by linguistic stimuli. Both of these factors modulate how frequency information is encoded and produced, but only the production-side modulations result in regularization (i. Read More


An essential step toward understanding neural circuits is linking their structure and their dynamics. In general, this relationship can be almost arbitrarily complex. Recent theoretical work has, however, begun to identify some broad principles underlying collective spiking activity in neural circuits. Read More


Individual computations and social interactions underlying collective behavior in groups of animals are of great ethological, behavioral, and theoretical interest. While complex individual behaviors have successfully been parsed into small dictionaries of stereotyped behavioral modes, studies of collective behavior largely ignored these findings; instead, their focus was on inferring single, mode-independent social interaction rules that reproduced macroscopic and often qualitative features of group behavior. Here we bring these two approaches together to predict individual swimming patterns of adult zebrafish in a group. Read More


A conceptual and computational framework is proposed for modelling of human sensorimotor control, and is exemplified for the sensorimotor task of steering a car. The framework emphasises control intermittency, and extends on existing models by suggesting that the nervous system implements intermittent control using a combination of (1) motor primitives, (2) prediction of sensory outcomes of motor actions, and (3) evidence accumulation of prediction errors. It is shown that approximate but useful sensory predictions in the intermittent control context can be constructed without detailed forward models, as a superposition of simple prediction primitives, resembling neurobiologically observed corollary discharges. Read More


We study a pulse-coupled dynamics of excitable elements in uncorrelated scale-free networks. Regimes of self-sustained activity are found for homogeneous and inhomogeneous couplings, in which the system displays a wide variety of behaviors, including periodic and irregular global spiking signals, as well as coherent oscillations, an unexpected form of synchronization. Our numerical results also show that the properties of the population firing rate depend on the size of the system, particularly its structure and average value over time. Read More


Our desire and fascination with intelligent machines dates back to the antiquity's mythical automaton Talos, Aristotle's mode of mechanical thought (syllogism) and Heron of Alexandria's mechanical machines and automata. However, the quest for Artificial General Intelligence (AGI) is troubled with repeated failures of strategies and approaches throughout the history. This decade has seen a shift in interest towards bio-inspired software and hardware, with the assumption that such mimicry entails intelligence. Read More


Calcium imaging has emerged as a workhorse method in neuroscience to investigate patterns of neuronal activity. Instrumentation to acquire calcium imaging movies has rapidly progressed and has become standard across labs. Still, algorithms to automatically detect and extract activity signals from calcium imaging movies are highly variable from~lab~to~lab and more advanced algorithms are continuously being developed. Read More


So-called sparse estimators arise in the context of model fitting, when one a priori assumes that only a few (unknown) model parameters deviate from zero. Sparsity constraints can be useful when the estimation problem is under-determined, i.e. Read More


The sure thing principle and the law of total probability are basic laws in classic probability theory. A disjunction fallacy leads to the violation of these two classical probability laws. In this paper, a new quantum dynamic belief decision making model based on quantum dynamic modelling and Dempster-Shafer (D-S) evidence theory is proposed to address this issue and model the real human decision-making process. Read More


The state-of-the-art method for automatically segmenting white matter bundles in diffusion-weighted MRI is tractography in conjunction with streamline cluster selection. This process involves long chains of processing steps which are not only computationally expensive but also complex to setup and tedious with respect to quality control. Direct bundle segmentation methods treat the task as a traditional image segmentation problem. Read More


Graph Signal Processing (GSP) is a promising method to analyze high-dimensional neuroimaging datasets while taking into account both the spatial and functional dependencies between brain signals. In the present work, we apply GSP with dimensionality reduction techniques to decode brain activity from real and simulated fMRI datasets. We introduce seven graphs obtained from a) geometric structure and/or b) functional connectivity between brain areas at rest and compare them when performing dimension reduction for classification. Read More


In the mammalian brain newly acquired memories are dependent on the hippocampus for maintenance and recall, but over time these functions are taken over by the neocortex through a process called memory consolidation. Thus, whereas recent memories are likely to be disrupted in the event of hippocampal damage, older memories are less vulnerable. However, if a consolidated memory is reactivated by a reminder, it can temporarily return to a hippocampus-dependent state. Read More


A major open challenge in neuroscience is the ability to measure and perturb neural activity in vivo from well-defined neural sub-populations at cellular resolution anywhere in the brain. However, limitations posed by scattering and absorption prohibit non-invasive (surface) multiphoton approaches for deep (>2mm) structures, while Gradient Refreactive Index (GRIN) endoscopes are thick and cause significant damage upon insertion. Here, we demonstrate a novel microendoscope to image neural activity at arbitrary depths via an ultrathin multimode optical fiber (MMF) probe that is 5-10X thinner than commercially available microendoscopes. Read More


Variational approaches to approximate Bayesian inference provide very efficient means of performing parameter estimation and model selection. Among these, so-called variational-Laplace or VL schemes rely on Gaussian approximations to posterior densities on model parameters. In this note, we review the main variants of VL approaches, that follow from considering nonlinear models of continuous and/or categorical data. Read More


Voltage-sensitive dye imaging (VSDi) has revealed fundamental properties of neocortical processing at mesoscopic scales. Since VSDi signals report the average membrane potential, it seems natural to use a mean-field formalism to model such signals. Here, we investigate a mean-field model of networks of Adaptive Exponential (AdEx) integrate-and-fire neurons, with conductance-based synaptic interactions. Read More


We perform new experiment using almost the same sample size considered by Tversky and Shafir to test the validity of classical probability theory in decision making. The results clearly indicate that the disjunction effect depends also on culture and more specifically on gender (females rather than males). We did more statistical analysis rather that putting the actual values done by previous authors. Read More