Quantitative Biology - Neurons and Cognition Publications (50)

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Quantitative Biology - Neurons and Cognition Publications

Enormous questions still loom for the emerging science of spontaneous thought: what, exactly, is spontaneous thought? Why does our brain engage in spontaneous forms of thinking, and when is this most likely to occur? And perhaps the question most interesting and accessible from a scientific perspective: how does the brain generate, elaborate, and evaluate its own spontaneous creations? The central aim of this volume is to bring together views from neuroscience, psychology, philosophy, phenomenology, history, education, contemplative traditions, and clinical practice in order to begin to address the ubiquitous but poorly understood mental phenomena that we collectively call 'spontaneous thought.' Perhaps no other mental experience is so familiar to us in daily life, and yet so difficult to understand and explain scientifically. The present volume represents the first effort to bring such highly diverse perspectives to bear on answering the what, when, why, and how of spontaneous thought. Read More


Community detection algorithms have been widely used to study the organization of complex systems like the brain. A principal appeal of these techniques is their ability to identify a partition of brain regions (or nodes) into communities, where nodes within a community are densely interconnected. In their simplest application, community detection algorithms are agnostic to the presence of community hierarchies, but a common characteristic of many neural systems is a nested hierarchy. Read More


Background: For newborn infants in critical care, continuous monitoring of brain function can help identify infants at-risk of brain injury. Quantitative features allow a consistent and reproducible approach to EEG analysis, but only when all implementation aspects are clearly defined. Methods: We detail quantitative features frequently used in neonatal EEG analysis and present a Matlab software package together with exact implementation details for all features. Read More


What happens inside the performers brain when he is performing and composing a particular raga. Are there some specific regions in brain which are activated when an artist is creating or imaging a raga in his brain. Do the regions remain the same when the artist is listening to the same raga sung by him. Read More


The activity of a neuronal network, characterized by action potentials (spikes) is constrained by the intrinsic properties of neurons and their interactions. When a neuronal network is submitted to external stimuli, the statistics of spikes changes, and becomes difficult to disentangle the influence of the stimuli from the intrinsic dynamics. Using the formalism of Gibbs distributions we analyze this problem in a specific model (Conductance-based Integrate-and-Fire), where the neuronal dynamics depends on the history of spikes of the network. Read More


This paper outlines a methodological approach to generate adaptive agents driving themselves near points of criticality. Using a synthetic approach we construct a conceptual model that, instead of specifying mechanistic requirements to generate criticality, exploits the maintenance of an organizational structure capable of reproducing critical behavior. Our approach captures the well-known principle of universality that classifies critical phenomena inside a few universality classes of systems without relying on specific mechanisms or topologies. Read More


EEG based brain state decoding has numerous applications. State of the art decoding is based on processing of the multivariate sensor space signal, however evidence is mounting that EEG source reconstruction can assist decoding. EEG source imaging leads to high-dimensional representations and rather strong a priori information must be invoked. Read More


Even this saying itself is a variant of a similar statement attributed to Bernard of Chartres in the 12th Century, and inspired the title for a book by Steven Hawking and an album by Oasis. Creative ideas beget other creative ideas and, as a result, modifications accumulate, and we see an overall increase in the complexity of cultural novelty over time, a phenomenon sometimes referred to as the ratchet effect (Tomasello, Kruger, & Ratner, 1993). Although we may never meet the people or objects that creatively influence us, by assimilating what we encounter around us and bringing to bear our own insights and perspectives, we all contribute in our own way, however small, to a second evolutionary process -- the evolution of culture. Read More


Despite our familiarity with and fondness of humor, until relatively recently very little was known about the underlying psychology of this complex and nuanced phenomenon. Recently, however, cognitive psychologists have begun investigating how people understand humor and why we find certain things funny. This chapter introduces a new cognitive approach to modeling humor that we refer to as the 'quantum approach', which will be explained here in intuitive, non-mathematical terms later (a formal treatment can be found in Gabora & Kitto, 2017). Read More


Optogenetics is an emerging field of neuroscience where neurons are genetically modified to express light-sensitive receptors that enable external control over when the neurons fire. Given the prominence of neuronal signaling within the brain and throughout the body, optogenetics has significant potential to improve the understanding of the nervous system and to develop treatments for neurological diseases. This paper uses a simple optogenetic model to compare the timing distortion between a randomly-generated target spike sequence and an externally-stimulated neuron spike sequence. Read More


Efficient complex systems have a modular structure, but modularity does not guarantee robustness, because efficiency also requires an ingenious interplay of the interacting modular components. The human brain is the elemental paradigm of an efficient robust modular system interconnected as a network of networks (NoN). Understanding the emergence of robustness in such modular architectures from the interconnections of its parts is a long-standing challenge that has concerned many scientists. Read More


This chapter revisits the concept of excitability, a basic system property of neurons. The focus is on excitable systems regarded as behaviors rather than dynamical systems. By this we mean open systems modulated by specific interconnection properties rather than closed systems classified by their parameter ranges. Read More


Elucidating principles that underlie computation in neural networks is currently a major research topic of interest in neuroscience. Transfer Entropy (TE) is increasingly used as a tool to bridge the gap between network structure, function, and behavior in fMRI studies. Computational models allow us to bridge the gap even further by directly associating individual neuron activity with behavior. Read More


Experimental data suggest that neural circuits configure their synaptic connectivity for a given computational task. They also point to dopamine-gated stochastic spine dynamics as an important underlying mechanism, and they show that the stochastic component of synaptic plasticity is surprisingly strong. We propose a model that elucidates how task-dependent self-configuration of neural circuits can emerge through these mechanisms. Read More


Serotonergic, noradrenergic and dopaminergic brainstem (including midbrain) neurons, often exhibit spontaneous and fairly regular spiking with frequencies of order a few Hz, though dopaminergic and noradrenergic neurons only exhibit such pacemaker-type activity in vitro or in vivo under special conditions. A large number of ion channel types contribute to such spiking so that detailed modeling of spike generation leads to the requirement of solving very large systems of differential equations. It is useful to have simplified mathematical models of spiking in such neurons so that, for example, features of inputs and output spike trains can be incorporated including stochastic effects for possible use in network models. Read More


Humans take advantage of real world symmetries for various tasks, yet capturing their superb symmetry perception mechanism into a computational model remains elusive. Encouraged by a new discovery (CVPR 2016) demonstrating extremely high inter-person accuracy of human perceived symmetries in the wild, we have created the first deep-learning neural network for reflection and rotation symmetry detection (Sym-NET), trained on photos from MS-COCO (Common Object in COntext) dataset with nearly 11K symmetry-labels from more than 400 human observers. We employ novel methods to convert discrete human labels into symmetry heatmaps, capture symmetry densely in an image and quantitatively evaluate Sym-NET against multiple existing computer vision algorithms. Read More


Cooperation and competition between human players in repeated microeconomic games offer a powerful window onto social phenomena such as the establishment, breakdown and repair of trust. This offers the prospect of particular insight into populations of subjects suffering from socially-debilitating conditions such as borderline personality disorder. However, although a suitable foundation for the quantitative analysis of such games exists, namely the Interactive Partially Observable Markov Decision Process (I-POMDP), computational considerations have hitherto limited its application. Read More


We consider the Watts-Strogatz small-world network consisting of subthreshold neurons which exhibit noise-induced spikings. This neuronal network has adaptive dynamic synaptic strengths governed by the spike-timing-dependent plasticity (STDP). In previous works without STDP, stochastic spike synchronization (SSS) between noise-induced spikings of subthreshold neurons was found to occur in a range of intermediate noise intensities through competition between the constructive and the destructive roles of noise. Read More


Message passing between components of a distributed physical system is non-instantaneous and contributes to determine the time scales of the emerging collective dynamics like an effective inertia. In biological neuron networks this inertia is due in part to local synaptic filtering of exchanged spikes, and in part to the distribution of the axonal transmission delays. How differently these two kinds of inertia affect the network dynamics is an open issue not yet addressed due to the difficulties in dealing with the non-Markovian nature of synaptic transmission. Read More


We explore statistical characteristics of avalanches associated with the dynamics of a complex-network model, where two modules corresponding to sensorial and symbolic memories interact, representing unconscious and conscious mental processes. The model illustrates Freud's ideas regarding the neuroses and that consciousness is related with symbolic and linguistic memory activity in the brain. It incorporates the Stariolo-Tsallis generalization of the Boltzmann Machine in order to model memory retrieval and associativity. Read More


Pain is among the most salient of experiences while also, curiously, being among the most malleable. A large body of research has revealed that a multitude of explicit strategies can be used to effectively alter the attention-demanding quality of acute and chronic pains and their associated neural correlates. However, thoughts that are spontaneous, rather than actively generated, are common in daily life, and so attention to pain can often temporally fluctuate because of ongoing self-generated experiences. Read More


This study proposes an approach to estimate the functional localization and connectivity from CBF and BOLD signals simultaneously measured by ASL (arterial spin labeling) MRI, especially using exploratory Structural Equation Modeling analysis. In a visual task experiment, the primary visual cortices were located by analyzing the perfusion data. In the resting state experiment, two structural equation models were estimated at each voxel regarding to the sensory-motor network and default-mode network. Read More


An often-overlooked characteristic of the human mind is its propensity to wander. Despite growing interest in the science of mind-wandering, most studies operationalize mind-wandering by its task-unrelated contents, which may be orthogonal to the processes constraining how thoughts are evoked and unfold over time. In this chapter, we emphasize the importance of incorporating such processes into current definitions of mind-wandering, and proposing that mind-wandering and other forms of spontaneous thought (such as dreaming and creativity) are mental states that arise and transition relatively freely due to an absence of constraints on cognition. Read More


Synchronization in neural networks is strongly tied to the implementation of cognitive processes, but abnormal neuronal synchronization has been linked to a number of brain disorders such as epilepsy and schizophrenia. Here we examine the effects of channel noise on the synchronization of small Hodgkin-Huxley neuronal networks. The principal feature of a Hodgkin-Huxley neuron is the existence of protein channels that transition between open and closed states with voltage dependent rate constants. Read More


Sleep paralysis is an experience of being temporarily unable to move or talk during the transitional periods between sleep and wakefulness: at sleep onset or upon awakening. Feeling of paralysis may be accompanied by a variety of vivid and intense sensory experiences, including mentation in visual, auditory, and tactile modalities, as well as a distinct feeling of presence. This chapter discusses a variety of sleep paralysis experiences from the perspective of enactive cognition and cultural neurophenomenology. Read More


The brain must robustly store a large number of memories, corresponding to the many events and scenes a person encounters over a lifetime. However, the number of memory states in existing neural network models either grows weakly with network size or recall performance fails catastrophically with vanishingly little noise. Here we show that it is possible to construct an associative content-addressable memory (ACAM) with exponentially many stable states and robust error-correction. Read More


Scene viewing is used to study attentional selection in complex but still controlled environments. One of the main observations on eye movements during scene viewing is the inhomogeneous distribution of fixation locations: While some parts of an image are fixated by almost all observers and are inspected repeatedly by the same observer, other image parts remain unfixated among observers even after long exploration intervals. Here, we apply spatial point processes to investigate the correlations between pairs of points. Read More


A recent paper suggests that Deep Neural Networks can be protected from gradient-based adversarial perturbations by driving the network activations into a highly saturated regime. Here we analyse such saturated networks and show that the attacks fail due to numerical limitations in the gradient computations. A simple stabilisation of the gradient estimates enables successful and efficient attacks. Read More


Psychiatric research has been hampered by an explanatory gap between psychiatric symptoms and their neural underpinnings, which has resulted in poor treatment outcomes. This situation has prompted us to shift from symptom-based diagnosis to data-driven diagnosis, aiming to redefine psychiatric disorders as disorders of neural circuitry. Promising candidates for data-driven diagnosis include resting-state functional connectivity MRI (rs-fcMRI)-based biomarkers. Read More


A fundamental explanandum of the hard problem of consciousness concerns the link between the physical and the phenomenal. That is to say, given that there are such things as physical processes and conscious experience, what is it about the particular physical processes (e.g. Read More


Miniscope calcium imaging is increasingly being used to monitor large populations of neuronal activities in freely behaving animals. However, due to the high background and low signal-to-noise ratio of the single-photon based imaging used in this technique, extraction of neural signals from the large numbers of imaged cells automatically has remained challenging. Here we describe a highly accurate framework for automatically identifying activated neurons and extracting calcium signals from the miniscope imaging data, seeds cleansing Constrained Nonnegative Matrix Factorization (sc-CNMF). Read More


Much has been learned about plasticity of biological synapses from empirical studies. Hebbian plasticity is driven by correlated activity of presynaptic and postsynaptic neurons. Synapses that converge onto the same neuron often behave as if they compete for a fixed resource; some survive the competition while others are eliminated. Read More


By focusing on melancholic features with biological homogeneity, this study aimed to identify a small number of critical functional connections (FCs) that were specific only to the melancholic type of MDD. On the resting-state fMRI data, classifiers were developed to differentiate MDD patients from healthy controls (HCs). The classification accuracy was improved from 50 % (93 MDD and 93 HCs) to 70% (66 melancholic MDD and 66 HCs), when we specifically focused on the melancholic MDD with moderate or severer level of depressive symptoms. Read More


The diffusion weighted images acquired with the multiband sequence or the Lifespan protocols shows a type of slice distortion artifact. We find that this artifact is caused by the eddy currents, which can be induced by the diffusion gradient associated with either current DW image or the previous DW images. The artifact can be corrected by further tuning the compensation circuit in the MR hardware, or by a correction algorithm which includes the diffusion gradients from the current and previous DW images. Read More


This paper describes an approach of using dynamic Structural Equation Modeling (SEM) analysis to estimate the connectivity networks from resting-state fMRI data measured by a multiband EPI sequence. Two structural equation models were estimated at each voxel with respect to the sensory-motor network and default-mode network. The resulting connectivity maps indicate that supplementary motor area has significant connections to left/right primary motor areas, and medial prefrontal cortex link significantly with posterior cingulate cortex and inferior parietal lobules. Read More


Functional magnetic resonance imaging (fMRI) has begun to narrow down the neural correlates of self-generated forms of thought, with current evidence pointing toward central roles for the default, frontoparietal, and visual networks. Recent work has linked the arising of thoughts more specifically to default network activity, but the limited temporal resolution of fMRI has precluded more detailed conclusions about where in the brain self-created mental content is generated and how this is achieved. Here I argue that the unparalleled spatiotemporal resolution of intracranial electrophysiology (iEEG) in human epilepsy patients can begin to provide answers to questions about the specific neural origins of self-generated thought. Read More


The central nervous system is composed of many individual units -- from cells to areas -- that are connected with one another in a complex pattern of functional interactions that supports perception, action, and cognition. One natural and parsimonious representation of such a system is a graph in which nodes (units) are connected by edges (interactions). While applicable across spatiotemporal scales, species, and cohorts, the traditional graph approach is unable to address the complexity of time-varying connectivity patterns that may be critically important for an understanding of emotional and cognitive state, task-switching, adaptation and development, or aging and disease progression. Read More


Multi-electrode arrays (MEA) are increasingly used to investigate spontaneous neuronal network activity. The recorded signals comprise several distinct components: Apart from artefacts without biological significance, one can distinguish between spikes (action potentials) and subthreshold fluctuations (local fields potentials). Here we aim to develop a theoretical model that allows for a compact and robust characterization of subthreshold fluctuations in terms of a Gaussian statistical field theory in two spatial and one temporal dimension. Read More


In previously identified forms of remote synchronization between two nodes, the intermediate portion of the network connecting the two nodes is not synchronized with them but generally exhibits some coherent dynamics. Here we report on a network phenomenon we call incoherence-mediated remote synchronization (IMRS), in which two non-contiguous parts of the network are identically synchronized while the dynamics of the intermediate part is statistically and information-theoretically incoherent. We identify mirror symmetry in the network structure as a mechanism allowing for such behavior, and show that IMRS is robust against dynamical noise as well as against parameter changes. Read More


We use a feed-forward artificial neural network with back-propagation through a single hidden layer to predict Barry Cottonfield's likely reply to this author's invitation to the "Once Upon a Daydream" junior prom at the Conard High School gymnasium back in 1997. To examine the network's ability to generalize to such a situation beyond specific training scenarios, we use a L2 regularization term in the cost function and examine performance over a range of regularization strengths. In addition, we examine the nonsensical decision-making strategies that emerge in Barry at times when he has recently engaged in a fight with his annoying kid sister Janice. Read More


Contemporary neuroscience has embraced network science to study the complex and self-organized structure of the human brain; one of the main outstanding issues is that of inferring from measure data, chiefly functional Magnetic Resonance Imaging (fMRI), the so-called effective connectivity in brain networks, that is the existing interactions among neuronal populations. This inverse problem is complicated by the fact that the BOLD (Blood Oxygenation Level Dependent) signal measured by fMRI represent a dynamic and nonlinear transformation (the hemodynamic response) of neuronal activity. In this paper, we consider resting state (rs) fMRI data; building upon a linear population model of the BOLD signal and a stochastic linear DCM model, the model parameters are estimated through an EM-type iterative procedure, which alternately estimates the neuronal activity by means of the Rauch-Tung-Striebel (RTS) smoother, updates the connections among neuronal states and refines the parameters of the hemodynamic model; sparsity in the interconnection structure is favoured using an iteratively reweighting scheme. Read More


Data-driven brain parcellations aim to provide a more accurate representation of an individual's functional connectivity, since they are able to capture individual variability that arises due to development or disease. This renders comparisons between the emerging brain connectivity networks more challenging, since correspondences between their elements are not preserved. Unveiling these correspondences is of major importance to keep track of local functional connectivity changes. Read More


The human visual system contains a hierarchical sequence of modules that take part in visual perception at different levels of abstraction, i.e., superordinate, basic, and subordinate levels. Read More


'If I cannot build it, I do not understand it.' So said Nobel laureate Richard Feynman, and by his metric, we understand a bit about physics, less about chemistry, and almost nothing about biology. When we fully understand a phenomenon, we can specify its entire sequence of events, causes, and effects so completely that it is possible to fully simulate it, with all its internal mechanisms intact. Read More


Hair cells, the sensory receptors of the internal ear, subserve different functions in various receptor organs: they detect oscillatory stimuli in the auditory system, but transduce constant and step stimuli in the vestibular and lateral-line systems. We show that a hair cell's function can be controlled experimentally by adjusting its mechanical load. By making bundles from a single organ operate as any of four distinct types of signal detector, we demonstrate that altering only a few key parameters can fundamentally change a sensory cell's role. Read More


Beta oscillations observed in motor cortical local field potentials (LFPs) recorded on separate electrodes of a multi-electrode array have been shown to exhibit non-zero phase shifts that organize into a planar wave propagation. Here, we generalize this concept by introducing additional classes of patterns that fully describe the spatial organization of beta oscillations. During a delayed reach-to-grasp task in monkey primary motor and dorsal premotor cortices we distinguish planar, synchronized, random, circular, and radial phase patterns. Read More


The brain processes visual inputs having structure over a large range of spatial scales. The precise mechanisms or algorithms used by the brain to achieve this feat are largely unknown and an open problem in visual neuroscience. In particular, the spatial extent in visual space over which primary visual cortex (V1) performs evidence integration has been shown to change as a function of contrast and other visual parameters, thus adapting scale in visual space in an input-dependent manner. Read More


Inspired by biophysical principles underlying nonlinear dendritic computation in neural circuits, we develop a scheme to train deep neural networks to make them robust to adversarial attacks. Our scheme generates highly nonlinear, saturated neural networks that achieve state of the art performance on gradient based adversarial examples on MNIST, despite never being exposed to adversarially chosen examples during training. Moreover, these networks exhibit unprecedented robustness to targeted, iterative schemes for generating adversarial examples, including second-order methods. Read More


In recent years, new technologies in neuroscience have made it possible to measure the activities of large numbers of neurons in behaving animals. For each neuron, a fluorescence trace is measured; this can be seen as a first-order approximation of the neuron's activity over time. Determining the exact time at which a neuron spikes on the basis of its fluorescence trace is an important open problem in the field of computational neuroscience. Read More


The human brain is one of the most complex dynamic systems that enables us to communicate in natural language. We have a good understanding of some principles underlying natural languages and language processing, some knowledge about socio-cultural conditions framing acquisition, and some insights about where activity is occurring in the brain. However, we were not yet able to understand the behavioural and mechanistic characteristics for natural language and how mechanisms in the brain allow to acquire and process language. Read More