45 research outputs found

    Population coding in the primary visual cortex

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    Ph.DDOCTOR OF PHILOSOPH

    The Manifold of Neural Responses Informs Physiological Circuits in the Visual System

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    The rapid development of multi-electrode and imaging techniques is leading to a data explosion in neuroscience, opening the possibility of truly understanding the organization and functionality of our visual systems. Furthermore, the need for more natural visual stimuli greatly increases the complexity of the data. Together, these create a challenge for machine learning. Our goal in this thesis is to develop one such technique. The central pillar of our contribution is designing a manifold of neurons, and providing an algorithmic approach to inferring it. This manifold is functional, in the sense that nearby neurons on the manifold respond similarly (in time) to similar aspects of the stimulus ensemble. By organizing the neurons, our manifold differs from other, standard manifolds as they are used in visual neuroscience which instead organize the stimuli. Our contributions to the machine learning component of the thesis are twofold. First, we develop a tensor representation of the data, adopting a multilinear view of potential circuitry. Tensor factorization then provides an intermediate representation between the neural data and the manifold. We found that the rank of the neural factor matrix can be used to select an appropriate number of tensor factors. Second, to apply manifold learning techniques, a similarity kernel on the data must be defined. Like many others, we employ a Gaussian kernel, but refine it based on a proposed graph sparsification technique—this makes the resulting manifolds less sensitive to the choice of bandwidth parameter. We apply this method to neuroscience data recorded from retina and primary visual cortex in the mouse. For the algorithm to work, however, the underlying circuitry must be exercised to as full an extent as possible. To this end, we develop an ensemble of flow stimuli, which simulate what the mouse would \u27see\u27 running through a field. Applying the algorithm to the retina reveals that neurons form clusters corresponding to known retinal ganglion cell types. In the cortex, a continuous manifold is found, indicating that, from a functional circuit point of view, there may be a continuum of cortical function types. Interestingly, both manifolds share similar global coordinates, which hint at what the key ingredients to vision might be. Lastly, we turn to perhaps the most widely used model for the cortex: deep convolutional networks. Their feedforward architecture leads to manifolds that are even more clustered than the retina, and not at all like that of the cortex. This suggests, perhaps, that they may not suffice as general models for Artificial Intelligence

    HIERARCHICAL NEURAL COMPUTATION IN THE MAMMALIAN VISUAL SYSTEM

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    Our visual system can efficiently extract behaviorally relevant information from ambiguous and noisy luminance patterns. Although we know much about the anatomy and physiology of the visual system, it remains obscure how the computation performed by individual visual neurons is constructed from the neural circuits. In this thesis, I designed novel statistical modeling approaches to study hierarchical neural computation, using electrophysiological recordings from several stages of the mammalian visual system. In Chapter 2, I describe a two-stage nonlinear model that characterized both synaptic current and spike response of retinal ganglion cells with unprecedented accuracy. I found that excitatory synaptic currents to ganglion cells are well described by excitatory inputs multiplied by divisive suppression, and that spike responses can be explained with the addition of a second stage of spiking nonlinearity and refractoriness. The structure of the model was inspired by known elements of the retinal circuit, and implies that presynaptic inhibition from amacrine cells is an important mechanism underlying ganglion cell computation. In Chapter 3, I describe a hierarchical stimulus-processing model of MT neurons in the context of a naturalistic optic flow stimulus. The model incorporates relevant nonlinear properties of upstream V1 processing and explained MT neuron responses to complex motion stimuli. MT neuron responses are shown to be best predicted from distinct excitatory and suppressive components. The direction-selective suppression can impart selectivity of MT neurons to complex velocity fields, and contribute to improved estimation of the three-dimensional velocity of moving objects. In Chapter 4, I present an extended model of MT neurons that includes both the stimulus-processing component and network activity reflected in local field potentials (LFPs). A significant fraction of the trial-to-trial variability of MT neuron responses is predictable from the LFPs in both passive fixation and a motion discrimination task. Moreover, the choice-related variability of MT neuron responses can be explained by their phase preferences in low-frequency band LFPs. These results suggest an important role of network activity in cortical function. Together, these results demonstrated that it is possible to infer the nature of neural computation from physiological recordings using statistical modeling approaches

    27th Annual Computational Neuroscience Meeting (CNS*2018): Part One

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    High-level visual object representation in juvenile and adult primates

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    Thesis: Ph. D., Massachusetts Institute of Technology, Department of Brain and Cognitive Sciences, 2018.Cataloged from PDF version of thesis.Includes bibliographical references (pages 109-130).Despite being reflexive, primate view invariant object recognition is a complex computational task. These computations are thought to reside in the ventral visual stream, specifically culminating in inferior temporal (IT) cortex. Recent research in machine learning has made great progress in modeling primate ventral visual stream computations. While the end result of current machine learning approaches produces models that are highly predictive of the adult state of the ventral stream, the learning approaches themselves are not biologically plausible, requiring tens of thousands to millions of human-labeled training points. Understanding primate visual development is therefore not only interesting from the perspective of neuroscience, but also has practical value in building more robust learning algorithms capable of functioning in domains where large amounts of human-labeled training information may be difficult or impossible to create. Better learning algorithms may also produce agents capable of adapting and behaving in the world not unlike humans. This thesis first describes work on predicting visual responses across the human ventral stream using convolutional neural networks (CNNs). We then describe a set of natural image statistics automatically incorporated into high-performing CNNs from supervised training-it is possible primate development incorporates these or similar natural image statistics into its synaptic strengths. Finally, we describe the first-large scale characterization of IT in 19-32 week old macaques. While we find longer response latencies in these younger animals, we do not find any differences in representation between adults and juveniles suggesting that, at 19-32 weeks of age, IT already supports robust object recognition consistent with adults. Our data provide an upper limit on the amount of training data needed to reach adult-level performance-approximately 2,800 hours of waking visual experience.by Darren Seibert.Ph. D

    Epälineaarisen visuaalisen prosessoinnin oppiminen luonnollisista kuvista

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    The paradigm of computational vision hypothesizes that any visual function -- such as the recognition of your grandparent -- can be replicated by computational processing of the visual input. What are these computations that the brain performs? What should or could they be? Working on the latter question, this dissertation takes the statistical approach, where the suitable computations are attempted to be learned from the natural visual data itself. In particular, we empirically study the computational processing that emerges from the statistical properties of the visual world and the constraints and objectives specified for the learning process. This thesis consists of an introduction and 7 peer-reviewed publications, where the purpose of the introduction is to illustrate the area of study to a reader who is not familiar with computational vision research. In the scope of the introduction, we will briefly overview the primary challenges to visual processing, as well as recall some of the current opinions on visual processing in the early visual systems of animals. Next, we describe the methodology we have used in our research, and discuss the presented results. We have included some additional remarks, speculations and conclusions to this discussion that were not featured in the original publications. We present the following results in the publications of this thesis. First, we empirically demonstrate that luminance and contrast are strongly dependent in natural images, contradicting previous theories suggesting that luminance and contrast were processed separately in natural systems due to their independence in the visual data. Second, we show that simple cell -like receptive fields of the primary visual cortex can be learned in the nonlinear contrast domain by maximization of independence. Further, we provide first-time reports of the emergence of conjunctive (corner-detecting) and subtractive (opponent orientation) processing due to nonlinear projection pursuit with simple objective functions related to sparseness and response energy optimization. Then, we show that attempting to extract independent components of nonlinear histogram statistics of a biologically plausible representation leads to projection directions that appear to differentiate between visual contexts. Such processing might be applicable for priming, \ie the selection and tuning of later visual processing. We continue by showing that a different kind of thresholded low-frequency priming can be learned and used to make object detection faster with little loss in accuracy. Finally, we show that in a computational object detection setting, nonlinearly gain-controlled visual features of medium complexity can be acquired sequentially as images are encountered and discarded. We present two online algorithms to perform this feature selection, and propose the idea that for artificial systems, some processing mechanisms could be selectable from the environment without optimizing the mechanisms themselves. In summary, this thesis explores learning visual processing on several levels. The learning can be understood as interplay of input data, model structures, learning objectives, and estimation algorithms. The presented work adds to the growing body of evidence showing that statistical methods can be used to acquire intuitively meaningful visual processing mechanisms. The work also presents some predictions and ideas regarding biological visual processing.Laskennallisen näön paradigma esittää, että mikä tahansa näkötoiminto - esimerkiksi jonkun esineen tunnistaminen - voidaan toistaa keinotekoisesti käyttäen laskennallisia menetelmiä. Minkälaisia nämä laskennalliset menetelmät voisivat olla, tai minkälaisia niiden tulisi olla? Tässä väitöskirjassa tutkitaan tilastollista lähestymistapaa näkemisen mekanismien muodostamiseen. Sovelletussa lähestymistavassa laskennallista käsittelyä yritetään muodostaa optimoimalla (tai 'oppimalla') siten, että toivotulle käsittelylle asetetaan erilaisia tavoitteita jonkin annetun luonnollisten kuvien joukon suhteen. Väitöskirja koostuu johdannosta ja seitsemästä kansainvälisillä foorumeilla julkaistusta tutkimusartikkelista. Johdanto esittelee väitöskirjan poikkitieteellistä tutkimusaluetta niille, jotka eivät entuudestaan tunne laskennallista näkötutkimusta. Johdannossa käydään läpi visuaalisen prosessoinnin haasteita sekä valotetaan hieman tämänhetkisiä mielipiteitä biologisista näkömekanismeista. Seuraavaksi lukija tutustutetaan työssä käytettyyn tutkimusmetodologiaan, jonka voi pitkälti nähdä koneoppimisen (tilastotieteen) soveltamisena. Johdannon lopuksi käydään läpi työn tutkimusartikkelit. Tämä katsaus on varustettu sellaisilla lisäkommenteilla, havainnoilla ja kritiikeillä, jotka eivät sisältyneet alkuperäisiin artikkeleihin. Varsinaiset tulokset väitöskirjassa liittyvät siihen, minkälaisia yksinkertaisia prosessointimekanismeja muodostuu yhdistelemällä erilaisia oppimistavoitteita, funktioluokkia, epälineaarisuuksia ja luonnollista kuvadataa. Työssä tarkastellaan erityisesti representaatioiden riippumattomuuteen ja harvuuteen tähtääviä oppimistavoitteita, mutta myös sellaisia, jotka pyrkivät edesauttamaan objektintunnistuksessa. Esitämme näiden aiheiden tiimoilta uusia löydöksiä, jotka listataan tarkemmin sekä englanninkielisessä tiivistelmässä että väitöskirjan alkusivuilla. Esitetty väitöskirjatyö tarjoaa lisänäyttöä siitä, että intuitiivisesti mielekkäitä visuaalisia prosessointimekanismeja voidaan muodostaa tilastollisin keinoin. Työ tarjoaa myös joitakin ennusteita ja ideoita liittyen biologisiin näkömekanismeihin

    A combined experimental and computational approach to investigate emergent network dynamics based on large-scale neuronal recordings

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    Sviluppo di un approccio integrato computazionale-sperimentale per lo studio di reti neuronali mediante registrazioni elettrofisiologich

    Spatial processing of conspecific signals in weakly electric fish: from sensory image to neural population coding

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    In this dissertation, I examine how an animal’s nervous system encodes spatially realistic conspecific signals in their environment and how the encoding mechanisms support behavioral sensitivity. I begin by modeling changes in the electrosensory signals exchanged by weakly electric fish in a social context. During this behavior, I estimate how the spatial structure of conspecific stimuli influences sensory responses at the electroreceptive periphery. I then quantify how space is represented in the hindbrain, specifically in the primary sensory area called the electrosensory lateral line lobe. I show that behavioral sensitivity is influenced by the heterogeneous properties of the pyramidal cell population. I further demonstrate that this heterogeneity serves to start segregating spatial and temporal information early in the sensory pathway. Lastly, I characterize the accuracy of spatial coding in this network and predict the role of network elements, such as correlated noise and feedback, in shaping the spatial information. My research provides a comprehensive understanding of spatial coding in the first stages of sensory processing in this system and allows us to better understand how network dynamics shape coding accuracy

    All-optical interrogation of neural circuits during behaviour

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    This thesis explores the fundamental question of how patterns of neural activity encode information and guide behaviour. To address this, one needs three things: a way to record neural activity so that one can correlate neuronal responses with environmental variables; a flexible and specific way to influence neural activity so that one can modulate the variables that may underlie how information is encoded; a robust behavioural paradigm that allows one to assess how modulation of both environmental and neural variables modify behaviour. Techniques combining all three would be transformative for investigating which features of neural activity, and which neurons, most influence behavioural output. Previous electrical and optogenetic microstimulation studies have told us much about the impact of spatially or genetically defined groups of neurons, however they lack the flexibility to probe the contribution of specific, functionally defined subsets. In this thesis I leverage a combination of existing technologies to approach this goal. I combine two-photon calcium imaging with two-photon optogenetics and digital holography to generate an “all-optical” method for simultaneous reading and writing of neural activity in vivo with high spatio-temporal resolution. Calcium imaging allows for cellular resolution recordings from neural populations. Two-photon optogenetics allows for targeted activation of individual cells. Digital holography, using spatial light modulators (SLMs), allows for simultaneous photostimulation of tens to hundreds of neurons in arbitrary spatial locations. Taken together, I demonstrate that this method allows one to map the functional signature of neurons in superficial mouse barrel cortex and to target photostimulation to functionally-defined subsets of cells. I develop a suite of software that allows for quick, intuitive execution of such experiments and I combine this with a behavioural paradigm testing the effect of targeted perturbations on behaviour. In doing so, I demonstrate that animals are able to reliably detect the targeted activation of tens of neurons, with some sensitive to as few as five cortical cells. I demonstrate that such learning can be specific to targeted cells, and that the lower bound of perception shifts with training. The temporal structure of such perturbations had little impact on behaviour, however different groups of neurons drive behaviour to different extents. In order to probe which characteristics underly such variation, I tested whether the sensory response strength or correlation structure of targeted ensembles influenced their behavioural salience. Whilst these final experiments were inconclusive, they demonstrate their feasibility and provide us with some key actionable improvements that could further strengthen the all-optical approach. This thesis therefore represents a significant step forward towards the goal of combining high resolution readout and perturbation of neural activity with behaviour in order to investigate which features of the neural code are behaviourally relevant
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