Scalable Tools for Information Extraction and Causal Modeling of Neural Data

Systems neuroscience has entered in the past 20 years into an era that one might call "large scale systems neuroscience". From tuning curves and single neuron recordings there has been a conceptual shift towards a more holistic understanding of how the neural circuits work and as a result how their representations produce neural tunings. With the introduction of a plethora of datasets in various scales, modalities, animals, and systems; we as a community have witnessed invaluable insights that can be gained from the collective view of a neural circuit which was not possible with small scale experimentation. The concurrency of the advances in neural recordings such as the production of wide field imaging technologies and neuropixels with the developments in statistical machine learning and specifically deep learning has brought system neuroscience one step closer to data science. With this abundance of data, the need for developing computational models has become crucial. We need to make sense of the data, and thus we need to build models that are constrained up to the acceptable amount of biological detail and probe those models in search of neural mechanisms. This thesis consists of sections covering a wide range of ideas from computer vision, statistics, machine learning, and dynamical systems. But all of these ideas share a common purpose, which is to help automate neuroscientific experimentation process in different levels. In chapters 1, 2, and 3, I develop tools that automate the process of extracting useful information from raw neuroscience data in the model organism C. elegans. The goal of this is to avoid manual labor and pave the way for high throughput data collection aiming at better quantification of variability across the population of worms. Due to its high level of structural and functional stereotypy, and its relative simplicity, the nematode C. elegans has been an attractive model organism for systems and developmental research. With 383 neurons in males and 302 neurons in hermaphrodites, the positions and function of neurons is remarkably conserved across individuals. Furthermore, C. elegans remains the only organism for which a complete cellular, lineage, and anatomical map of the entire nervous system has been described for both sexes. Here, I describe the analysis pipeline that we developed for the recently proposed NeuroPAL technique in C. elegans. Our proposed pipeline consists of atlas building (chapter 1), registration, segmentation, neural tracking (chapter 2), and signal extraction (chapter 3). I emphasize that categorizing the analysis techniques as a pipeline consisting of the above steps is general and can be applied to virtually every single animal model and emerging imaging modality. I use the language of probabilistic generative modeling and graphical models to communicate the ideas in a rigorous form, therefore some familiarity with those concepts could help the reader navigate through the chapters of this thesis more easily. In chapters 4 and 5 I build models that aim to automate hypothesis testing and causal interrogation of neural circuits. The notion of functional connectivity (FC) has been instrumental in our understanding of how information propagates in a neural circuit. However, an important limitation is that current techniques do not dissociate between causal connections and purely functional connections with no mechanistic correspondence. I start chapter 4 by introducing causal inference as a unifying language for the following chapters. In chapter 4 I define the notion of interventional connectivity (IC) as a way to summarize the effect of stimulation in a neural circuit providing a more mechanistic description of the information flow. I then investigate which functional connectivity metrics are best predictive of IC in simulations and real data. Following this framework, I discuss how stimulations and interventions can be used to improve fitting and generalization properties of time series models. Building on the literature of model identification and active causal discovery I develop a switching time series model and a method for finding stimulation patterns that help the model to generalize to the vicinity of the observed neural trajectories. Finally in chapter 5 I develop a new FC metric that separates the transferred information from one variable to the other into unique and synergistic sources. In all projects, I have abstracted out concepts that are specific to the datasets at hand and developed the methods in the most general form. This makes the presented methods applicable to a broad range of datasets, potentially leading to new findings. In addition, all projects are accompanied with extensible and documented code packages, allowing theorists to repurpose the modules for novel applications and experimentalists to run analysis on their datasets efficiently and scalably. In summary my main contribution in this thesis are the following: 1) Building the first atlases of hermaphrodite and male C. elegans and developing a generic statistical framework for constructing atlases for a broad range of datasets. 2) Developing a semi-automated analysis pipeline for neural registration, segmentation, and tracking in C. elegans. 3) Extending the framework of non-negative matrix factorization to datasets with deformable motion and developing algorithms for joint tracking and signal demixing from videos of semi-immobilized C. elegans. 4) Defining the notion of interventional connectivity (IC) as a way to summarize the effect of stimulation in a neural circuit and investigating which functional connectivity metrics are best predictive of IC in simulations and real data. 5) Developing a switching time series model and a method for finding stimulation patterns that help the model to generalize to the vicinity of the observed neural trajectories. 6) Developing a new functional connectivity metric that separates the transferred information from one variable to the other into unique and synergistic sources. 7) Implementing extensible, well documented, open source code packages for each of the above contributions

Modélisation stochastique pour l'analyse d'images texturées (approches Bayésiennes pour la caractérisation dans le domaine des transformées)

Le travail présenté dans cette thèse s inscrit dans le cadre de la modélisation d images texturées à l aide des représentations multi-échelles et multi-orientations. Partant des résultats d études en neurosciences assimilant le mécanisme de la perception humaine à un schéma sélectif spatio-fréquentiel, nous proposons de caractériser les images texturées par des modèles probabilistes associés aux coefficients des sous-bandes. Nos contributions dans ce contexte concernent dans un premier temps la proposition de différents modèles probabilistes permettant de prendre en compte le caractère leptokurtique ainsi que l éventuelle asymétrie des distributions marginales associées à un contenu texturée. Premièrement, afin de modéliser analytiquement les statistiques marginales des sous-bandes, nous introduisons le modèle Gaussien généralisé asymétrique. Deuxièmement, nous proposons deux familles de modèles multivariés afin de prendre en compte les dépendances entre coefficients des sous-bandes. La première famille regroupe les processus à invariance sphérique pour laquelle nous montrons qu il est pertinent d associer une distribution caractéristique de type Weibull. Concernant la seconde famille, il s agit des lois multivariées à copules. Après détermination de la copule caractérisant la structure de la dépendance adaptée à la texture, nous proposons une extension multivariée de la distribution Gaussienne généralisée asymétrique à l aide de la copule Gaussienne. L ensemble des modèles proposés est comparé quantitativement en terme de qualité d ajustement à l aide de tests statistiques d adéquation dans un cadre univarié et multivarié. Enfin, une dernière partie de notre étude concerne la validation expérimentale des performances de nos modèles à travers une application de recherche d images par le contenu textural. Pour ce faire, nous dérivons des expressions analytiques de métriques probabilistes mesurant la similarité entre les modèles introduits, ce qui constitue selon nous une troisième contribution de ce travail. Finalement, une étude comparative est menée visant à confronter les modèles probabilistes proposés à ceux de l état de l art.In this thesis we study the statistical modeling of textured images using multi-scale and multi-orientation representations. Based on the results of studies in neuroscience assimilating the human perception mechanism to a selective spatial frequency scheme, we propose to characterize textures by probabilistic models of subband coefficients.Our contributions in this context consist firstly in the proposition of probabilistic models taking into account the leptokurtic nature and the asymmetry of the marginal distributions associated with a textured content. First, to model analytically the marginal statistics of subbands, we introduce the asymmetric generalized Gaussian model. Second, we propose two families of multivariate models to take into account the dependencies between subbands coefficients. The first family includes the spherically invariant processes that we characterize using Weibull distribution. The second family is this of copula based multivariate models. After determination of the copula characterizing the dependence structure adapted to the texture, we propose a multivariate extension of the asymmetric generalized Gaussian distribution using Gaussian copula. All proposed models are compared quantitatively using both univariate and multivariate statistical goodness of fit tests. Finally, the last part of our study concerns the experimental validation of the performance of proposed models through texture based image retrieval. To do this, we derive closed-form metrics measuring the similarity between probabilistic models introduced, which we believe is the third contribution of this work. A comparative study is conducted to compare the proposed probabilistic models to those of the state-of-the-art.BORDEAUX1-Bib.electronique (335229901) / SudocSudocFranceF

Flood dynamics derived from video remote sensing

Flooding is by far the most pervasive natural hazard, with the human impacts of floods expected to worsen in the coming decades due to climate change. Hydraulic models are a key tool for understanding flood dynamics and play a pivotal role in unravelling the processes that occur during a flood event, including inundation flow patterns and velocities. In the realm of river basin dynamics, video remote sensing is emerging as a transformative tool that can offer insights into flow dynamics and thus, together with other remotely sensed data, has the potential to be deployed to estimate discharge. Moreover, the integration of video remote sensing data with hydraulic models offers a pivotal opportunity to enhance the predictive capacity of these models. Hydraulic models are traditionally built with accurate terrain, flow and bathymetric data and are often calibrated and validated using observed data to obtain meaningful and actionable model predictions. Data for accurately calibrating and validating hydraulic models are not always available, leaving the assessment of the predictive capabilities of some models deployed in flood risk management in question. Recent advances in remote sensing have heralded the availability of vast video datasets of high resolution. The parallel evolution of computing capabilities, coupled with advancements in artificial intelligence are enabling the processing of data at unprecedented scales and complexities, allowing us to glean meaningful insights into datasets that can be integrated with hydraulic models. The aims of the research presented in this thesis were twofold. The first aim was to evaluate and explore the potential applications of video from air- and space-borne platforms to comprehensively calibrate and validate two-dimensional hydraulic models. The second aim was to estimate river discharge using satellite video combined with high resolution topographic data. In the first of three empirical chapters, non-intrusive image velocimetry techniques were employed to estimate river surface velocities in a rural catchment. For the first time, a 2D hydraulicvmodel was fully calibrated and validated using velocities derived from Unpiloted Aerial Vehicle (UAV) image velocimetry approaches. This highlighted the value of these data in mitigating the limitations associated with traditional data sources used in parameterizing two-dimensional hydraulic models. This finding inspired the subsequent chapter where river surface velocities, derived using Large Scale Particle Image Velocimetry (LSPIV), and flood extents, derived using deep neural network-based segmentation, were extracted from satellite video and used to rigorously assess the skill of a two-dimensional hydraulic model. Harnessing the ability of deep neural networks to learn complex features and deliver accurate and contextually informed flood segmentation, the potential value of satellite video for validating two dimensional hydraulic model simulations is exhibited. In the final empirical chapter, the convergence of satellite video imagery and high-resolution topographical data bridges the gap between visual observations and quantitative measurements by enabling the direct extraction of velocities from video imagery, which is used to estimate river discharge. Overall, this thesis demonstrates the significant potential of emerging video-based remote sensing datasets and offers approaches for integrating these data into hydraulic modelling and discharge estimation practice. The incorporation of LSPIV techniques into flood modelling workflows signifies a methodological progression, especially in areas lacking robust data collection infrastructure. Satellite video remote sensing heralds a major step forward in our ability to observe river dynamics in real time, with potentially significant implications in the domain of flood modelling science

Machine Learning Approaches to Human Body Shape Analysis

Soft biometrics, biomedical sciences, and many other fields of study pay particular attention to the study of the geometric description of the human body, and its variations. Although multiple contributions, the interest is particularly high given the non-rigid nature of the human body, capable of assuming different poses, and numerous shapes due to variable body composition. Unfortunately, a well-known costly requirement in data-driven machine learning, and particularly in the human-based analysis, is the availability of data, in the form of geometric information (body measurements) with related vision information (natural images, 3D mesh, etc.). We introduce a computer graphics framework able to generate thousands of synthetic human body meshes, representing a population of individuals with stratified information: gender, Body Fat Percentage (BFP), anthropometric measurements, and pose. This contribution permits an extensive analysis of different bodies in different poses, avoiding the demanding, and expensive acquisition process. We design a virtual environment able to take advantage of the generated bodies, to infer the body surface area (BSA) from a single view. The framework permits to simulate the acquisition process of newly introduced RGB-D devices disentangling different noise components (sensor noise, optical distortion, body part occlusions). Common geometric descriptors in soft biometric, as well as in biomedical sciences, are based on body measurements. Unfortunately, as we prove, these descriptors are not pose invariant, constraining the usability in controlled scenarios. We introduce a differential geometry approach assuming body pose variations as isometric transformations of the body surface, and body composition changes covariant to the body surface area. This setting permits the use of the Laplace-Beltrami operator on the 2D body manifold, describing the body with a compact, efficient, and pose invariant representation. We design a neural network architecture able to infer important body semantics from spectral descriptors, closing the gap between abstract spectral features, and traditional measurement-based indices. Studying the manifold of body shapes, we propose an innovative generative adversarial model able to learn the body shapes. The method permits to generate new bodies with unseen geometries as a walk on the latent space, constituting a significant advantage over traditional generative methods

High Performance Video Stream Analytics System for Object Detection and Classification

Due to the recent advances in cameras, cell phones and camcorders, particularly the resolution at which they can record an image/video, large amounts of data are generated daily. This video data is often so large that manually inspecting it for object detection and classification can be time consuming and error prone, thereby it requires automated analysis to extract useful information and meta-data. The automated analysis from video streams also comes with numerous challenges such as blur content and variation in illumination conditions and poses. We investigate an automated video analytics system in this thesis which takes into account the characteristics from both shallow and deep learning domains. We propose fusion of features from spatial frequency domain to perform highly accurate blur and illumination invariant object classification using deep learning networks. We also propose the tuning of hyper-parameters associated with the deep learning network through a mathematical model. The mathematical model used to support hyper-parameter tuning improved the performance of the proposed system during training. The outcomes of various hyper-parameters on system's performance are compared. The parameters that contribute towards the most optimal performance are selected for the video object classification. The proposed video analytics system has been demonstrated to process a large number of video streams and the underlying infrastructure is able to scale based on the number and size of the video stream(s) being processed. The extensive experimentation on publicly available image and video datasets reveal that the proposed system is significantly more accurate and scalable and can be used as a general purpose video analytics system.N/

Head-Driven Phrase Structure Grammar

Head-Driven Phrase Structure Grammar (HPSG) is a constraint-based or declarative approach to linguistic knowledge, which analyses all descriptive levels (phonology, morphology, syntax, semantics, pragmatics) with feature value pairs, structure sharing, and relational constraints. In syntax it assumes that expressions have a single relatively simple constituent structure. This volume provides a state-of-the-art introduction to the framework. Various chapters discuss basic assumptions and formal foundations, describe the evolution of the framework, and go into the details of the main syntactic phenomena. Further chapters are devoted to non-syntactic levels of description. The book also considers related fields and research areas (gesture, sign languages, computational linguistics) and includes chapters comparing HPSG with other frameworks (Lexical Functional Grammar, Categorial Grammar, Construction Grammar, Dependency Grammar, and Minimalism)

Head-Driven Phrase Structure Grammar

Head-Driven Phrase Structure Grammar (HPSG) is a constraint-based or declarative approach to linguistic knowledge, which analyses all descriptive levels (phonology, morphology, syntax, semantics, pragmatics) with feature value pairs, structure sharing, and relational constraints. In syntax it assumes that expressions have a single relatively simple constituent structure. This volume provides a state-of-the-art introduction to the framework. Various chapters discuss basic assumptions and formal foundations, describe the evolution of the framework, and go into the details of the main syntactic phenomena. Further chapters are devoted to non-syntactic levels of description. The book also considers related fields and research areas (gesture, sign languages, computational linguistics) and includes chapters comparing HPSG with other frameworks (Lexical Functional Grammar, Categorial Grammar, Construction Grammar, Dependency Grammar, and Minimalism)

CONTACTLESS FINGERPRINT BIOMETRICS: ACQUISITION, PROCESSING, AND PRIVACY PROTECTION

Biometrics is defined by the International Organization for Standardization (ISO) as \u201cthe automated recognition of individuals based on their behavioral and biological characteristics\u201d Examples of distinctive features evaluated by biometrics, called biometric traits, are behavioral characteristics like the signature, gait, voice, and keystroke, and biological characteristics like the fingerprint, face, iris, retina, hand geometry, palmprint, ear, and DNA. The biometric recognition is the process that permits to establish the identity of a person, and can be performed in two modalities: verification, and identification. The verification modality evaluates if the identity declared by an individual corresponds to the acquired biometric data. Differently, in the identification modality, the recognition application has to determine a person's identity by comparing the acquired biometric data with the information related to a set of individuals. Compared with traditional techniques used to establish the identity of a person, biometrics offers a greater confidence level that the authenticated individual is not impersonated by someone else. Traditional techniques, in fact, are based on surrogate representations of the identity, like tokens, smart cards, and passwords, which can easily be stolen or copied with respect to biometric traits. This characteristic permitted a wide diffusion of biometrics in different scenarios, like physical access control, government applications, forensic applications, logical access control to data, networks, and services. Most of the biometric applications, also called biometric systems, require performing the acquisition process in a highly controlled and cooperative manner. In order to obtain good quality biometric samples, the acquisition procedures of these systems need that the users perform deliberate actions, assume determinate poses, and stay still for a time period. Limitations regarding the applicative scenarios can also be present, for example the necessity of specific light and environmental conditions. Examples of biometric technologies that traditionally require constrained acquisitions are based on the face, iris, fingerprint, and hand characteristics. Traditional face recognition systems need that the users take a neutral pose, and stay still for a time period. Moreover, the acquisitions are based on a frontal camera and performed in controlled light conditions. Iris acquisitions are usually performed at a distance of less than 30 cm from the camera, and require that the user assume a defined pose and stay still watching the camera. Moreover they use near infrared illumination techniques, which can be perceived as dangerous for the health. Fingerprint recognition systems and systems based on the hand characteristics require that the users touch the sensor surface applying a proper and uniform pressure. The contact with the sensor is often perceived as unhygienic and/or associated to a police procedure. This kind of constrained acquisition techniques can drastically reduce the usability and social acceptance of biometric technologies, therefore decreasing the number of possible applicative contexts in which biometric systems could be used. In traditional fingerprint recognition systems, the usability and user acceptance are not the only negative aspects of the used acquisition procedures since the contact of the finger with the sensor platen introduces a security lack due to the release of a latent fingerprint on the touched surface, the presence of dirt on the surface of the finger can reduce the accuracy of the recognition process, and different pressures applied to the sensor platen can introduce non-linear distortions and low-contrast regions in the captured samples. Other crucial aspects that influence the social acceptance of biometric systems are associated to the privacy and the risks related to misuses of biometric information acquired, stored and transmitted by the systems. One of the most important perceived risks is related to the fact that the persons consider the acquisition of biometric traits as an exact permanent filing of their activities and behaviors, and the idea that the biometric systems can guarantee recognition accuracy equal to 100\% is very common. Other perceived risks consist in the use of the collected biometric data for malicious purposes, for tracing all the activities of the individuals, or for operating proscription lists. In order to increase the usability and the social acceptance of biometric systems, researchers are studying less-constrained biometric recognition techniques based on different biometric traits, for example, face recognition systems in surveillance applications, iris recognition techniques based on images captured at a great distance and on the move, and contactless technologies based on the fingerprint and hand characteristics. Other recent studies aim to reduce the real and perceived privacy risks, and consequently increase the social acceptance of biometric technologies. In this context, many studies regard methods that perform the identity comparison in the encrypted domain in order to prevent possible thefts and misuses of biometric data. The objective of this thesis is to research approaches able to increase the usability and social acceptance of biometric systems by performing less-constrained and highly accurate biometric recognitions in a privacy compliant manner. In particular, approaches designed for high security contexts are studied in order improve the existing technologies adopted in border controls, investigative, and governmental applications. Approaches based on low cost hardware configurations are also researched with the aim of increasing the number of possible applicative scenarios of biometric systems. The privacy compliancy is considered as a crucial aspect in all the studied applications. Fingerprint is specifically considered in this thesis, since this biometric trait is characterized by high distinctivity and durability, is the most diffused trait in the literature, and is adopted in a wide range of applicative contexts. The studied contactless biometric systems are based on one or more CCD cameras, can use two-dimensional or three-dimensional samples, and include privacy protection methods. The main goal of these systems is to perform accurate and privacy compliant recognitions in less-constrained applicative contexts with respect to traditional fingerprint biometric systems. Other important goals are the use of a wider fingerprint area with respect to traditional techniques, compatibility with the existing databases, usability, social acceptance, and scalability. The main contribution of this thesis consists in the realization of novel biometric systems based on contactless fingerprint acquisitions. In particular, different techniques for every step of the recognition process based on two-dimensional and three-dimensional samples have been researched. Novel techniques for the privacy protection of fingerprint data have also been designed. The studied approaches are multidisciplinary since their design and realization involved optical acquisition systems, multiple view geometry, image processing, pattern recognition, computational intelligence, statistics, and cryptography. The implemented biometric systems and algorithms have been applied to different biometric datasets describing a heterogeneous set of applicative scenarios. Results proved the feasibility of the studied approaches. In particular, the realized contactless biometric systems have been compared with traditional fingerprint recognition systems, obtaining positive results in terms of accuracy, usability, user acceptability, scalability, and security. Moreover, the developed techniques for the privacy protection of fingerprint biometric systems showed satisfactory performances in terms of security, accuracy, speed, and memory usage