Characterizing Retinal Ganglion Cell Responses to Electrical Stimulation Using Generalized Linear Models

The ability to preferentially stimulate different retinal pathways is an important area of research for improving visual prosthetics. Recent work has shown that different classes of retinal ganglion cells (RGCs) have distinct linear electrical input filters for low-amplitude white noise stimulation. The aim of this study is to provide a statistical framework for characterizing how RGCs respond to white-noise electrical stimulation. We used a nested family of Generalized Linear Models (GLMs) to partition neural responses into different components-progressively adding covariates to the GLM which captured non-stationarity in neural activity, a linear dependence on the stimulus, and any remaining non-linear interactions. We found that each of these components resulted in increased model performance, but that even the non-linear model left a substantial fraction of neural variability unexplained. The broad goal of this paper is to provide a much-needed theoretical framework to objectively quantify stimulus paradigms in terms of the types of neural responses that they elicit (linear vs. non-linear vs. stimulus-independent variability). In turn, this aids the prosthetic community in the search for optimal stimulus parameters that avoid indiscriminate retinal activation and adaptation caused by excessively large stimulus pulses, and avoid low fidelity responses (low signal-to-noise ratio) caused by excessively weak stimulus pulses

Developing robust movement decoders for local field potentials

textBrain Computer Interfaces (BCI) are devices that translate acquired neural signals to command and control signals. Applications of BCI include neural rehabilitation and neural prosthesis (thought controlled wheelchair, thought controlled speller etc.) to aid patients with disabilities and to augment human computer interaction. A successful practical BCI requires a faithful acquisition modality to record high quality neural signals; a signal processing system to construct appropriate features from these signals; and an algorithm to translate these features to appropriate outputs. Intracortical recordings like local field potentials provide reliable high SNR signals over long periods and suit BCI applications well. However, the non-stationarity of neural signals poses a challenge in robust decoding of subject behavior. Most BCI research focuses either on developing daily re-calibrated decoders that require exhaustive training sessions; or on providing cross-validation results. Such results ignore the variation of signal characteristics over different sessions and provide an optimistic estimate of BCI performance. Specifically, traditional BCI algorithms fail to perform at the same level on chronological data recordings. Neural signals are susceptible to variations in signal characteristics due to changes in subject behavior and learning, and variability in electrode characteristics due to tissue interactions. While training day-specific BCI overcomes signal variability, BCI re-training causes user frustration and exhaustion. This dissertation presents contributions to solve these challenges in BCI research. Specifically, we developed decoders trained on a single recording session and applied them on subsequently recorded sessions. This strategy evaluates BCI in a practical scenario with a potential to alleviate BCI user frustration without compromising performance. The initial part of the dissertation investigates extracting features that remain robust to changes in neural signal over several days of recordings. It presents a qualitative feature extraction technique based on ranking the instantaneous power of multichannel data. These qualitative features remain robust to outliers and changes in the baseline of neural recordings, while extracting discriminative information. These features form the foundation in developing robust decoders. Next, this dissertation presents a novel algorithm based on the hypothesis that multiple neural spatial patterns describe the variation in behavior. The presented algorithm outperforms the traditional methods in decoding over chronological recordings. Adapting such a decoder over multiple recording sessions (over 6 weeks) provided > 90% accuracy in decoding eight movement directions. In comparison, performance of traditional algorithms like Common Spatial Patterns deteriorates to 16% over the same time. Over time, adaptation reinforces some spatial patterns while diminishing others. Characterizing these spatial patterns reduces model complexity without user input, while retaining the same accuracy levels. Lastly, this dissertation provides an algorithm that overcomes the variation in recording quality. Chronic electrode implantation causes changes in signal-to-noise ratio (SNR) of neural signals. Thus, some signals and their corresponding features available during training become unavailable during testing and vice-versa. The proposed algorithm uses prior knowledge on spatial pattern evolution to estimate unknown neural features. This algorithm overcomes SNR variations and provides up to 93% decoding of eight movement directions over 6 weeks. Since model training requires only one session, this strategy reduces user frustration. In a practical closed-loop BCI, the user learns to produce stable spatial patterns, which improves performance of the proposed algorithms.Electrical and Computer Engineerin

Modelling multivariate discrete data with latent Gaussian processes

Multivariate count data are common in some fields, such as sports, neuroscience, and text mining. Models that can accurately perform factor analysis are required, especially for structured data, such as time-series count matrices. We present Poisson Factor Analysis using Latent Gaussian Processes, a novel method for analyzing multivariate count data. Our approach allows for non-i.i.d observations, which are linked in the latent space using a Gaussian Process. Due to an exponential non-linearity in the model, there is no closed form solution. Thus, we resort to an expectation maximization approach with a Laplace approximation for tractable inference. We present results on several data sets, both synthetic and real, of a comparison with other factor analysis methods. Our method is both qualitatively and quantitatively superior for non-i.i.d Poisson data, because the assumptions it makes are well suited for the data

Electroencephalography (EEG)-based Brain-Computer Interfaces

International audienceBrain-Computer Interfaces (BCI) are systems that can translate the brain activity patterns of a user into messages or commands for an interactive application. The brain activity which is processed by the BCI systems is usually measured using Electroencephalography (EEG). In this article, we aim at providing an accessible and up-to-date overview of EEG-based BCI, with a main focus on its engineering aspects. We notably introduce some basic neuroscience background, and explain how to design an EEG-based BCI, in particular reviewing which signal processing, machine learning, software and hardware tools to use. We present Brain Computer Interface applications, highlight some limitations of current systems and suggest some perspectives for the field

Classification of Frequency and Phase Encoded Steady State Visual Evoked Potentials for Brain Computer Interface Speller Applications using Convolutional Neural Networks

Over the past decade there have been substantial improvements in vision based Brain-Computer Interface (BCI) spellers for quadriplegic patient populations. This thesis contains a review of the numerous bio-signals available to BCI researchers, as well as a brief chronology of foremost decoding methodologies used to date. Recent advances in classification accuracy and information transfer rate can be primarily attributed to time consuming patient specific parameter optimization procedures. The aim of the current study was to develop analysis software with potential ‘plug-in-and-play’ functionality. To this end, convolutional neural networks, presently established as state of the art analytical techniques for image processing, were utilized. The thesis herein defines deep convolutional neural network architecture for the offline classification of phase and frequency encoded SSVEP bio-signals. Networks were trained using an extensive 35 participant open source Electroencephalographic (EEG) benchmark dataset (Department of Bio-medical Engineering, Tsinghua University, Beijing). Average classification accuracies of 82.24% and information transfer rates of 22.22 bpm were achieved on a BCI naïve participant dataset for a 40 target alphanumeric display, in absence of any patient specific parameter optimization

From locomotion to dance and back : exploring rhythmic sensorimotor synchronization

Le rythme est un aspect important du mouvement et de la perception de l’environnement. Lorsque l’on danse, la pulsation musicale induit une activité neurale oscillatoire qui permet au système nerveux d’anticiper les évènements musicaux à venir. Le système moteur peut alors s’y synchroniser. Cette thèse développe de nouvelles techniques d’investigation des rythmes neuraux non strictement périodiques, tels que ceux qui régulent le tempo naturellement variable de la marche ou la perception rythmes musicaux. Elle étudie des réponses neurales reflétant la discordance entre ce que le système nerveux anticipe et ce qu’il perçoit, et qui sont nécessaire pour adapter la synchronisation de mouvements à un environnement variable. Elle montre aussi comment l’activité neurale évoquée par un rythme musical complexe est renforcée par les mouvements qui y sont synchronisés. Enfin, elle s’intéresse à ces rythmes neuraux chez des patients ayant des troubles de la marche ou de la conscience.Rhythms are central in human behaviours spanning from locomotion to music performance. In dance, self-sustaining and dynamically adapting neural oscillations entrain to the regular auditory inputs that is the musical beat. This entrainment leads to anticipation of forthcoming sensory events, which in turn allows synchronization of movements to the perceived environment. This dissertation develops novel technical approaches to investigate neural rhythms that are not strictly periodic, such as naturally tempo-varying locomotion movements and rhythms of music. It studies neural responses reflecting the discordance between what the nervous system anticipates and the actual timing of events, and that are critical for synchronizing movements to a changing environment. It also shows how the neural activity elicited by a musical rhythm is shaped by how we move. Finally, it investigates such neural rhythms in patient with gait or consciousness disorders

Unsupervised methods for large-scale, cell-resolution neural data analysis

In order to keep up with the volume of data, as well as the complexity of experiments and models in modern neuroscience, we need scalable and principled analytic programmes that take into account the scientific goals and the challenges of biological experiments. This work focuses on algorithms that tackle problems throughout the whole data analysis process. I first investigate how to best transform two-photon calcium imaging microscopy recordings – sets of contiguous images – into an easier-to-analyse matrix containing time courses of individual neurons. For this I first estimate how the true fluorescence signal gets transformed by tissue artefacts and the microscope setup, by learning the parameters of a realistic physical model from recorded data. Next, I describe how individual neural cell bodies may be segmented from the images, based on a cost function tailored to neural characteristics. Finally, I describe an interpretable non-linear dynamical model of neural population activity, which provides immediate scientific insight into complex system behaviour, and may spawn a new way of investigating stochastic non-linear dynamical systems. I hope the algorithms described here will not only be integrated into analytic pipelines of neural recordings, but also point out that algorithmic design should be informed by communication with the broader community, understanding and tackling the challenges inherent in experimental biological science

Discovering Causal Relations and Equations from Data

Physics is a field of science that has traditionally used the scientific method to answer questions about why natural phenomena occur and to make testable models that explain the phenomena. Discovering equations, laws and principles that are invariant, robust and causal explanations of the world has been fundamental in physical sciences throughout the centuries. Discoveries emerge from observing the world and, when possible, performing interventional studies in the system under study. With the advent of big data and the use of data-driven methods, causal and equation discovery fields have grown and made progress in computer science, physics, statistics, philosophy, and many applied fields. All these domains are intertwined and can be used to discover causal relations, physical laws, and equations from observational data. This paper reviews the concepts, methods, and relevant works on causal and equation discovery in the broad field of Physics and outlines the most important challenges and promising future lines of research. We also provide a taxonomy for observational causal and equation discovery, point out connections, and showcase a complete set of case studies in Earth and climate sciences, fluid dynamics and mechanics, and the neurosciences. This review demonstrates that discovering fundamental laws and causal relations by observing natural phenomena is being revolutionised with the efficient exploitation of observational data, modern machine learning algorithms and the interaction with domain knowledge. Exciting times are ahead with many challenges and opportunities to improve our understanding of complex systems.Comment: 137 page

Towards efficient and robust reinforcement learning via synthetic environments and offline data

Over the past decade, Deep Reinforcement Learning (RL) has driven many advances in sequential decision-making, including remarkable applications in superhuman Go-playing, robotic control, and automated algorithm discovery. However, despite these successes, deep RL is also notoriously sample-inefficient, usually generalizes poorly to settings beyond the original environment, and can be unstable during training. Moreover, the conventional RL setting still relies on exploring and learning tabula-rasa in new environments and does not make use of pre-existing data. This thesis investigates two promising directions to address these challenges. First, we explore the use of synthetic data and environments in order to broaden an agent's experience. Second, we propose principled techniques to leverage pre-existing datasets, thereby reducing or replacing the need for costly online data collection. The first part of the thesis focuses on the generation of synthetic data and environments to train RL agents. While there is a rich history in model-based RL of leveraging a learned dynamics model to improve sample efficiency, these methods are usually restricted to single-task settings. To overcome this limitation, we propose Augmented World Models, a novel approach designed for offline-to-online transfer where the test dynamics may differ from the training data. Our method augments a learned dynamics model with simple transformations that seek to capture potential changes in the physical properties of a robot, leading to more robust policies. Additionally, we train the agent with the sampled augmentation as context for test-time inference, significantly improving zero-shot generalization to novel dynamics. Going beyond commonly used forward dynamics models, we propose an alternative paradigm, Synthetic Experience Replay, which uses generative modeling to directly model and upsample the agent's training data distribution. Leveraging recent advances in diffusion generative models, our approach outperforms and is composable with standard data augmentation, and is particularly effective in low-data regimes. Furthermore, our method opens the door for certain RL agents to train stably with much larger networks than before. In the second part of the thesis, we explore a complementary direction to data efficiency where we can leverage pre-existing data. While adjacent fields of machine learning, such as computer vision and natural language processing, have made significant progress in scaling data and model size, traditional RL algorithms can find it difficult to incorporate additional data due to the need for on-policy data. We begin by investigating a principled method for incorporating expert demonstrations to accelerate online RL, KL-regularization to a behavioral prior, and identify a pathology stemming from the behavioral prior having uncalibrated uncertainties. We show that standard parameterizations of the behavioral reference policy can lead to unstable training dynamics, and propose a solution, Non-Parametric Prior Actor–Critic, that represents the new state-of-the-art in locomotion and dexterous manipulation tasks. Furthermore, we make advances in offline reinforcement learning, with which agents can be trained without any online data collection at all. In this domain, we elucidate the design space of offline model-based RL algorithms and highlight where prior methods use suboptimal heuristics and choices for hyperparameters. By rigorously searching through this space, we show that we can vastly improve standard algorithms and provide insights into which design choices are most important. Finally, we make progress towards extending offline RL to pixel-based environments by presenting Vision Datasets for Deep Data-Driven RL, the first comprehensive and publicly available evaluation suite for this field, alongside simple model-based and model-free baselines for assessing future progress in this domain. In conclusion, this thesis represents explorations toward making RL algorithms more efficient and readily deployable in the real world. Further progress along these directions may bring us closer to the ultimate goal of more generally capable agents, that are able to both generate appropriate learning environments for themselves and bootstrap learning from vast quantities of pre-existing data