2,259 research outputs found
Computational techniques to interpret the neural code underlying complex cognitive processes
Advances in large-scale neural recording technology have significantly improved the
capacity to further elucidate the neural code underlying complex cognitive processes.
This thesis aimed to investigate two research questions in rodent models. First, what
is the role of the hippocampus in memory and specifically what is the underlying
neural code that contributes to spatial memory and navigational decision-making.
Second, how is social cognition represented in the medial prefrontal cortex at the
level of individual neurons. To start, the thesis begins by investigating memory and
social cognition in the context of healthy and diseased states that use non-invasive
methods (i.e. fMRI and animal behavioural studies). The main body of the thesis
then shifts to developing our fundamental understanding of the neural mechanisms
underpinning these cognitive processes by applying computational techniques to ana lyse stable large-scale neural recordings. To achieve this, tailored calcium imaging
and behaviour preprocessing computational pipelines were developed and optimised
for use in social interaction and spatial navigation experimental analysis. In parallel,
a review was conducted on methods for multivariate/neural population analysis. A
comparison of multiple neural manifold learning (NML) algorithms identified that non linear algorithms such as UMAP are more adaptable across datasets of varying noise
and behavioural complexity. Furthermore, the review visualises how NML can be
applied to disease states in the brain and introduces the secondary analyses that
can be used to enhance or characterise a neural manifold. Lastly, the preprocessing
and analytical pipelines were combined to investigate the neural mechanisms in volved in social cognition and spatial memory. The social cognition study explored
how neural firing in the medial Prefrontal cortex changed as a function of the social
dominance paradigm, the "Tube Test". The univariate analysis identified an ensemble
of behavioural-tuned neurons that fire preferentially during specific behaviours such
as "pushing" or "retreating" for the animalâs own behaviour and/or the competitorâs
behaviour. Furthermore, in dominant animals, the neural population exhibited greater
average firing than that of subordinate animals. Next, to investigate spatial memory,
a spatial recency task was used, where rats learnt to navigate towards one of three
reward locations and then recall the rewarded location of the session. During the
task, over 1000 neurons were recorded from the hippocampal CA1 region for five rats
over multiple sessions. Multivariate analysis revealed that the sequence of neurons encoding an animalâs spatial position leading up to a rewarded location was also active
in the decision period before the animal navigates to the rewarded location. The result
posits that prospective replay of neural sequences in the hippocampal CA1 region
could provide a mechanism by which decision-making is supported
An ensemble model for predictive energy performance:Closing the gap between actual and predicted energy use in residential buildings
The design stage of a building plays a pivotal role in influencing its life cycle and overall performance. Accurate predictions of a building's performance are crucial for informed decision-making, particularly in terms of energy performance, given the escalating global awareness of climate change and the imperative to enhance energy efficiency in buildings. However, a well-documented energy performance gap persists between actual and predicted energy consumption, primarily attributed to the unpredictable nature of occupant behavior.Existing methodologies for predicting and simulating occupant behavior in buildings frequently neglect or exclusively concentrate on particular behaviors, resulting in uncertainties in energy performance predictions. Machine learning approaches have exhibited increased accuracy in predicting occupant energy behavior, yet the majority of extant studies focus on specific behavior types rather than investigating the interactions among all contributing factors. This dissertation delves into the building energy performance gap, with a particular emphasis on the influence of occupants on energy performance. A comprehensive literature review scrutinizes machine learning models employed for predicting occupants' behavior in buildings and assesses their performance. The review uncovers knowledge gaps, as most studies are case-specific and lack a consolidated database to examine diverse behaviors across various building types.An ensemble model integrating occupant behavior parameters is devised to enhance the accuracy of energy performance predictions in residential buildings. Multiple algorithms are examined, with the selection of algorithms contingent upon evaluation metrics. The ensemble model is validated through a case study that compares actual energy consumption with the predictions of the ensemble model and an EnergyPlus simulation that takes occupant behavior factors into account.The findings demonstrate that the ensemble model provides considerably more accurate predictions of actual energy consumption compared to the EnergyPlus simulation. This dissertation also addresses the research limitations, including the reusability of the model and the requirement for additional datasets to bolster confidence in the model's applicability across diverse building types and occupant behavior patterns.In summary, this dissertation presents an ensemble model that endeavors to bridge the gap between actual and predicted energy usage in residential buildings by incorporating occupant behavior parameters, leading to more precise energy performance predictions and promoting superior energy management strategies
LIPIcs, Volume 251, ITCS 2023, Complete Volume
LIPIcs, Volume 251, ITCS 2023, Complete Volum
On the Utility of Representation Learning Algorithms for Myoelectric Interfacing
Electrical activity produced by muscles during voluntary movement is a reflection of the firing patterns of relevant motor neurons and, by extension, the latent motor intent driving the movement. Once transduced via electromyography (EMG) and converted into digital form, this activity can be processed to provide an estimate of the original motor intent and is as such a feasible basis for non-invasive efferent neural interfacing. EMG-based motor intent decoding has so far received the most attention in the field of upper-limb prosthetics, where alternative means of interfacing are scarce and the utility of better control apparent. Whereas myoelectric prostheses have been available since the 1960s, available EMG control interfaces still lag behind the mechanical capabilities of the artificial limbs they are intended to steerâa gap at least partially due to limitations in current methods for translating EMG into appropriate motion commands. As the relationship between EMG signals and concurrent effector kinematics is highly non-linear and apparently stochastic, finding ways to accurately extract and combine relevant information from across electrode sites is still an active area of inquiry.This dissertation comprises an introduction and eight papers that explore issues afflicting the status quo of myoelectric decoding and possible solutions, all related through their use of learning algorithms and deep Artificial Neural Network (ANN) models. Paper I presents a Convolutional Neural Network (CNN) for multi-label movement decoding of high-density surface EMG (HD-sEMG) signals. Inspired by the successful use of CNNs in Paper I and the work of others, Paper II presents a method for automatic design of CNN architectures for use in myocontrol. Paper III introduces an ANN architecture with an appertaining training framework from which simultaneous and proportional control emerges. Paper Iv introduce a dataset of HD-sEMG signals for use with learning algorithms. Paper v applies a Recurrent Neural Network (RNN) model to decode finger forces from intramuscular EMG. Paper vI introduces a Transformer model for myoelectric interfacing that do not need additional training data to function with previously unseen users. Paper vII compares the performance of a Long Short-Term Memory (LSTM) network to that of classical pattern recognition algorithms. Lastly, paper vIII describes a framework for synthesizing EMG from multi-articulate gestures intended to reduce training burden
Glioblastoma cell fate is differentially regulated by the microenvironments of the tumor bulk and infiltrative margin
Glioblastoma (GBM) recurrence originates from invasive margin cells that escape surgical debulking, but to what extent these cells resemble their bulk counterparts remains unclear. Here, we generated three immunocompetent somatic GBM mouse models, driven by subtype-associated mutations, to compare matched bulk and margin cells. We find that, regardless of mutations, tumors converge on common sets of neural-like cellular states. However, bulk and margin have distinct biology. Injury-like programs associated with immune infiltration dominate in the bulk, leading to the generation of lowly proliferative injured neural progenitor-like cells (iNPCs). iNPCs account for a significant proportion of dormant GBM cells and are induced by interferon signaling within TÂ cell niches. In contrast, developmental-like trajectories are favored within the immune-cold margin microenvironment resulting in differentiation toward invasive astrocyte-like cells. These findings suggest that the regional tumor microenvironment dominantly controls GBM cell fate and biological vulnerabilities identified in the bulk may not extend to the margin residuum
Singularity Formation in the High-Dimensional Euler Equations and Sampling of High-Dimensional Distributions by Deep Generative Networks
High dimensionality brings both opportunities and challenges to the study of applied mathematics. This thesis consists of two parts. The first part explores the singularity formation of the axisymmetric incompressible Euler equations with no swirl in ââż, which is closely related to the Millennium Prize Problem on the global singularity of the Navier-Stokes equations. In this part, the high dimensionality contributes to the singularity formation in finite time by enhancing the strength of the vortex stretching term. The second part focuses on sampling from a high-dimensional distribution using deep generative networks, which has wide applications in the Bayesian inverse problem and the image synthesis task. The high dimensionality in this part becomes a significant challenge to the numerical algorithms, known as the curse of dimensionality.
In the first part of this thesis, we consider the singularity formation in two scenarios. In the first scenario, for the axisymmetric Euler equations with no swirl, we consider the case when the initial condition for the angular vorticity is Cα Hölder continuous. We provide convincing numerical examples where the solutions develop potential self-similar blow-up in finite time when the Hölder exponent α < α*, and this upper bound α* can asymptotically approach 1 - 2/n. This result supports a conjecture from Drivas and Elgindi [37], and generalizes it to the high-dimensional case. This potential blow-up is insensitive to the perturbation of initial data. Based on assumptions summarized from numerical experiments, we study a limiting case of the Euler equations, and obtain α* = 1 - 2/n which agrees with the numerical result. For the general case, we propose a relatively simple one-dimensional model and numerically verify its approximation to the Euler equations. This one-dimensional model might suggest a possible way to show this finite-time blow-up scenario analytically. Compared to the first proved blow-up result of the 3D axisymmetric Euler equations with no swirl and Hölder continuous initial data by Elgindi in [40], our potential blow-up scenario has completely different scaling behavior and regularity of the initial condition. In the second scenario, we consider using smooth initial data, but modify the Euler equations by adding a factor Δ as the coefficient of the convection terms to weaken the convection effect. The new model is called the weak convection model. We provide convincing numerical examples of the weak convection model where the solutions develop potential self-similar blow-up in finite time when the convection strength Δ < Δ*, and this upper bound Δ* should be close to 1 - 2/n. This result is closely related to the infinite-dimensional case of an open question [37] stated by Drivas and Elgindi. Our numerical observations also inspire us to approximate the weak convection model with a one-dimensional model. We give a rigorous proof that the one-dimensional model will develop finite-time blow-up if Δ < 1 - 2/n, and study the approximation quality of the one-dimensional model to the weak convection model numerically, which could be beneficial to a rigorous proof of the potential finite-time blow-up.
In the second part of the thesis, we propose the Multiscale Invertible Generative Network (MsIGN) to sample from high-dimensional distributions by exploring the low-dimensional structure in the target distribution. The MsIGN models a transport map from a known reference distribution to the target distribution, and thus is very efficient in generating uncorrelated samples compared to MCMC-type methods. The MsIGN captures multiple modes in the target distribution by generating new samples hierarchically from a coarse scale to a fine scale with the help of a novel prior conditioning layer. The hierarchical structure of the MsIGN also allows training in a coarse-to-fine scale manner. The Jeffreys divergence is used as the objective function in training to avoid mode collapse. Importance sampling based on the prior conditioning layer is leveraged to estimate the Jeffreys divergence, which is intractable in previous deep generative networks. Numerically, when applied to two Bayesian inverse problems, the MsIGN clearly captures multiple modes in the high-dimensional posterior and approximates the posterior accurately, demonstrating its superior performance compared with previous methods. We also provide an ablation study to show the necessity of our proposed network architecture and training algorithm for the good numerical performance. Moreover, we also apply the MsIGN to the image synthesis task, where it achieves superior performance in terms of bits-per-dimension value over other flow-based generative models and yields very good interpretability of its neurons in intermediate layers.</p
Introduction to Riemannian Geometry and Geometric Statistics: from basic theory to implementation with Geomstats
International audienceAs data is a predominant resource in applications, Riemannian geometry is a natural framework to model and unify complex nonlinear sources of data.However, the development of computational tools from the basic theory of Riemannian geometry is laborious.The work presented here forms one of the main contributions to the open-source project geomstats, that consists in a Python package providing efficient implementations of the concepts of Riemannian geometry and geometric statistics, both for mathematicians and for applied scientists for whom most of the difficulties are hidden under high-level functions. The goal of this monograph is two-fold. First, we aim at giving a self-contained exposition of the basic concepts of Riemannian geometry, providing illustrations and examples at each step and adopting a computational point of view. The second goal is to demonstrate how these concepts are implemented in Geomstats, explaining the choices that were made and the conventions chosen. The general concepts are exposed and specific examples are detailed along the text.The culmination of this implementation is to be able to perform statistics and machine learning on manifolds, with as few lines of codes as in the wide-spread machine learning tool scikit-learn. We exemplify this with an introduction to geometric statistics
Patient-independent epileptic seizure detection by stable feature selection
The detection of epileptic seizures in EEG signals is a challenging task because it requires careful review of multi-channel EEG recordings over a lengthy time interval. In general, EEG-based seizure detection is strongly dependent on the ability to select descriptive features that are also stable in the sense that they are not sensitive to changes in the training data. This study proposes and investigates a patient-independent seizure detection model that uses stable EEG-based features obtained by comparing multiple feature selection methods. The schemes considered can be divided into five categories, often referred to as similarity, information theoretic, sparse learning, statistical, and graph centrality feature selection methods. The stability of the features these schemes produce was evaluated by random forest classification, using the intersection, frequency, correlation, and similarity measures. In experiments with Temple University Hospitalâs Seizure database of EEG records of 341 patients, unsupervised graph centrality feature selection was the most effective method, with a correct classification rate of 91.5%
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
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