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We study a new two-time-scale stochastic gradient method for solving optimization problems, where the gradients are computed with the aid of an auxiliary variable under samples generated by time-varying Markov random processes parameterized by the underlying optimization variable. These time-varying samples make gradient directions in our update biased and dependent, which can potentially lead to the divergence of the iterates. In our two-time-scale approach, one scale is to estimate the true gradient from these samples, which is then used to update the estimate of the optimal solution. While these two iterates are implemented simultaneously, the former is updated "faster" (using bigger step sizes) than the latter (using smaller step sizes). Our first contribution is to characterize the finite-time complexity of the proposed two-time-scale stochastic gradient method. In particular, we provide explicit formulas for the convergence rates of this method under different structural assumptions, namely, strong convexity, convexity, the Polyak-Lojasiewicz condition, and general non-convexity. We apply our framework to two problems in control and reinforcement learning. First, we look at the standard online actor-critic algorithm over finite state and action spaces and derive a convergence rate of O(k^(-2/5)), which recovers the best known rate derived specifically for this problem. Second, we study an online actor-critic algorithm for the linear-quadratic regulator and show that a convergence rate of O(k^(-2/3)) is achieved. This is the first time such a result is known in the literature. Finally, we support our theoretical analysis with numerical simulations where the convergence rates are visualized.

The approximate uniform sampling of graph realizations with a given degree sequence is an everyday task in several social science, computer science, engineering etc. projects. One approach is using Markov chains. The best available current result about the well-studied switch Markov chain is that it is rapidly mixing on P-stable degree sequences (see DOI:10.1016/j.ejc.2021.103421). The switch Markov chain does not change any degree sequence. However, there are cases where degree intervals are specified rather than a single degree sequence. (A natural scenario where this problem arises is in hypothesis testing on social networks that are only partially observed.) Rechner, Strowick, and M\"uller-Hannemann introduced in 2018 the notion of degree interval Markov chain which uses three (separately well-studied) local operations (switch, hinge-flip and toggle), and employing on degree sequence realizations where any two sequences under scrutiny have very small coordinate-wise distance. Recently Amanatidis and Kleer published a beautiful paper (arXiv:2110.09068), showing that the degree interval Markov chain is rapidly mixing if the sequences are coming from a system of very thin intervals which are centered not far from a regular degree sequence. In this paper we extend substantially their result, showing that the degree interval Markov chain is rapidly mixing if the intervals are centred at P-stable degree sequences.

Stochastic partial differential equations (SPDEs) are the mathematical tool of choice for modelling spatiotemporal PDE-dynamics under the influence of randomness. Based on the notion of mild solution of an SPDE, we introduce a novel neural architecture to learn solution operators of PDEs with (possibly stochastic) forcing from partially observed data. The proposed Neural SPDE model provides an extension to two popular classes of physics-inspired architectures. On the one hand, it extends Neural CDEs and variants -- continuous-time analogues of RNNs -- in that it is capable of processing incoming sequential information arriving irregularly in time and observed at arbitrary spatial resolutions. On the other hand, it extends Neural Operators -- generalizations of neural networks to model mappings between spaces of functions -- in that it can parameterize solution operators of SPDEs depending simultaneously on the initial condition and a realization of the driving noise. By performing operations in the spectral domain, we show how a Neural SPDE can be evaluated in two ways, either by calling an ODE solver (emulating a spectral Galerkin scheme), or by solving a fixed point problem. Experiments on various semilinear SPDEs, including the stochastic Navier-Stokes equations, demonstrate how the Neural SPDE model is capable of learning complex spatiotemporal dynamics in a resolution-invariant way, with better accuracy and lighter training data requirements compared to alternative models, and up to 3 orders of magnitude faster than traditional solvers.

Molecular dynamics (MD) has long been the \emph{de facto} choice for modeling complex atomistic systems from first principles, and recently deep learning become a popular way to accelerate it. Notwithstanding, preceding approaches depend on intermediate variables such as the potential energy or force fields to update atomic positions, which requires additional computations to perform back-propagation. To waive this requirement, we propose a novel model called ScoreMD by directly estimating the gradient of the log density of molecular conformations. Moreover, we analyze that diffusion processes highly accord with the principle of enhanced sampling in MD simulations, and is therefore a perfect match to our sequential conformation generation task. That is, ScoreMD perturbs the molecular structure with a conditional noise depending on atomic accelerations and employs conformations at previous timeframes as the prior distribution for sampling. Another challenge of modeling such a conformation generation process is that the molecule is kinetic instead of static, which no prior studies strictly consider. To solve this challenge, we introduce a equivariant geometric Transformer as a score function in the diffusion process to calculate the corresponding gradient. It incorporates the directions and velocities of atomic motions via 3D spherical Fourier-Bessel representations. With multiple architectural improvements, we outperforms state-of-the-art baselines on MD17 and isomers of C7O2H10. This research provides new insights into the acceleration of new material and drug discovery.

In this work, we introduce a novel approach to formulating an artificial viscosity for shock capturing in nonlinear hyperbolic systems by utilizing the property that the solutions of hyperbolic conservation laws are not reversible in time in the vicinity of shocks. The proposed approach does not require any additional governing equations or a priori knowledge of the hyperbolic system in question, is independent of the mesh and approximation order, and requires the use of only one tunable parameter. The primary novelty is that the resulting artificial viscosity is unique for each component of the conservation law which is advantageous for systems in which some components exhibit discontinuities while others do not. The efficacy of the method is shown in numerical experiments of multi-dimensional hyperbolic conservation laws such as nonlinear transport, Euler equations, and ideal magnetohydrodynamics using a high-order discontinuous spectral element method on unstructured grids.

We introduce a novel methodology for particle filtering in dynamical systems where the evolution of the signal of interest is described by a SDE and observations are collected instantaneously at prescribed time instants. The new approach includes the discretisation of the SDE and the design of efficient particle filters for the resulting discrete-time state-space model. The discretisation scheme converges with weak order 1 and it is devised to create a sequential dependence structure along the coordinates of the discrete-time state vector. We introduce a class of space-sequential particle filters that exploits this structure to improve performance when the system dimension is large. This is numerically illustrated by a set of computer simulations for a stochastic Lorenz 96 system with additive noise. The new space-sequential particle filters attain approximately constant estimation errors as the dimension of the Lorenz 96 system is increased, with a computational cost that increases polynomially, rather than exponentially, with the system dimension. Besides the new numerical scheme and particle filters, we provide in this paper a general framework for discrete-time filtering in continuous-time dynamical systems described by a SDE and instantaneous observations. Provided that the SDE is discretised using a weakly-convergent scheme, we prove that the marginal posterior laws of the resulting discrete-time state-space model converge to the posterior marginal posterior laws of the original continuous-time state-space model under a suitably defined metric. This result is general and not restricted to the numerical scheme or particle filters specifically studied in this manuscript.

The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an increasing interest in the adaptive processing of graphs, which led to the development of different neural network-based methodologies. In this thesis, we take a different route and develop a Bayesian Deep Learning framework for graph learning. The dissertation begins with a review of the principles over which most of the methods in the field are built, followed by a study on graph classification reproducibility issues. We then proceed to bridge the basic ideas of deep learning for graphs with the Bayesian world, by building our deep architectures in an incremental fashion. This framework allows us to consider graphs with discrete and continuous edge features, producing unsupervised embeddings rich enough to reach the state of the art on several classification tasks. Our approach is also amenable to a Bayesian nonparametric extension that automatizes the choice of almost all model's hyper-parameters. Two real-world applications demonstrate the efficacy of deep learning for graphs. The first concerns the prediction of information-theoretic quantities for molecular simulations with supervised neural models. After that, we exploit our Bayesian models to solve a malware-classification task while being robust to intra-procedural code obfuscation techniques. We conclude the dissertation with an attempt to blend the best of the neural and Bayesian worlds together. The resulting hybrid model is able to predict multimodal distributions conditioned on input graphs, with the consequent ability to model stochasticity and uncertainty better than most works. Overall, we aim to provide a Bayesian perspective into the articulated research field of deep learning for graphs.

The conjoining of dynamical systems and deep learning has become a topic of great interest. In particular, neural differential equations (NDEs) demonstrate that neural networks and differential equation are two sides of the same coin. Traditional parameterised differential equations are a special case. Many popular neural network architectures, such as residual networks and recurrent networks, are discretisations. NDEs are suitable for tackling generative problems, dynamical systems, and time series (particularly in physics, finance, ...) and are thus of interest to both modern machine learning and traditional mathematical modelling. NDEs offer high-capacity function approximation, strong priors on model space, the ability to handle irregular data, memory efficiency, and a wealth of available theory on both sides. This doctoral thesis provides an in-depth survey of the field. Topics include: neural ordinary differential equations (e.g. for hybrid neural/mechanistic modelling of physical systems); neural controlled differential equations (e.g. for learning functions of irregular time series); and neural stochastic differential equations (e.g. to produce generative models capable of representing complex stochastic dynamics, or sampling from complex high-dimensional distributions). Further topics include: numerical methods for NDEs (e.g. reversible differential equations solvers, backpropagation through differential equations, Brownian reconstruction); symbolic regression for dynamical systems (e.g. via regularised evolution); and deep implicit models (e.g. deep equilibrium models, differentiable optimisation). We anticipate this thesis will be of interest to anyone interested in the marriage of deep learning with dynamical systems, and hope it will provide a useful reference for the current state of the art.

This book develops an effective theory approach to understanding deep neural networks of practical relevance. Beginning from a first-principles component-level picture of networks, we explain how to determine an accurate description of the output of trained networks by solving layer-to-layer iteration equations and nonlinear learning dynamics. A main result is that the predictions of networks are described by nearly-Gaussian distributions, with the depth-to-width aspect ratio of the network controlling the deviations from the infinite-width Gaussian description. We explain how these effectively-deep networks learn nontrivial representations from training and more broadly analyze the mechanism of representation learning for nonlinear models. From a nearly-kernel-methods perspective, we find that the dependence of such models' predictions on the underlying learning algorithm can be expressed in a simple and universal way. To obtain these results, we develop the notion of representation group flow (RG flow) to characterize the propagation of signals through the network. By tuning networks to criticality, we give a practical solution to the exploding and vanishing gradient problem. We further explain how RG flow leads to near-universal behavior and lets us categorize networks built from different activation functions into universality classes. Altogether, we show that the depth-to-width ratio governs the effective model complexity of the ensemble of trained networks. By using information-theoretic techniques, we estimate the optimal aspect ratio at which we expect the network to be practically most useful and show how residual connections can be used to push this scale to arbitrary depths. With these tools, we can learn in detail about the inductive bias of architectures, hyperparameters, and optimizers.

The last decade has witnessed an experimental revolution in data science and machine learning, epitomised by deep learning methods. Indeed, many high-dimensional learning tasks previously thought to be beyond reach -- such as computer vision, playing Go, or protein folding -- are in fact feasible with appropriate computational scale. Remarkably, the essence of deep learning is built from two simple algorithmic principles: first, the notion of representation or feature learning, whereby adapted, often hierarchical, features capture the appropriate notion of regularity for each task, and second, learning by local gradient-descent type methods, typically implemented as backpropagation. While learning generic functions in high dimensions is a cursed estimation problem, most tasks of interest are not generic, and come with essential pre-defined regularities arising from the underlying low-dimensionality and structure of the physical world. This text is concerned with exposing these regularities through unified geometric principles that can be applied throughout a wide spectrum of applications. Such a 'geometric unification' endeavour, in the spirit of Felix Klein's Erlangen Program, serves a dual purpose: on one hand, it provides a common mathematical framework to study the most successful neural network architectures, such as CNNs, RNNs, GNNs, and Transformers. On the other hand, it gives a constructive procedure to incorporate prior physical knowledge into neural architectures and provide principled way to build future architectures yet to be invented.