Markov jump processes are continuous-time stochastic processes with a wide range of applications in both natural and social sciences. Despite their widespread use, inference in these models is highly non-trivial and typically proceeds via either Monte Carlo or expectation-maximization methods. In this work we introduce an alternative, variational inference algorithm for Markov jump processes which relies on neural ordinary differential equations, and is trainable via back-propagation. Our methodology learns neural, continuous-time representations of the observed data, that are used to approximate the initial distribution and time-dependent transition probability rates of the posterior Markov jump process. The time-independent rates of the prior process are in contrast trained akin to generative adversarial networks. We test our approach on synthetic data sampled from ground-truth Markov jump processes, experimental switching ion channel data and molecular dynamics simulations. Source code to reproduce our experiments is available online.
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Gaussian Partial Information Decomposition: Bias Correction and Application to High-dimensional Data
Recent advances in neuroscientific experimental techniques have enabled us to simultaneously record the activity of thousands of neurons across multiple brain regions. This has led to a growing need for computational tools capable of analyzing how task-relevant information is represented and communicated between several brain regions. Partial information decompositions (PIDs) have emerged as one such tool, quantifying how much unique, redundant and synergistic information two or more brain regions carry about a task-relevant message. However, computing PIDs is computationally challenging in practice, and statistical issues such as the bias and variance of estimates remain largely unexplored. In this paper, we propose a new method for efficiently computing and estimating a PID definition on multivariate Gaussian distributions. We show empirically that our method satisfies an intuitive additivity property, and recovers the ground truth in a battery of canonical examples, even at high dimensionality. We also propose and evaluate, for the first time, a method to correct the bias in PID estimates at finite sample sizes. Finally, we demonstrate that our Gaussian PID effectively characterizes inter-areal interactions in the mouse brain, revealing higher redundancy between visual areas when a stimulus is behaviorally relevant.
Canonical models of Markov decision processes (MDPs) usually consider geometric discounting based on a constant discount factor. While this standard modeling approach has led to many elegant results, some recent studies indicate the necessity of modeling time-varying discounting in certain applications. This paper studies a model of infinite-horizon MDPs with time-varying discount factors. We take a game-theoretic perspective -- whereby each time step is treated as an independent decision maker with their own (fixed) discount factor -- and we study the subgame perfect equilibrium (SPE) of the resulting game as well as the related algorithmic problems. We present a constructive proof of the existence of an SPE and demonstrate the EXPTIME-hardness of computing an SPE. We also turn to the approximate notion of $\epsilon$-SPE and show that an $\epsilon$-SPE exists under milder assumptions. An algorithm is presented to compute an $\epsilon$-SPE, of which an upper bound of the time complexity, as a function of the convergence property of the time-varying discount factor, is provided.
Designing efficient and rigorous numerical methods for sequential decision-making under uncertainty is a difficult problem that arises in many applications frameworks. In this paper we focus on the numerical solution of a subclass of impulse control problem for piecewise deterministic Markov process (PDMP) when the jump times are hidden. We first state the problem as a partially observed Markov decision process (POMDP) on a continuous state space and with controlled transition kernels corresponding to some specific skeleton chains of the PDMP. Then we proceed to build a numerically tractable approximation of the POMDP by tailor-made discretizations of the state spaces. The main difficulty in evaluating the discretization error come from the possible random or boundary jumps of the PDMP between consecutive epochs of the POMDP and requires special care. Finally we extensively discuss the practical construction of discretization grids and illustrate our method on simulations.
We consider the general class of time-homogeneous dynamical systems, both discrete and continuous, and study the problem of learning a meaningful representation of the state from observed data. This is instrumental for the task of learning a forward transfer operator of the system, that in turn can be used for forecasting future states or observables. The representation, typically parametrized via a neural network, is associated with a projection operator and is learned by optimizing an objective function akin to that of canonical correlation analysis (CCA). However, unlike CCA, our objective avoids matrix inversions and therefore is generally more stable and applicable to challenging scenarios. Our objective is a tight relaxation of CCA and we further enhance it by proposing two regularization schemes, one encouraging the orthogonality of the components of the representation while the other exploiting Chapman-Kolmogorov's equation. We apply our method to challenging discrete dynamical systems, discussing improvements over previous methods, as well as to continuous dynamical systems.
Extreme heatwave sampling and prediction with analog Markov chain and comparisons with deep learning
We present a data-driven emulator, stochastic weather generator (SWG), suitable for estimating probabilities of prolonged heatwaves in France and Scandinavia. This emulator is based on the method of analogs of circulation to which we add temperature and soil moisture as predictor fields. We train the emulator on an intermediate complexity climate model run and show that it is capable of predicting conditional probabilities (forecasting) of heatwaves out of sample. Special attention is payed that this prediction is evaluated using proper score appropriate for rare events. To accelerate the computation of analogs dimensionality reduction techniques are applied and the performance is evaluated. The probabilistic prediction achieved with SWG is compared with the one achieved with Convolutional Neural Network (CNN). With the availability of hundreds of years of training data CNNs perform better at the task of probabilistic prediction. In addition, we show that the SWG emulator trained on 80 years of data is capable of estimating extreme return times of order of thousands of years for heatwaves longer than several days more precisely than the fit based on generalised extreme value distribution. Finally, the quality of its synthetic extreme teleconnection patterns obtained with stochastic weather generator is studied. We showcase two examples of such synthetic teleconnection patterns for heatwaves in France and Scandinavia that compare favorably to the very long climate model control run.
Neural networks have achieved remarkable performance in various application domains. Nevertheless, a large number of weights in pre-trained deep neural networks prohibit them from being deployed on smartphones and embedded systems. It is highly desirable to obtain lightweight versions of neural networks for inference in edge devices. Many cost-effective approaches were proposed to prune dense and convolutional layers that are common in deep neural networks and dominant in the parameter space. However, a unified theoretical foundation for the problem mostly is missing. In this paper, we identify the close connection between matrix spectrum learning and neural network training for dense and convolutional layers and argue that weight pruning is essentially a matrix sparsification process to preserve the spectrum. Based on the analysis, we also propose a matrix sparsification algorithm tailored for neural network pruning that yields better pruning result. We carefully design and conduct experiments to support our arguments. Hence we provide a consolidated viewpoint for neural network pruning and enhance the interpretability of deep neural networks by identifying and preserving the critical neural weights.
Discrimination between objects, in particular quantum states, is one of the most fundamental tasks in (quantum) information theory. Recent years have seen significant progress towards extending the framework to point-to-point quantum channels. However, with technological progress the focus of the field is shifting to more complex structures: Quantum networks. In contrast to channels, networks allow for intermediate access points where information can be received, processed and reintroduced into the network. In this work we study the discrimination of quantum networks and its fundamental limitations. In particular when multiple uses of the network are at hand, the rooster of available strategies becomes increasingly complex. The simplest quantum network that capturers the structure of the problem is given by a quantum superchannel. We discuss the available classes of strategies when considering $n$ copies of a superchannel and give fundamental bounds on the asymptotically achievable rates in an asymmetric discrimination setting. Furthermore, we discuss achievability, symmetric network discrimination, the strong converse exponent, generalization to arbitrary quantum networks and finally an application to an active version of the quantum illumination problem.
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.
The essence of multivariate sequential learning is all about how to extract dependencies in data. These data sets, such as hourly medical records in intensive care units and multi-frequency phonetic time series, often time exhibit not only strong serial dependencies in the individual components (the "marginal" memory) but also non-negligible memories in the cross-sectional dependencies (the "joint" memory). Because of the multivariate complexity in the evolution of the joint distribution that underlies the data generating process, we take a data-driven approach and construct a novel recurrent network architecture, termed Memory-Gated Recurrent Networks (mGRN), with gates explicitly regulating two distinct types of memories: the marginal memory and the joint memory. Through a combination of comprehensive simulation studies and empirical experiments on a range of public datasets, we show that our proposed mGRN architecture consistently outperforms state-of-the-art architectures targeting multivariate time series.
Deep learning methods for graphs achieve remarkable performance on many node-level and graph-level prediction tasks. However, despite the proliferation of the methods and their success, prevailing Graph Neural Networks (GNNs) neglect subgraphs, rendering subgraph prediction tasks challenging to tackle in many impactful applications. Further, subgraph prediction tasks present several unique challenges, because subgraphs can have non-trivial internal topology, but also carry a notion of position and external connectivity information relative to the underlying graph in which they exist. Here, we introduce SUB-GNN, a subgraph neural network to learn disentangled subgraph representations. In particular, we propose a novel subgraph routing mechanism that propagates neural messages between the subgraph's components and randomly sampled anchor patches from the underlying graph, yielding highly accurate subgraph representations. SUB-GNN specifies three channels, each designed to capture a distinct aspect of subgraph structure, and we provide empirical evidence that the channels encode their intended properties. We design a series of new synthetic and real-world subgraph datasets. Empirical results for subgraph classification on eight datasets show that SUB-GNN achieves considerable performance gains, outperforming strong baseline methods, including node-level and graph-level GNNs, by 12.4% over the strongest baseline. SUB-GNN performs exceptionally well on challenging biomedical datasets when subgraphs have complex topology and even comprise multiple disconnected components.
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