Spurio Mancini et al. (2022) (SM22 hereafter), the exploration of high-dimensional parameter spaces in particular, developed CosmoPower, a suite of - O(100) parameters and higher - necessary to accurately neural network emulators of cosmological power spectra model the physical signals and their several systematic that replaces the computation of these quantities traditionally contaminants. Sampling the posterior distribution performed with Einstein-Boltzmann solvers such in these high-dimensional spaces represents a significant as the Code for Anisotropies in the Microwave Background computational challenge for Markov Chain Monte Carlo (CAMB, Lewis & Challinor 2011) or the Cosmic (MCMC) algorithms (Roberts et al. 1997; Katafygiotis Linear Anisotropy Solving System (CLASS, Blas et al. & Zuev 2008; Liu 2009), which are traditionally used 2011). In SM22 the authors show how Bayesian inference in cosmological analyses (Lewis & Bridle 2002; Audren of cosmological parameters can be accelerated by several et al. 2013; Brinckmann & Lesgourgues 2019; Torrado & orders of magnitude using CosmoPower; the speed-up becomes Lewis 2021). Gradient-based inference methods, such as particularly relevant when the emulators are employed Hamiltonian Monte Carlo (HMC, Duane et al. 1987; Neal within an inference pipeline that can be run on 1996) and variational inference (VI, Hoffman et al. 2013; graphics processing units (GPUs). Blei et al. 2017), manage to concentrate the sampling An additional advantage in using machine learning in regions of high posterior mass, even in large parameter emulators is that they efficiently provide accurate derivatives spaces, provided one has efficient access to accurate with respect to their input parameters. This is derivatives of the likelihood function with respect to made possible by the automatic differentiation features the model parameters (Brooks et al. 2011; Neal 2011; implemented in the libraries routinely used to build these Zhang et al. 2017; Betancourt 2017).

Predicting the presence of major depressive disorder (MDD) using behavioural and cognitive signals is a highly non-trivial task. The heterogeneous clinical profile of MDD means that any given speech, facial expression and/or observed cognitive pattern may be associated with a unique combination of depressive symptoms. Conventional discriminative machine learning models potentially lack the complexity to robustly model this heterogeneity. Bayesian networks, however, may instead be well-suited to such a scenario. These networks are probabilistic graphical models that efficiently describe the joint probability distribution over a set of random variables by explicitly capturing their conditional dependencies. This framework provides further advantages over standard discriminative modelling by offering the possibility to incorporate expert opinion in the graphical structure of the models, generating explainable model predictions, informing about the uncertainty of predictions, and naturally handling missing data. In this study, we apply a Bayesian framework to capture the relationships between depression, depression symptoms, and features derived from speech, facial expression and cognitive game data collected at thymia.

Training normalizing flow generative models can be challenging due to the need to calculate computationally expensive determinants of Jacobians. This paper studies the likelihood-free training of flows and proposes the energy objective, an alternative sample-based loss based on proper scoring rules. The energy objective is determinant-free and supports flexible model architectures that are not easily compatible with maximum likelihood training, including semi-autoregressive energy flows, a novel model family that interpolates between fully autoregressive and non-autoregressive models. Energy flows feature competitive sample quality, posterior inference, and generation speed relative to likelihood-based flows; this performance is decorrelated from the quality of log-likelihood estimates, which are generally very poor. Our findings question the use of maximum likelihood as an objective or a metric, and contribute to a scientific study of its role in generative modeling.

When analyzing real-world data it is common to work with event ensembles, which comprise sets of observations that collectively constrain the parameters of an underlying model of interest. Such models often have a hierarchical structure, where "local" parameters impact individual events and "global" parameters influence the entire dataset. We introduce practical approaches for optimal dataset-wide probabilistic inference in cases where the likelihood is intractable, but simulations can be realized via forward modeling. We construct neural estimators for the likelihood(-ratio) or posterior and show that explicitly accounting for the model's hierarchical structure can lead to tighter parameter constraints. We ground our discussion using case studies from the physical sciences, focusing on examples from particle physics (particle collider data) and astrophysics (strong gravitational lensing observations).

Diffusion models have achieved state-of-the-art performance in generating many different kinds of data, including images, text, and videos. Despite their success, there has been limited research on how the underlying diffusion process and the final convergent prior can affect generative performance; this research has also been limited to continuous data types and a score-based diffusion framework. To fill this gap, we explore how different discrete diffusion kernels (which converge to different prior distributions) affect the performance of diffusion models for graphs. To this end, we developed a novel formulation of a family of discrete diffusion kernels which are easily adjustable to converge to different Bernoulli priors, and we study the effect of these different kernels on generative performance. We show that the quality of generated graphs is sensitive to the prior used, and that the optimal choice cannot be explained by obvious statistics or metrics, which challenges the intuitions which previous works have suggested.

Diffusion Schr\"odinger bridges (DSB) have recently emerged as a powerful framework for recovering stochastic dynamics via their marginal observations at different time points. Despite numerous successful applications, existing algorithms for solving DSBs have so far failed to utilize the structure of aligned data, which naturally arises in many biological phenomena. In this paper, we propose a novel algorithmic framework that, for the first time, solves DSBs while respecting the data alignment. Our approach hinges on a combination of two decades-old ideas: The classical Schr\"odinger bridge theory and Doob's $h$-transform. Compared to prior methods, our approach leads to a simpler training procedure with lower variance, which we further augment with principled regularization schemes. This ultimately leads to sizeable improvements across experiments on synthetic and real data, including the tasks of rigid protein docking and temporal evolution of cellular differentiation processes.

We propose a new model, independent linear Markov game, for multi-agent reinforcement learning with a large state space and a large number of agents. This is a class of Markov games with independent linear function approximation, where each agent has its own function approximation for the state-action value functions that are marginalized by other players' policies. We design new algorithms for learning the Markov coarse correlated equilibria (CCE) and Markov correlated equilibria (CE) with sample complexity bounds that only scale polynomially with each agent's own function class complexity, thus breaking the curse of multiagents. In contrast, existing works for Markov games with function approximation have sample complexity bounds scale with the size of the \emph{joint action space} when specialized to the canonical tabular Markov game setting, which is exponentially large in the number of agents. Our algorithms rely on two key technical innovations: (1) utilizing policy replay to tackle non-stationarity incurred by multiple agents and the use of function approximation; (2) separating learning Markov equilibria and exploration in the Markov games, which allows us to use the full-information no-regret learning oracle instead of the stronger bandit-feedback no-regret learning oracle used in the tabular setting. Furthermore, we propose an iterative-best-response type algorithm that can learn pure Markov Nash equilibria in independent linear Markov potential games. In the tabular case, by adapting the policy replay mechanism for independent linear Markov games, we propose an algorithm with $\widetilde{O}(\epsilon^{-2})$ sample complexity to learn Markov CCE, which improves the state-of-the-art result $\widetilde{O}(\epsilon^{-3})$ in Daskalakis et al. 2022, where $\epsilon$ is the desired accuracy, and also significantly improves other problem parameters.

A directed acyclic graph (DAG) provides valuable prior knowledge that is often discarded in regression tasks in machine learning. We show that the independences arising from the presence of collider structures in DAGs provide meaningful inductive biases, which constrain the regression hypothesis space and improve predictive performance. We introduce collider regression, a framework to incorporate probabilistic causal knowledge from a collider in a regression problem. When the hypothesis space is a reproducing kernel Hilbert space, we prove a strictly positive generalisation benefit under mild assumptions and provide closed-form estimators of the empirical risk minimiser. Experiments on synthetic and climate model data demonstrate performance gains of the proposed methodology.

In this article, I take inspiration from stochastic thermodynamics to derive a problem formulation for online learning in uncertain MDPs while grounded in system dynamics. The system balances the diffusion process with drif dynamics as a way to formulate the explorationexploitation trade-off. To this effect, I make an explicit link between the information entropy and the stochastic dynamics of a system coupled to an environment. I analyze various sources of entropy production: due to the decision-maker's uncertainty about the system-environment interaction characteristics; due to the stochastic nature of system dynamics; and the interaction of the decision maker's knowledge with system dynamics. This analysis provides a framework that can be formulated either as a maximum entropy program to derive efficient policies that balance the exploration and exploitation trade-off, or as a modified cost optimization program that includes informational costs and benefits.

Conditional independence (CI) testing is frequently used in data analysis and machine learning for various scientific fields and it forms the basis of constraint-based causal discovery. Oftentimes, CI testing relies on strong, rather unrealistic assumptions. One of these assumptions is homoskedasticity, in other words, a constant conditional variance is assumed. We frame heteroskedasticity in a structural causal model framework and present an adaptation of the partial correlation CI test that works well in the presence of heteroskedastic noise, given that expert knowledge about the heteroskedastic relationships is available. Further, we provide theoretical consistency results for the proposed CI test which carry over to causal discovery under certain assumptions. Numerical causal discovery experiments demonstrate that the adapted partial correlation CI test outperforms the standard test in the presence of heteroskedasticity and is on par for the homoskedastic case. Finally, we discuss the general challenges and limits as to how expert knowledge about heteroskedasticity can be accounted for in causal discovery.