Bayesian inference is a powerful framework for making probabilistic inferences and decisions under uncertainty. Fundamental choices in modern Bayesian workflows concern the specification of the likelihood function and prior distributions, the posterior approximator, and the data. Each choice can significantly influence model-based inference and subsequent decisions, thereby necessitating sensitivity analysis. In this work, we propose a multifaceted approach to integrate sensitivity analyses into amortized Bayesian inference (ABI, i.e., simulation-based inference with neural networks). First, we utilize weight sharing to encode the structural similarities between alternative likelihood and prior specifications in the training process with minimal computational overhead. Second, we leverage the rapid inference of neural networks to assess sensitivity to various data perturbations or pre-processing procedures. In contrast to most other Bayesian approaches, both steps circumvent the costly bottleneck of refitting the model(s) for each choice of likelihood, prior, or dataset. Finally, we propose to use neural network ensembles to evaluate variation in results induced by unreliable approximation on unseen data. We demonstrate the effectiveness of our method in applied modeling problems, ranging from the estimation of disease outbreak dynamics and global warming thresholds to the comparison of human decision-making models. Our experiments showcase how our approach enables practitioners to effectively unveil hidden relationships between modeling choices and inferential conclusions.

Bayesian model comparison (BMC) offers a principled approach for assessing the relative merits of competing computational models and propagating uncertainty into model selection decisions. However, BMC is often intractable for the popular class of hierarchical models due to their high-dimensional nested parameter structure. To address this intractability, we propose a deep learning method for performing BMC on any set of hierarchical models which can be instantiated as probabilistic programs. Since our method enables amortized inference, it allows efficient re-estimation of posterior model probabilities and fast performance validation prior to any real-data application. In a series of extensive validation studies, we benchmark the performance of our method against the state-of-the-art bridge sampling method and demonstrate excellent amortized inference across all BMC settings. We then showcase our method by comparing four hierarchical evidence accumulation models that have previously been deemed intractable for BMC due to partly implicit likelihoods. Additionally, we demonstrate how transfer learning can be leveraged to enhance training efficiency. We provide reproducible code for all analyses and an open-source implementation of our method.

Feature alignment methods are used in many scientific disciplines for data pooling, annotation, and comparison. As an instance of a permutation learning problem, feature alignment presents significant statistical and computational challenges. In this work, we propose the covariance alignment model to study and compare various alignment methods and establish a minimax lower bound for covariance alignment that has a non-standard dimension scaling because of the presence of a nuisance parameter. This lower bound is in fact minimax optimal and is achieved by a natural quasi MLE. However, this estimator involves a search over all permutations which is computationally infeasible even when the problem has moderate size. To overcome this limitation, we show that the celebrated Gromov-Wasserstein algorithm from optimal transport which is more amenable to fast implementation even on large-scale problems is also minimax optimal. These results give the first statistical justification for the deployment of the Gromov-Wasserstein algorithm in practice.

Working with multiple variables they usually contain difficult to control complex dependencies. This article proposes extraction of their individual information, e.g. $\overline{X|Y}$ as random variable containing information from $X$, but with removed information about $Y$, by using $(x,y) \leftrightarrow (\bar{x}=\textrm{CDF}_{X|Y=y}(x),y)$ reversible normalization. One application can be decoupling of individual information of variables: reversibly transform $(X_1,\ldots,X_n)\leftrightarrow(\tilde{X}_1,\ldots \tilde{X}_n)$ together containing the same information, but being independent: $\forall_{i\neq j} \tilde{X}_i\perp \tilde{X}_j, \tilde{X}_i\perp X_j$. It requires detailed models of complex conditional probability distributions - it is generally a difficult task, but here can be done through multiple dependency reducing iterations, using imperfect methods (here HCR: Hierarchical Correlation Reconstruction). It could be also used for direct mutual information - evaluating direct information transfer: without use of intermediate variables. For causality direction there is discussed multi-feature Granger causality, e.g. to trace various types of individual information transfers between such decoupled variables, including propagation time (delay).

While deep learning has achieved remarkable success, there is no clear explanation about why it works so well. In order to discuss this question quantitatively, we need a mathematical framework that explains what learning is in the first place. After several considerations, we succeeded in constructing a mathematical framework that can provide a unified understanding of all types of learning, including deep learning and learning in the brain. We call it learning principle, and it follows that all learning is equivalent to estimating the probability of input data. We not only derived this principle, but also mentioned its application to actual machine learning models. For example, we found that conventional supervised learning is equivalent to estimating conditional probabilities, and succeeded in making supervised learning more effective and generalized. We also proposed a new method of defining the values of estimated probability using differentiation, and showed that unsupervised learning can be performed on arbitrary dataset without any prior knowledge. Namely, this method is a general-purpose machine learning in the true sense. Moreover, we succeeded in describing the learning mechanism in the brain by considering the time evolution of a fully or partially connected model and applying this new method. The learning principle provides solutions to many unsolved problems in deep learning and cognitive neuroscience.

This study employs Bayesian methodologies to explore the influence of player or positional factors in predicting the probability of a shot resulting in a goal, measured by the expected goals (xG) metric. Utilising publicly available data from StatsBomb, Bayesian hierarchical logistic regressions are constructed, analysing approximately 10,000 shots from the English Premier League to ascertain whether positional or player-level effects impact xG. The findings reveal positional effects in a basic model that includes only distance to goal and shot angle as predictors, highlighting that strikers and attacking midfielders exhibit a higher likelihood of scoring. However, these effects diminish when more informative predictors are introduced. Nevertheless, even with additional predictors, player-level effects persist, indicating that certain players possess notable positive or negative xG adjustments, influencing their likelihood of scoring a given chance. The study extends its analysis to data from Spain's La Liga and Germany's Bundesliga, yielding comparable results. Additionally, the paper assesses the impact of prior distribution choices on outcomes, concluding that the priors employed in the models provide sound results but could be refined to enhance sampling efficiency for constructing more complex and extensive models feasibly.

Machine learning models offer the potential to understand diverse datasets in a data-driven way, powering insights into individual disease experiences and ensuring equitable healthcare. In this study, we explore Bayesian inference for characterising symptom sequences, and the associated modelling challenges. We adapted the Mallows model to account for partial rankings and right-censored data, employing custom MCMC fitting. Our evaluation, encompassing synthetic data and a primary progressive aphasia dataset, highlights the model's efficacy in revealing mean orderings and estimating ranking variance. This holds the potential to enhance clinical comprehension of symptom occurrence. However, our work encounters limitations concerning model scalability and small dataset sizes.

A popular perspective in Reinforcement learning (RL) casts the problem as probabilistic inference on a graphical model of the Markov decision process (MDP). The core object of study is the probability of each state-action pair being visited under the optimal policy. Previous approaches to approximate this quantity can be arbitrarily poor, leading to algorithms that do not implement genuine statistical inference and consequently do not perform well in challenging problems. In this work, we undertake a rigorous Bayesian treatment of the posterior probability of state-action optimality and clarify how it flows through the MDP. We first reveal that this quantity can indeed be used to generate a policy that explores efficiently, as measured by regret. Unfortunately, computing it is intractable, so we derive a new variational Bayesian approximation yielding a tractable convex optimization problem and establish that the resulting policy also explores efficiently. We call our approach VAPOR and show that it has strong connections to Thompson sampling, K-learning, and maximum entropy exploration. We conclude with some experiments demonstrating the performance advantage of a deep RL version of VAPOR.

Effective and rapid decision-making from randomized controlled trials (RCTs) requires unbiased and precise treatment effect inferences. Two strategies to address this requirement are to adjust for covariates that are highly correlated with the outcome, and to leverage historical control information via Bayes' theorem. We propose a new Bayesian prognostic covariate adjustment methodology, referred to as Bayesian PROCOVA, that combines these two strategies. Covariate adjustment in Bayesian PROCOVA is based on generative artificial intelligence (AI) algorithms that construct a digital twin generator (DTG) for RCT participants. The DTG is trained on historical control data and yields a digital twin (DT) probability distribution for each RCT participant's outcome under the control treatment. The expectation of the DT distribution, referred to as the prognostic score, defines the covariate for adjustment. Historical control information is leveraged via an additive mixture prior with two components: an informative prior probability distribution specified based on historical control data, and a weakly informative prior distribution. The mixture weight determines the extent to which posterior inferences are drawn from the informative component, versus the weakly informative component. This weight has a prior distribution as well, and so the entire additive mixture prior is completely pre-specifiable without involving any RCT information. We establish an efficient Gibbs algorithm for sampling from the posterior distribution, and derive closed-form expressions for the posterior mean and variance of the treatment effect parameter conditional on the weight, in Bayesian PROCOVA. We evaluate efficiency gains of Bayesian PROCOVA via its bias control and variance reduction compared to frequentist PROCOVA in simulation studies that encompass different discrepancies. These gains translate to smaller RCTs.

Bayesian inference can quantify uncertainty in the predictions of neural networks using posterior distributions for model parameters and network output. By looking at these posterior distributions, one can separate the origin of uncertainty into aleatoric and epistemic contributions. One goal of uncertainty quantification is to inform on prediction accuracy. Here we show that prediction accuracy depends on both epistemic and aleatoric uncertainty in an intricate fashion that cannot be understood in terms of marginalized uncertainty distributions alone. How the accuracy relates to epistemic and aleatoric uncertainties depends not only on the model architecture, but also on the properties of the dataset. We discuss the significance of these results for active learning and introduce a novel acquisition function that outperforms common uncertainty-based methods. To arrive at our results, we approximated the posteriors using deep ensembles, for fully-connected, convolutional and attention-based neural networks.