Gaussian Process Networks (GPNs) are a class of directed graphical models which employ Gaussian processes as priors for the conditional expectation of each variable given its parents in the network. The model allows the description of continuous joint distributions in a compact but flexible manner with minimal parametric assumptions on the dependencies between variables. Bayesian structure learning of GPNs requires computing the posterior over graphs of the network and is computationally infeasible even in low dimensions. This work implements Monte Carlo and Markov Chain Monte Carlo methods to sample from the posterior distribution of network structures. As such, the approach follows the Bayesian paradigm, comparing models via their marginal likelihood and computing the posterior probability of the GPN features. Simulation studies show that our method outperforms state-of-the-art algorithms in recovering the graphical structure of the network and provides an accurate approximation of its posterior distribution.

This study aims to comprehensively investigate the deep ensemble approach, an approximate Bayesian inference, in the multi-output regression task for predicting the aerodynamic performance of a missile configuration. To this end, the effect of the number of neural networks used in the ensemble, which has been blindly adopted in previous studies, is scrutinized. As a result, an obvious trend towards underestimation of uncertainty as it increases is observed for the first time, and in this context, we propose the deep ensemble framework that applies the post-hoc calibration method to improve its uncertainty quantification performance. It is compared with Gaussian process regression and is shown to have superior performance in terms of regression accuracy ($\uparrow55\sim56\%$), reliability of estimated uncertainty ($\uparrow38\sim77\%$), and training efficiency ($\uparrow78\%$). Finally, the potential impact of the suggested framework on the Bayesian optimization is briefly examined, indicating that deep ensemble without calibration may lead to unintended exploratory behavior. This UQ framework can be seamlessly applied and extended to any regression task, as no special assumptions have been made for the specific problem used in this study.

Optimal Transport has received much attention in Machine Learning as it allows to compare probability distributions by exploiting the geometry of the underlying space. However, in its original formulation, solving this problem suffers from a significant computational burden. Thus, a meaningful line of work consists at proposing alternatives to reduce this burden while still enjoying its properties. In this thesis, we focus on alternatives which use projections on subspaces. The main such alternative is the Sliced-Wasserstein distance, which we first propose to extend to Riemannian manifolds in order to use it in Machine Learning applications for which using such spaces has been shown to be beneficial in the recent years. We also study sliced distances between positive measures in the so-called unbalanced OT problem. Back to the original Euclidean Sliced-Wasserstein distance between probability measures, we study the dynamic of gradient flows when endowing the space with this distance in place of the usual Wasserstein distance. Then, we investigate the use of the Busemann function, a generalization of the inner product in metric spaces, in the space of probability measures. Finally, we extend the subspace detour approach to incomparable spaces using the Gromov-Wasserstein distance.

Spurious correlations in the data, where multiple cues are predictive of the target labels, often lead to a phenomenon known as simplicity bias, where a model relies on erroneous, easy-to-learn cues while ignoring reliable ones. In this work, we propose an ensemble diversification framework exploiting Diffusion Probabilistic Models (DPMs) for shortcut bias mitigation. We show that at particular training intervals, DPMs can generate images with novel feature combinations, even when trained on images displaying correlated input features. We leverage this crucial property to generate synthetic counterfactuals to increase model diversity via ensemble disagreement. We show that DPM-guided diversification is sufficient to remove dependence on primary shortcut cues, without a need for additional supervised signals. We further empirically quantify its efficacy on several diversification objectives, and finally show improved generalization and diversification performance on par with prior work that relies on auxiliary data collection.

We investigate the stationary (late-time) training regime of single- and two-layer linear neural networks within the continuum limit of stochastic gradient descent (SGD) for synthetic Gaussian data. In the case of a single-layer network in the weakly oversampled regime, the spectrum of the noise covariance matrix deviates notably from the Hessian, which can be attributed to the broken detailed balance of SGD dynamics. The weight fluctuations are in this case generally anisotropic, but experience an isotropic loss. For a two-layer network, we obtain the stochastic dynamics of the weights in each layer and analyze the associated stationary covariances. We identify the inter-layer coupling as a new source of anisotropy for the weight fluctuations. In contrast to the single-layer case, the weight fluctuations experience an anisotropic loss, the flatness of which is inversely related to the fluctuation variance. We thereby provide an analytical derivation of the recently observed inverse variance-flatness relation in a deep linear network model.

Retrosynthesis poses a fundamental challenge in biopharmaceuticals, aiming to aid chemists in finding appropriate reactant molecules and synthetic pathways given determined product molecules. With the reactant and product represented as 2D graphs, retrosynthesis constitutes a conditional graph-to-graph generative task. Inspired by the recent advancements in discrete diffusion models for graph generation, we introduce Retrosynthesis Diffusion (RetroDiff), a novel diffusion-based method designed to address this problem. However, integrating a diffusion-based graph-to-graph framework while retaining essential chemical reaction template information presents a notable challenge. Our key innovation is to develop a multi-stage diffusion process. In this method, we decompose the retrosynthesis procedure to first sample external groups from the dummy distribution given products and then generate the external bonds to connect the products and generated groups. Interestingly, such a generation process is exactly the reverse of the widely adapted semi-template retrosynthesis procedure, i.e. from reaction center identification to synthon completion, which significantly reduces the error accumulation. Experimental results on the benchmark have demonstrated the superiority of our method over all other semi-template methods.

Mutation validation (MV) is a recently proposed approach for model selection, garnering significant interest due to its unique characteristics and potential benefits compared to the widely used cross-validation (CV) method. In this study, we empirically compared MV and $k$-fold CV using benchmark and real-world datasets. By employing Bayesian tests, we compared generalization estimates yielding three posterior probabilities: practical equivalence, CV superiority, and MV superiority. We also evaluated the differences in the capacity of the selected models and computational efficiency. We found that both MV and CV select models with practically equivalent generalization performance across various machine learning algorithms and the majority of benchmark datasets. MV exhibited advantages in terms of selecting simpler models and lower computational costs. However, in some cases MV selected overly simplistic models leading to underfitting and showed instability in hyperparameter selection. These limitations of MV became more evident in the evaluation of a real-world neuroscientific task of predicting sex at birth using brain functional connectivity.

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.