We present a novel theoretical interpretation of AlphaFold1 that reveals the potential of generalized Bayesian updating for probabilistic deep learning. The seminal breakthrough of AlphaFold1 in protein structure prediction by deep learning relied on a learned potential energy function, in contrast to the later end-to-end architectures of AlphaFold2 and AlphaFold3. While this potential was originally justified by referring to physical potentials of mean force (PMFs), we reinterpret AlphaFold1's potential as an instance of {\em probability kinematics} -- also known as {\em Jeffrey conditioning} -- a principled but under-recognised generalization of conventional Bayesian updating. Probability kinematics accommodates uncertain or {\em soft} evidence in the form of updated probabilities over a partition. This perspective reveals AlphaFold1's potential as a form of generalized Bayesian updating, rather than a thermodynamic potential. To confirm our probabilistic framework's scope and precision, we analyze a synthetic 2D model in which an angular random walk prior is updated with evidence on distances via probability kinematics, mirroring AlphaFold1's approach. This theoretical contribution connects AlphaFold1 to a broader class of well-justified Bayesian methods, allowing precise quantification, surpassing merely qualitative heuristics based on PMFs. Our contribution is theoretical: we replace AlphaFold1's heuristic analogy with a principled probabilistic framework, tested in a controlled synthetic setting where correctness can be assessed. More broadly, our results point to the considerable promise of probability kinematics for probabilistic deep learning, by allowing the formulation of complex models from a few simpler components.

Probabilistic relational models such as parametric factor graphs enable efficient (lifted) inference by exploiting the indistinguishability of objects. In lifted inference, a representative of indistinguishable objects is used for computations. To obtain a relational (i.e., lifted) representation, the Advanced Colour Passing (ACP) algorithm is the state of the art. The ACP algorithm, however, requires underlying distributions, encoded as potential-based factorisations, to exactly match to identify and exploit indistinguishabilities. Hence, ACP is unsuitable for practical applications where potentials learned from data inevitably deviate even if associated objects are indistinguishable. To mitigate this problem, we introduce the $\varepsilon$-Advanced Colour Passing ($\varepsilon$-ACP) algorithm, which allows for a deviation of potentials depending on a hyperparameter $\varepsilon$. $\varepsilon$-ACP efficiently uncovers and exploits indistinguishabilities that are not exact. We prove that the approximation error induced by $\varepsilon$-ACP is strictly bounded and our experiments show that the approximation error is close to zero in practice.

Federated learning (FL) is a privacy-preserving machine learning paradigm that enables collaborative model training across multiple distributed clients without disclosing their raw data. Personalized federated learning (pFL) has gained increasing attention for its ability to address data heterogeneity. However, most existing pFL methods assume that each client's data follows a single distribution and learn one client-level personalized model for each client. This assumption often fails in practice, where a single client may possess data from multiple sources or domains, resulting in significant intra-client heterogeneity and suboptimal performance. To tackle this challenge, we propose pFedBayesPT, a fine-grained instance-wise pFL framework based on visual prompt tuning. Specifically, we formulate instance-wise prompt generation from a Bayesian perspective and model the prompt posterior as an implicit distribution to capture diverse visual semantics. We derive a variational training objective under the semi-implicit variational inference framework. Extensive experiments on benchmark datasets demonstrate that pFedBayesPT consistently outperforms existing pFL methods under both feature and label heterogeneity settings.

Neural density estimation has seen widespread applications in the gravitational-wave (GW) data analysis, which enables real-time parameter estimation for compact binary coalescences and enhances rapid inference for subsequent analysis such as population inference. In this work, we explore the application of using the Kolmogorov-Arnold network (KAN) to construct efficient and interpretable neural density estimators for lightweight posterior construction of GW catalogs. By replacing conventional activation functions with learnable splines, KAN achieves superior interpretability, higher accuracy, and greater parameter efficiency on related scientific tasks. Leveraging this feature, we propose a KAN-based neural density estimator, which ingests megabyte-scale GW posterior samples and compresses them into model weights of tens of kilobytes. Subsequently, analytic expressions requiring only several kilobytes can be further distilled from these neural network weights with minimal accuracy trade-off. In practice, GW posterior samples with fidelity can be regenerated rapidly using the model weights or analytic expressions for subsequent analysis. Our lightweight posterior construction strategy is expected to facilitate user-level data storage and transmission, paving a path for efficient analysis of numerous GW events in the next-generation GW detectors.

Preference-based reinforcement learning has gained prominence as a strategy for training agents in environments where the reward signal is difficult to specify or misaligned with human intent. However, its effectiveness is often limited by the high cost and low availability of reliable human input, especially in domains where expert feedback is scarce or errors are costly. To address this, we propose a novel framework that combines two complementary strategies: probabilistic crowd modelling to handle noisy, multi-annotator feedback, and active learning to prioritize feedback on the most informative agent actions. We extend the Advise algorithm to support multiple trainers, estimate their reliability online, and incorporate entropy-based query selection to guide feedback requests. We evaluate our approach in a set of environments that span both synthetic and real-world-inspired settings, including 2D games (Taxi, Pacman, Frozen Lake) and a blood glucose control task for Type 1 Diabetes using the clinically approved UVA/Padova simulator. Our preliminary results demonstrate that agents trained with feedback on uncertain trajectories exhibit faster learning in most tasks, and we outperform the baselines for the blood glucose control task.

Molecular structure generation is a fundamental problem that involves determining the 3D positions of molecules' constituents. It has crucial biological applications, such as molecular docking, protein folding, and molecular design. Recent advances in generative modeling, such as diffusion models and flow matching, have made great progress on these tasks by modeling molecular conformations as a distribution. In this work, we focus on flow matching and adopt an energy-based perspective to improve training and inference of structure generation models. Our view results in a mapping function, represented by a deep network, that is directly learned to \textit{iteratively} map random configurations, i.e. samples from the source distribution, to target structures, i.e. points in the data manifold. This yields a conceptually simple and empirically effective flow matching setup that is theoretically justified and has interesting connections to fundamental properties such as idempotency and stability, as well as the empirically useful techniques such as structure refinement in AlphaFold. Experiments on protein docking as well as protein backbone generation consistently demonstrate the method's effectiveness, where it outperforms recent baselines of task-associated flow matching and diffusion models, using a similar computational budget.

The contextual duelling bandit problem models adaptive recommender systems, where the algorithm presents a set of items to the user, and the user's choice reveals their preference. This setup is well suited for implicit choices users make when navigating a content platform, but does not capture other possible comparison queries. Motivated by the fact that users provide more reliable feedback after consuming items, we propose a new bandit model that can be described as follows. The algorithm recommends one item per time step; after consuming that item, the user is asked to compare it with another item chosen from the user's consumption history. Importantly, in our model, this comparison item can be chosen without incurring any additional regret, potentially leading to better performance. However, the regret analysis is challenging because of the temporal dependency in the user's history. To overcome this challenge, we first show that the algorithm can construct informative queries provided the history is rich, i.e., satisfies a certain diversity condition. We then show that a short initial random exploration phase is sufficient for the algorithm to accumulate a rich history with high probability. This result, proven via matrix concentration bounds, yields $O(\sqrt{T})$ regret guarantees. Additionally, our simulations show that reusing past items for comparisons can lead to significantly lower regret than only comparing between simultaneously recommended items.

In this PhD thesis, we propose a novel framework for uncertainty quantification in machine learning, which is based on proper scores. Uncertainty quantification is an important cornerstone for trustworthy and reliable machine learning applications in practice. Usually, approaches to uncertainty quantification are problem-specific, and solutions and insights cannot be readily transferred from one task to another. Proper scores are loss functions minimized by predicting the target distribution. Due to their very general definition, proper scores apply to regression, classification, or even generative modeling tasks. We contribute several theoretical results, that connect epistemic uncertainty, aleatoric uncertainty, and model calibration with proper scores, resulting in a general and widely applicable framework. We achieve this by introducing a general bias-variance decomposition for strictly proper scores via functional Bregman divergences. Specifically, we use the kernel score, a kernel-based proper score, for evaluating sample-based generative models in various domains, like image, audio, and natural language generation. This includes a novel approach for uncertainty estimation of large language models, which outperforms state-of-the-art baselines. Further, we generalize the calibration-sharpness decomposition beyond classification, which motivates the definition of proper calibration errors. We then introduce a novel estimator for proper calibration errors in classification, and a novel risk-based approach to compare different estimators for squared calibration errors. Last, we offer a decomposition of the kernel spherical score, another kernel-based proper score, allowing a more fine-grained and interpretable evaluation of generative image models.

Many modern probabilistic models rely on SDEs, but their adoption is hampered by instability, poor inductive bias outside bounded domains, and reliance on restrictive dynamics or training tricks. While recent work constrains SDEs to compact spaces using reflected dynamics, these approaches lack continuous dynamics and efficient high-order solvers, limiting interpretability and applicability. We propose a novel class of neural SDEs on compact polyhedral spaces with continuous dynamics, amenable to higher-order solvers, and with favorable inductive bias.

Accurate modelling and quantification of predictive uncertainty is crucial in deep learning since it allows a model to make safer decisions when the data is ambiguous and facilitates the users' understanding of the model's confidence in its predictions. Along with the tremendously increasing research focus on \emph{graph neural networks} (GNNs) in recent years, there have been numerous techniques which strive to capture the uncertainty in their predictions. However, most of these approaches are specifically designed for node or link-level tasks and cannot be directly applied to graph-level learning problems. In this paper, we propose a novel variational modelling framework for the \emph{posterior predictive distribution}~(PPD) to obtain uncertainty-aware prediction in graph-level learning tasks. Based on a graph-level embedding derived from one of the existing GNNs, our framework can learn the PPD in a data-adaptive fashion. Experimental results on several benchmark datasets exhibit the effectiveness of our approach.