Graph encoder embedding, a recent technique for graph data, offers speed and scalability in producing vertex-level representations from binary graphs. In this paper, we extend the applicability of this method to a general graph model, which includes weighted graphs, distance matrices, and kernel matrices. We prove that the encoder embedding satisfies the law of large numbers and the central limit theorem on a per-observation basis. Under certain condition, it achieves asymptotic normality on a per-class basis, enabling optimal classification through discriminant analysis. These theoretical findings are validated through a series of experiments involving weighted graphs, as well as text and image data transformed into general graph representations using appropriate distance metrics.

In recent years, the inconsistency in Bayesian deep learning has garnered increasing attention. Tempered or generalized posterior distributions often offer a direct and effective solution to this issue. However, understanding the underlying causes and evaluating the effectiveness of generalized posteriors remain active areas of research. In this study, we introduce a unified theoretical framework to attribute Bayesian inconsistency to model misspecification and inadequate priors. We interpret the generalization of the posterior with a temperature factor as a correction for misspecified models through adjustments to the joint probability model, and the recalibration of priors by redistributing probability mass on models within the hypothesis space using data samples. Additionally, we highlight a distinctive feature of Laplace approximation, which ensures that the generalized normalizing constant can be treated as invariant, unlike the typical scenario in general Bayesian learning where this constant varies with model parameters post-generalization. Building on this insight, we propose the generalized Laplace approximation, which involves a simple adjustment to the computation of the Hessian matrix of the regularized loss function. This method offers a flexible and scalable framework for obtaining high-quality posterior distributions. We assess the performance and properties of the generalized Laplace approximation on state-of-the-art neural networks and real-world datasets.

Diffusion models have become a leading method for generativ e modeling of both image and scientific data. As these models are costly to train and evaluate, reducing the inference cost for diffusion models remains a maj or goal. Inspired by the recent empirical success in accelerating diffusion mod els via the parallel sampling technique [1], we propose to divide the sampling proce ss into O (1) blocks with parallelizable Picard iterations within each block. R igorous theoretical analysis reveals that our algorithm achieves null O (poly log d) overall time complexity, marking the first implementation with provable sub-linear complexi ty w.r .t. the data dimension d. Our analysis is based on a generalized version of Girsanov' s theorem and is compatible with both the SDE and probability fl ow ODE implementations. Our results shed light on the potential of fast a nd efficient sampling of high-dimensional data on fast-evolving modern large-me mory GPU clusters.

Denoising diffusion bridge models (DDBMs) are a powerful variant of diffusion models for interpolating between two arbitrary paired distributions given as endpoints. Despite their promising performance in tasks like image translation, DDBMs require a computationally intensive sampling process that involves the simulation of a (stochastic) differential equation through hundreds of network evaluations. In this work, we present diffusion bridge implicit models (DBIMs) for accelerated sampling of diffusion bridges without extra training. We generalize DDBMs via a class of non-Markovian diffusion bridges defined on the discretized timesteps concerning sampling, which share the same training objective as DDBMs. These generalized diffusion bridges give rise to generative processes ranging from stochastic to deterministic (i.e., an implicit probabilistic model) while being up to 25$\times$ faster than the vanilla sampler of DDBMs. Moreover, the deterministic sampling procedure yielded by DBIMs enables faithful encoding and reconstruction by a booting noise used in the initial sampling step, and allows us to perform semantically meaningful interpolation in image translation tasks by regarding the booting noise as the latent variable.

PAC-Bayesian analysis is a frequentist framework for incorporating prior knowledge into learning. It was inspired by Bayesian learning, which allows sequential data processing and naturally turns posteriors from one processing step into priors for the next. However, despite two and a half decades of research, the ability to update priors sequentially without losing confidence information along the way remained elusive for PAC-Bayes. While PAC-Bayes allows construction of data-informed priors, the final confidence intervals depend only on the number of points that were not used for the construction of the prior, whereas confidence information in the prior, which is related to the number of points used to construct the prior, is lost. This limits the possibility and benefit of sequential prior updates, because the final bounds depend only on the size of the final batch. We present a novel and, in retrospect, surprisingly simple and powerful PAC-Bayesian procedure that allows sequential prior updates with no information loss. The procedure is based on a novel decomposition of the expected loss of randomized classifiers. The decomposition rewrites the loss of the posterior as an excess loss relative to a downscaled loss of the prior plus the downscaled loss of the prior, which is bounded recursively. As a side result, we also present a generalization of the split-kl and PAC-Bayes-split-kl inequalities to discrete random variables, which we use for bounding the excess losses, and which can be of independent interest. In empirical evaluation the new procedure significantly outperforms state-of-the-art.

Continuous-time generative models, such as Flow Matching (FM), construct probability paths to transport between one distribution and another through the simulation-free learning of the neural ordinary differential equations (ODEs). During inference, however, the learned model often requires multiple neural network evaluations to accurately integrate the flow, resulting in a slow sampling speed. We attribute the reason to the inherent (joint) heterogeneity of source and/or target distributions, namely the singularity problem, which poses challenges for training the neural ODEs effectively. To address this issue, we propose a more general framework, termed Switched FM (SFM), that eliminates singularities via switching ODEs, as opposed to using a uniform ODE in FM. Importantly, we theoretically show that FM cannot transport between two simple distributions due to the existence and uniqueness of initial value problems of ODEs, while these limitations can be well tackled by SFM. From an orthogonal perspective, our framework can seamlessly integrate with the existing advanced techniques, such as minibatch optimal transport, to further enhance the straightness of the flow, yielding a more efficient sampling process with reduced costs. We demonstrate the effectiveness of the newly proposed SFM through several numerical examples.

Directed acyclic graph (DAG) learning is a rapidly expanding field of research. Though the field has witnessed remarkable advances over the past few years, it remains statistically and computationally challenging to learn a single (point estimate) DAG from data, let alone provide uncertainty quantification. Our article addresses the difficult task of quantifying graph uncertainty by developing a variational Bayes inference framework based on novel distributions that have support directly on the space of DAGs. The distributions, which we use to form our prior and variational posterior, are induced by a projection operation, whereby an arbitrary continuous distribution is projected onto the space of sparse weighted acyclic adjacency matrices (matrix representations of DAGs) with probability mass on exact zeros. Though the projection constitutes a combinatorial optimization problem, it is solvable at scale via recently developed techniques that reformulate acyclicity as a continuous constraint. We empirically demonstrate that our method, ProDAG, can deliver accurate inference, and often outperforms existing state-of-the-art alternatives.

Label differential privacy (DP) is a framework that protects the privacy of labels in training datasets, while the feature vectors are public. Existing approaches protect the privacy of labels by flipping them randomly, and then train a model to make the output approximate the privatized label. However, as the number of classes $K$ increases, stronger randomization is needed, thus the performances of these methods become significantly worse. In this paper, we propose a vector approximation approach, which is easy to implement and introduces little additional computational overhead. Instead of flipping each label into a single scalar, our method converts each label into a random vector with $K$ components, whose expectations reflect class conditional probabilities. Intuitively, vector approximation retains more information than scalar labels. A brief theoretical analysis shows that the performance of our method only decays slightly with $K$. Finally, we conduct experiments on both synthesized and real datasets, which validate our theoretical analysis as well as the practical performance of our method.

The generation of ligands that both are tailored to a given protein pocket and exhibit a range of desired chemical properties is a major challenge in structure-based drug design. Here, we propose an in-silico approach for the $\textit{de novo}$ generation of 3D ligand structures using the equivariant diffusion model PILOT, combining pocket conditioning with a large-scale pre-training and property guidance. Its multi-objective trajectory-based importance sampling strategy is designed to direct the model towards molecules that not only exhibit desired characteristics such as increased binding affinity for a given protein pocket but also maintains high synthetic accessibility. This ensures the practicality of sampled molecules, thus maximizing their potential for the drug discovery pipeline. PILOT significantly outperforms existing methods across various metrics on the common benchmark dataset CrossDocked2020. Moreover, we employ PILOT to generate novel ligands for unseen protein pockets from the Kinodata-3D dataset, which encompasses a substantial portion of the human kinome. The generated structures exhibit predicted $IC_{50}$ values indicative of potent biological activity, which highlights the potential of PILOT as a powerful tool for structure-based drug design.

This paper presents an innovative approach, called credal wrapper, to formulating a credal set representation of model averaging for Bayesian neural networks (BNNs) and deep ensembles, capable of improving uncertainty estimation in classification tasks. Given a finite collection of single distributions derived from BNNs or deep ensembles, the proposed approach extracts an upper and a lower probability bound per class, acknowledging the epistemic uncertainty due to the availability of a limited amount of sampled predictive distributions. Such probability intervals over classes can be mapped on a convex set of probabilities (a 'credal set') from which, in turn, a unique prediction can be obtained using a transformation called 'intersection probability transformation'. In this article, we conduct extensive experiments on multiple out-of-distribution (OOD) detection benchmarks, encompassing various dataset pairs (CIFAR10/100 vs SVHN/Tiny-ImageNet, CIFAR10 vs CIFAR10-C, CIFAR100 vs CIFAR100-C and ImageNet vs ImageNet-O) and using different network architectures (such as VGG16, Res18/50, EfficientNet B2, and ViT Base). Compared to BNN and deep ensemble baselines, the proposed credal representation methodology exhibits superior performance in uncertainty estimation and achieves lower expected calibration error on OOD samples.