We present a generative modeling approach based on the variational inference framework for likelihood-free simulation-based inference. The method leverages latent variables within variational autoencoders to efficiently estimate complex posterior distributions arising from stochastic simulations. We explore two variations of this approach distinguished by their treatment of the prior distribution. The first model adapts the prior based on observed data using a multivariate prior network, enhancing generalization across various posterior queries. In contrast, the second model utilizes a standard Gaussian prior, offering simplicity while still effectively capturing complex posterior distributions. We demonstrate the efficacy of these models on well-established benchmark problems, achieving results comparable to flow-based approaches while maintaining computational efficiency and scalability.

We propose a Bayesian neural network-based continual learning algorithm using Variational Inference, aiming to overcome several drawbacks of existing methods. Specifically, in continual learning scenarios, storing network parameters at each step to retain knowledge poses challenges. This is compounded by the crucial need to mitigate catastrophic forgetting, particularly given the limited access to past datasets, which complicates maintaining correspondence between network parameters and datasets across all sessions. Current methods using Variational Inference with KL divergence risk catastrophic forgetting during uncertain node updates and coupled disruptions in certain nodes. To address these challenges, we propose the following strategies. To reduce the storage of the dense layer parameters, we propose a parameter distribution learning method that significantly reduces the storage requirements. In the continual learning framework employing variational inference, our study introduces a regularization term that specifically targets the dynamics and population of the mean and variance of the parameters. This term aims to retain the benefits of KL divergence while addressing related challenges. To ensure proper correspondence between network parameters and the data, our method introduces an importance-weighted Evidence Lower Bound term to capture data and parameter correlations. This enables storage of common and distinctive parameter hyperspace bases. The proposed method partitions the parameter space into common and distinctive subspaces, with conditions for effective backward and forward knowledge transfer, elucidating the network-parameter dataset correspondence. The experimental results demonstrate the effectiveness of our method across diverse datasets and various combinations of sequential datasets, yielding superior performance compared to existing approaches.

Structure-based molecule optimization (SBMO) aims to optimize molecules with both continuous coordinates and discrete types against protein targets. A promising direction is to exert gradient guidance on generative models given its remarkable success in images, but it is challenging to guide discrete data and risks inconsistencies between modalities. To this end, we leverage a continuous and differentiable space derived through Bayesian inference, presenting Molecule Joint Optimization (MolJO), the first gradient-based SBMO framework that facilitates joint guidance signals across different modalities while preserving SE(3)-equivariance. We introduce a novel backward correction strategy that optimizes within a sliding window of the past histories, allowing for a seamless trade-off between explore-and-exploit during optimization. Our proposed MolJO achieves state-of-the-art performance on CrossDocked2020 benchmark (Success Rate 51.3% , Vina Dock -9.05 and SA 0.78), more than 4x improvement in Success Rate compared to the gradient-based counterpart, and 2x "Me-Better" Ratio as much as 3D baselines. Furthermore, we extend MolJO to a wide range of optimization settings, including multi-objective optimization and challenging tasks in drug design such as R-group optimization and scaffold hopping, further underscoring its versatility and potential.

The multivariate Gaussian distribution underpins myriad operations-research, decision-analytic, and machine-learning models (e.g., Bayesian optimization, Gaussian influence diagrams, and variational autoencoders). However, despite recent advances in adversarial machine learning (AML), inference for Gaussian models in the presence of an adversary is notably understudied. Therefore, we consider a self-interested attacker who wishes to disrupt a decisionmaker's conditional inference and subsequent actions by corrupting a set of evidentiary variables. To avoid detection, the attacker also desires the attack to appear plausible wherein plausibility is determined by the density of the corrupted evidence. We consider white- and grey-box settings such that the attacker has complete and incomplete knowledge about the decisionmaker's underlying multivariate Gaussian distribution, respectively. Select instances are shown to reduce to quadratic and stochastic quadratic programs, and structural properties are derived to inform solution methods. We assess the impact and efficacy of these attacks in three examples, including, real estate evaluation, interest rate estimation and signals processing. Each example leverages an alternative underlying model, thereby highlighting the attacks' broad applicability. Through these applications, we also juxtapose the behavior of the white- and grey-box attacks to understand how uncertainty and structure affect attacker behavior.

Recent advancements in Markov chain Monte Carlo (MCMC) sampling and surrogate modelling have significantly enhanced the feasibility of Bayesian analysis across engineering fields. However, the selection and integration of surrogate models and cutting-edge MCMC algorithms, often depend on ad-hoc decisions. A systematic assessment of their combined influence on analytical accuracy and efficiency is notably lacking. The present work offers a comprehensive comparative study, employing a scalable case study in computational mechanics focused on the inference of spatially varying material parameters, that sheds light on the impact of methodological choices for surrogate modelling and sampling. We show that a priori training of the surrogate model introduces large errors in the posterior estimation even in low to moderate dimensions. We introduce a simple active learning strategy based on the path of the MCMC algorithm that is superior to all a priori trained models, and determine its training data requirements. We demonstrate that the choice of the MCMC algorithm has only a small influence on the amount of training data but no significant influence on the accuracy of the resulting surrogate model. Further, we show that the accuracy of the posterior estimation largely depends on the surrogate model, but not even a tailored surrogate guarantees convergence of the MCMC.Finally, we identify the forward model as the bottleneck in the inference process, not the MCMC algorithm. While related works focus on employing advanced MCMC algorithms, we demonstrate that the training data requirements render the surrogate modelling approach infeasible before the benefits of these gradient-based MCMC algorithms on cheap models can be reaped.

Bayesian reasoning in linear mixed-effects models (LMMs) is challenging and often requires advanced sampling techniques like Markov chain Monte Carlo (MCMC). A common approach is to write the model in a probabilistic programming language and then sample via Hamiltonian Monte Carlo (HMC). However, there are many ways a user can transform a model that make inference more or less efficient. In particular, marginalizing some variables can greatly improve inference but is difficult for users to do manually. We develop an algorithm to easily marginalize random effects in LMMs. A naive approach introduces cubic time operations within an inference algorithm like HMC, but we reduce the running time to linear using fast linear algebra techniques. We show that marginalization is always beneficial when applicable and highlight improvements in various models, especially ones from cognitive sciences.

Learning dynamical models from data is not only fundamental but also holds great promise for advancing principle discovery, time-series prediction, and controller design. Among various approaches, Gaussian Process State-Space Models (GPSSMs) have recently gained significant attention due to their combination of flexibility and interpretability. However, for online learning, the field lacks an efficient method suitable for scenarios where prior information regarding data distribution and model function is limited. To address this issue, this paper proposes a recursive GPSSM method with adaptive capabilities for both operating domains and Gaussian process (GP) hyperparameters. Specifically, we first utilize first-order linearization to derive a Bayesian update equation for the joint distribution between the system state and the GP model, enabling closed-form and domain-independent learning. Second, an online selection algorithm for inducing points is developed based on informative criteria to achieve lightweight learning. Third, to support online hyperparameter optimization, we recover historical measurement information from the current filtering distribution. Comprehensive evaluations on both synthetic and real-world datasets demonstrate the superior accuracy, computational efficiency, and adaptability of our method compared to state-of-the-art online GPSSM techniques.

Test-time adaptation (TTA) is an effective approach to mitigate performance degradation of trained models when encountering input distribution shifts at test time. However, existing TTA methods often suffer significant performance drops when facing additional class distribution shifts. We first analyze TTA methods under label distribution shifts and identify the presence of class-wise confusion patterns commonly observed across different covariate shifts. Based on this observation, we introduce label Distribution shift-Aware prediction Refinement for Test-time adaptation (DART), a novel TTA method that refines the predictions by focusing on class-wise confusion patterns. DART trains a prediction refinement module during an intermediate time by exposing it to several batches with diverse class distributions using the training dataset. This module is then used during test time to detect and correct class distribution shifts, significantly improving pseudo-label accuracy for test data. Our method exhibits 5-18% gains in accuracy under label distribution shifts on CIFAR-10C, without any performance degradation when there is no label distribution shift. Extensive experiments on CIFAR, PACS, OfficeHome, and ImageNet benchmarks demonstrate DART's ability to correct inaccurate predictions caused by test-time distribution shifts. This improvement leads to enhanced performance in existing TTA methods, making DART a valuable plug-in tool.

We propose ODTE, a new ensemble that uses oblique decision trees as base classifiers. Additionally, we introduce STree, the base algorithm for growing oblique decision trees, which leverages support vector machines to define hyperplanes within the decision nodes. We embed a multiclass strategy -- one-vs-one or one-vs-rest -- at the decision nodes, allowing the model to directly handle non-binary classification tasks without the need to cluster instances into two groups, as is common in other approaches from the literature. In each decision node, only the best-performing model SVM -- the one that minimizes an impurity measure for the n-ary classification -- is retained, even if the learned SVM addresses a binary classification subtask. An extensive experimental study involving 49 datasets and various state-of-the-art algorithms for oblique decision tree ensembles has been conducted. Our results show that ODTE ranks consistently above its competitors, achieving significant performance gains when hyperparameters are carefully tuned. Moreover, the oblique decision trees learned through STree are more compact than those produced by other algorithms evaluated in our experiments.

This paper presents a novel approach for nonlinear assimilation called score-based sequential Langevin sampling (SSLS) within a recursive Bayesian framework. SSLS decomposes the assimilation process into a sequence of prediction and update steps, utilizing dynamic models for prediction and observation data for updating via score-based Langevin Monte Carlo. An annealing strategy is incorporated to enhance convergence and facilitate multi-modal sampling. The convergence of SSLS in TV-distance is analyzed under certain conditions, providing insights into error behavior related to hyper-parameters. Numerical examples demonstrate its outstanding performance in high-dimensional and nonlinear scenarios, as well as in situations with sparse or partial measurements. Furthermore, SSLS effectively quantifies the uncertainty associated with the estimated states, highlighting its potential for error calibration.