Probability estimation of tree topologies is one of the fundamental tasks in phylogenetic inference. The recently proposed subsplit Bayesian networks (SBNs) provide a powerful probabilistic graphical model for tree topology probability estimation by properly leveraging the hierarchical structure of phylogenetic trees. However, the expectation maximization (EM) method currently used for learning SBN parameters does not scale up to large data sets. In this paper, we introduce several computationally efficient methods for training SBNs and show that variance reduction could be the key for better performance. Furthermore, we also introduce the variance reduction technique to improve the optimization of SBN parameters for variational Bayesian phylogenetic inference (VBPI). Extensive synthetic and real data experiments demonstrate that our methods outperform previous baseline methods on the tasks of tree topology probability estimation as well as Bayesian phylogenetic inference using SBNs.

In recent years, neural networks (NNs) have become increasingly popular for surrogate modeling tasks in mechanics and materials modeling applications. While traditional NNs are deterministic functions that rely solely on data to learn the input--output mapping, casting NN training within a Bayesian framework allows to quantify uncertainties, in particular epistemic uncertainties that arise from lack of training data, and to integrate a priori knowledge via the Bayesian prior. However, the high dimensionality and non-physicality of the NN parameter space, and the complex relationship between parameters (NN weights) and predicted outputs, renders both prior design and posterior inference challenging. In this work we present a novel BNN training scheme based on anchored ensembling that can integrate a priori information available in the function space, from e.g. low-fidelity models. The anchoring scheme makes use of low-rank correlations between NN parameters, learnt from pre-training to realizations of the functional prior. We also perform a study to demonstrate how correlations between NN weights, which are often neglected in existing BNN implementations, is critical to appropriately transfer knowledge between the function-space and parameter-space priors. Performance of our novel BNN algorithm is first studied on a small 1D example to illustrate the algorithm's behavior in both interpolation and extrapolation settings. Then, a thorough assessment is performed on a multi--input--output materials surrogate modeling example, where we demonstrate the algorithm's capabilities both in terms of accuracy and quality of the uncertainty estimation, for both in-distribution and out-of-distribution data.

In the realm of drug discovery, DNA-encoded library (DEL) screening technology has emerged as an efficient method for identifying high-affinity compounds. However, DEL screening faces a significant challenge: noise arising from nonspecific interactions within complex biological systems. Neural networks trained on DEL libraries have been employed to extract compound features, aiming to denoise the data and uncover potential binders to the desired therapeutic target. Nevertheless, the inherent structure of DEL, constrained by the limited diversity of building blocks, impacts the performance of compound encoders. Moreover, existing methods only capture compound features at a single level, further limiting the effectiveness of the denoising strategy. To mitigate these issues, we propose a Multimodal Pretraining DEL-Fusion model (MPDF) that enhances encoder capabilities through pretraining and integrates compound features across various scales. We develop pretraining tasks applying contrastive objectives between different compound representations and their text descriptions, enhancing the compound encoders' ability to acquire generic features. Furthermore, we propose a novel DEL-fusion framework that amalgamates compound information at the atomic, submolecular, and molecular levels, as captured by various compound encoders. The synergy of these innovations equips MPDF with enriched, multi-scale features, enabling comprehensive downstream denoising. Evaluated on three DEL datasets, MPDF demonstrates superior performance in data processing and analysis for validation tasks. Notably, MPDF offers novel insights into identifying high-affinity molecules, paving the way for improved DEL utility in drug discovery.

Estimating spatially distributed information through the interpolation of scattered observation datasets often overlooks the critical role of domain knowledge in understanding spatial dependencies. Additionally, the features of these data sets are typically limited to the spatial coordinates of the scattered observation locations. In this paper, we propose a hybrid framework that integrates data-driven spatial dependency feature extraction with rule-assisted spatial dependency function mapping to augment domain knowledge. We demonstrate the superior performance of our framework in two comparative application scenarios, highlighting its ability to capture more localized spatial features in the reconstructed distribution fields. Furthermore, we underscore its potential to enhance nonlinear estimation capabilities through the application of transformed fuzzy rules and to quantify the inherent uncertainties associated with the observation data sets. Our framework introduces an innovative approach to spatial information estimation by synergistically combining observational data with rule-assisted domain knowledge.

Probabilistic relational models provide a well-established formalism to combine first-order logic and probabilistic models, thereby allowing to represent relationships between objects in a relational domain. At the same time, the field of artificial intelligence requires increasingly large amounts of relational training data for various machine learning tasks. Collecting real-world data, however, is often challenging due to privacy concerns, data protection regulations, high costs, and so on. To mitigate these challenges, the generation of synthetic data is a promising approach. In this paper, we solve the problem of generating synthetic relational data via probabilistic relational models. In particular, we propose a fully-fledged pipeline to go from relational database to probabilistic relational model, which can then be used to sample new synthetic relational data points from its underlying probability distribution. As part of our proposed pipeline, we introduce a learning algorithm to construct a probabilistic relational model from a given relational database.

Bayesian inference often faces a trade-off between computational speed and sampling accuracy. We propose an adaptive workflow that integrates rapid amortized inference with gold-standard MCMC techniques to achieve both speed and accuracy when performing inference on many observed datasets. Our approach uses principled diagnostics to guide the choice of inference method for each dataset, moving along the Pareto front from fast amortized sampling to slower but guaranteed-accurate MCMC when necessary. By reusing computations across steps, our workflow creates synergies between amortized and MCMC-based inference. We demonstrate the effectiveness of this integrated approach on a generalized extreme value task with 1000 observed data sets, showing 90x time efficiency gains while maintaining high posterior quality.

In the early stages of drug discovery, decisions regarding which experiments to pursue can be influenced by computational models. These decisions are critical due to the time-consuming and expensive nature of the experiments. Therefore, it is becoming essential to accurately quantify the uncertainty in machine learning predictions, such that resources can be used optimally and trust in the models improves. While computational methods for drug discovery often suffer from limited data and sparse experimental observations, additional information can exist in the form of censored labels that provide thresholds rather than precise values of observations. However, the standard approaches that quantify uncertainty in machine learning cannot fully utilize censored labels. In this work, we adapt ensemble-based, Bayesian, and Gaussian models with tools to learn from censored labels by using the Tobit model from survival analysis. Our results demonstrate that despite the partial information available in censored labels, they are essential to accurately and reliably model the real pharmaceutical setting.

Gaussian process (GP) models that combine both categorical and continuous input variables have found use in longitudinal data analysis of and computer experiments. However, standard inference for these models has the typical cubic scaling, and common scalable approximation schemes for GPs cannot be applied since the covariance function is non-continuous. In this work, we derive a basis function approximation scheme for mixed-domain covariance functions, which scales linearly with respect to the number of observations and total number of basis functions. The proposed approach is naturally applicable to also Bayesian GP regression with discrete observation models. We demonstrate the scalability of the approach and compare model reduction techniques for additive GP models in a longitudinal data context. We confirm that we can approximate the exact GP model accurately in a fraction of the runtime compared to fitting the corresponding exact model. In addition, we demonstrate a scalable model reduction workflow for obtaining smaller and more interpretable models when dealing with a large number of candidate predictors.

Missing data is commonly encountered in practice, and when the missingness is non-ignorable, effective remediation depends on knowledge of the missingness mechanism. Learning the underlying missingness mechanism from the data is not possible in general, so adversaries can exploit this fact by maliciously engineering non-ignorable missingness mechanisms. Such Adversarial Missingness (AM) attacks have only recently been motivated and introduced, and then successfully tailored to mislead causal structure learning algorithms into hiding specific cause-and-effect relationships. However, existing AM attacks assume the modeler (victim) uses full-information maximum likelihood methods to handle the missing data, and are of limited applicability when the modeler uses different remediation strategies. In this work we focus on associational learning in the context of AM attacks. We consider (i) complete case analysis, (ii) mean imputation, and (iii) regression-based imputation as alternative strategies used by the modeler. Instead of combinatorially searching for missing entries, we propose a novel probabilistic approximation by deriving the asymptotic forms of these methods used for handling the missing entries. We then formulate the learning of the adversarial missingness mechanism as a bi-level optimization problem. Experiments on generalized linear models show that AM attacks can be used to change the p-values of features from significant to insignificant in real datasets, such as the California-housing dataset, while using relatively moderate amounts of missingness (<20%). Additionally, we assess the robustness of our attacks against defense strategies based on data valuation.

Estimating collision probabilities between robots and environmental obstacles or other moving agents is crucial to ensure safety during path planning. This is an important building block of modern planning algorithms in many application scenarios such as autonomous driving, where noisy sensors perceive obstacles. While many approaches exist, they either provide too conservative estimates of the collision probabilities or are computationally intensive due to their sampling-based nature. To deal with these issues, we introduce Deep Collision Probability Fields, a neural-based approach for computing collision probabilities of arbitrary objects with arbitrary unimodal uncertainty distributions. Our approach relegates the computationally intensive estimation of collision probabilities via sampling at the training step, allowing for fast neural network inference of the constraints during planning. In extensive experiments, we show that Deep Collision Probability Fields can produce reasonably accurate collision probabilities (up to 10^{-3}) for planning and that our approach can be easily plugged into standard path planning approaches to plan safe paths on 2-D maps containing uncertain static and dynamic obstacles. Additional material, code, and videos are available at https://sites.google.com/view/ral-dcpf.