In drug discovery, aqueous solubility is an important pharmacokinetic property which affects absorption and assay availability of drug. Thus, in silico prediction of solubility has been studied for its utility in virtual screening and lead optimization. Recently, machine learning (ML) methods using experimental data has been popular because physics-based methods like quantum mechanics and molecular dynamics are not suitable for high-throughput tasks due to its computational costs. However, ML method can exhibit over-fitting problem in a data-deficient condition, and this is the case for most chemical property datasets. In addition, ML methods are regarded as a black box function in that it is difficult to interpret contribution of hidden features to outputs, hindering analysis and modification of structure-activity relationship. To deal with mentioned issues, we developed Bayesian graph neural networks (GNNs) with the self-attention readout layer. Unlike most GNNs using self-attention in node updates, self-attention applied at readout layer enabled a model to improve prediction performance as well as to identify atom-wise importance, which can help lead optimization as exemplified for three FDA-approved drugs. Also, Bayesian inference enables us to separate more or less accurate results according to uncertainty in solubility prediction task We expect that our accurate, reliable and interpretable model can be used for more careful decision-making and various applications in the development of drugs.

Driven by the critical needs of biomanufacturing 4.0, we introduce a probabilistic knowledge graph hybrid model characterizing the risk- and science-based understanding of bioprocess mechanisms. It can faithfully capture the important properties, including nonlinear reactions, partially observed state, and nonstationary dynamics. Given very limited real process observations, we derive a posterior distribution quantifying model estimation uncertainty. To avoid the evaluation of intractable likelihoods, Approximate Bayesian Computation sampling with Sequential Monte Carlo (ABC-SMC) is utilized to approximate the posterior distribution. Under high stochastic and model uncertainties, it is computationally expensive to match output trajectories. Therefore, we create a linear Gaussian dynamic Bayesian network (LG-DBN) auxiliary likelihood-based ABC-SMC approach. Through matching the summary statistics driven through LG-DBN likelihood that can capture critical interactions and variations, the proposed algorithm can accelerate hybrid model inference, support process monitoring, and facilitate mechanism learning and robust control.

This paper is concerned with forecast error, particularly in relation to loss reserving. This is generally regarded as consisting of three components, namely parameter, process and model errors. The first two of these components, and their estimation, are well understood, but less so model error. Model error itself is considered in two parts: one part that is capable of estimation from past data (internal model error), and another part that is not (external model error). Attention is focused here on internal model error. Estimation of this error component is approached by means of Bayesian model averaging, using the Bayesian interpretation of the LASSO. This is used to generate a set of admissible models, each with its prior probability and the likelihood of observed data. A posterior on the model set, conditional on the data, results, and an estimate of model error (contained in a loss reserve) is obtained as the variance of the loss reserve according to this posterior. The population of models entering materially into the support of the posterior may turn out to be thinner than desired, and bootstrapping of the LASSO is used to gain bulk. This provides the bonus of an estimate of parameter error also. It turns out that the estimates of parameter and model errors are entangled, and dissociation of them is at least difficult, and possibly not even meaningful. These matters are discussed. The majority of the discussion applies to forecasting generally, but numerical illustration of the concepts is given in relation to insurance data and the problem of insurance loss reserving.

Probabilistic predictions from neural networks which account for predictive uncertainty during classification is crucial in many real-world and high-impact decision making settings. However, in practice most datasets are trained on non-probabilistic neural networks which by default do not capture this inherent uncertainty. This well-known problem has led to the development of post-hoc calibration procedures, such as Platt scaling (logistic), isotonic and beta calibration, which transforms the scores into well calibrated empirical probabilities. A plausible alternative to the calibration approach is to use Bayesian neural networks, which directly models a predictive distribution. Although they have been applied to images and text datasets, they have seen limited adoption in the tabular and small data regime. In this paper, we demonstrate that Bayesian neural networks yields competitive performance when compared to calibrated neural networks and conduct experiments across a wide array of datasets.

Over the course of the last several years, a significant amount of scholarly attention has been drawn to the issue of feature selection. At a high level, feature selection can be considered as a branch of reducing data dimensionality of which the two primary methods are feature learning and feature selection. The problem of feature learning involves the creation of new features from the original data. In contrast, the feature selection problem does not change the original representation of the data variables, so the physical meaning of each variable is preserved. To be more specific, the feature selection problem can be subdivided into two scenarios: supervised and unsupervised. Since we do not have target variables, selecting unsupervised features is more challenging. Typically, the unsupervised feature selection relies on matrix decomposition (Cheng et al., 2005; Liberty et al., 2007; Martinsson et al., 2011; Lu, 2022a), filter (Dash et al., 2002), and embeddings (Dy & Brodley, 2004; Hou et al., 2011). On the other hand, matrix decomposition algorithms such as QR decomposition, and singular value decomposition have been used extensively over the years to reveal hidden structures of data matrices in scientific and engineering areas such as collaborative filtering (Marlin, 2003; Lim & Teh, 2007; Mnih & Salakhutdinov, 2007; Lu, 2022c;a), recommendation systems (Lu, 2022c), clustering and classification (Li et al., 2009; Wang et al., 2013).

We rigorously prove that deep Gaussian process priors can outperform Gaussian process priors if the target function has a compositional structure. To this end, we study information-theoretic lower bounds for posterior contraction rates for Gaussian process regression in a continuous regression model. We show that if the true function is a generalized additive function, then the posterior based on any mean-zero Gaussian process can only recover the truth at a rate that is strictly slower than the minimax rate by a factor that is polynomially suboptimal in the sample size $n$.

Importance sampling (IS) is a powerful Monte Carlo (MC) methodology for approximating integrals, for instance in the context of Bayesian inference. In IS, the samples are simulated from the so-called proposal distribution, and the choice of this proposal is key for achieving a high performance. In adaptive IS (AIS) methods, a set of proposals is iteratively improved. AIS is a relevant and timely methodology although many limitations remain yet to be overcome, e.g., the curse of dimensionality in high-dimensional and multi-modal problems. Moreover, the Hamiltonian Monte Carlo (HMC) algorithm has become increasingly popular in machine learning and statistics. HMC has several appealing features such as its exploratory behavior, especially in high-dimensional targets, when other methods suffer. In this paper, we introduce the novel Hamiltonian adaptive importance sampling (HAIS) method. HAIS implements a two-step adaptive process with parallel HMC chains that cooperate at each iteration. The proposed HAIS efficiently adapts a population of proposals, extracting the advantages of HMC. HAIS can be understood as a particular instance of the generic layered AIS family with an additional resampling step. HAIS achieves a significant performance improvement in high-dimensional problems w.r.t. state-of-the-art algorithms. We discuss the statistical properties of HAIS and show its high performance in two challenging examples.

Surrogate models are used to alleviate the computational burden in engineering tasks, which require the repeated evaluation of computationally demanding models of physical systems, such as the efficient propagation of uncertainties. For models that show a strongly non-linear dependence on their input parameters, standard surrogate techniques, such as polynomial chaos expansion, are not sufficient to obtain an accurate representation of the original model response. Through applying a rational approximation instead, the approximation error can be efficiently reduced for models whose non-linearity is accurately described through a rational function. Specifically, our aim is to approximate complex-valued models. A common approach to obtain the coefficients in the surrogate is to minimize the sample-based error between model and surrogate in the least-square sense. In order to obtain an accurate representation of the original model and to avoid overfitting, the sample set has be two to three times the number of polynomial terms in the expansion. For models that require a high polynomial degree or are high-dimensional in terms of their input parameters, this number often exceeds the affordable computational cost. To overcome this issue, we apply a sparse Bayesian learning approach to the rational approximation. Through a specific prior distribution structure, sparsity is induced in the coefficients of the surrogate model. The denominator polynomial coefficients as well as the hyperparameters of the problem are determined through a type-II-maximum likelihood approach. We apply a quasi-Newton gradient-descent algorithm in order to find the optimal denominator coefficients and derive the required gradients through application of $\mathbb{CR}$-calculus.

Experimental data is costly to obtain, which makes it difficult to calibrate complex models. For many models an experimental design that produces the best calibration given a limited experimental budget is not obvious. This paper introduces a deep reinforcement learning (RL) algorithm for design of experiments that maximizes the information gain measured by Kullback-Leibler (KL) divergence obtained via the Kalman filter (KF). This combination enables experimental design for rapid online experiments where traditional methods are too costly. We formulate possible configurations of experiments as a decision tree and a Markov decision process (MDP), where a finite choice of actions is available at each incremental step. Once an action is taken, a variety of measurements are used to update the state of the experiment. This new data leads to a Bayesian update of the parameters by the KF, which is used to enhance the state representation. In contrast to the Nash-Sutcliffe efficiency (NSE) index, which requires additional sampling to test hypotheses for forward predictions, the KF can lower the cost of experiments by directly estimating the values of new data acquired through additional actions. In this work our applications focus on mechanical testing of materials. Numerical experiments with complex, history-dependent models are used to verify the implementation and benchmark the performance of the RL-designed experiments.

Ensemble weather forecasts based on multiple runs of numerical weather prediction models typically show systematic errors and require post-processing to obtain reliable forecasts. Accurately modeling multivariate dependencies is crucial in many practical applications, and various approaches to multivariate post-processing have been proposed where ensemble predictions are first post-processed separately in each margin and multivariate dependencies are then restored via copulas. These two-step methods share common key limitations, in particular the difficulty to include additional predictors in modeling the dependencies. We propose a novel multivariate post-processing method based on generative machine learning to address these challenges. In this new class of nonparametric data-driven distributional regression models, samples from the multivariate forecast distribution are directly obtained as output of a generative neural network. The generative model is trained by optimizing a proper scoring rule which measures the discrepancy between the generated and observed data, conditional on exogenous input variables. Our method does not require parametric assumptions on univariate distributions or multivariate dependencies and allows for incorporating arbitrary predictors. In two case studies on multivariate temperature and wind speed forecasting at weather stations over Germany, our generative model shows significant improvements over state-of-the-art methods and particularly improves the representation of spatial dependencies.