We introduce GAUCHE, a library for GAUssian processes in CHEmistry. Gaussian processes have long been a cornerstone of probabilistic machine learning, affording particular advantages for uncertainty quantification and Bayesian optimisation. Extending Gaussian processes to chemical representations, however, is nontrivial, necessitating kernels defined over structured inputs such as graphs, strings and bit vectors. By defining such kernels in GAUCHE, we seek to open the door to powerful tools for uncertainty quantification and Bayesian optimisation in chemistry. Motivated by scenarios frequently encountered in experimental chemistry, we showcase applications for GAUCHE in molecular discovery and chemical reaction optimisation. The codebase is made available at https://github.com/leojklarner/gauche

With the growth of neural network size, model compression has attracted increasing interest in recent research. As one of the most common techniques, pruning has been studied for a long time. By exploiting the structured sparsity of the neural network, existing methods can prune neurons instead of individual weights. However, in most existing pruning methods, surviving neurons are randomly connected in the neural network without any structure, and the non-zero weights within each neuron are also randomly distributed. Such irregular sparse structure can cause very high control overhead and irregular memory access for the hardware and even increase the neural network computational complexity. In this paper, we propose a three-layer hierarchical prior to promote a more regular sparse structure during pruning. The proposed three-layer hierarchical prior can achieve per-neuron weight-level structured sparsity and neuron-level structured sparsity. We derive an efficient Turbo-variational Bayesian inferencing (Turbo-VBI) algorithm to solve the resulting model compression problem with the proposed prior. The proposed Turbo-VBI algorithm has low complexity and can support more general priors than existing model compression algorithms. Simulation results show that our proposed algorithm can promote a more regular structure in the pruned neural networks while achieving even better performance in terms of compression rate and inferencing accuracy compared with the baselines.

While the Bayesian decision-theoretic framework offers an elegant solution to the problem of decision making under uncertainty, one question is how to appropriately select the prior distribution. One idea is to employ a worst-case prior. However, this is not as easy to specify in sequential decision making as in simple statistical estimation problems. This paper studies (sometimes approximate) minimax-Bayes solutions for various reinforcement learning problems to gain insights into the properties of the corresponding priors and policies. We find that while the worst-case prior depends on the setting, the corresponding minimax policies are more robust than those that assume a standard (i.e. uniform) prior.

In this big data era, it is hard for the current generation to find the right data from the huge amount of data contained within online platforms. In such a situation, there is a need for an information filtering system that might help them find the information they are looking for. In recent years, a research field has emerged known as recommender systems. Recommenders have become important as they have many real-life applications. This paper reviews the different techniques and developments of recommender systems in e-commerce, e-tourism, e-resources, e-government, e-learning, and e-library. By analyzing recent work on this topic, we will be able to provide a detailed overview of current developments and identify existing difficulties in recommendation systems. The final results give practitioners and researchers the necessary guidance and insights into the recommendation system and its application.

In this article, we propose a novel pessimism-based Bayesian learning method for optimal dynamic treatment regimes in the offline setting. When the coverage condition does not hold, which is common for offline data, the existing solutions would produce sub-optimal policies. The pessimism principle addresses this issue by discouraging recommendation of actions that are less explored conditioning on the state. However, nearly all pessimism-based methods rely on a key hyper-parameter that quantifies the degree of pessimism, and the performance of the methods can be highly sensitive to the choice of this parameter. We propose to integrate the pessimism principle with Thompson sampling and Bayesian machine learning for optimizing the degree of pessimism. We derive a credible set whose boundary uniformly lower bounds the optimal Q-function, and thus we do not require additional tuning of the degree of pessimism. We develop a general Bayesian learning method that works with a range of models, from Bayesian linear basis model to Bayesian neural network model. We develop the computational algorithm based on variational inference, which is highly efficient and scalable. We establish the theoretical guarantees of the proposed method, and show empirically that it outperforms the existing state-of-the-art solutions through both simulations and a real data example.

Over the past three decades, the logic programming paradigm has been successfully expanded to support probabilistic modeling, inference and learning. The resulting paradigm of probabilistic logic programming (PLP) and its programming languages owes much of its success to a declarative semantics, the so-called distribution semantics. However, the distribution semantics is limited to discrete random variables only. While PLP has been extended in various ways for supporting hybrid, that is, mixed discrete and continuous random variables, we are still lacking a declarative semantics for hybrid PLP that not only generalizes the distribution semantics and the modeling language but also the standard inference algorithm that is based on knowledge compilation. We contribute the hybrid distribution semantics together with the hybrid PLP language DC-ProbLog and its inference engine infinitesimal algebraic likelihood weighting (IALW). These have the original distribution semantics, standard PLP languages such as ProbLog, and standard inference engines for PLP based on knowledge compilation as special cases. Thus, we generalize the state-of-the-art of PLP towards hybrid PLP in three different aspects: semantics, language and inference. Furthermore, IALW is the first inference algorithm for hybrid probabilistic programming based on knowledge compilation.

In fields such as medicine and drug discovery, the ultimate goal of a classification is not to guess a class, but to choose the optimal course of action among a set of possible ones, usually not in one-one correspondence with the set of classes. This decision-theoretic problem requires sensible probabilities for the classes. Probabilities conditional on the features are computationally almost impossible to find in many important cases. The main idea of the present work is to calculate probabilities conditional not on the features, but on the trained classifier's output. This calculation is cheap, needs to be made only once, and provides an output-to-probability "transducer" that can be applied to all future outputs of the classifier. In conjunction with problem-dependent utilities, the probabilities of the transducer allow us to find the optimal choice among the classes or among a set of more general decisions, by means of expected-utility maximization. This idea is demonstrated in a simplified drug-discovery problem with a highly imbalanced dataset. The transducer and utility maximization together always lead to improved results, sometimes close to theoretical maximum, for all sets of problem-dependent utilities. The one-time-only calculation of the transducer also provides, automatically: (i) a quantification of the uncertainty about the transducer itself; (ii) the expected utility of the augmented algorithm (including its uncertainty), which can be used for algorithm selection; (iii) the possibility of using the algorithm in a "generative mode", useful if the training dataset is biased.

Bayesian model comparison (BMC) offers a principled probabilistic approach to study and rank competing models. In standard BMC, we construct a discrete probability distribution over the set of possible models, conditional on the observed data of interest. These posterior model probabilities (PMPs) are measures of uncertainty, but -- when derived from a finite number of observations -- are also uncertain themselves. In this paper, we conceptualize distinct levels of uncertainty which arise in BMC. We explore a fully probabilistic framework for quantifying meta-uncertainty, resulting in an applied method to enhance any BMC workflow. Drawing on both Bayesian and frequentist techniques, we represent the uncertainty over the uncertain PMPs via meta-models which combine simulated and observed data into a predictive distribution for PMPs on new data. We demonstrate the utility of the proposed method in the context of conjugate Bayesian regression, likelihood-based inference with Markov chain Monte Carlo, and simulation-based inference with neural networks.

We present the E-UC$^3$RL algorithm for regret minimization in Stochastic Contextual Markov Decision Processes (CMDPs). The algorithm operates under the minimal assumptions of realizable function class and access to \emph{offline} least squares and log loss regression oracles. Our algorithm is efficient (assuming efficient offline regression oracles) and enjoys a regret guarantee of $ \widetilde{O}(H^3 \sqrt{T |S| |A|d_{\mathrm{E}}(\mathcal{P}) \log (|\mathcal{F}| |\mathcal{P}|/ \delta) )}) , $ with $T$ being the number of episodes, $S$ the state space, $A$ the action space, $H$ the horizon, $\mathcal{P}$ and $\mathcal{F}$ are finite function classes used to approximate the context-dependent dynamics and rewards, respectively, and $d_{\mathrm{E}}(\mathcal{P})$ is the Eluder dimension of $\mathcal{P}$ w.r.t the Hellinger distance. To the best of our knowledge, our algorithm is the first efficient and rate-optimal regret minimization algorithm for CMDPs that operates under the general offline function approximation setting. In addition, we extend the Eluder dimension to general bounded metrics which may be of separate interest.

The parameters of a machine learning model are typically learned by minimizing a loss function on a set of training data. However, this can come with the risk of overtraining; in order for the model to generalize well, it is of great importance that we are able to find the optimal parameter for the model on the entire population -- not only on the given training sample. In this paper, we construct valid confidence sets for this optimal parameter of a machine learning model, which can be generated using only the training data without any knowledge of the population. We then show that studying the distribution of this confidence set allows us to assign a notion of confidence to arbitrary regions of the parameter space, and we demonstrate that this distribution can be well-approximated using bootstrapping techniques.