Related papers: Preferential Multi-Objective Bayesian Optimization…

Multi fidelity Bayesian optimization (MFBO) leverages experimental and or computational data of varying quality and resource cost to optimize towards desired maxima cost effectively. This approach is particularly attractive for chemical…

High throughput screening of compounds (chemicals) is an essential part of drug discovery [7], involving thousands to millions of compounds, with the purpose of identifying candidate hits. Most statistical tools, including the industry…

Predicting a ligand's bound pose to a target protein is a key component of early-stage computational drug discovery. Recent developments in machine learning methods have focused on improving pose quality at the cost of model runtime. For…

Drug-drug interactions (DDIs) are a leading cause of preventable adverse events, often complicating treatment and increasing healthcare costs. At the same time, knowing which drugs do not interact is equally important, as such knowledge…

Feature selection is a combinatorial optimization problem that is NP-hard. Conventional approaches often employ heuristic or greedy strategies, which are prone to premature convergence and may fail to capture subtle yet informative…

Rapid discovery and synthesis of new materials requires intelligent data acquisition strategies to navigate large design spaces. A popular strategy is Bayesian optimization, which aims to find candidates that maximize material properties;…

To optimize efficiently over discrete data and with only few available target observations is a challenge in Bayesian optimization. We propose a continuous relaxation of the objective function and show that inference and optimization can be…

We propose HydraScreen, a deep-learning approach that aims to provide a framework for more robust machine-learning-accelerated drug discovery. HydraScreen utilizes a state-of-the-art 3D convolutional neural network, designed for the…

We consider Bayesian optimization of expensive-to-evaluate experiments that generate vector-valued outcomes over which a decision-maker (DM) has preferences. These preferences are encoded by a utility function that is not known in closed…

Active search is a learning paradigm for actively identifying as many members of a given class as possible. A critical target scenario is high-throughput screening for scientific discovery, such as drug or materials discovery. In this…

The discovery of peptides having high biological activity is very challenging mainly because there is an enormous diversity of compounds and only a minority have the desired properties. To lower cost and reduce the time to obtain promising…

Bayesian optimization has been successfully applied throughout Chemical Engineering for the optimization of functions that are expensive-to-evaluate, or where gradients are not easily obtainable. However, domain experts often possess…

We devise an approach for targeted molecular design, a problem of interest in computational drug discovery: given a target protein site, we wish to generate a chemical with both high binding affinity to the target and satisfactory…

In the drug repurposing approach, the chemically diverse and potentially safe molecules can be explored as therapeutic potential out of those originally targeted indications. However, the intellectual property rights, and competitive…

Predicting the bioactivity of a ligand is one of the hardest and most important challenges in computer-aided drug discovery. Despite years of data collection and curation efforts by research organizations worldwide, bioactivity data remains…

Prediction of protein-ligand interactions (PLI) plays a crucial role in drug discovery as it guides the identification and optimization of molecules that effectively bind to target proteins. Despite remarkable advances in deep…

The field of machine learning for drug discovery is witnessing an explosion of novel methods. These methods are often benchmarked on simple physicochemical properties such as solubility or general druglikeness, which can be readily…

We present a novel preference learning framework to capture participant preferences efficiently within limited interaction rounds. It involves three main contributions. First, we develop a variational Bayesian approach to infer the…

Virtual screening (VS) is an essential task in drug discovery, focusing on the identification of small-molecule ligands that bind to specific protein pockets. Existing deep learning methods, from early regression models to recent…

Drug discovery is a complex process that involves sequentially screening and examining a vast array of molecules to identify those with the target properties. This process, also referred to as sequential experimentation, faces challenges…