Related papers: Preferential Multi-Objective Bayesian Optimization…

The discovery of therapeutic molecules is fundamentally a multi-objective optimization problem. One formulation of the problem is to identify molecules that simultaneously exhibit strong binding affinity for a target protein, minimal…

Drug discovery seeks molecules (ligands) that bind strongly and selectively to a target protein. However, fewer than 5% of candidate ligands pass the bar for even the early stages of drug discovery. Furthermore, we want methods that work…

Accurately predicting protein-ligand binding free energies (BFEs) remains a central challenge in drug discovery, particularly because the most reliable methods, such as free energy perturbation (FEP), are computationally intensive and…

Drug discovery through virtual screening (VS) has become a popular strategy for identifying hits against protein targets. Alongside VS, molecular design further expands accessible chemical space. Together, these approaches have the…

We introduce a new ligand-based virtual screening (LBVS) framework that uses piecewise linear (PL) Morse theory to predict ligand binding potential. We model ligands as simplicial complexes via a pruned Delaunay triangulation, and catalogue…

Virtual Screening is an essential technique in the early phases of drug discovery, aimed at identifying promising drug candidates from vast molecular libraries. Recently, ligand-based virtual screening has garnered significant attention due…

The accurate screening of candidate drug ligands against target proteins through computational approaches is of prime interest to drug development efforts. Such virtual screening depends in part on methods to predict the binding affinity…

Preference-based many-objective optimization faces two obstacles: an expanding space of trade-offs and heterogeneous, context-dependent human value structures. Towards this, we propose a Bayesian framework that learns a small set of latent…

Efficient optimization of molecules with targeted properties remains a significant challenge due to the vast size and discrete nature of chemical compound space. Conventional machine-learning-based optimization approaches typically require…

Virtual screening (VS) is a critical step in computer-aided drug discovery, aiming to identify molecules that bind to a specific target receptor like protein. Traditional VS methods, such as docking, are often too time-consuming for…

The arc of drug discovery entails a multiparameter optimization problem spanning vast length scales. They key parameters range from solubility (angstroms) to protein-ligand binding (nanometers) to in vivo toxicity (meters). Through feature…

Identification of optimal dose combinations in early phase dose-finding trials is challenging, due to the trade-off between precisely estimating the many parameters required to flexibly model the possibly non-monotonic dose-response…

Bayesian optimization offers a sample-efficient framework for navigating the exploration-exploitation trade-off in the vast design space of biological sequences. Whereas it is possible to optimize the various properties of interest jointly…

Early phase, personalized dose-finding trials for combination therapies seek to identify patient-specific optimal biological dose (OBD) combinations, which are defined as safe dose combinations which maximize therapeutic benefit for a…

We study the problem of performing automated experiment design for drug screening through Bayesian inference and optimisation. In particular, we compare and contrast the behaviour of linear-Gaussian models and Gaussian processes, when used…

This study introduces BIRDSHOT, an integrated Bayesian materials discovery framework designed to efficiently explore complex compositional spaces while optimizing multiple material properties. We applied this framework to the CoCrFeNiVAl…

Molecular docking is a core tool in drug discovery for predicting ligand-target interactions. Despite the availability of diverse search-based and machine learning approaches, no single docking algorithm consistently dominates, as…

Bayesian optimization is an effective method for finding extrema of a black-box function. We propose a new type of Bayesian optimization for learning user preferences in high-dimensional spaces. The central assumption is that the underlying…

Precision cancer medicine aims to determine the optimal treatment for each patient. In-vitro cancer drug sensitivity screens combined with multi-omics characterization of the cancer cells have become an important tool to achieve this aim.…

Virtual screening, which identifies potential drugs from vast compound databases to bind with a particular protein pocket, is a critical step in AI-assisted drug discovery. Traditional docking methods are highly time-consuming, and can only…