Related papers: Towards Precision Protein-Ligand Affinity Predicti…

Large Artificial Neural Network (ANN) models have demonstrated success in various domains, including general text and image generation, drug discovery, and protein-RNA (ribonucleic acid) binding tasks. However, these models typically demand…

Molecular docking is a cornerstone of drug discovery to unveil the mechanism of ligand-receptor interactions. With the recent development of deep learning in the field of artificial intelligence, innovative methods were developed for…

Recent advances in image-based saliency prediction are approaching gold standard performance levels on existing benchmarks. Despite this success, we show that predicting fixations across multiple saliency datasets remains challenging due to…

Accurate prediction of protein stability changes upon single-site variations (DDG) is important for protein design, as well as our understanding of the mechanism of genetic diseases. The performance of high-throughput computational methods…

Computational approaches to drug discovery can reduce the time and cost associated with experimental assays and enable the screening of novel chemotypes. Structure-based drug design methods rely on scoring functions to rank and predict…

The increasing volume of drug combinations in modern therapeutic regimens needs reliable methods for predicting drug-drug interactions (DDIs). While Large Language Models (LLMs) have revolutionized various domains, their potential in…

Predicting the effect of mutations in proteins is one of the most critical challenges in protein engineering; by knowing the effect a substitution of one (or several) residues in the protein's sequence has on its overall properties, could…

Data-driven science is an emerging paradigm where scientific discoveries depend on the execution of computational AI models against rich, discipline-specific datasets. With modern machine learning frameworks, anyone can develop and execute…

In 2023, the U.S. Food and Drug Administration issued guidance for adjustment of covariates in randomized clinical trials, emphasizing its role in enhancing precision and power through prognostic baseline variables. Despite its potential,…

Artificial intelligence (AI) is increasingly used in every stage of drug development. One challenge facing drug discovery AI is that drug pharmacokinetic (PK) datasets are often collected independently from each other, often with limited…

We introduce the Local Intersectional Visual Spaces (LIVS) dataset, a benchmark for multi-criteria alignment, developed through a two-year participatory process with 30 community organizations to support the pluralistic alignment of…

Accurately predicting the three-dimensional structures of protein-ligand complexes remains a fundamental challenge in computational drug discovery that limits the pace and success of therapeutic design. Deep learning methods have recently…

The rapid evolution of molecular dynamics (MD) methods, including machine-learned dynamics, has outpaced the development of standardized tools for method validation. Objective comparison between simulation approaches is often hindered by…

Is it feasible to create an analysis paradigm that can analyze and then accurately and quickly predict known drugs from experimental data? PharML.Bind is a machine learning toolkit which is able to accomplish this feat. Utilizing deep…

Summary: Protein quality assessment is a long-standing problem in bioinformatics. For more than a decade we have developed state-of-art predictors by carefully selecting and optimising inputs to a machine learning method. The correlation…

There is widespread optimism that frontier Large Language Models (LLMs) and LLM-augmented systems have the potential to rapidly accelerate scientific discovery across disciplines. Today, many benchmarks exist to measure LLM knowledge and…

Deep learning promises to dramatically improve scoring functions for molecular docking, leading to substantial advances in binding pose prediction and virtual screening. To train scoring functions-and to perform molecular docking-one must…

The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor…

In most practical applications such as recommendation systems, display advertising, and so forth, the collected data often contains missing values and those missing values are generally missing-not-at-random, which deteriorates the…

Machine learning systems deployed in the wild are often trained on a source distribution but deployed on a different target distribution. Unlabeled data can be a powerful point of leverage for mitigating these distribution shifts, as it is…