Related papers: Lo-Hi: Practical ML Drug Discovery Benchmark

Several recently devised machine learning (ML) algorithms have shown improved accuracy for various predictive problems. Model searches, which explore to find an optimal ML algorithm and hyperparameter values for the target problem, play a…

While deep learning has revolutionized computer-aided drug discovery, the AI community has predominantly focused on model innovation and placed less emphasis on establishing best benchmarking practices. We posit that without a sound model…

Generation of drug-like molecules with high binding affinity to target proteins remains a difficult and resource-intensive task in drug discovery. Existing approaches primarily employ reinforcement learning, Markov sampling, or deep…

De novo molecule generation can suffer from data inefficiency; requiring large amounts of training data or many sampled data points to conduct objective optimization. The latter is a particular disadvantage when combining deep generative…

As machine learning (ML) is more tightly woven into society, it is imperative that we better characterize ML's strengths and limitations if we are to employ it responsibly. Existing benchmark environments for ML, such as board and video…

Discovering new medicines is the hallmark of human endeavor to live a better and longer life. Yet the pace of discovery has slowed down as we need to venture into more wildly unexplored biomedical space to find one that matches today's high…

Predicting drug properties is key in drug discovery to enable de-risking of assets before expensive clinical trials, and to find highly active compounds faster. Interest from the Machine Learning community has led to the release of a…

Molecular optimization is a fundamental goal in the chemical sciences and is of central interest to drug and material design. In recent years, significant progress has been made in solving challenging problems across various aspects of…

Due to their excellent drug-like and pharmacokinetic properties, small molecule drugs are widely used to treat various diseases, making them a critical component of drug discovery. In recent years, with the rapid development of deep…

Drug-target interaction (DTI) prediction plays a very important role in drug development and drug discovery. Biochemical experiments or \textit{in vitro} methods are very expensive, laborious and time-consuming. Therefore, \textit{in…

With the development of computer-assisted techniques, research communities including biochemistry and deep learning have been devoted into the drug discovery field for over a decade. Various applications of deep learning have drawn great…

Traditional drug discovery is a long, expensive, and complex process. Advances in Artificial Intelligence (AI) and Machine Learning (ML) are beginning to change this narrative. Here, we provide a comprehensive overview of different AI and…

Publicly available collections of drug-like molecules have grown to comprise 10s of billions of possibilities in recent history due to advances in chemical synthesis. Traditional methods for identifying "hit" molecules from a large…

Molecular machine learning has been maturing rapidly over the last few years. Improved methods and the presence of larger datasets have enabled machine learning algorithms to make increasingly accurate predictions about molecular…

In recent years, machine learning has been proposed as a promising strategy to build accurate scoring functions for computational docking finalized to numerically empowered drug discovery. However, the latest studies have suggested that…

A central task in computational drug discovery is to construct models from known active molecules to find further promising molecules for subsequent screening. However, typically only very few active molecules are known. Therefore, few-shot…

Development of new medications is a very lengthy and costly process. Finding novel indications for existing drugs, or drug repositioning, can serve as a useful strategy to shorten the development cycle. In this study, we present an approach…

Efficient exploration of the chemical space to search the candidate drugs that satisfy various constraints is a fundamental task of drug discovery. Advanced deep generative methods attempt to optimize the molecules in the compact latent…

Drug discovery is crucial for identifying candidate drugs for various diseases.However, its low success rate often results in a scarcity of annotations, posing a few-shot learning problem. Existing methods primarily focus on single-scale…

Large Language Models (LLM) are increasingly used for software development, yet existing benchmarks for LLM-based coding assistance do not reflect the constraints of High Energy Physics (HEP) and High Performance Computing (HPC) software.…