Scientific discovery in the age of artificial intelligence

H Wang, T Fu, Y Du, W Gao, K Huang, Z Liu… - Nature, 2023 - nature.com
Artificial intelligence (AI) is being increasingly integrated into scientific discovery to augment
and accelerate research, helping scientists to generate hypotheses, design experiments …

Machine learning for synthetic data generation: a review

Y Lu, M Shen, H Wang, X Wang, C van Rechem… - arXiv preprint arXiv …, 2023 - arxiv.org
Machine learning heavily relies on data, but real-world applications often encounter various
data-related issues. These include data of poor quality, insufficient data points leading to …

Sample efficiency matters: a benchmark for practical molecular optimization

W Gao, T Fu, J Sun, C Coley - Advances in neural …, 2022 - proceedings.neurips.cc
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 …

Multimodal learning with graphs

Y Ektefaie, G Dasoulas, A Noori, M Farhat… - Nature Machine …, 2023 - nature.com
Artificial intelligence for graphs has achieved remarkable success in modelling complex
systems, ranging from dynamic networks in biology to interacting particle systems in physics …

Regression transformer enables concurrent sequence regression and generation for molecular language modelling

J Born, M Manica - Nature Machine Intelligence, 2023 - nature.com
Despite tremendous progress of generative models in the natural sciences, their
controllability remains challenging. One fundamentally missing aspect of molecular or …

A survey on deep graph generation: Methods and applications

Y Zhu, Y Du, Y Wang, Y Xu, J Zhang… - Learning on Graphs …, 2022 - proceedings.mlr.press
Graphs are ubiquitous in encoding relational information of real-world objects in many
domains. Graph generation, whose purpose is to generate new graphs from a distribution …

Molgensurvey: A systematic survey in machine learning models for molecule design

Y Du, T Fu, J Sun, S Liu - arXiv preprint arXiv:2203.14500, 2022 - arxiv.org
Molecule design is a fundamental problem in molecular science and has critical applications
in a variety of areas, such as drug discovery, material science, etc. However, due to the large …

Reinforced genetic algorithm for structure-based drug design

T Fu, W Gao, C Coley, J Sun - Advances in Neural …, 2022 - proceedings.neurips.cc
Abstract Structure-based drug design (SBDD) aims to discover drug candidates by finding
molecules (ligands) that bind tightly to a disease-related protein (targets), which is the …

State-specific protein–ligand complex structure prediction with a multiscale deep generative model

Z Qiao, W Nie, A Vahdat, TF Miller III… - Nature Machine …, 2024 - nature.com
The binding complexes formed by proteins and small molecule ligands are ubiquitous and
critical to life. Despite recent advancements in protein structure prediction, existing …

A perspective on explanations of molecular prediction models

GP Wellawatte, HA Gandhi, A Seshadri… - Journal of Chemical …, 2023 - ACS Publications
Chemists can be skeptical in using deep learning (DL) in decision making, due to the lack of
interpretability in “black-box” models. Explainable artificial intelligence (XAI) is a branch of …