Graph representation learning in biomedicine and healthcare

MM Li, K Huang, M Zitnik - Nature Biomedical Engineering, 2022 - nature.com
Networks—or graphs—are universal descriptors of systems of interacting elements. In
biomedicine and healthcare, they can represent, for example, molecular interactions …

A comprehensive survey on deep graph representation learning

W Ju, Z Fang, Y Gu, Z Liu, Q Long, Z Qiao, Y Qin… - Neural Networks, 2024 - Elsevier
Graph representation learning aims to effectively encode high-dimensional sparse graph-
structured data into low-dimensional dense vectors, which is a fundamental task that has …

Generative models for molecular discovery: Recent advances and challenges

C Bilodeau, W **, T Jaakkola… - Wiley …, 2022 - Wiley Online Library
Abstract Development of new products often relies on the discovery of novel molecules.
While conventional molecular design involves using human expertise to propose …

Artificial intelligence foundation for therapeutic science

K Huang, T Fu, W Gao, Y Zhao, Y Roohani… - Nature chemical …, 2022 - nature.com
Artificial intelligence (AI) is poised to transform therapeutic science. Therapeutics Data
Commons is an initiative to access and evaluate AI capability across therapeutic modalities …

Gflownet foundations

Y Bengio, S Lahlou, T Deleu, EJ Hu, M Tiwari… - The Journal of Machine …, 2023 - dl.acm.org
Generative Flow Networks (GFlowNets) have been introduced as a method to sample a
diverse set of candidates in an active learning context, with a training objective that makes …

Flow network based generative models for non-iterative diverse candidate generation

E Bengio, M Jain, M Korablyov… - Advances in Neural …, 2021 - proceedings.neurips.cc
This paper is about the problem of learning a stochastic policy for generating an object (like
a molecular graph) from a sequence of actions, such that the probability of generating an …

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 …

Therapeutics data commons: Machine learning datasets and tasks for drug discovery and development

K Huang, T Fu, W Gao, Y Zhao, Y Roohani… - arxiv preprint arxiv …, 2021 - arxiv.org
Therapeutics machine learning is an emerging field with incredible opportunities for
innovatiaon and impact. However, advancement in this field requires formulation of …

Trajectory balance: Improved credit assignment in gflownets

N Malkin, M Jain, E Bengio, C Sun… - Advances in Neural …, 2022 - proceedings.neurips.cc
Generative flow networks (GFlowNets) are a method for learning a stochastic policy for
generating compositional objects, such as graphs or strings, from a given unnormalized …

Cf-gnnexplainer: Counterfactual explanations for graph neural networks

A Lucic, MA Ter Hoeve, G Tolomei… - International …, 2022 - proceedings.mlr.press
Given the increasing promise of graph neural networks (GNNs) in real-world applications,
several methods have been developed for explaining their predictions. Existing methods for …