Machine learning methods for small data challenges in molecular science

B Dou, Z Zhu, E Merkurjev, L Ke, L Chen… - Chemical …, 2023 - ACS Publications
Small data are often used in scientific and engineering research due to the presence of
various constraints, such as time, cost, ethics, privacy, security, and technical limitations in …

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 …

What can large language models do in chemistry? a comprehensive benchmark on eight tasks

T Guo, B Nan, Z Liang, Z Guo… - Advances in …, 2023 - proceedings.neurips.cc
Abstract Large Language Models (LLMs) with strong abilities in natural language
processing tasks have emerged and have been applied in various kinds of areas such as …

Deep learning methods for molecular representation and property prediction

Z Li, M Jiang, S Wang, S Zhang - Drug Discovery Today, 2022 - Elsevier
Highlights•The deep learning method could effectively represent the molecular structure and
predict molecular property through diversified models.•One, two, and three-dimensional …

Artificial intelligence in drug toxicity prediction: recent advances, challenges, and future perspectives

TTV Tran, A Surya Wibowo, H Tayara… - Journal of chemical …, 2023 - ACS Publications
Toxicity prediction is a critical step in the drug discovery process that helps identify and
prioritize compounds with the greatest potential for safe and effective use in humans, while …

Enhancing activity prediction models in drug discovery with the ability to understand human language

P Seidl, A Vall, S Hochreiter… - … on Machine Learning, 2023 - proceedings.mlr.press
Activity and property prediction models are the central workhorses in drug discovery and
materials sciences, but currently, they have to be trained or fine-tuned for new tasks. Without …

Condensing graphs via one-step gradient matching

W Jin, X Tang, H Jiang, Z Li, D Zhang, J Tang… - Proceedings of the 28th …, 2022 - dl.acm.org
As training deep learning models on large dataset takes a lot of time and resources, it is
desired to construct a small synthetic dataset with which we can train deep learning models …

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 …

Few-shot molecular property prediction via hierarchically structured learning on relation graphs

W Ju, Z Liu, Y Qin, B Feng, C Wang, Z Guo, X Luo… - Neural Networks, 2023 - Elsevier
This paper studies few-shot molecular property prediction, which is a fundamental problem
in cheminformatics and drug discovery. More recently, graph neural network based model …

Graph rationalization with environment-based augmentations

G Liu, T Zhao, J Xu, T Luo, M Jiang - Proceedings of the 28th ACM …, 2022 - dl.acm.org
Rationale is defined as a subset of input features that best explains or supports the
prediction by machine learning models. Rationale identification has improved the …