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 …

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 …

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 …

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 …

Learning subpocket prototypes for generalizable structure-based drug design

Z Zhang, Q Liu - International Conference on Machine …, 2023 - proceedings.mlr.press
Generating molecules with high binding affinities to target proteins (aka structure-based
drug design) is a fundamental and challenging task in drug discovery. Recently, deep …

Graph-based molecular representation learning

Z Guo, K Guo, B Nan, Y Tian, RG Iyer, Y Ma… - arXiv preprint arXiv …, 2022 - arxiv.org
Molecular representation learning (MRL) is a key step to build the connection between
machine learning and chemical science. In particular, it encodes molecules as numerical …

Context-enriched molecule representations improve few-shot drug discovery

J Schimunek, P Seidl, L Friedrich, D Kuhn… - arXiv preprint arXiv …, 2023 - arxiv.org
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 …

Few-shot learning on graphs

C Zhang, K Ding, J Li, X Zhang, Y Ye… - arXiv preprint arXiv …, 2022 - arxiv.org
Graph representation learning has attracted tremendous attention due to its remarkable
performance in many real-world applications. However, prevailing supervised graph …

Meta-learning adaptive deep kernel gaussian processes for molecular property prediction

W Chen, A Tripp, JM Hernández-Lobato - arXiv preprint arXiv:2205.02708, 2022 - arxiv.org
We propose Adaptive Deep Kernel Fitting with Implicit Function Theorem (ADKF-IFT), a
novel framework for learning deep kernel Gaussian processes (GPs) by interpolating …