Exploring chemical reaction space with machine learning models: Representation and feature perspective

Y Ding, B Qiang, Q Chen, Y Liu… - Journal of Chemical …, 2024 - ACS Publications
Chemical reactions serve as foundational building blocks for organic chemistry and drug
design. In the era of large AI models, data-driven approaches have emerged to innovate the …

Pre-training with fractional denoising to enhance molecular property prediction

Y Ni, S Feng, X Hong, Y Sun, WY Ma, ZM Ma… - Nature Machine …, 2024 - nature.com
Deep learning methods have been considered promising for accelerating molecular
screening in drug discovery and material design. Due to the limited availability of labelled …

Impact of Domain Knowledge and Multi-Modality on Intelligent Molecular Property Prediction: A Systematic Survey

T Kuang, P Liu, Z Ren - Big Data Mining and Analytics, 2024 - ieeexplore.ieee.org
The precise prediction of molecular properties is essential for advancements in drug
development, particularly in virtual screening and compound optimization. The recent …

A deep learning framework for predicting molecular property based on multi-type features fusion

M Ma, X Lei - Computers in Biology and Medicine, 2024 - Elsevier
Extracting expressive molecular features is essential for molecular property prediction.
Sequence-based representation is a common representation of molecules, which ignores …

Mmpolymer: A multimodal multitask pretraining framework for polymer property prediction

F Wang, W Guo, M Cheng, S Yuan, H Xu… - Proceedings of the 33rd …, 2024 - dl.acm.org
Polymers are high-molecular-weight compounds constructed by the covalent bonding of
numerous identical or similar monomers so that their 3D structures are complex yet exhibit …

Multi-modal representation learning for molecular property prediction: sequence, graph, geometry

Z Wang, T Jiang, J Wang, Q Xuan - arxiv preprint arxiv:2401.03369, 2024 - arxiv.org
Recent years have seen a rapid growth of machine learning in cheminformatics problems. In
order to tackle the problem of insufficient training data in reality, more and more researchers …

Non-homophilic graph pre-training and prompt learning

X Yu, J Zhang, Y Fang, R Jiang - arxiv preprint arxiv:2408.12594, 2024 - arxiv.org
Graphs are ubiquitous for modeling complex relationships between objects across various
fields. Graph neural networks (GNNs) have become a mainstream technique for graph …

Unimap: universal smiles-graph representation learning

S Feng, L Yang, Y Huang, Y Ni, W Ma, Y Lan - arxiv preprint arxiv …, 2023 - arxiv.org
Molecular representation learning is fundamental for many drug related applications. Most
existing molecular pre-training models are limited in using single molecular modality, either …

MOAT: Graph prompting for 3D molecular graphs

Q Long, Y Yan, W Cui, W Ju, Z Zhu, Y Zhou… - Proceedings of the 33rd …, 2024 - dl.acm.org
Molecular property prediction stands as a cornerstone task in AI-driven drug design and
discovery, wherein the atoms within a molecule serve as nodes, collectively forming a graph …

A survey on multi-view fusion for predicting links in biomedical bipartite networks: Methods and applications

Y Qian, Y Wang, J Liu, Q Zou, Y Ding, X Guo, W Ding - Information Fusion, 2025 - Elsevier
Biomedical research increasingly relies on the analysis of complex interactions between
biological entities, such as genes, proteins, and drugs. Although advancements in …