[HTML][HTML] Protein–protein interaction prediction with deep learning: A comprehensive review

F Soleymani, E Paquet, H Viktor, W Michalowski… - Computational and …, 2022 - Elsevier
Most proteins perform their biological function by interacting with themselves or other
molecules. Thus, one may obtain biological insights into protein functions, disease …

Knowledge graph-enhanced molecular contrastive learning with functional prompt

Y Fang, Q Zhang, N Zhang, Z Chen, X Zhuang… - Nature Machine …, 2023 - nature.com
Deep learning models can accurately predict molecular properties and help making the
search for potential drug candidates faster and more efficient. Many existing methods are …

Application of message passing neural networks for molecular property prediction

M Tang, B Li, H Chen - Current Opinion in Structural Biology, 2023 - Elsevier
Accurate molecular property prediction, as one of the classical cheminformatics topics, plays
a prominent role in the fields of computer-aided drug design. For instance, property …

Structure-aware interactive graph neural networks for the prediction of protein-ligand binding affinity

S Li, J Zhou, T Xu, L Huang, F Wang, H **ong… - Proceedings of the 27th …, 2021 - dl.acm.org
Drug discovery often relies on the successful prediction of protein-ligand binding affinity.
Recent advances have shown great promise in applying graph neural networks (GNNs) for …

One transformer can understand both 2d & 3d molecular data

S Luo, T Chen, Y Xu, S Zheng, TY Liu… - The Eleventh …, 2022 - openreview.net
Unlike vision and language data which usually has a unique format, molecules can naturally
be characterized using different chemical formulations. One can view a molecule as a 2D …

Geomgcl: Geometric graph contrastive learning for molecular property prediction

S Li, J Zhou, T Xu, D Dou, H **ong - … of the AAAI conference on artificial …, 2022 - ojs.aaai.org
Recently many efforts have been devoted to applying graph neural networks (GNNs) to
molecular property prediction which is a fundamental task for computational drug and …

Molecular contrastive learning with chemical element knowledge graph

Y Fang, Q Zhang, H Yang, X Zhuang, S Deng… - Proceedings of the …, 2022 - ojs.aaai.org
Molecular representation learning contributes to multiple downstream tasks such as
molecular property prediction and drug design. To properly represent molecules, graph …

DSTG: deconvoluting spatial transcriptomics data through graph-based artificial intelligence

Q Song, J Su - Briefings in bioinformatics, 2021 - academic.oup.com
Recent development of spatial transcriptomics (ST) is capable of associating spatial
information at different spots in the tissue section with RNA abundance of cells within each …

Understanding the limitations of deep models for molecular property prediction: Insights and solutions

J **a, L Zhang, X Zhu, Y Liu, Z Gao… - Advances in …, 2023 - proceedings.neurips.cc
Abstract Molecular Property Prediction (MPP) is a crucial task in the AI-driven Drug
Discovery (AIDD) pipeline, which has recently gained considerable attention thanks to …

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 …