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 …

Retrosynthesis prediction with an iterative string editing model

Y Han, X Xu, CY Hsieh, K Ding, H Xu, R Xu… - Nature …, 2024 - nature.com
Retrosynthesis is a crucial task in drug discovery and organic synthesis, where artificial
intelligence (AI) is increasingly employed to expedite the process. However, existing …

Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review

G Gricourt, P Meyer, T Duigou, JL Faulon - ACS Synthetic Biology, 2024 - ACS Publications
Retrosynthesis aims to efficiently plan the synthesis of desirable chemicals by strategically
breaking down molecules into readily available building block compounds. Having a long …

Artificial intelligence in drug development

K Zhang, X Yang, Y Wang, Y Yu, N Huang, G Li, X Li… - Nature Medicine, 2025 - nature.com
Drug development is a complex and time-consuming endeavor that traditionally relies on the
experience of drug developers and trial-and-error experimentation. The advent of artificial …

Challenging complexity with simplicity: Rethinking the role of single-step models in computer-aided synthesis planning

J Li, K Lin, J Pei, L Lai - Journal of Chemical Information and …, 2024 - ACS Publications
Computer-assisted synthesis planning has become increasingly important in drug discovery.
While deep-learning models have shown remarkable progress in achieving high accuracies …

MotifPiece: A Data-Driven Approach for Effective Motif Extraction and Molecular Representation Learning

Z Yu, H Gao - arXiv preprint arXiv:2312.15387, 2023 - arxiv.org
Motif extraction is an important task in motif based molecular representation learning.
Previously, machine learning approaches employing either rule-based or string-based …

Retro-BLEU: quantifying chemical plausibility of retrosynthesis routes through reaction template sequence analysis

J Li, L Fang, JG Lou - Digital Discovery, 2024 - pubs.rsc.org
Computer-assisted methods have emerged as valuable tools for retrosynthesis analysis.
However, quantifying the plausibility of generated retrosynthesis routes remains a …

Single-step retrosynthesis prediction via multitask graph representation learning

PC Zhao, XX Wei, Q Wang, QH Wang, JN Li… - Nature …, 2025 - nature.com
Inferring appropriate synthesis reaction (ie, retrosynthesis) routes for newly designed
molecules is vital. Recently, computational methods have produced promising single-step …

Applications of Transformers in Computational Chemistry: Recent Progress and Prospects

R Wang, Y Ji, Y Li, ST Lee - The Journal of Physical Chemistry …, 2024 - ACS Publications
The powerful data processing and pattern recognition capabilities of machine learning (ML)
technology have provided technical support for the innovation in computational chemistry …

Repurposing quantum chemical descriptor datasets for on-the-fly generation of informative reaction representations: application to hydrogen atom transfer reactions

JE Alfonso-Ramos, RM Neeser, T Stuyver - Digital Discovery, 2024 - pubs.rsc.org
In this work, we explore how existing datasets of quantum chemical properties can be
repurposed to build data-efficient downstream machine learning models, with a particular …