Chemical Reaction Prediction

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17 papers4 papers in the last four weeks, up 33% on the four weeks before. 0.0% of all new papers.

Synthetic reaction data from transformation rules for graph-to-sequence pretraining in biodegradation pathway prediction
Oct 14, 2026Irsyaad Rijwan, Liam Brydon, Aidan Jared +1Chemical Reaction Prediction Synthetic Data Pretraining
School of Computer Science, University of Auckland, Auckland, New Zealand. · enviPath Limited, Auckland, New Zealand.
Elucidating the Space of Enzymatic Reaction: A Unified Benchmark and Pretrained Model
Oct 8, 2026Yutong Hu, Tianming Huang, Yanbo Zhao +6Sequence-to-Sequence Models Chemical Reaction Prediction
Shanghai Jiao Tong University · Shanghai Artificial Intelligence Laboratory · The University of Sydney
Neural Petri flows for chemical reactions
Oct 6, 2026Jose Eduardo Escrig Molina, Daniel ProbstAI-Assisted Scientific Research Chemical Reaction Prediction
Bioinformatics Group Bioprocess Engineering Group Wageningen Unversity Wageningen, the Netherlands
FREA: A Multi-Source Expert Benchmark for Reaction Feasibility Verification
Oct 5, 2026Botao Yu, Bo Zhou, Daniel Adu-Ampratwum +7LLM Evaluation AI-Assisted Scientific Research
Department of Computer Science and Engineering, The Ohio State University · Department of Pharmaceutical Sciences, University of Illinois Chicago · College of Pharmacy, The Ohio State University +3
Learning Transferable Reaction Mechanisms from Visual Chemical Knowledge
Sep 27, 2026Yujian Yuan, Jiaxin Xu, Xin Cai +4Visual Representation Learning Transfer Learning
The Hong Kong University of Science and Technology · The Chinese University of Hong Kong · University of Edinburgh
Mechanistic Reaction Prediction via Discrete Flow Matching on Graph-Structured Electron Occupation
Aug 27, 2026Nguyen Xuan-Vu, Octavian Susanu, Daniel Armstrong +1Chemical Reaction Prediction Discrete Flow Matching
École Polytechnique Fédérale de Lausanne (EPFL) · National Centre of Competence in Research (NCCR) Catalysis
Role-Aware Morgan Fingerprints for Reaction Yield Prediction
Aug 26, 2026Chinmay Mirji, Prashant Shekhar, Foram Madiyar +1Chemical Reaction Prediction Molecular Property Prediction
Aerospace Engineering Embry-Riddle Aeronautical University Daytona Beach, Florida · Mathematics Embry-Riddle Aeronautical University Daytona Beach, Florida · Chemistry Bethune Cookman University Daytona Beach, Florida
Training Chemical Plausibility-Aware Large Language Models for Single-Step Retrosynthesis
Aug 19, 2026Bogdan Zagribelnyy, Ivan Ilin, Nikita Bondarev +5Chemical Reaction Prediction Retrosynthesis
Insilico Medicine AI Limited, Abu Dhabi, UAE · Insilico Medicine Canada Inc., Montreal, Quebec, Canada · Insilico Medicine Hong Kong Ltd., Hong Kong SAR, China
RxnCLF: Contrastive Transformation-Aware Reaction Foundation Model for Improved Reactivity Prediction
Aug 6, 2026Yiting Zheng, Cheng Fang, Anthony Donofrio +1Representation Learning Graph Representation Learning
Discovery Chemistry, Merck & Co., Inc. Boston, MA, USA · Discovery Chemistry, Merck & Co., Inc. Cambridge, MA, USA
ReactionAtlas: Ab origine exploration of chemical reaction networks with machine learning
Jun 29, 2026Stefan Gugler, Max Eissler, Khaled Kahouli +1Generative Modeling Chemical Reaction Prediction
BIFOLD – Berlin Institute for the Foundations of Learning and Data, Berlin, Germany. · Machine Learning Group, TU Berlin, Berlin, Germany. · Department of Artificial Intelligence, Korea University, Seoul, South Korea. +1
RETROSPECT: RETROsynthesis via Sequential Prediction, and Chemically Transformed-ranking
Jun 5, 2026Raja Sekhar Pappala, Shreyas Vinaya Sathyanarayana, Ronit Kumar Choudhary +2Transformer Learning to Rank
Mstack AI
From Answers to States: Verifiable Process-Level Evaluation of Chemical Reasoning in Large Language Models
Jun 2, 2026Hongyu Guo, Hao Li, He Cao +2LLM Evaluation Chemical Reasoning in LLMs
Peking University, Shenzhen Graduate School · International Digital Economy Academy (IDEA)
SciCore-Mol: Augmenting Large Language Models with Pluggable Molecular Cognition Modules
May 21, 2026Yuxuan Chen, Changwei Lv, Yunduo Xiao +5AI-Assisted Scientific Research Chemical Reaction Prediction
School of Electronic and Computer Engineering, Peking University, Shenzhen, China · Tsinghua University, Beijing, China · School of Intelligence Science and Technology, Nanjing University, Suzhou, China
HiRes: Inspectable Precedent Memory for Reaction Condition Recommendation
May 20, 2026Shreyas Vinaya Sathyanarayana, Raja Sekhar Pappala, Deepak WarrierRepresentation Learning Molecular Representation Learning
Mstack AI Bangalore, India
ConRetroBert: EMA Stabilized Dual Encoders for Template-Based Single-Step Retrosynthesis
May 12, 2026Mohammad Jahid Ibna Basher, Ali Khodabandeh Yalabadi, Ivan Garibay +1Dense Retrieval Retrosynthesis
Department of Industrial Engineering University of Central Florida Orlando, FL 32816
ARMOR: An Agentic Framework for Reaction Feasibility Prediction via Adaptive Utility-aware Multi-tool Reasoning
May 8, 2026Ye Liu, Botao Yu, Xinyi Ling +2Computational Quantum Chemistry LLM Tool Use
Department of Biomedical Informatics The Ohio State University · Department of Computer Science and Engineering The Ohio State University · Division of Medicinal Chemistry and Pharmacognosy The Ohio State University +1
Large Language Models Transform Organic Synthesis From Reaction Prediction to Automation
Aug 7, 2025Kartar Kumar, Rajesh Kumar, Nikesh LagunAI-Assisted Scientific Research Laboratory Automation
Department of Computer Science, Institute of Business Administration (IBA), Karachi, Pakistan · International Research Center for Complexity Sciences, Hangzhou International Innovation Institute, Beihang University, Hangzhou 311115, China · School of Computer Science and Engineering, University of Electronic Science and Technology of China, Chengdu 611731, China

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Synthetic reaction data from transformation rules for graph-to-sequence pretraining in biodegradation pathway prediction

Irsyaad Rijwan, Liam Brydon, Aidan Jared, Jörg Simon Wicker

School of Computer Science, University of Auckland, Auckland, New Zealand. · enviPath Limited, Auckland, New Zealand.

Chemical Reaction Prediction Synthetic Data Pretraining Synthetic Data Generation AI-Assisted Scientific Research

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The scarcity of observed biodegradation reactions constrains the training of product and pathway predictors. We present enviGraph, a framework that generates and curates synthetic reaction data, uses these data to pretrain a graph-to-sequence predictor, and fine-tunes the predictor on observed environmental reactions for product and recursive pathway prediction. Applying inherited environmental transformation rules to structures from PubChem, NORMAN SusDat and EPA DSSTox, followed by curation, produces 776,851 canonical parent-product pairs for pretraining. We compare this dataset with three United States Patent and Trademark Office (USPTO) reaction datasets: USPTO-50K, USPTO-MIT and USPTO-Stereo. We evaluate enviGraph and the sequence-based enviFormer using ten folds split by pathway on the EAWAG Biocatalysis/Biodegradation Database (BBD), regulatory pesticide biodegradation data (Soil) and activated-sludge biodegradation data (Sludge). For both predictors, synthetic pretraining gives the highest BBD mean precision-recall area under the curve (PR-AUC) among the evaluated pretraining datasets for single-generation and multi-generation prediction. enviGraph achieves BBD single-generation PR-AUC of

0.202 \pm 0.050

with synthetic pretraining, compared with

0.169 \pm 0.065

for the retrospectively selected strongest USPTO condition, USPTO-Stereo (mean

\pm

sample standard deviation across folds). Its exact BBD top-1 and top-5 accuracies with synthetic pretraining are 0.355 and 0.594. The strongest USPTO conditions give higher PR-AUC means than synthetic pretraining in most Soil and Sludge comparisons. enviGraph has higher Soil multi-generation PR-AUC means than enviFormer under each of the four main pretraining datasets, and with synthetic pretraining it also leads enviFormer on BBD single-generation PR-AUC and exact top-1 and top-5 accuracy.