mlsanityData to 7 Oct 2026

"Found in Translation": Predicting Outcomes of Complex Organic Chemistry Reactions using Neural Sequence-to-Sequence Models

arXiv 1711.04810 ↗First posted 13 Nov 2017cs.LG stat.MLcited by 54

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Abstract (arXiv)

There is an intuitive analogy of an organic chemist's understanding of a compound and a language speaker's understanding of a word. Consequently, it is possible to introduce the basic concepts and analyze potential impacts of linguistic analysis to the world of organic chemistry. In this work, we cast the reaction prediction task as a translation problem by introducing a template-free sequence-to-sequence model, trained end-to-end and fully data-driven. We propose a novel way of tokenization, which is arbitrarily extensible with reaction information. With this approach, we demonstrate results superior to the state-of-the-art solution by a significant margin on the top-1 accuracy. Specifically, our approach achieves an accuracy of 80.1% without relying on auxiliary knowledge such as reaction templates. Also, 66.4% accuracy is reached on a larger and noisier dataset.

Key facts. Cited by 54 papers in the map (data through 7 Oct 2026). First posted on arXiv 13 Nov 2017.

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Citing papers per year: 2021: 14; 2022: 9; 2023: 9; 2024: 6; 2025: 6; 2026: 10.

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  1. 2023MLAgentBench: Evaluating Language Agents on Machine Learning Experimentationcited by 339
  2. 2023Large Language Models on Graphs: A Comprehensive Surveycited by 190
  3. 2021Geometric Deep Learning on Molecular Representationscited by 113
  4. 2023Unifying Molecular and Textual Representations via Multi-task Language Modellingcited by 92
  5. 202314 Examples of How LLMs Can Transform Materials Science and Chemistry: A Reflection on a Large Language Model Hackathoncited by 85
  6. 2023MolXPT: Wrapping Molecules with Text for Generative Pre-trainingcited by 81
  7. 2021Permutation invariant graph-to-sequence model for template-free retrosynthesis and reaction predictioncited by 66
  8. 2022Regression Transformer: Concurrent sequence regression and generation for molecular language modelingcited by 49
  9. 2022Root-aligned SMILES: A Tight Representation for Chemical Reaction Predictioncited by 49
  10. 2022TransPolymer: a Transformer-based language model for polymer property predictionscited by 43
  11. 2021Chemical-Reaction-Aware Molecule Representation Learningcited by 36
  12. 2022MOFormer: Self-Supervised Transformer model for Metal-Organic Framework Property Predictioncited by 28
38 more
  1. 2021Self-Improved Retrosynthetic Planningcited by 23
  2. 2024Accurate and efficient structure elucidation from routine one-dimensional NMR spectra using multitask machine learningcited by 21
  3. 2022BARTSmiles: Generative Masked Language Models for Molecular Representationscited by 18
  4. 2021Non-Autoregressive Electron Redistribution Modeling for Reaction Predictioncited by 17
  5. 2021TITAN: T Cell Receptor Specificity Prediction with Bimodal Attention Networkscited by 15
  6. 2021Retrosynthetic Planning with Experience-Guided Monte Carlo Tree Searchcited by 14
  7. 2021Modern Hopfield Networks for Few- and Zero-Shot Reaction Template Predictioncited by 13
  8. 2022SemiRetro: Semi-template framework boosts deep retrosynthesis predictioncited by 13
  9. 2022Toward automatic generation of control structures for process flow diagrams with large language modelscited by 12
  10. 2025MOFGPT: Generative Design of Metal-Organic Frameworks using Language Modelscited by 11
  11. 2021Hybrid quantum-classical machine learning for generative chemistry and drug designcited by 10
  12. 2022Learning from flowsheets: A generative transformer model for autocompletion of flowsheetscited by 10
  13. 2023Deep Learning Methods for Small Molecule Drug Discovery: A Surveycited by 10
  14. 2021Robust PDF Document Conversion Using Recurrent Neural Networkscited by 9
  15. 2024Equivariant Denoisers Cannot Copy Graphs: Align Your Graph Diffusion Modelscited by 7
  16. 2021Dataset Bias in the Natural Sciences: A Case Study in Chemical Reaction Prediction and Synthesis Designcited by 6
  17. 2023Language models in molecular discoverycited by 6
  18. 2024Aligning Transformers with Continuous Feedback via Energy Rank Alignmentcited by 6
  19. 2025Challenging reaction prediction models to generalize to novel chemistrycited by 6
  20. 2022Pre-training Transformers for Molecular Property Prediction Using Reaction Predictioncited by 5
  21. 2023AI for Interpretable Chemistry: Predicting Radical Mechanistic Pathways via Contrastive Learningcited by 5
  22. 2021Using Molecular Embeddings in QSAR Modeling: Does it Make a Difference?cited by 4
  23. 2023Holistic chemical evaluation reveals pitfalls in reaction prediction modelscited by 4
  24. 2024Tokenization for Molecular Foundation Modelscited by 4
  25. 2021Automated and Explainable Ontology Extension Based on Deep Learning: A Case Study in the Chemical Domaincited by 3
  26. 2024SMI-Editor: Edit-based SMILES Language Model with Fragment-level Supervisioncited by 3
  27. 2021Gemini: Dynamic Bias Correction for Autonomous Experimentation and Molecular Simulationcited by 2
  28. 2025ExLM: Rethinking the Impact of [MASK] Tokens in Masked Language Modelscited by 2
  29. 2025Predicting Chemical Reaction Outcomes Based on Electron Movements Using Machine Learningcited by 2
  30. 2024Multi-view biomedical foundation models for molecule-target and property predictioncited by 1
  31. 2025Large Language Models Transform Organic Synthesis From Reaction Prediction to Automationcited by 1
  32. 2026SynRXN: An Open Benchmark and Curated Dataset for Computational Reaction Modelingcited by 1
  33. 2026Agentic generation of verifiable rules for deterministic, self-expanding reaction classificationcited by 1
  34. 2025Attending on Multilevel Structure of Proteins enables Accurate Prediction of Cold-Start Drug-Target Interactionscited by 0
  35. 2026Beyond Learning on Molecules by Weakly Supervising on Moleculescited by 0
  36. 2026Driving Reaction Trajectories via Latent Flow Matchingcited by 0
  37. 2026RxnNano:Training Compact LLMs for Chemical Reaction and Retrosynthesis Prediction via Hierarchical Curriculum Learningcited by 0
  38. 2026CompleteRXN: Toward Completing Open Chemical Reaction Databasescited by 0

50 most cited of 54 All 54 (JSON)