mlsanityData to 14 Oct 2026

Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction

arXiv 1811.02633 ↗First posted 6 Nov 2018physics.chem-ph cs.LGcited by 229

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Abstract (arXiv)

Organic synthesis is one of the key stumbling blocks in medicinal chemistry. A necessary yet unsolved step in planning synthesis is solving the forward problem: given reactants and reagents, predict the products. Similar to other work, we treat reaction prediction as a machine translation problem between SMILES strings of reactants-reagents and the products. We show that a multi-head attention Molecular Transformer model outperforms all algorithms in the literature, achieving a top-1 accuracy above 90% on a common benchmark dataset. Our algorithm requires no handcrafted rules, and accurately predicts subtle chemical transformations. Crucially, our model can accurately estimate its own uncertainty, with an uncertainty score that is 89% accurate in terms of classifying whether a prediction is correct. Furthermore, we show that the model is able to handle inputs without reactant-reagent split and including stereochemistry, which makes our method universally applicable.

Key facts. Cited by 229 papers in the map (data through 14 Oct 2026). First posted on arXiv 6 Nov 2018.

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Citing papers per year: 2021: 20; 2022: 27; 2023: 42; 2024: 45; 2025: 56; 2026: 39.

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  1. 2023ChemCrow: Augmenting large-language models with chemistry toolscited by 631
  2. 2021A Survey of Transformerscited by 401
  3. 2021Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Developmentcited by 264
  4. 2021Large-Scale Chemical Language Representations Capture Molecular Structure and Propertiescited by 206
  5. 2025Remasking Discrete Diffusion Models with Inference-Time Scalingcited by 189
  6. 2023What can Large Language Models do in chemistry? A comprehensive benchmark on eight taskscited by 185
  7. 2022Graph neural networks for materials science and chemistrycited by 182
  8. 2024Simple Guidance Mechanisms for Discrete Diffusion Modelscited by 155
  9. 2024LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Datasetcited by 128
  10. 2021Geometric Deep Learning on Molecular Representationscited by 113
  11. 2023Unifying Molecular and Textual Representations via Multi-task Language Modellingcited by 93
  12. 202314 Examples of How LLMs Can Transform Materials Science and Chemistry: A Reflection on a Large Language Model Hackathoncited by 86
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  1. 2023InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug Discoverycited by 86
  2. 2024Scientific Large Language Models: A Survey on Biological & Chemical Domainscited by 80
  3. 2022SELFIES and the future of molecular string representationscited by 76
  4. 2021Permutation invariant graph-to-sequence model for template-free retrosynthesis and reaction predictioncited by 68
  5. 2024Efficient Evolutionary Search Over Chemical Space with Large Language Modelscited by 61
  6. 2023Language models can generate molecules, materials, and protein binding sites directly in three dimensions as XYZ, CIF, and PDB filescited by 59
  7. 2024Developing ChemDFM as a large language foundation model for chemistrycited by 52
  8. 2022Root-aligned SMILES: A Tight Representation for Chemical Reaction Predictioncited by 51
  9. 2022Graph-based Molecular Representation Learningcited by 51
  10. 2022Regression Transformer: Concurrent sequence regression and generation for molecular language modelingcited by 50
  11. 2022polyBERT: A chemical language model to enable fully machine-driven ultrafast polymer informaticscited by 48
  12. 2023Gotta be SAFE: A New Framework for Molecular Designcited by 48
  13. 2021Amortized Tree Generation for Bottom-up Synthesis Planning and Synthesizable Molecular Designcited by 44
  14. 2022TransPolymer: a Transformer-based language model for polymer property predictionscited by 43
  15. 2025SciToolAgent: A Knowledge Graph-Driven Scientific Agent for Multi-Tool Integrationcited by 43
  16. 2023RetroBridge: Modeling Retrosynthesis with Markov Bridgescited by 36
  17. 2024ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedbackcited by 33
  18. 2024Unraveling Molecular Structure: A Multimodal Spectroscopic Dataset for Chemistrycited by 31
  19. 2023MeLM, a generative pretrained language modeling framework that solves forward and inverse mechanics problemscited by 29
  20. 2022MOFormer: Self-Supervised Transformer model for Metal-Organic Framework Property Predictioncited by 28
  21. 2021Dual-view Molecule Pre-trainingcited by 27
  22. 2023nach0: Multimodal Natural and Chemical Languages Foundation Modelcited by 26
  23. 2022Bidirectional Generation of Structure and Properties Through a Single Molecular Foundation Modelcited by 25
  24. 2024Double-Ended Synthesis Planning with Goal-Constrained Bidirectional Searchcited by 24
  25. 2024Large Language Models in Drug Discovery and Development: From Disease Mechanisms to Clinical Trialscited by 24
  26. 2021Self-Improved Retrosynthetic Planningcited by 23
  27. 2024Practical and efficient quantum circuit synthesis and transpiling with Reinforcement Learningcited by 22
  28. 2021Relative Molecule Self-Attention Transformercited by 21
  29. 2023PeptideBERT: A Language Model based on Transformers for Peptide Property Predictioncited by 21
  30. 2024Setting the Record Straight on Transformer Oversmoothingcited by 21
  31. 2022BARTSmiles: Generative Masked Language Models for Molecular Representationscited by 18
  32. 2021Non-Autoregressive Electron Redistribution Modeling for Reaction Predictioncited by 17
  33. 2023Transformers in Healthcare: A Surveycited by 17
  34. 2023Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst Designcited by 17
  35. 2021C5T5: Controllable Generation of Organic Molecules with Transformerscited by 16
  36. 2023Conformal Autoregressive Generation: Beam Search with Coverage Guaranteescited by 16
  37. 2024Clustering in pure-attention hardmax transformers and its role in sentiment analysiscited by 15
  38. 2022Graph Neural Networks for Temperature-Dependent Activity Coefficient Prediction of Solutes in Ionic Liquidscited by 14

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