mlsanityData to 14 Oct 2026

DrugAssist: A Large Language Model for Molecule Optimization

arXiv 2401.10334 ↗First posted 28 Dec 2023q-bio.QM cs.AI cs.CLcited by 59

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Abstract (arXiv)

Recently, the impressive performance of large language models (LLMs) on a wide range of tasks has attracted an increasing number of attempts to apply LLMs in drug discovery. However, molecule optimization, a critical task in the drug discovery pipeline, is currently an area that has seen little involvement from LLMs. Most of existing approaches focus solely on capturing the underlying patterns in chemical structures provided by the data, without taking advantage of expert feedback. These non-interactive approaches overlook the fact that the drug discovery process is actually one that requires the integration of expert experience and iterative refinement. To address this gap, we propose DrugAssist, an interactive molecule optimization model which performs optimization through human-machine dialogue by leveraging LLM's strong interactivity and generalizability. DrugAssist has achieved leading results in both single and multiple property optimization, simultaneously showcasing immense potential in transferability and iterative optimization. In addition, we publicly release a large instruction-based dataset called MolOpt-Instructions for fine-tuning language models on molecule optimization tasks. We have made our code and data publicly available at https://github.com/blazerye/DrugAssist, which we hope to pave the way for future research in LLMs' application for drug discovery.

Key facts. Cited by 59 papers in the map (data through 14 Oct 2026). Builds on 22 of its 46 references that are in the map. First posted on arXiv 28 Dec 2023.

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22 of 46 references.

References · 22

  1. 2022Training language models to follow instructions with human feedbackcited by 15,971
  2. 2021LoRA: Low-Rank Adaptation of Large Language Modelscited by 14,380
  3. 2023Llama 2: Open Foundation and Fine-Tuned Chat Modelscited by 13,028
  4. 2022PaLM: Scaling Language Modeling with Pathwayscited by 5,326
  5. 2023Siren's Song in the AI Ocean: A Survey on Hallucination in Large Language Modelscited by 698
  6. 2018Junction Tree Variational Autoencoder for Molecular Graph Generationcited by 652
  7. 2018GraphVAE: Towards Generation of Small Graphs Using Variational Autoencoderscited by 383
  8. 2023ChatDoctor: A Medical Chat Model Fine-Tuned on a Large Language Model Meta-AI (LLaMA) Using Medical Domain Knowledgecited by 325
  9. 2023MedAlpaca -- An Open-Source Collection of Medical Conversational AI Models and Training Datacited by 286
  10. 2017Molecular De Novo Design through Deep Reinforcement Learningcited by 267
  11. 2023How Abilities in Large Language Models are Affected by Supervised Fine-tuning Data Compositioncited by 223
  12. 2020Hierarchical Generation of Molecular Graphs using Structural Motifscited by 208
10 more
  1. 2018Constrained Graph Variational Autoencoders for Molecule Designcited by 185
  2. 2023Macaw-LLM: Multi-Modal Language Modeling with Image, Audio, Video, and Text Integrationcited by 172
  3. 2023Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Modelscited by 133
  4. 2023BioMedGPT: Open Multimodal Generative Pre-trained Transformer for BioMedicinecited by 100
  5. 2018Learning Multimodal Graph-to-Graph Translation for Molecular Optimizationcited by 88
  6. 2023A Systematic Evaluation of GPT-4V's Multimodal Capability for Medical Image Analysiscited by 37
  7. 2017Molecular Generation with Recurrent Neural Networks (RNNs)cited by 36
  8. 2023ChatGPT-powered Conversational Drug Editing Using Retrieval and Domain Feedbackcited by 31
  9. 2023A Comprehensive Evaluation of GPT-4V on Knowledge-Intensive Visual Question Answeringcited by 23
  10. 2023Retrieval-augmented Multi-modal Chain-of-Thoughts Reasoning for Large Language Modelscited by 18

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Citing papers per year: 2024: 16; 2025: 26; 2026: 17.

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  1. 2025AlphaEvolve: A coding agent for scientific and algorithmic discoverycited by 867
  2. 2024LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Datasetcited by 128
  3. 2025Towards Scientific Intelligence: A Survey of LLM-based Scientific Agentscited by 98
  4. 2024A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discoverycited by 96
  5. 2024A Systematic Survey on Large Language Models for Algorithm Designcited by 69
  6. 2024Efficient Evolutionary Search Over Chemical Space with Large Language Modelscited by 61
  7. 2025A Survey on the Optimization of Large Language Model-based Agentscited by 46
  8. 2024ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedbackcited by 33
  9. 2024LICO: Large Language Models for In-Context Molecular Optimizationcited by 26
  10. 2024Speak-to-Structure: Evaluating LLMs in Open-domain Natural Language-Driven Molecule Generationcited by 25
  11. 2025DrugPilot: LLM-based Parameterized Reasoning Agent for Drug Discoverycited by 19
  12. 2024ChemEval: A Comprehensive Multi-Level Chemical Evaluation for Large Language Modelscited by 18
38 more
  1. 2024Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Surveycited by 17
  2. 2025GeLLMO: Generalizing Large Language Models for Multi-property Molecule Optimizationcited by 17
  3. 2025A Survey of Large Language Models for Text-Guided Molecular Discovery: from Molecule Generation to Optimizationcited by 13
  4. 2024MolReFlect: Towards In-Context Fine-grained Alignments between Molecules and Textscited by 11
  5. 2025POLO: Preference-Guided Multi-Turn Reinforcement Learning for Lead Optimizationcited by 11
  6. 2024Can LLMs Generate Diverse Molecules? Towards Alignment with Structural Diversitycited by 9
  7. 2025Evolving Roles of LLMs in Scientific Innovation: Assistant, Collaborator, Scientist, and Evaluatorcited by 9
  8. 2025From Hypothesis to Publication: A Comprehensive Survey of AI-Driven Research Support Systemscited by 8
  9. 2025mCLM: A Modular Chemical Language Model that Generates Functional and Makeable Moleculescited by 8
  10. 2024Bioinformatics and Biomedical Informatics with ChatGPT: Year One Reviewcited by 4
  11. 2026MolMem: Memory-Augmented Agentic Reinforcement Learning for Sample-Efficient Molecular Optimizationcited by 4
  12. 2024Instruction-Based Molecular Graph Generation with Unified Text-Graph Diffusion Modelcited by 3
  13. 2024SwiftDossier: Tailored Automatic Dossier for Drug Discovery with LLMs and Agentscited by 3
  14. 2025Exploring Modularity of Agentic Systems for Drug Discoverycited by 3
  15. 2025DrugMCTS: a drug repurposing framework combining multi-agent, RAG and Monte Carlo Tree Searchcited by 3
  16. 2025Generative AI for Healthcare: Fundamentals, Challenges, and Perspectivescited by 3
  17. 2025BioMedGPT-Mol: Multi-task Learning for Molecular Understanding and Generationcited by 3
  18. 2025SciEvalKit: An Open-source Evaluation Toolkit for Scientific General Intelligencecited by 3
  19. 2026M^4olGen: Multi-Agent, Multi-Stage Molecular Generation under Precise Multi-Property Constraintscited by 3
  20. 2024Atomas: Hierarchical Alignment on Molecule-Text for Unified Molecule Understanding and Generationcited by 2
  21. 2025Large Language Models for Controllable Multi-property Multi-objective Molecule Optimizationcited by 2
  22. 2025GP-MoLFormer-Sim: Test Time Molecular Optimization through Contextual Similarity Guidancecited by 2
  23. 2025Breaking Bad Molecules: Are MLLMs Ready for Structure-Level Molecular Detoxification?cited by 2
  24. 2025Round-trip Reinforcement Learning: Self-Consistent Training for Better Chemical LLMscited by 2
  25. 2026LLM-Guided Dynamic Action Spaces for Synthesizable Molecular Optimizationcited by 2
  26. 2025MolEditRL: Structure-Preserving Molecular Editing via Discrete Diffusion and Reinforcement Learningcited by 1
  27. 2025A Dataset for Distilling Knowledge Priors from Literature for Therapeutic Designcited by 1
  28. 2025Coder as Editor: Code-driven Interpretable Molecular Optimizationcited by 1
  29. 2025Eliminating Agentic Workflow for Introduction Generation with Parametric Stage Tokenscited by 1
  30. 2026SLIM: Sparse Latent Steering for Interpretable and Property-Directed LLM-Based Molecular Editingcited by 1
  31. 2026Agents on a Tree: Pathwise Coordination for Multi-Objective Molecular Optimizationcited by 1
  32. 2024M3-20M: A Large-Scale Multi-Modal Molecule Dataset for AI-driven Drug Design and Discoverycited by 0
  33. 2025MolErr2Fix: Benchmarking LLM Trustworthiness in Chemistry via Modular Error Detection, Localization, Explanation, and Revisioncited by 0
  34. 2025Generative Artificial Intelligence in Bioinformatics: A Systematic Review of Models, Applications, and Methodological Advancescited by 0
  35. 2025FRAGMENTA: End-to-end Fragmentation-based Generative Model with Agentic Tuning for Drug Lead Optimizationcited by 0
  36. 2026AROMA: Augmented Reasoning Over a Multimodal Architecture for Virtual Cell Genetic Perturbation Modelingcited by 0
  37. 2026C-MORAL: Controllable Multi-Objective Molecular Optimization with Reinforcement Alignment for LLMscited by 0
  38. 2026MolWorld: Molecule World Models for Actionable Molecular Optimizationcited by 0

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