Unifying Molecular and Textual Representations via Multi-task Language Modelling
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Abstract (arXiv)
The recent advances in neural language models have also been successfully applied to the field of chemistry, offering generative solutions for classical problems in molecular design and synthesis planning. These new methods have the potential to fuel a new era of data-driven automation in scientific discovery. However, specialized models are still typically required for each task, leading to the need for problem-specific fine-tuning and neglecting task interrelations. The main obstacle in this field is the lack of a unified representation between natural language and chemical representations, complicating and limiting human-machine interaction. Here, we propose the first multi-domain, multi-task language model that can solve a wide range of tasks in both the chemical and natural language domains. Our model can handle chemical and natural language concurrently, without requiring expensive pre-training on single domains or task-specific models. Interestingly, sharing weights across domains remarkably improves our model when benchmarked against state-of-the-art baselines on single-domain and cross-domain tasks. In particular, sharing information across domains and tasks gives rise to large improvements in cross-domain tasks, the magnitude of which increase with scale, as measured by more than a dozen of relevant metrics. Our work suggests that such models can robustly and efficiently accelerate discovery in physical sciences by superseding problem-specific fine-tuning and enhancing human-model interactions.
Key facts. Cited by 92 papers in the map (data through 7 Oct 2026). Builds on 26 of its 62 references that are in the map. First posted on arXiv 29 Jan 2023.
Builds on
26 of 62 references.
References · 26
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Citing papers per year: 2023: 12; 2024: 41; 2025: 27; 2026: 12.
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- 2023ChemCrow: Augmenting large-language models with chemistry toolscited by 609
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- 2024A Review of Large Language Models and Autonomous Agents in Chemistrycited by 96
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- 2024Scientific Large Language Models: A Survey on Biological & Chemical Domainscited by 80
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- 2024BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuningcited by 54
- 2024Developing ChemDFM as a large language foundation model for chemistrycited by 51
- 2024A Sober Look at LLMs for Material Discovery: Are They Actually Good for Bayesian Optimization Over Molecules?cited by 46
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- 2024LLaMo: Large Language Model-based Molecular Graph Assistantcited by 22
- 2024L+M-24: Building a Dataset for Language + Molecules @ ACL 2024cited by 21
- 2024MoleculeQA: A Dataset to Evaluate Factual Accuracy in Molecular Comprehensioncited by 19
- 2024ReactXT: Understanding Molecular "Reaction-ship" via Reaction-Contextualized Molecule-Text Pretrainingcited by 19
- 2025RAG-Enhanced Collaborative LLM Agents for Drug Discoverycited by 18
- 2024HIGHT: Hierarchical Graph Tokenization for Molecule-Language Alignmentcited by 17
- 2023Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst Designcited by 16
- 2024Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Surveycited by 16
- 2025Mol-LLaMA: Towards General Understanding of Molecules in Large Molecular Language Modelcited by 16
- 2024From Words to Molecules: A Survey of Large Language Models in Chemistrycited by 14
- 2024PRESTO: Progressive Pretraining Enhances Synthetic Chemistry Outcomescited by 14
- 2023SynerGPT: In-Context Learning for Personalized Drug Synergy Prediction and Drug Designcited by 13
- 2023Transformers and Large Language Models for Chemistry and Drug Discoverycited by 13
- 2023ReactionT5: a large-scale pre-trained model towards application of limited reaction datacited by 13
- 2024Regress, Don't Guess -- A Regression-like Loss on Number Tokens for Language Modelscited by 12
- 2023From Artificially Real to Real: Leveraging Pseudo Data from Large Language Models for Low-Resource Molecule Discoverycited by 11
- 2024Learning Multi-view Molecular Representations with Structured and Unstructured Knowledgecited by 11
- 2024From Generalist to Specialist: A Survey of Large Language Models for Chemistrycited by 11
- 2025Large language models as uncertainty-calibrated optimizers for experimental discoverycited by 10
- 2024Can LLMs Generate Diverse Molecules? Towards Alignment with Structural Diversitycited by 9
- 2025Enhancing Chemical Reaction and Retrosynthesis Prediction with Large Language Model and Dual-task Learningcited by 9
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- 2025A Survey of AI for Materials Science: Foundation Models, LLM Agents, Datasets, and Toolscited by 7
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- 2024ALMol: Aligned Language-Molecule Translation LLMs through Offline Preference Contrastive Optimisationcited by 3
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50 most cited of 92 All 92 (JSON)
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- 2026CoMPASS: Collaborative Molecular Property Prediction via Adaptive Small-Large Model Synergy31 Aug 2026
- 2026Gene Expression-Informed Jointly Controlled Generative Modeling for Precision Molecular Design13 Jul 2026
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- 2026From Knowledge to Action: Outcomes of the 2025 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry4 May 2026
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- 2026Enhanced Drug-drug Interaction Prediction Using Adaptive Knowledge Integration13 Mar 2026
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- 2026Retrieval-Augmented Foundation Models for Matched Molecular Pair Transformations to Recapitulate Medicinal Chemistry Intuition18 Feb 2026
- 2026Transformer-Based Approach for Automated Functional Group Replacement in Chemical Compounds12 Jan 2026
- 2026Towards Compositional Generalization in LLMs for Smart Contract Security: A Case Study on Reentrancy Vulnerabilities11 Jan 2026
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- 2025RTMol: Rethinking Molecule-text Alignment in a Round-trip View15 Nov 2025
- 2025Chain-of-Generation: Progressive Latent Diffusion for Text-Guided Molecular Design14 Nov 2025
- 2025ChEmREF: Evaluating Language Model Readiness for Chemical Emergency Response13 Nov 2025
- 2025Bridging the Gap Between Molecule and Textual Descriptions via Substructure-aware Alignment30 Oct 2025
- 2025KnowMol: Advancing Molecular Large Language Models with Multi-Level Chemical Knowledge22 Oct 2025
- 2025MoRA: On-the-fly Molecule-aware Low-Rank Adaptation Framework for LLM-based Multi-Modal Molecular Assistant14 Oct 2025
- 2025Training Text-to-Molecule Models with Context-Aware Tokenization30 Aug 2025
- 2025MolErr2Fix: Benchmarking LLM Trustworthiness in Chemistry via Modular Error Detection, Localization, Explanation, and Revision26 Aug 2025
- 2025HSA-Net: Hierarchical and Structure-Aware Framework for Efficient and Scalable Molecular Language Modeling10 Aug 2025
- 2025MolSnap: Snap-Fast Molecular Generation with Latent Variational Mean Flow7 Aug 2025
- 2025ChemActor: Enhancing Automated Extraction of Chemical Synthesis Actions with LLM-Generated Data30 Jun 2025
- 2025A Survey of AI for Materials Science: Foundation Models, LLM Agents, Datasets, and Tools25 Jun 2025
- 2025ModuLM: Enabling Modular and Multimodal Molecular Relational Learning with Large Language Models1 Jun 2025
- 2025Improving Chemical Understanding of LLMs via SMILES Parsing22 May 2025
- 2025Enhancing Chemical Reaction and Retrosynthesis Prediction with Large Language Model and Dual-task Learning5 May 2025
- 2025Large language models as uncertainty-calibrated optimizers for experimental discovery8 Apr 2025
- 2025We Need Improved Data Curation and Attribution in AI for Scientific Discovery3 Apr 2025
- 2025Unified Cross-Scale 3D Generation and Understanding via Autoregressive Modeling20 Mar 2025
- 2025GraphT5: Unified Molecular Graph-Language Modeling via Multi-Modal Cross-Token Attention7 Mar 2025
- 2025RAG-Enhanced Collaborative LLM Agents for Drug Discovery22 Feb 2025
- 2025Mol-LLaMA: Towards General Understanding of Molecules in Large Molecular Language Model19 Feb 2025
- 2025Automatic Annotation Augmentation Boosts Translation between Molecules and Natural Language10 Feb 2025
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- 2025Omni-Mol: Multitask Molecular Model for Any-to-any Modalities3 Feb 2025
- 2024From Generalist to Specialist: A Survey of Large Language Models for Chemistry28 Dec 2024
- 2024Property Enhanced Instruction Tuning for Multi-task Molecule Generation with Large Language Models24 Dec 2024
- 2024GeomCLIP: Contrastive Geometry-Text Pre-training for Molecules16 Nov 2024
- 2024Exploring Optimal Transport-Based Multi-Grained Alignments for Text-Molecule Retrieval4 Nov 2024
- 2024Regress, Don't Guess -- A Regression-like Loss on Number Tokens for Language Models4 Nov 2024
- 2024LLaMo: Large Language Model-based Molecular Graph Assistant31 Oct 2024
- 2024Chemical Language Model Linker: blending text and molecules with modular adapters26 Oct 2024
- 2024Can LLMs Generate Diverse Molecules? Towards Alignment with Structural Diversity4 Oct 2024
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- 2024Uncertainty-Guided Likelihood Tree Searchcited by 4
- 2024Uncertainty-Guided Likelihood Tree Search4 Jul 2024
- 2024ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback15 Feb 2024
- 2023Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst Design22 Oct 2023
- 2023ChemCrow: Augmenting large-language models with chemistry toolscited by 609
- 2023Large Language Models on Graphs: A Comprehensive Surveycited by 190
- 2023Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Modelscited by 131
- 2023MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adaptercited by 128
- 2024A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discoverycited by 96
- 2023InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug Discoverycited by 86
- 2024Scientific Large Language Models: A Survey on Biological & Chemical Domainscited by 80
- 2024Efficient Evolutionary Search Over Chemical Space with Large Language Modelscited by 59
- 2024BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuningcited by 54
- 2024Developing ChemDFM as a large language foundation model for chemistrycited by 51
- 2024A Sober Look at LLMs for Material Discovery: Are They Actually Good for Bayesian Optimization Over Molecules?cited by 46
- 2024MolecularGPT: Open Large Language Model (LLM) for Few-Shot Molecular Property Predictioncited by 24
12 most cited of 76 All 76 (JSON)
- 2026MolSC: Leveraging Substituent Contributions to Enhance Fine-grained Molecular Understanding in LLMs19 Sep 2026
- 2026Dynamic language model representations for multi-objective reaction optimisation10 Sep 2026
- 2026CoMPASS: Collaborative Molecular Property Prediction via Adaptive Small-Large Model Synergy31 Aug 2026
- 2026Gene Expression-Informed Jointly Controlled Generative Modeling for Precision Molecular Design13 Jul 2026
- 2026MolSafeEval: A Benchmark for Uncovering Safety Risks in AI-Generated Molecules1 Jul 2026
- 2026From Knowledge to Action: Outcomes of the 2025 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry4 May 2026
- 2026BiMol-Diff: A Unified Diffusion Framework for Molecular Generation and Captioning27 Apr 2026
- 2026Enhanced Drug-drug Interaction Prediction Using Adaptive Knowledge Integration13 Mar 2026
- 2026Chem4DLLM: 4D Multimodal LLMs for Chemical Dynamics Understanding12 Mar 2026
- 2026Transformer-Based Approach for Automated Functional Group Replacement in Chemical Compounds12 Jan 2026
- 2026Towards Compositional Generalization in LLMs for Smart Contract Security: A Case Study on Reentrancy Vulnerabilities11 Jan 2026
- 2025NMIRacle: Multi-modal Generative Molecular Elucidation from IR and NMR Spectra17 Dec 2025
12 newest of 76 All 76 (JSON)