# Unifying Molecular and Textual Representations via Multi-task Language Modelling

arXiv: https://arxiv.org/abs/2301.12586 · HTML: https://mlsanity.com/paper/2301.12586/

## Key facts

- Cited by 93 papers in the map (data through 14 Oct 2026).
- Builds on 26 of its 62 references that are in the map.
- First posted on arXiv 29 Jan 2023.

## Builds on (most cited first, 26 of 26)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [BERT: Pre-training of Deep Bidirectional Transformers for Language Understanding](https://mlsanity.com/paper/1810.04805/) (2018)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (2020)
- [An Image is Worth 16x16 Words: Transformers for Image Recognition at Scale](https://mlsanity.com/paper/2010.11929/) (2020)
- [Training language models to follow instructions with human feedback](https://mlsanity.com/paper/2203.02155/) (2022)
- [Exploring the Limits of Transfer Learning with a Unified Text-to-Text Transformer](https://mlsanity.com/paper/1910.10683/) (2019)
- [Chain-of-Thought Prompting Elicits Reasoning in Large Language Models](https://mlsanity.com/paper/2201.11903/) (2022)
- [Evaluating Large Language Models Trained on Code](https://mlsanity.com/paper/2107.03374/) (2021)
- [Hierarchical Text-Conditional Image Generation with CLIP Latents](https://mlsanity.com/paper/2204.06125/) (2022)
- [Photorealistic Text-to-Image Diffusion Models with Deep Language Understanding](https://mlsanity.com/paper/2205.11487/) (2022)
- [Scaling Instruction-Finetuned Language Models](https://mlsanity.com/paper/2210.11416/) (2022)
- [Multitask Prompted Training Enables Zero-Shot Task Generalization](https://mlsanity.com/paper/2110.08207/) (2021)
- [Solving Quantitative Reasoning Problems with Language Models](https://mlsanity.com/paper/2206.14858/) (2022)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [Complexity-Based Prompting for Multi-Step Reasoning](https://mlsanity.com/paper/2210.00720/) (2022)
- [Towards Understanding and Mitigating Social Biases in Language Models](https://mlsanity.com/paper/2106.13219/) (2021)
- [Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction](https://mlsanity.com/paper/1811.02633/) (2018)
- [Fr'echet ChemNet Distance: A metric for generative models for molecules in drug discovery](https://mlsanity.com/paper/1803.09518/) (2018)
- [Can large language models reason about medical questions?](https://mlsanity.com/paper/2207.08143/) (2022)
- [Gradio: Hassle-Free Sharing and Testing of ML Models in the Wild](https://mlsanity.com/paper/1906.02569/) (2019)
- [Translation between Molecules and Natural Language](https://mlsanity.com/paper/2204.11817/) (2022)
- [Language Models are Few-shot Multilingual Learners](https://mlsanity.com/paper/2109.07684/) (2021)
- [Mapping the Space of Chemical Reactions Using Attention-Based Neural Networks](https://mlsanity.com/paper/2012.06051/) (2020)
- ["Found in Translation": Predicting Outcomes of Complex Organic Chemistry Reactions using Neural Sequence-to-Sequence Models](https://mlsanity.com/paper/1711.04810/) (2017)
- [Regression Transformer: Concurrent sequence regression and generation for molecular language modeling](https://mlsanity.com/paper/2202.01338/) (2022)
- [Accelerating Material Design with the Generative Toolkit for Scientific Discovery](https://mlsanity.com/paper/2207.03928/) (2022)

## Built on by (most cited first, 30 of 93)

- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [Large Language Models on Graphs: A Comprehensive Survey](https://mlsanity.com/paper/2312.02783/) (2023)
- [Mol-Instructions: A Large-Scale Biomolecular Instruction Dataset for Large Language Models](https://mlsanity.com/paper/2306.08018/) (2023)
- [MolCA: Molecular Graph-Language Modeling with Cross-Modal Projector and Uni-Modal Adapter](https://mlsanity.com/paper/2310.12798/) (2023)
- [A Review of Large Language Models and Autonomous Agents in Chemistry](https://mlsanity.com/paper/2407.01603/) (2024)
- [A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery](https://mlsanity.com/paper/2406.10833/) (2024)
- [InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug Discovery](https://mlsanity.com/paper/2311.16208/) (2023)
- [Scientific Large Language Models: A Survey on Biological & Chemical Domains](https://mlsanity.com/paper/2401.14656/) (2024)
- [Efficient Evolutionary Search Over Chemical Space with Large Language Models](https://mlsanity.com/paper/2406.16976/) (2024)
- [BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning](https://mlsanity.com/paper/2402.17810/) (2024)
- [Developing ChemDFM as a large language foundation model for chemistry](https://mlsanity.com/paper/2401.14818/) (2024)
- [A Sober Look at LLMs for Material Discovery: Are They Actually Good for Bayesian Optimization Over Molecules?](https://mlsanity.com/paper/2402.05015/) (2024)
- [ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback](https://mlsanity.com/paper/2402.10980/) (2024)
- [MolecularGPT: Open Large Language Model (LLM) for Few-Shot Molecular Property Prediction](https://mlsanity.com/paper/2406.12950/) (2024)
- [MolTC: Towards Molecular Relational Modeling In Language Models](https://mlsanity.com/paper/2402.03781/) (2024)
- [MoleculeQA: A Dataset to Evaluate Factual Accuracy in Molecular Comprehension](https://mlsanity.com/paper/2403.08192/) (2024)
- [LLaMo: Large Language Model-based Molecular Graph Assistant](https://mlsanity.com/paper/2411.00871/) (2024)
- [L+M-24: Building a Dataset for Language + Molecules @ ACL 2024](https://mlsanity.com/paper/2403.00791/) (2024)
- [ReactXT: Understanding Molecular "Reaction-ship" via Reaction-Contextualized Molecule-Text Pretraining](https://mlsanity.com/paper/2405.14225/) (2024)
- [RAG-Enhanced Collaborative LLM Agents for Drug Discovery](https://mlsanity.com/paper/2502.17506/) (2025)
- [Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst Design](https://mlsanity.com/paper/2310.14420/) (2023)
- [Leveraging Biomolecule and Natural Language through Multi-Modal Learning: A Survey](https://mlsanity.com/paper/2403.01528/) (2024)
- [HIGHT: Hierarchical Graph Tokenization for Molecule-Language Alignment](https://mlsanity.com/paper/2406.14021/) (2024)
- [Mol-LLaMA: Towards General Understanding of Molecules in Large Molecular Language Model](https://mlsanity.com/paper/2502.13449/) (2025)
- [From Words to Molecules: A Survey of Large Language Models in Chemistry](https://mlsanity.com/paper/2402.01439/) (2024)
- [PRESTO: Progressive Pretraining Enhances Synthetic Chemistry Outcomes](https://mlsanity.com/paper/2406.13193/) (2024)
- [SynerGPT: In-Context Learning for Personalized Drug Synergy Prediction and Drug Design](https://mlsanity.com/paper/2307.11694/) (2023)
- [Transformers and Large Language Models for Chemistry and Drug Discovery](https://mlsanity.com/paper/2310.06083/) (2023)
- [ReactionT5: a large-scale pre-trained model towards application of limited reaction data](https://mlsanity.com/paper/2311.06708/) (2023)
- [Regress, Don't Guess -- A Regression-like Loss on Number Tokens for Language Models](https://mlsanity.com/paper/2411.02083/) (2024)

## 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.