# Empowering Molecule Discovery for Molecule-Caption Translation with Large Language Models: A ChatGPT Perspective

arXiv: https://arxiv.org/abs/2306.06615 · HTML: https://mlsanity.com/paper/2306.06615/

## Key facts

- Cited by 92 papers in the map (data through 14 Oct 2026).
- Builds on 25 of its 73 references that are in the map.
- First posted on arXiv 11 Jun 2023.

## Builds on (most cited first, 25 of 25)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Language Models are Few-Shot Learners](https://mlsanity.com/paper/2005.14165/) (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)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [PaLM: Scaling Language Modeling with Pathways](https://mlsanity.com/paper/2204.02311/) (2022)
- [MiniGPT-4: Enhancing Vision-Language Understanding with Advanced Large Language Models](https://mlsanity.com/paper/2304.10592/) (2023)
- [LaMDA: Language Models for Dialog Applications](https://mlsanity.com/paper/2201.08239/) (2022)
- [What Makes Good In-Context Examples for GPT-3?](https://mlsanity.com/paper/2101.06804/) (2021)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Automatic Chain of Thought Prompting in Large Language Models](https://mlsanity.com/paper/2210.03493/) (2022)
- [Learning To Retrieve Prompts for In-Context Learning](https://mlsanity.com/paper/2112.08633/) (2021)
- [MetaICL: Learning to Learn In Context](https://mlsanity.com/paper/2110.15943/) (2021)
- [ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction](https://mlsanity.com/paper/2010.09885/) (2020)
- [TALLRec: An Effective and Efficient Tuning Framework to Align Large Language Model with Recommendation](https://mlsanity.com/paper/2305.00447/) (2023)
- [Grammar Variational Autoencoder](https://mlsanity.com/paper/1703.01925/) (2017)
- [Translation between Molecules and Natural Language](https://mlsanity.com/paper/2204.11817/) (2022)
- [Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing](https://mlsanity.com/paper/2212.10789/) (2022)
- [A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language](https://mlsanity.com/paper/2209.05481/) (2022)
- [Syntax-Directed Variational Autoencoder for Structured Data](https://mlsanity.com/paper/1802.08786/) (2018)
- [SMILES Transformer: Pre-trained Molecular Fingerprint for Low Data Drug Discovery](https://mlsanity.com/paper/1911.04738/) (2019)
- [Generative Diffusion Models on Graphs: Methods and Applications](https://mlsanity.com/paper/2302.02591/) (2023)
- [MolGenSurvey: A Systematic Survey in Machine Learning Models for Molecule Design](https://mlsanity.com/paper/2203.14500/) (2022)
- [ChatGPT: A Meta-Analysis after 2.5 Months](https://mlsanity.com/paper/2302.13795/) (2023)
- [Deep Learning Methods for Small Molecule Drug Discovery: A Survey](https://mlsanity.com/paper/2303.00313/) (2023)

## Built on by (most cited first, 30 of 92)

- [A Survey on RAG Meeting LLMs: Towards Retrieval-Augmented Large Language Models](https://mlsanity.com/paper/2405.06211/) (2024)
- [Large Language Models for Information Retrieval: A Survey](https://mlsanity.com/paper/2308.07107/) (2023)
- [Exploring the Potential of Large Language Models (LLMs) in Learning on Graphs](https://mlsanity.com/paper/2307.03393/) (2023)
- [Large Language Models on Graphs: A Comprehensive Survey](https://mlsanity.com/paper/2312.02783/) (2023)
- [Recommender Systems in the Era of Large Language Models (LLMs)](https://mlsanity.com/paper/2307.02046/) (2023)
- [ChemLLM: A Chemical Large Language Model](https://mlsanity.com/paper/2402.06852/) (2024)
- [BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations](https://mlsanity.com/paper/2310.07276/) (2023)
- [InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug Discovery](https://mlsanity.com/paper/2311.16208/) (2023)
- [LLM and Simulation as Bilevel Optimizers: A New Paradigm to Advance Physical Scientific Discovery](https://mlsanity.com/paper/2405.09783/) (2024)
- [A Survey of Attacks on Large Vision-Language Models: Resources, Advances, and Future Trends](https://mlsanity.com/paper/2407.07403/) (2024)
- [GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text](https://mlsanity.com/paper/2308.06911/) (2023)
- [Knowledge Graph Retrieval-Augmented Generation for LLM-based Recommendation](https://mlsanity.com/paper/2501.02226/) (2025)
- [BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning](https://mlsanity.com/paper/2402.17810/) (2024)
- [BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments](https://mlsanity.com/paper/2405.17631/) (2024)
- [Can Large Language Models Empower Molecular Property Prediction?](https://mlsanity.com/paper/2307.07443/) (2023)
- [A Survey of Mamba](https://mlsanity.com/paper/2408.01129/) (2024)
- [TokenRec: Learning to Tokenize ID for LLM-based Generative Recommendation](https://mlsanity.com/paper/2406.10450/) (2024)
- [Graph Machine Learning in the Era of Large Language Models (LLMs)](https://mlsanity.com/paper/2404.14928/) (2024)
- [Speak-to-Structure: Evaluating LLMs in Open-domain Natural Language-Driven Molecule Generation](https://mlsanity.com/paper/2412.14642/) (2024)
- [CheatAgent: Attacking LLM-Empowered Recommender Systems via LLM Agent](https://mlsanity.com/paper/2504.13192/) (2025)
- [Certified Robustness for Large Language Models with Self-Denoising](https://mlsanity.com/paper/2307.07171/) (2023)
- [MoleculeQA: A Dataset to Evaluate Factual Accuracy in Molecular Comprehension](https://mlsanity.com/paper/2403.08192/) (2024)
- [Benchmarking Retrieval-Augmented Generation for Chemistry](https://mlsanity.com/paper/2505.07671/) (2025)
- [A quantitative analysis of knowledge-learning preferences in large language models in molecular science](https://mlsanity.com/paper/2402.04119/) (2024)
- [Large Language Models are In-Context Molecule Learners](https://mlsanity.com/paper/2403.04197/) (2024)
- [ChemEval: A Comprehensive Multi-Level Chemical Evaluation for Large Language Models](https://mlsanity.com/paper/2409.13989/) (2024)
- [RAG-Enhanced Collaborative LLM Agents for Drug Discovery](https://mlsanity.com/paper/2502.17506/) (2025)
- [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)
- [RemoteRAG: A Privacy-Preserving LLM Cloud RAG Service](https://mlsanity.com/paper/2412.12775/) (2024)

## Abstract (arXiv)

Molecule discovery plays a crucial role in various scientific fields, advancing the design of tailored materials and drugs. However, most of the existing methods heavily rely on domain experts, require excessive computational cost, or suffer from sub-optimal performance. On the other hand, Large Language Models (LLMs), like ChatGPT, have shown remarkable performance in various cross-modal tasks due to their powerful capabilities in natural language understanding, generalization, and in-context learning (ICL), which provides unprecedented opportunities to advance molecule discovery. Despite several previous works trying to apply LLMs in this task, the lack of domain-specific corpus and difficulties in training specialized LLMs still remain challenges. In this work, we propose a novel LLM-based framework (MolReGPT) for molecule-caption translation, where an In-Context Few-Shot Molecule Learning paradigm is introduced to empower molecule discovery with LLMs like ChatGPT to perform their in-context learning capability without domain-specific pre-training and fine-tuning. MolReGPT leverages the principle of molecular similarity to retrieve similar molecules and their text descriptions from a local database to enable LLMs to learn the task knowledge from context examples. We evaluate the effectiveness of MolReGPT on molecule-caption translation, including molecule understanding and text-based molecule generation. Experimental results show that compared to fine-tuned models, MolReGPT outperforms MolT5-base and is comparable to MolT5-large without additional training. To the best of our knowledge, MolReGPT is the first work to leverage LLMs via in-context learning in molecule-caption translation for advancing molecule discovery. Our work expands the scope of LLM applications, as well as providing a new paradigm for molecule discovery and design.