# DrugChat: Towards Enabling ChatGPT-Like Capabilities on Drug Molecule Graphs

arXiv: https://arxiv.org/abs/2309.03907 · HTML: https://mlsanity.com/paper/2309.03907/

## Key facts

- Cited by 40 papers in the map (data through 14 Oct 2026).
- Builds on 7 of its 16 references that are in the map.
- First posted on arXiv 18 May 2023.

## Builds on (most cited first, 7 of 7)

- [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)
- [LLaMA: Open and Efficient Foundation Language Models](https://mlsanity.com/paper/2302.13971/) (2023)
- [Visual Instruction Tuning](https://mlsanity.com/paper/2304.08485/) (2023)
- [MiniGPT-4: Enhancing Vision-Language Understanding with Advanced Large Language Models](https://mlsanity.com/paper/2304.10592/) (2023)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)

## Built on by (most cited first, 30 of 40)

- [Accessing GPT-4 level Mathematical Olympiad Solutions via Monte Carlo Tree Self-refine with LLaMa-3 8B](https://mlsanity.com/paper/2406.07394/) (2024)
- [LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset](https://mlsanity.com/paper/2402.09391/) (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)
- [Developing ChemDFM as a large language foundation model for chemistry](https://mlsanity.com/paper/2401.14818/) (2024)
- [Making Large Language Models Perform Better in Knowledge Graph Completion](https://mlsanity.com/paper/2310.06671/) (2023)
- [Scientists' First Exam: Probing Cognitive Abilities of MLLM via Perception, Understanding, and Reasoning](https://mlsanity.com/paper/2506.10521/) (2025)
- [Graph Machine Learning in the Era of Large Language Models (LLMs)](https://mlsanity.com/paper/2404.14928/) (2024)
- [Data-Centric Foundation Models in Computational Healthcare: A Survey](https://mlsanity.com/paper/2401.02458/) (2024)
- [UniMoT: Unified Molecule-Text Language Model with Discrete Token Representation](https://mlsanity.com/paper/2408.00863/) (2024)
- [MoleculeQA: A Dataset to Evaluate Factual Accuracy in Molecular Comprehension](https://mlsanity.com/paper/2403.08192/) (2024)
- [ProtLLM: An Interleaved Protein-Language LLM with Protein-as-Word Pre-Training](https://mlsanity.com/paper/2403.07920/) (2024)
- [ChemEval: A Comprehensive Multi-Level Chemical Evaluation for Large Language Models](https://mlsanity.com/paper/2409.13989/) (2024)
- [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)
- [PRESTO: Progressive Pretraining Enhances Synthetic Chemistry Outcomes](https://mlsanity.com/paper/2406.13193/) (2024)
- [LLMs as Visual Explainers: Advancing Image Classification with Evolving Visual Descriptions](https://mlsanity.com/paper/2311.11904/) (2023)
- [Geometry Informed Tokenization of Molecules for Language Model Generation](https://mlsanity.com/paper/2408.10120/) (2024)
- [A Recent Survey of Heterogeneous Transfer Learning](https://mlsanity.com/paper/2310.08459/) (2023)
- [FedMentalCare: Towards Privacy-Preserving Fine-Tuned LLMs to Analyze Mental Health Status Using Federated Learning Framework](https://mlsanity.com/paper/2503.05786/) (2025)
- [KnowMol: Advancing Molecular Large Language Models with Multi-Level Chemical Knowledge](https://mlsanity.com/paper/2510.19484/) (2025)
- [Mol-LLM: Multimodal Generalist Molecular LLM with Improved Graph Utilization](https://mlsanity.com/paper/2502.02810/) (2025)
- [K-Paths: Reasoning over Graph Paths for Drug Repurposing and Drug Interaction Prediction](https://mlsanity.com/paper/2502.13344/) (2025)
- [Large Language Models Meet Text-Attributed Graphs: A Survey of Integration Frameworks and Applications](https://mlsanity.com/paper/2510.21131/) (2025)
- [GPT vs Human for Scientific Reviews: A Dual Source Review on Applications of ChatGPT in Science](https://mlsanity.com/paper/2312.03769/) (2023)
- [Bridging Text and Molecule: A Survey on Multimodal Frameworks for Molecule](https://mlsanity.com/paper/2403.13830/) (2024)
- [Bioinformatics and Biomedical Informatics with ChatGPT: Year One Review](https://mlsanity.com/paper/2403.15274/) (2024)
- [T-Rex: Text-assisted Retrosynthesis Prediction](https://mlsanity.com/paper/2401.14637/) (2024)
- [DRAK: Unlocking Molecular Insights with Domain-Specific Retrieval-Augmented Knowledge in LLMs](https://mlsanity.com/paper/2406.18535/) (2024)
- [Instruction-Based Molecular Graph Generation with Unified Text-Graph Diffusion Model](https://mlsanity.com/paper/2408.09896/) (2024)

## Abstract (arXiv)

A ChatGPT-like system for drug compounds could be a game-changer in pharmaceutical research, accelerating drug discovery, enhancing our understanding of structure-activity relationships, guiding lead optimization, aiding drug repurposing, reducing the failure rate, and streamlining clinical trials. In this work, we make an initial attempt towards enabling ChatGPT-like capabilities on drug molecule graphs, by developing a prototype system DrugChat. DrugChat works in a similar way as ChatGPT. Users upload a compound molecule graph and ask various questions about this compound. DrugChat will answer these questions in a multi-turn, interactive manner. The DrugChat system consists of a graph neural network (GNN), a large language model (LLM), and an adaptor. The GNN takes a compound molecule graph as input and learns a representation for this graph. The adaptor transforms the graph representation produced by the GNN into another representation that is acceptable to the LLM. The LLM takes the compound representation transformed by the adaptor and users' questions about this compound as inputs and generates answers. All these components are trained end-to-end. To train DrugChat, we collected instruction tuning datasets which contain 10,834 drug compounds and 143,517 question-answer pairs. The code and data is available at urlhttps://github.com/UCSD-AI4H/drugchat