# ChatGPT-powered Conversational Drug Editing Using Retrieval and Domain Feedback

arXiv: https://arxiv.org/abs/2305.18090 · HTML: https://mlsanity.com/paper/2305.18090/

## Key facts

- Cited by 31 papers in the map (data through 14 Oct 2026).
- Builds on 48 of its 97 references that are in the map.
- First posted on arXiv 29 May 2023.

## Builds on (most cited first, 30 of 48)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [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)
- [Hierarchical Text-Conditional Image Generation with CLIP Latents](https://mlsanity.com/paper/2204.06125/) (2022)
- [Large Language Models are Zero-Shot Reasoners](https://mlsanity.com/paper/2205.11916/) (2022)
- [Learning Phrase Representations using RNN Encoder-Decoder for Statistical Machine Translation](https://mlsanity.com/paper/1406.1078/) (2014)
- [GLIDE: Towards Photorealistic Image Generation and Editing with Text-Guided Diffusion Models](https://mlsanity.com/paper/2112.10741/) (2021)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Scaling Instruction-Finetuned Language Models](https://mlsanity.com/paper/2210.11416/) (2022)
- [XLNet: Generalized Autoregressive Pretraining for Language Understanding](https://mlsanity.com/paper/1906.08237/) (2019)
- [Pre-train, Prompt, and Predict: A Systematic Survey of Prompting Methods in Natural Language Processing](https://mlsanity.com/paper/2107.13586/) (2021)
- [Rethinking the Role of Demonstrations: What Makes In-Context Learning Work?](https://mlsanity.com/paper/2202.12837/) (2022)
- [Large Language Models Are Human-Level Prompt Engineers](https://mlsanity.com/paper/2211.01910/) (2022)
- [StyleCLIP: Text-Driven Manipulation of StyleGAN Imagery](https://mlsanity.com/paper/2103.17249/) (2021)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [An Explanation of In-context Learning as Implicit Bayesian Inference](https://mlsanity.com/paper/2111.02080/) (2021)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [Tensor field networks: Rotation- and translation-equivariant neural networks for 3D point clouds](https://mlsanity.com/paper/1802.08219/) (2018)
- [Galactica: A Large Language Model for Science](https://mlsanity.com/paper/2211.09085/) (2022)
- [Large Language Models Can Self-Improve](https://mlsanity.com/paper/2210.11610/) (2022)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [MineDojo: Building Open-Ended Embodied Agents with Internet-Scale Knowledge](https://mlsanity.com/paper/2206.08853/) (2022)
- [Equivariant message passing for the prediction of tensorial properties and molecular spectra](https://mlsanity.com/paper/2102.03150/) (2021)
- [Analyzing Learned Molecular Representations for Property Prediction](https://mlsanity.com/paper/1904.01561/) (2019)
- [Do Prompt-Based Models Really Understand the Meaning of their Prompts?](https://mlsanity.com/paper/2109.01247/) (2021)
- [AutoPrompt: Eliciting Knowledge from Language Models with Automatically Generated Prompts](https://mlsanity.com/paper/2010.15980/) (2020)
- [Molecular Graph Convolutions: Moving Beyond Fingerprints](https://mlsanity.com/paper/1603.00856/) (2016)
- [PTR: Prompt Tuning with Rules for Text Classification](https://mlsanity.com/paper/2105.11259/) (2021)

## Built on by (most cited first, 30 of 31)

- [Prompt Injection attack against LLM-integrated Applications](https://mlsanity.com/paper/2306.05499/) (2023)
- [LlaSMol: Advancing Large Language Models for Chemistry with a Large-Scale, Comprehensive, High-Quality Instruction Tuning Dataset](https://mlsanity.com/paper/2402.09391/) (2024)
- [A Comprehensive Survey of Scientific Large Language Models and Their Applications in Scientific Discovery](https://mlsanity.com/paper/2406.10833/) (2024)
- [Scientific Large Language Models: A Survey on Biological & Chemical Domains](https://mlsanity.com/paper/2401.14656/) (2024)
- [DrugAssist: A Large Language Model for Molecule Optimization](https://mlsanity.com/paper/2401.10334/) (2023)
- [BioDiscoveryAgent: An AI Agent for Designing Genetic Perturbation Experiments](https://mlsanity.com/paper/2405.17631/) (2024)
- [BioPlanner: Automatic Evaluation of LLMs on Protocol Planning in Biology](https://mlsanity.com/paper/2310.10632/) (2023)
- [ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback](https://mlsanity.com/paper/2402.10980/) (2024)
- [LICO: Large Language Models for In-Context Molecular Optimization](https://mlsanity.com/paper/2406.18851/) (2024)
- [Large Language Models in Drug Discovery and Development: From Disease Mechanisms to Clinical Trials](https://mlsanity.com/paper/2409.04481/) (2024)
- [Symmetry-Informed Geometric Representation for Molecules, Proteins, and Crystalline Materials](https://mlsanity.com/paper/2306.09375/) (2023)
- [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)
- [Monte Carlo Thought Search: Large Language Model Querying for Complex Scientific Reasoning in Catalyst Design](https://mlsanity.com/paper/2310.14420/) (2023)
- [LLMs as Visual Explainers: Advancing Image Classification with Evolving Visual Descriptions](https://mlsanity.com/paper/2311.11904/) (2023)
- [BioKGBench: A Knowledge Graph Checking Benchmark of AI Agent for Biomedical Science](https://mlsanity.com/paper/2407.00466/) (2024)
- [BioMaze: Benchmarking and Enhancing Large Language Models for Biological Pathway Reasoning](https://mlsanity.com/paper/2502.16660/) (2025)
- [From Text to Life: On the Reciprocal Relationship between Artificial Life and Large Language Models](https://mlsanity.com/paper/2407.09502/) (2024)
- [Reflections from the 2024 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry](https://mlsanity.com/paper/2411.15221/) (2024)
- [Image and Data Mining in Reticular Chemistry Using GPT-4V](https://mlsanity.com/paper/2312.05468/) (2023)
- [Entropy-Reinforced Planning with Large Language Models for Drug Discovery](https://mlsanity.com/paper/2406.07025/) (2024)
- [Computational Protein Science in the Era of Large Language Models (LLMs)](https://mlsanity.com/paper/2501.10282/) (2025)
- [GPT vs Human for Scientific Reviews: A Dual Source Review on Applications of ChatGPT in Science](https://mlsanity.com/paper/2312.03769/) (2023)
- [De Novo Molecular Design Enabled by Direct Preference Optimization and Curriculum Learning](https://mlsanity.com/paper/2504.01389/) (2025)
- [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)
- [How to Enable Effective Cooperation Between Humans and NLP Models: A Survey of Principles, Formalizations, and Beyond](https://mlsanity.com/paper/2501.05714/) (2025)
- [Towards Diverse Scientific Hypothesis Search with Large Language Models](https://mlsanity.com/paper/2606.10587/) (2026)
- [Deciphering Scientific Reasoning Steps from Outcome Data for Molecule Optimization](https://mlsanity.com/paper/2603.20262/) (2026)
- [C-MORAL: Controllable Multi-Objective Molecular Optimization with Reinforcement Alignment for LLMs](https://mlsanity.com/paper/2604.23061/) (2026)

## Abstract (arXiv)

Recent advancements in conversational large language models (LLMs), such as ChatGPT, have demonstrated remarkable promise in various domains, including drug discovery. However, existing works mainly focus on investigating the capabilities of conversational LLMs on chemical reaction and retrosynthesis. While drug editing, a critical task in the drug discovery pipeline, remains largely unexplored. To bridge this gap, we propose ChatDrug, a framework to facilitate the systematic investigation of drug editing using LLMs. ChatDrug jointly leverages a prompt module, a retrieval and domain feedback (ReDF) module, and a conversation module to streamline effective drug editing. We empirically show that ChatDrug reaches the best performance on 33 out of 39 drug editing tasks, encompassing small molecules, peptides, and proteins. We further demonstrate, through 10 case studies, that ChatDrug can successfully identify the key substructures (e.g., the molecule functional groups, peptide motifs, and protein structures) for manipulation, generating diverse and valid suggestions for drug editing. Promisingly, we also show that ChatDrug can offer insightful explanations from a domain-specific perspective, enhancing interpretability and enabling informed decision-making. This research sheds light on the potential of ChatGPT and conversational LLMs for drug editing. It paves the way for a more efficient and collaborative drug discovery pipeline, contributing to the advancement of pharmaceutical research and development.