# Multi-modal Molecule Structure-text Model for Text-based Retrieval and Editing

arXiv: https://arxiv.org/abs/2212.10789 · HTML: https://mlsanity.com/paper/2212.10789/

## Key facts

- Cited by 166 papers in the map (data through 14 Oct 2026).
- Builds on 29 of its 87 references that are in the map.
- First posted on arXiv 21 Dec 2022.

## Builds on (most cited first, 29 of 29)

- [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)
- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [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)
- [A Style-Based Generator Architecture for Generative Adversarial Networks](https://mlsanity.com/paper/1812.04948/) (2018)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [GLIDE: Towards Photorealistic Image Generation and Editing with Text-Guided Diffusion Models](https://mlsanity.com/paper/2112.10741/) (2021)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [StyleCLIP: Text-Driven Manipulation of StyleGAN Imagery](https://mlsanity.com/paper/2103.17249/) (2021)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [E(n) Equivariant Graph Neural Networks](https://mlsanity.com/paper/2102.09844/) (2021)
- [Open-vocabulary Object Detection via Vision and Language Knowledge Distillation](https://mlsanity.com/paper/2104.13921/) (2021)
- [Convolutional Networks on Graphs for Learning Molecular Fingerprints](https://mlsanity.com/paper/1509.09292/) (2015)
- [Contrastive Multi-View Representation Learning on Graphs](https://mlsanity.com/paper/2006.05582/) (2020)
- [MineDojo: Building Open-Ended Embodied Agents with Internet-Scale Knowledge](https://mlsanity.com/paper/2206.08853/) (2022)
- [InfoGraph: Unsupervised and Semi-supervised Graph-Level Representation Learning via Mutual Information Maximization](https://mlsanity.com/paper/1908.01000/) (2019)
- [Pre-training Molecular Graph Representation with 3D Geometry](https://mlsanity.com/paper/2110.07728/) (2021)
- [Pre-Trained Language Models for Interactive Decision-Making](https://mlsanity.com/paper/2202.01771/) (2022)
- [Hierarchical Generation of Molecular Graphs using Structural Motifs](https://mlsanity.com/paper/2002.03230/) (2020)
- [Construction of the Literature Graph in Semantic Scholar](https://mlsanity.com/paper/1805.02262/) (2018)
- [Geometric Deep Learning on Molecular Representations](https://mlsanity.com/paper/2107.12375/) (2021)
- [N-Gram Graph: Simple Unsupervised Representation for Graphs, with Applications to Molecules](https://mlsanity.com/paper/1806.09206/) (2018)
- [Molecular Geometry Pretraining with SE(3)-Invariant Denoising Distance Matching](https://mlsanity.com/paper/2206.13602/) (2022)
- [DrugOOD: Out-of-Distribution (OOD) Dataset Curator and Benchmark for AI-aided Drug Discovery -- A Focus on Affinity Prediction Problems with Noise Annotations](https://mlsanity.com/paper/2201.09637/) (2022)
- [Retrieval-based Controllable Molecule Generation](https://mlsanity.com/paper/2208.11126/) (2022)
- [Evaluating Self-Supervised Learning for Molecular Graph Embeddings](https://mlsanity.com/paper/2206.08005/) (2022)

## Built on by (most cited first, 30 of 166)

- [A Survey on RAG Meeting LLMs: Towards Retrieval-Augmented Large Language Models](https://mlsanity.com/paper/2405.06211/) (2024)
- [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)
- [AdaShield: Safeguarding Multimodal Large Language Models from Structure-based Attack via Adaptive Shield Prompting](https://mlsanity.com/paper/2403.09513/) (2024)
- [Rethinking Interpretability in the Era of Large Language Models](https://mlsanity.com/paper/2402.01761/) (2024)
- [Graph Foundation Models: Concepts, Opportunities and Challenges](https://mlsanity.com/paper/2310.11829/) (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)
- [Empowering Molecule Discovery for Molecule-Caption Translation with Large Language Models: A ChatGPT Perspective](https://mlsanity.com/paper/2306.06615/) (2023)
- [InstructMol: Multi-Modal Integration for Building a Versatile and Reliable Molecular Assistant in Drug Discovery](https://mlsanity.com/paper/2311.16208/) (2023)
- [A Survey of Graph Meets Large Language Model: Progress and Future Directions](https://mlsanity.com/paper/2311.12399/) (2023)
- [ZeroG: Investigating Cross-dataset Zero-shot Transferability in Graphs](https://mlsanity.com/paper/2402.11235/) (2024)
- [GIT-Mol: A Multi-modal Large Language Model for Molecular Science with Graph, Image, and Text](https://mlsanity.com/paper/2308.06911/) (2023)
- [Scientific Large Language Models: A Survey on Biological & Chemical Domains](https://mlsanity.com/paper/2401.14656/) (2024)
- [ProtST: Multi-Modality Learning of Protein Sequences and Biomedical Texts](https://mlsanity.com/paper/2301.12040/) (2023)
- [Foundation Model for Advancing Healthcare: Challenges, Opportunities, and Future Directions](https://mlsanity.com/paper/2404.03264/) (2024)
- [A Survey of Large Language Models for Graphs](https://mlsanity.com/paper/2405.08011/) (2024)
- [GIMLET: A Unified Graph-Text Model for Instruction-Based Molecule Zero-Shot Learning](https://mlsanity.com/paper/2306.13089/) (2023)
- [Visual-RolePlay: Universal Jailbreak Attack on MultiModal Large Language Models via Role-playing Image Character](https://mlsanity.com/paper/2405.20773/) (2024)
- [Towards 3D Molecule-Text Interpretation in Language Models](https://mlsanity.com/paper/2401.13923/) (2024)
- [A Text-guided Protein Design Framework](https://mlsanity.com/paper/2302.04611/) (2023)
- [Efficient Evolutionary Search Over Chemical Space with Large Language Models](https://mlsanity.com/paper/2406.16976/) (2024)
- [MolFM: A Multimodal Molecular Foundation Model](https://mlsanity.com/paper/2307.09484/) (2023)
- [Enhancing Activity Prediction Models in Drug Discovery with the Ability to Understand Human Language](https://mlsanity.com/paper/2303.03363/) (2023)
- [GLBench: A Comprehensive Benchmark for Graph with Large Language Models](https://mlsanity.com/paper/2407.07457/) (2024)
- [ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback](https://mlsanity.com/paper/2402.10980/) (2024)
- [A Group Symmetric Stochastic Differential Equation Model for Molecule Multi-modal Pretraining](https://mlsanity.com/paper/2305.18407/) (2023)
- [ChatGPT-powered Conversational Drug Editing Using Retrieval and Domain Feedback](https://mlsanity.com/paper/2305.18090/) (2023)
- [Text-Guided Molecule Generation with Diffusion Language Model](https://mlsanity.com/paper/2402.13040/) (2024)

## Abstract (arXiv)

There is increasing adoption of artificial intelligence in drug discovery. However, existing studies use machine learning to mainly utilize the chemical structures of molecules but ignore the vast textual knowledge available in chemistry. Incorporating textual knowledge enables us to realize new drug design objectives, adapt to text-based instructions and predict complex biological activities. Here we present a multi-modal molecule structure-text model, MoleculeSTM, by jointly learning molecules' chemical structures and textual descriptions via a contrastive learning strategy. To train MoleculeSTM, we construct a large multi-modal dataset, namely, PubChemSTM, with over 280,000 chemical structure-text pairs. To demonstrate the effectiveness and utility of MoleculeSTM, we design two challenging zero-shot tasks based on text instructions, including structure-text retrieval and molecule editing. MoleculeSTM has two main properties: open vocabulary and compositionality via natural language. In experiments, MoleculeSTM obtains the state-of-the-art generalization ability to novel biochemical concepts across various benchmarks.