# A Molecular Multimodal Foundation Model Associating Molecule Graphs with Natural Language

arXiv: https://arxiv.org/abs/2209.05481 · HTML: https://mlsanity.com/paper/2209.05481/

## Key facts

- Cited by 131 papers in the map (data through 14 Oct 2026).
- Builds on 41 of its 80 references that are in the map.
- First posted on arXiv 12 Sep 2022.

## Builds on (most cited first, 30 of 41)

- [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)
- [PyTorch: An Imperative Style, High-Performance Deep Learning Library](https://mlsanity.com/paper/1912.01703/) (2019)
- [A Simple Framework for Contrastive Learning of Visual Representations](https://mlsanity.com/paper/2002.05709/) (2020)
- [Representation Learning with Contrastive Predictive Coding](https://mlsanity.com/paper/1807.03748/) (2018)
- [Momentum Contrast for Unsupervised Visual Representation Learning](https://mlsanity.com/paper/1911.05722/) (2019)
- [Inductive Representation Learning on Large Graphs](https://mlsanity.com/paper/1706.02216/) (2017)
- [How Powerful are Graph Neural Networks?](https://mlsanity.com/paper/1810.00826/) (2018)
- [Scaling Up Visual and Vision-Language Representation Learning With Noisy Text Supervision](https://mlsanity.com/paper/2102.05918/) (2021)
- [Neural Message Passing for Quantum Chemistry](https://mlsanity.com/paper/1704.01212/) (2017)
- [Open Graph Benchmark: Datasets for Machine Learning on Graphs](https://mlsanity.com/paper/2005.00687/) (2020)
- [BioBERT: a pre-trained biomedical language representation model for biomedical text mining](https://mlsanity.com/paper/1901.08746/) (2019)
- [Unsupervised Feature Learning via Non-Parametric Instance-level Discrimination](https://mlsanity.com/paper/1805.01978/) (2018)
- [SciBERT: A Pretrained Language Model for Scientific Text](https://mlsanity.com/paper/1903.10676/) (2019)
- [Learning deep representations by mutual information estimation and maximization](https://mlsanity.com/paper/1808.06670/) (2018)
- [Oscar: Object-Semantics Aligned Pre-training for Vision-Language Tasks](https://mlsanity.com/paper/2004.06165/) (2020)
- [Graph Contrastive Learning with Augmentations](https://mlsanity.com/paper/2010.13902/) (2020)
- [Deep Graph Infomax](https://mlsanity.com/paper/1809.10341/) (2018)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [Strategies for Pre-training Graph Neural Networks](https://mlsanity.com/paper/1905.12265/) (2019)
- [Automatic chemical design using a data-driven continuous representation of molecules](https://mlsanity.com/paper/1610.02415/) (2016)
- [Junction Tree Variational Autoencoder for Molecular Graph Generation](https://mlsanity.com/paper/1802.04364/) (2018)
- [Supervision Exists Everywhere: A Data Efficient Contrastive Language-Image Pre-training Paradigm](https://mlsanity.com/paper/2110.05208/) (2021)
- [ChemBERTa: Large-Scale Self-Supervised Pretraining for Molecular Property Prediction](https://mlsanity.com/paper/2010.09885/) (2020)
- [GraphAF: a Flow-based Autoregressive Model for Molecular Graph Generation](https://mlsanity.com/paper/2001.09382/) (2020)
- [Grammar Variational Autoencoder](https://mlsanity.com/paper/1703.01925/) (2017)
- [Adversarial Graph Augmentation to Improve Graph Contrastive Learning](https://mlsanity.com/paper/2106.05819/) (2021)
- [MoFlow: An Invertible Flow Model for Generating Molecular Graphs](https://mlsanity.com/paper/2006.10137/) (2020)
- [GraphDF: A Discrete Flow Model for Molecular Graph Generation](https://mlsanity.com/paper/2102.01189/) (2021)
- [Translation between Molecules and Natural Language](https://mlsanity.com/paper/2204.11817/) (2022)

## Built on by (most cited first, 30 of 131)

- [A Comprehensive Survey of AI-Generated Content (AIGC): A History of Generative AI from GAN to ChatGPT](https://mlsanity.com/paper/2303.04226/) (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)
- [Graph Foundation Models: Concepts, Opportunities and Challenges](https://mlsanity.com/paper/2310.11829/) (2023)
- [BioT5: Enriching Cross-modal Integration in Biology with Chemical Knowledge and Natural Language Associations](https://mlsanity.com/paper/2310.07276/) (2023)
- [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)
- [MolXPT: Wrapping Molecules with Text for Generative Pre-training](https://mlsanity.com/paper/2305.10688/) (2023)
- [Scientific Large Language Models: A Survey on Biological & Chemical Domains](https://mlsanity.com/paper/2401.14656/) (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)
- [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)
- [GOFA: A Generative One-For-All Model for Joint Graph Language Modeling](https://mlsanity.com/paper/2407.09709/) (2024)
- [BioT5+: Towards Generalized Biological Understanding with IUPAC Integration and Multi-task Tuning](https://mlsanity.com/paper/2402.17810/) (2024)
- [MolFM: A Multimodal Molecular Foundation Model](https://mlsanity.com/paper/2307.09484/) (2023)
- [SNIP: Bridging Mathematical Symbolic and Numeric Realms with Unified Pre-training](https://mlsanity.com/paper/2310.02227/) (2023)
- [A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers](https://mlsanity.com/paper/2508.21148/) (2025)
- [ChemReasoner: Heuristic Search over a Large Language Model's Knowledge Space using Quantum-Chemical Feedback](https://mlsanity.com/paper/2402.10980/) (2024)
- [Graph Machine Learning in the Era of Large Language Models (LLMs)](https://mlsanity.com/paper/2404.14928/) (2024)
- [Towards Graph Foundation Models: Learning Generalities Across Graphs via Task-Trees](https://mlsanity.com/paper/2412.16441/) (2024)
- [ChatGPT-powered Conversational Drug Editing Using Retrieval and Domain Feedback](https://mlsanity.com/paper/2305.18090/) (2023)
- [Heterogeneous Contrastive Learning for Foundation Models and Beyond](https://mlsanity.com/paper/2404.00225/) (2024)
- [ProtT3: Protein-to-Text Generation for Text-based Protein Understanding](https://mlsanity.com/paper/2405.12564/) (2024)
- [Speak-to-Structure: Evaluating LLMs in Open-domain Natural Language-Driven Molecule Generation](https://mlsanity.com/paper/2412.14642/) (2024)

## Abstract (arXiv)

Although artificial intelligence (AI) has made significant progress in understanding molecules in a wide range of fields, existing models generally acquire the single cognitive ability from the single molecular modality. Since the hierarchy of molecular knowledge is profound, even humans learn from different modalities including both intuitive diagrams and professional texts to assist their understanding. Inspired by this, we propose a molecular multimodal foundation model which is pretrained from molecular graphs and their semantically related textual data (crawled from published Scientific Citation Index papers) via contrastive learning. This AI model represents a critical attempt that directly bridges molecular graphs and natural language. Importantly, through capturing the specific and complementary information of the two modalities, our proposed model can better grasp molecular expertise. Experimental results show that our model not only exhibits promising performance in cross-modal tasks such as cross-modal retrieval and molecule caption, but also enhances molecular property prediction and possesses capability to generate meaningful molecular graphs from natural language descriptions. We believe that our model would have a broad impact on AI-empowered fields across disciplines such as biology, chemistry, materials, environment, and medicine, among others.