# Leveraging Chemistry Foundation Models to Facilitate Structure Focused Retrieval Augmented Generation in Multi-Agent Workflows for Catalyst and Materials Design

arXiv: https://arxiv.org/abs/2408.11793 · HTML: https://mlsanity.com/paper/2408.11793/

## Key facts

- Cited by 3 papers in the map (data through 14 Oct 2026).
- Placed in Medical and biomedical RAG, one of 15 directions in Retrieval-augmented generation.
- Builds on 21 of its 44 references that are in the map.
- First posted on arXiv 21 Aug 2024.

## Placed in

- Retrieval-augmented generation / [Medical and biomedical RAG](https://mlsanity.com/rag/medical-and-biomedical-rag/)
- LLM agents and tool use / [Medical and scientific domain agents](https://mlsanity.com/agents/medical-and-scientific-domain-agents/)

## Builds on (most cited first, 21 of 21)

- [Learning Transferable Visual Models From Natural Language Supervision](https://mlsanity.com/paper/2103.00020/) (2021)
- [Retrieval-Augmented Generation for Knowledge-Intensive NLP Tasks](https://mlsanity.com/paper/2005.11401/) (2020)
- [Self-RAG: Learning to Retrieve, Generate, and Critique through Self-Reflection](https://mlsanity.com/paper/2310.11511/) (2023)
- [MoleculeNet: A Benchmark for Molecular Machine Learning](https://mlsanity.com/paper/1703.00564/) (2017)
- [ChemCrow: Augmenting large-language models with chemistry tools](https://mlsanity.com/paper/2304.05376/) (2023)
- [Adaptive-RAG: Learning to Adapt Retrieval-Augmented Large Language Models through Question Complexity](https://mlsanity.com/paper/2403.14403/) (2024)
- [Retrieval-Augmented Generation for AI-Generated Content: A Survey](https://mlsanity.com/paper/2402.19473/) (2024)
- [Molecular Transformer - A Model for Uncertainty-Calibrated Chemical Reaction Prediction](https://mlsanity.com/paper/1811.02633/) (2018)
- [Large-Scale Chemical Language Representations Capture Molecular Structure and Properties](https://mlsanity.com/paper/2106.09553/) (2021)
- [A Survey on Retrieval-Augmented Text Generation](https://mlsanity.com/paper/2202.01110/) (2022)
- [ChemBERTa-2: Towards Chemical Foundation Models](https://mlsanity.com/paper/2209.01712/) (2022)
- [Mapping the Space of Chemical Reactions Using Attention-Based Neural Networks](https://mlsanity.com/paper/2012.06051/) (2020)
- [ProtAgents: Protein discovery via large language model multi-agent collaborations combining physics and machine learning](https://mlsanity.com/paper/2402.04268/) (2024)
- [ChatGPT Chemistry Assistant for Text Mining and Prediction of MOF Synthesis](https://mlsanity.com/paper/2306.11296/) (2023)
- [TransPolymer: a Transformer-based language model for polymer property predictions](https://mlsanity.com/paper/2209.01307/) (2022)
- [AtomAgents: Alloy design and discovery through physics-aware multi-modal multi-agent artificial intelligence](https://mlsanity.com/paper/2407.10022/) (2024)
- [LLaMP: Large Language Model Made Powerful for High-fidelity Materials Knowledge Retrieval and Distillation](https://mlsanity.com/paper/2401.17244/) (2024)
- [Take and Took, Gaggle and Goose, Book and Read: Evaluating the Utility of Vector Differences for Lexical Relation Learning](https://mlsanity.com/paper/1509.01692/) (2015)
- [A graph representation of molecular ensembles for polymer property prediction](https://mlsanity.com/paper/2205.08619/) (2022)
- [GPT-MolBERTa: GPT Molecular Features Language Model for molecular property prediction](https://mlsanity.com/paper/2310.03030/) (2023)
- [Transformers and Large Language Models for Chemistry and Drug Discovery](https://mlsanity.com/paper/2310.06083/) (2023)

## Built on by (most cited first, 3 of 3)

- [Towards Scientific Discovery with Generative AI: Progress, Opportunities, and Challenges](https://mlsanity.com/paper/2412.11427/) (2024)
- [TopoMAS: Large Language Model Driven Topological Materials Multiagent System](https://mlsanity.com/paper/2507.04053/) (2025)
- [MADD: Multi-Agent Drug Discovery Orchestra](https://mlsanity.com/paper/2511.08217/) (2025)

## Abstract (arXiv)

Molecular property prediction and generative design via deep learning models has been the subject of intense research given its potential to accelerate development of new, high-performance materials. More recently, these workflows have been significantly augmented with the advent of large language models (LLMs) and systems of autonomous agents capable of utilizing pre-trained models to make predictions in the context of more complex research tasks. While effective, there is still room for substantial improvement within agentic systems on the retrieval of salient information for material design tasks. Within this context, alternative uses of predictive deep learning models, such as leveraging their latent representations to facilitate cross-modal retrieval augmented generation within agentic systems for task-specific materials design, has remained unexplored. Herein, we demonstrate that large, pre-trained chemistry foundation models can serve as a basis for enabling structure-focused, semantic chemistry information retrieval for both small-molecules, complex polymeric materials, and reactions. Additionally, we show the use of chemistry foundation models in conjunction with multi-modal models such as OpenCLIP facilitate unprecedented queries and information retrieval across multiple characterization data domains. Finally, we demonstrate the integration of these models within multi-agent systems to facilitate structure and topological-based natural language queries and information retrieval for different research tasks.