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

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 LLM-driven 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 the agentic systems on the retrieval of salient information for material design tasks. Moreover, alternative uses of predictive deep learning models, such as leveraging their latent representations to facilitate cross-modal retrieval augmented generation within agentic systems to enable task-specific materials design, has remained unexplored. Herein, we demonstrate that large, pre-trained chemistry foundation models can serve as a basis for enabling 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 image models such as OpenCLIP facilitate unprecedented queries and information retrieval across multiple characterization data domains. Finally, we demonstrate the integration of these systems within multi-agent systems to facilitate structure and topological-based natural language queries and information retrieval for complex research tasks.

Language models in molecular discovery

The success of language models, especially transformer-based architectures, has trickled into other domains giving rise to "scientific language models" that operate on small molecules, proteins or polymers. In chemistry, language models contribute to accelerating the molecule discovery cycle as evidenced by promising recent findings in early-stage drug discovery. Here, we review the role of language models in molecular discovery, underlining their strength in de novo drug design, property prediction and reaction chemistry. We highlight valuable open-source software assets thus lowering the entry barrier to the field of scientific language modeling. Last, we sketch a vision for future molecular design that combines a chatbot interface with access to computational chemistry tools. Our contribution serves as a valuable resource for researchers, chemists, and AI enthusiasts interested in understanding how language models can and will be used to accelerate chemical discovery.