Poster
in
Workshop: Accessible and Efficient Foundation Models for Biological Discovery
Geometric Algebra based encoding for graph prompting
Sotirios Panagiotis Chytas · Rudrasis Chakraborty · Vikas Singh
Keywords: [ PPI ] [ Fock space ] [ LLM ] [ Algebraic representation ]
Recent results show that modern Large Language Models (LLM) are indeed capable of understanding and answering questions about structured data such as graphs. %Works like GraphToken and GraphLLM have demonstrated, Existing proposals often use some description of the graph to create an ``augmented'' prompt fed to the LLM. For a chosen class of graphs, if a well-tailored graph encoder is deployed to play together with a pre-trained LLM, the model can answer graph-related questions well. %In this work, we expand greatly on these approaches. Existing solutions to graph-based prompts range from graph serialization to graph transformers. In this work, we show that the use of a parameter-free graph encoder based on Fock space representations, a concept borrowed from mathematical physics, is remarkably versatile in this problem setting. The simple construction, inherited directly from the theory with a few small adjustments, can provide rich and informative graph encodings, for a wide range of different graphs. We investigate the use of this idea for prefix-tuned prompts leveraging the capabilities of a pre-trained, frozen LLM. The modifications lead to a model that can answer graph-related questions -- from simple graphs to proteins to hypergraphs -- effectively and with minimal, if any, adjustments to the architecture. Our work significantly simplifies existing solutions and generalizes well to multiple different graph-based structures effortlessly.