Thought Graph: Generating Thought Process for Biological Reasoning

arXiv:2403.07144v1 Announce Type: new
Abstract: We present the Thought Graph as a novel framework to support complex reasoning and use gene set analysis as an example to uncover semantic relationships between biological processes. Our framework stands out for its ability to provide a deeper understanding of gene sets, significantly surpassing GSEA by 40.28% and LLM baselines by 5.38% based on cosine similarity to human annotations. Our analysis further provides insights into future directions of biological processes naming, and implications for …

abstract analysis arxiv cs.cl example framework gene graph novel process processes reasoning relationships semantic set support thought type understanding