Thought Graph: Generating Thought Process for Biological Reasoning
<|reference_start|>Thought Graph: Generating Thought Process for Biological Reasoning: 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 bioinformatics and precision medicine.<|reference_end|>
@article{hsu2024thought,
    title={Thought Graph: Generating Thought Process for Biological Reasoning},
    author={Chi-Yang Hsu, Kyle Cox, Jiawei Xu, Zhen Tan, Tianhua Zhai, Mengzhou
  Hu, Dexter Pratt, Tianlong Chen, Ziniu Hu, Ying Ding},
    journal={arXiv preprint arXiv:2403.07144},
    year={2024},
    doi={10.1145/3589335.3651572},
    archivePrefix={arXiv},
    eprint={2403.07144},
    primaryClass={cs.CL}
}