Network for knowledge Organization (NEKO): An AI knowledge mining workflow for synthetic biology research
Zhengyang Xiao, Himadri B. Pakrasi, Yixin Chen, Yinjie Tang
Abstract
Large language models (LLMs) can complete general scientific question-and-answer, yet they are constrained by their pretraining cut-off dates and lack the ability to provide specific, cited scientific knowledge. Here, we introduce Ne twork for K nowledge O rganization (NEKO), a workflow that uses LLM Qwen to extract knowledge through scientific literature text mining. When user inputs a keyword of interest, NEKO can generate knowledge graphs to link bioinformation entities and produce comprehensive summaries from PubMed search. NEKO significantly enhance LLM ability and has immediate applications in daily academic tasks such as education of young scientists, literature review, paper writing, experiment planning/troubleshooting, and new ideas/hypothesis generation. We exemplified this workflow's applicability through several case studies on yeast fermentation and cyanobacterial biorefinery. NEKO's output is more informative, specific, and actionable than GPT-4's zero-shot Q&A. NEKO offers flexible, lightweight local deployment options. NEKO democratizes artificial intelligence (AI) tools, making scientific foundation model more accessible to researchers without excessive computational power. • NEKO enhances LLMs by integrating PubMed searches. • NEKO's RAG output is more specific and actionable than GPT-4's zero-shot Q&A. • This work democratizes AI tools by enabling lightweight, local deployment, making LLM/AI tools accessible to researchers.