MicroTraitLLM: A Microbial-focused Large Language Model for Researchers

Thursday, May 29, 2025

1:00 PM-3:00 PM

BIOMED Master's Thesis Defense

Title:
MicroTraitLLM: A Microbial-focused Large Language Model for Researchers

Speaker:
Glen Rogers, Master's Candidate
School of Biomedical Engineering, Science and Health Systems
Drexel University
 
Advisor:
Gail Rosen, PhD
Professor
Department of Electrical and Computer Engineering
EESI Lab
College of Engineering
Drexel University

Details:
Large Language Models (LLMs) have become a focal point of biological and bioinformatics research in recent years. The vast number of applications, in combination with rapidly improving models, make LLMs an enticing point of investigation. However, LLMs often hallucinate if they are not provided with domain-specific information, which can misinform users. Additionally, with the vast number of applications being served in the eukaryotic domain, there has been little investigative research into LLM applications for prokaryotes, which has seen a surge in investigative research thanks to new high-throughput techniques. Furthermore, the current LLM tools for microbe-specific tasks provide insufficient citations, have a restrictive knowledge cutoff, or are too generalized for microbial researchers.
 
Here we present MicroTraitLLM, a retrieval-augmented generation (RAG) system LLM which utilizes zero-shot and single-shot prompting to give specific, citation-based answers for researchers. Its connection to the PubMed Central live-updating, Open Access article database allows for the LLM to remain up-to-date on breakthroughs in the prokaryotic field. MicroTraitLLM can utilize various LLMs for its procedural answer generation, allowing for the user to customize their experience with the LLM they prefer the most. The tool is also instructed on citations, ensuring proper citations for a variety of formats. We show that MicroTraitLLM can respond in a similar time frame to many popular commercial LLMs, maintain relevant literature search, and provides informative answers to microbial experts.

Contact Information

Natalia Broz
njb33@drexel.edu