Stanley Ta

MicrobeRT is a framework of fine-tuned language models for metagenomic analysis, achieving strong performance in taxonomic classification, antibiotic resistance detection, and pathogenicity assessment.

TaxTriage is a metagenomic analysis pipeline that detects putative pathogens in sequencing data using read classification, mapping, and de novo assembly, with comparable performance to cloud-based tools.

This study evaluates parameter-efficient fine-tuning in genomic classification and finds it underperforms compared to full and partial fine-tuning methods.