Common Failure Modes in Pathogen Genomics Machine Learning Pipelines: Lessons for AMR, Fungal and Viral Drug Discovery

Machine learning (ML) promises transformative gains in pathogen genomics — from antimicrobial resistance (AMR) prediction to fungal target identification and rapid viral variant characterization. Yet, across research and translational environments, pipelines that integrate high-throughput sequencing with ML models regularly fail to deliver robust, generalizable outcomes.