Harmon Bhasin, Kevin Flyangolts, Dianzhuo Wang +9cs.AI
As pathogen genomic surveillance scales, the bottleneck is shifting from data generation to analysis. We present BioSecBench-Surveillance, a verifiable benchmark of 100 evaluations testing whether AI agents can infer the right analysis pipeline from raw sequencing data and surveillance context. Each evaluation gives an agent only the data and context a human analyst would have, then grades its structured answer deterministically. The tasks span seven categories, from taxonomic classification to genetic-engineering detection, across diverse sample types and sequencing technologies. Across 3,962 gradable attempts from sixteen model-harness pairs, the strongest configuration cleared only about half. Opus 4.8 with PI led at 50.2 percent, with a 95 percent confidence interval of 40.1 to 60.3 percent across 83 evaluations, tied with GPT-5.5 with Codex at 50.2 percent, with a 95 percent confidence interval of 40.8 to 59.6 percent, followed by Opus 4.7 with PI at 49.6 percent, with a 95 percent confidence interval of 40.0 to 59.2 percent, and Sonnet 4.6 with PI at 48.6 percent, with a 95 percent confidence interval of 38.9 to 58.3 percent. Even when agents invoked the correct workflows, their mistakes came from the choices around them, such as which references, thresholds, filters, and normalization to apply. BioSecBench-Surveillance provides a standard for measuring whether agents can be trusted to perform genomic surveillance when the next outbreak arrives.
Hantavirus genomic surveillance is limited by the distribution of sequence data, non-IID source heterogeneity, and constrained expert-review capacity. We propose HantaWatch, a federated learning framework that enables laboratories and surveillance sites to collaboratively train sequence-based models without sharing raw data. HantaWatch integrates k-mer feature extraction, source-aware federated client construction, adaptive DU-FedProx optimization, surveillance-specific model selection, and prediction-only triage. Experiments on binary and multi-class tasks show that HantaWatch supports high-risk screening, outbreak-associated prediction, clade classification, and clinical-syndrome categorization while balancing predictive performance, false-negative risk, and update stability. The framework converts model output into risk scores, confidence estimates, uncertainty flags, and ranked expert-review priorities. HantaWatch therefore provides a practical federated decision-support layer for decentralized Hantavirus surveillance, supporting expert prioritization without replacing laboratory or public-health interpretation.