C-G.C.05: Grounding AI Agents in Viral Genomics: A Deterministic Retrieval Layer for Reliable Autonomous Surveillance
Sarah Gurev
Broad Institute, MIT, FutureHouse
Patrick Varilly
Broad Institute
Krithik Ramesh
Lyra Labs
Nuala A. O'Leary
NCBI
Jonah Cool
Anthropic
Bernhard Y. Renard
Hasso Plattner Institute
Pardis C. Sabeti
Broad Institute, Harvard, Howard Hughes Medical Institute
Laura Luebbert
Broad Institute, FutureHouse, Harvard
[sponser-meet-now-chat][/sponser-meet-now-chat]
As Large Language Models (LLMs) transition from conversational assistants to autonomous research agents, their ability to interface with primary genomic databases becomes critical. However, the stochastic nature of LLMs is fundamentally at odds with the deterministic precision required for viral sequence retrieval. When navigating the multi-dimensional metadata of repositories like NCBI Virus, state-of-the-art agents (including GPT-5.5, Claude Sonnet 4, Edison and Biomni) frequently "hallucinate" query parameters or fail to navigate complex web-based filtering logic, leading to corrupted datasets and invalid downstream biological conclusions.
We present gget virus, a programmatic framework that formalizes the full filtering logic of the NCBI Virus portal into a deterministic system. To evaluate its impact, we developed VirBench, a curated benchmark of 120 complex virological queries. We demonstrate that unconstrained AI agents achieve a retrieval accuracy of only 16.9-91.3% with high inter-run variability. By equipping these agents with gget virus as a tool-use layer, accuracy increases to >90% across all systems, while ensuring exact-match semantics. Furthermore, the framework's "metadata-first" retrieval strategy reduces data transfer by >98% compared to bulk download methods. By bridging the gap between natural language intent and precise data acquisition, gget virus provides the necessary infrastructure for reproducible, AI-driven viral discovery and genomic surveillance. The manual and source code are available at https://scverse.org/gget/en/virus.html and https://github.com/scverse/gget/blob/main/gget/gget_virus.py, respectively.
Co-authors: Sarah Gurev, Patrick Varilly, Krithik Ramesh, Nuala A. O'Leary, Jonah Cool, Bernhard Y. Renard, Pardis C. Sabeti, Laura Luebbert
Contact Attendee
Warning: Attempt to read property "user_email" on string in /home/1276969.cloudwaysapps.com/ydbgzhdjeq/public_html/wp-content/plugins/my-conference-now/functions.php on line 2826