AskBeacon-performing genomic data exchange and analytics with natural language

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• dc.contributor.author Wickramarachchi, Anuradha
• dc.contributor.author Tonni, Shakila
• dc.contributor.author Majumdar, Sonali
• dc.contributor.author Karimi, Sarvnaz
• dc.contributor.author Kõks, Sulev
• dc.contributor.author Hosking, Brendan
• dc.contributor.author Rambla de Argila, Jordi
• dc.contributor.author Twine, Natalie A.
• dc.contributor.author Jain, Yatish
• dc.contributor.author Bauer, Denis C.
• dc.date.accessioned 2025-05-14T06:01:11Z
• dc.date.available 2025-05-14T06:01:11Z
• dc.date.issued 2025
• dc.description.abstract Motivation: Enabling clinicians and researchers to directly interact with global genomic data resources by removing technological barriers is vital for medical genomics. AskBeacon enables large language models (LLMs) to be applied to securely shared cohorts via the Global Alliance for Genomics and Health Beacon protocol. By simply "asking" Beacon, actionable insights can be gained, analyzed, and made publication-ready. Results: In the Parkinson's Progression Markers Initiative (PPMI), we use natural language to ask whether the sex-differences observed in Parkinson's disease are due to X-linked or autosomal markers. AskBeacon returns a publication-ready visualization showing that for PPMI the autosomal marker occurred 1.4 times more often in males with Parkinson's disease than females, compared to no differences for the X-linked marker. We evaluate commercial and open-weight LLM models, as well as different architectures to identify the best strategy for translating research questions to Beacon queries. AskBeacon implements extensive safety guardrails to ensure that genomic data is not exposed to the LLM directly, and that generated code for data extraction, analysis and visualization process is sanitized and hallucination resistant, so data cannot be leaked or falsified. Availability and implementation: AskBeacon is available at https://github.com/aehrc/AskBeacon.
• dc.format.mimetype application/pdf
• dc.identifier.citation Wickramarachchi A, Tonni S, Majumdar S, Karimi S, Kõks S, Hosking B, et al. AskBeacon-performing genomic data exchange and analytics with natural language. Bioinformatics. 2025 Mar 4;41(3):btaf079. DOI: 10.1093/bioinformatics/btaf079
• dc.identifier.doi http://dx.doi.org/10.1093/bioinformatics/btaf079
• dc.identifier.issn 1367-4803
• dc.identifier.uri http://hdl.handle.net/10230/70381
• dc.language.iso eng
• dc.publisher Oxford University Press
• dc.relation.ispartof Bioinformatics. 2025 Mar 4;41(3):btaf079
• dc.rights © The Author(s) 2025. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.other Genòmica
• dc.title AskBeacon-performing genomic data exchange and analytics with natural language
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion