{"paper":{"title":"Gene-R1: Reasoning with Data-Augmented Lightweight LLMs for Gene Set Analysis","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cs.AI"],"primary_cat":"q-bio.GN","authors_text":"Qiao Jin, Yifan Yang, Zhiyong Lu, Zhizheng Wang","submitted_at":"2025-09-11T17:14:08Z","abstract_excerpt":"The gene set analysis (GSA) is a foundational approach for uncovering the molecular functions associated with a group of genes. Recently, LLM-powered methods have emerged to annotate gene sets with biological functions together with coherent explanatory insights. However, existing studies primarily focus on proprietary models, which have been shown to outperform their open-source counterparts despite concerns over cost and data privacy. Furthermore, no research has investigated the application of advanced reasoning strategies to the GSA task. To address this gap, we introduce Gene-R1, a data-a"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2509.10575","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2509.10575/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}