{"ID":2871511,"CreatedAt":"2026-06-01T04:54:23.091178241Z","UpdatedAt":"2026-06-01T04:54:23.091178241Z","DeletedAt":null,"paper_url":"https://arxiv.org/abs/2509.12266","arxiv_id":"2509.12266","title":"Genome-Factory: A Library for Tuning, Deploying, and Interpreting Genomic Foundation Models","abstract":"We introduce Genome-Factory, the first integrated Python library for tuning, deploying, and interpreting genomic foundation models. Our core contribution is to simplify and unify the workflow for genomic model development: data collection, model tuning, inference, benchmarking, and interpretability. For data collection, Genome-Factory offers an automated pipeline to download genomic sequences and preprocess them. For model tuning, Genome-Factory supports both full and parameter-efficient fine-tuning across diverse genomic models. For inference, Genome-Factory enables both embedding extraction and DNA sequence generation. For benchmarking, we include two existing benchmarks and provide a flexible interface to incorporate additional benchmarks. For interpretability, Genome-Factory introduces an open-source biological interpreter based on a sparse auto-encoder. We validate the utility of Genome-Factory across three dimensions: (i) Compatibility with diverse models and fine-tuning methods; (ii) Benchmarking downstream performance using two open-source benchmarks; (iii) Biological interpretation of learned representations with DNABERT-2. These results highlight its practical value for real-world genomic analysis. GitHub: https://github.com/WeiminWu2000/Genome_Factory.","short_abstract":"We introduce Genome-Factory, the first integrated Python library for tuning, deploying, and interpreting genomic foundation models. Our core contribution is to simplify and unify the workflow for genomic model development: data collection, model tuning, inference, benchmarking, and interpretability. For data collection...","url_abs":"https://arxiv.org/abs/2509.12266","url_pdf":"https://arxiv.org/pdf/2509.12266v2","authors":"[\"Weimin Wu\",\"Xuefeng Song\",\"Yibo Wen\",\"Qinjie Lin\",\"Zhihan Zhou\",\"Jerry Yao-Chieh Hu\",\"Zhong Wang\",\"Han Liu\"]","published":"2025-09-13T03:31:55Z","proceeding":"q-bio.GN","tasks":"[\"q-bio.GN\",\"cs.LG\"]","methods":"[]","has_code":false,"code_links":[{"ID":609866,"CreatedAt":"2026-06-01T04:54:23.091178241Z","UpdatedAt":"2026-06-01T04:54:23.091178241Z","DeletedAt":null,"paper_id":2871511,"paper_url":"https://arxiv.org/abs/2509.12266","paper_title":"Genome-Factory: A Library for Tuning, Deploying, and Interpreting Genomic Foundation Models","repo_url":"https://github.com/WeiminWu2000/Genome_Factory","is_official":false,"mentioned_in_paper":false,"mentioned_in_github":true,"github_stars":0}]}