{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/venusfactory-a-unified-platform-for-protein","title":"VenusFactory: A Unified Platform for Protein Engineering Data Retrieval and Language Model Fine-Tuning","arxiv_id":"2503.15438","date":"2025-03-19","proceeding":null,"authors":["Yang Tan","Chen Liu","Jingyuan Gao","Banghao Wu","Mingchen Li","Ruilin Wang","Lingrong Zhang","Huiqun Yu","Guisheng Fan","Liang Hong","Bingxin Zhou"],"abstract":"Natural language processing (NLP) has significantly influenced scientific domains beyond human language, including protein engineering, where pre-trained protein language models (PLMs) have demonstrated remarkable success. However, interdisciplinary adoption remains limited due to challenges in data collection, task benchmarking, and application. This work presents VenusFactory, a versatile engine that integrates biological data retrieval, standardized task benchmarking, and modular fine-tuning of PLMs. VenusFactory supports both computer science and biology communities with choices of both a command-line execution and a Gradio-based no-code interface, integrating $40+$ protein-related datasets and $40+$ popular PLMs. All implementations are open-sourced on https://github.com/tyang816/VenusFactory.","url_abs":"https://arxiv.org/abs/2503.15438v1","url_pdf":"https://arxiv.org/pdf/2503.15438v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"venusfactory-a-unified-platform-for-protein","repo_url":"https://github.com/tyang816/venusfactory","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"benchmarking","task_name":"Benchmarking"},{"task_slug":"language-modeling","task_name":"Language Modeling"},{"task_slug":"language-modelling","task_name":"Language Modelling"},{"task_slug":"retrieval","task_name":"Retrieval"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"syntology_url":null,"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}