VenusFactory: A Unified Platform for Protein Engineering Data Retrieval and Language Model Fine-Tuning

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.