Biology-Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability of Large Language Models

• URL: http://arxiv.org/abs/2412.19191v2
• Date: Tue, 23 Sep 2025 12:55:03 GMT
• Title: Biology-Instructions: A Dataset and Benchmark for Multi-Omics Sequence Understanding Capability of Large Language Models
• Authors: Haonan He, Yuchen Ren, Yining Tang, Ziyang Xu, Junxian Li, Minghao Yang, Di Zhang, Dong Yuan, Tao Chen, Shufei Zhang, Yuqiang Li, Nanqing Dong, Wanli Ouyang, Dongzhan Zhou, Peng Ye,
• Abstract summary: We introduce Biology-Instructions, the first large-scale instruction-tuning dataset for multi-omics biological sequences.<n>This dataset bridges large language models (LLMs) and complex biological sequence-related tasks, enhancing their versatility and reasoning.<n>We also highlight significant limitations of current state-of-the-art LLMs on multi-omics tasks without specialized training.
• Score: 55.74944165932666
• License: http://arxiv.org/licenses/nonexclusive-distrib/1.0/
• Abstract: Large language models (LLMs) have shown remarkable capabilities in general domains, but their application to multi-omics biology remains underexplored. To address this gap, we introduce Biology-Instructions, the first large-scale instruction-tuning dataset for multi-omics biological sequences, including DNA, RNA, proteins, and multi-molecules. This dataset bridges LLMs and complex biological sequence-related tasks, enhancing their versatility and reasoning while maintaining conversational fluency. We also highlight significant limitations of current state-of-the-art LLMs on multi-omics tasks without specialized training. To overcome this, we propose ChatMultiOmics, a strong baseline with a novel three-stage training pipeline, demonstrating superior biological understanding through Biology-Instructions. Both resources are publicly available, paving the way for better integration of LLMs in multi-omics analysis. The Biology-Instructions is publicly available at: https://github.com/hhnqqq/Biology-Instructions.

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