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arXiv · 2410.11499

BSM: Small but Powerful Biological Sequence Model for Genes and Proteins

Weixi Xiang·Xueting Han·Xiujuan Chai·Jing Bai
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Abstract

Modeling biological sequences such as DNA, RNA, and proteins is crucial for understanding complex processes like gene regulation and protein synthesis. However, most current models either focus on a single type or treat multiple types of data separately, limiting their ability to capture cross-modal relationships. We propose that by learning the relationships between these modalities, the model can enhance its understanding of each type. To address this, we introduce BSM, a small but powerful mixed-modal biological sequence foundation model, trained on three types of data: RefSeq, Gene Related Sequences, and interleaved biological sequences from the web. These datasets capture the genetic flow, gene-protein relationships, and the natural co-occurrence of diverse biological data, respectively. By training on mixed-modal data, BSM significantly enhances learning efficiency and cross-modal representation, outperforming models trained solely on unimodal data. With only 110M parameters, BSM achieves performance comparable to much larger models across both single-modal and mixed-modal tasks, and uniquely demonstrates in-context learning capability for mixed-modal tasks, which is absent in existing models. Further scaling to 270M parameters demonstrates even greater performance gains, highlighting the potential of BSM as a significant advancement in multimodal biological sequence modeling.

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Weixi Xiang, Xueting Han, Xiujuan Chai, Jing Bai. 2024-10-15. BSM: Small but Powerful Biological Sequence Model for Genes and Proteins. https://arxiv.org/abs/2410.11499

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