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

arXiv: https://arxiv.org/abs/2410.11499 · HTML: https://mlsanity.com/paper/2410.11499/

## Key facts

- Cited by 1 papers in the map (data through 14 Oct 2026).
- Builds on 16 of its 46 references that are in the map.
- First posted on arXiv 15 Oct 2024.

## Builds on (most cited first, 16 of 16)

- [The Llama 3 Herd of Models](https://mlsanity.com/paper/2407.21783/) (2024)
- [RoFormer: Enhanced Transformer with Rotary Position Embedding](https://mlsanity.com/paper/2104.09864/) (2021)
- [FlashAttention-2: Faster Attention with Better Parallelism and Work Partitioning](https://mlsanity.com/paper/2307.08691/) (2023)
- [Gemma 2: Improving Open Language Models at a Practical Size](https://mlsanity.com/paper/2408.00118/) (2024)
- [Phi-3 Technical Report: A Highly Capable Language Model Locally on Your Phone](https://mlsanity.com/paper/2404.14219/) (2024)
- [The FineWeb Datasets: Decanting the Web for the Finest Text Data at Scale](https://mlsanity.com/paper/2406.17557/) (2024)
- [Textbooks Are All You Need](https://mlsanity.com/paper/2306.11644/) (2023)
- [Large Language Models: A Survey](https://mlsanity.com/paper/2402.06196/) (2024)
- [Evaluating Protein Transfer Learning with TAPE](https://mlsanity.com/paper/1906.08230/) (2019)
- [HyenaDNA: Long-Range Genomic Sequence Modeling at Single Nucleotide Resolution](https://mlsanity.com/paper/2306.15794/) (2023)
- [ProtTrans: Towards Cracking the Language of Life's Code Through Self-Supervised Deep Learning and High Performance Computing](https://mlsanity.com/paper/2007.06225/) (2020)
- [ProGen2: Exploring the Boundaries of Protein Language Models](https://mlsanity.com/paper/2206.13517/) (2022)
- [DNABERT-2: Efficient Foundation Model and Benchmark For Multi-Species Genome](https://mlsanity.com/paper/2306.15006/) (2023)
- [Caduceus: Bi-Directional Equivariant Long-Range DNA Sequence Modeling](https://mlsanity.com/paper/2403.03234/) (2024)
- [Does your data spark joy? Performance gains from domain upsampling at the end of training](https://mlsanity.com/paper/2406.03476/) (2024)
- [ncRNA Classification with Graph Convolutional Networks](https://mlsanity.com/paper/1905.06515/) (2019)

## Built on by (most cited first, 1 of 1)

- [Life-Code: Central Dogma Modeling with Multi-Omics Sequence Unification](https://mlsanity.com/paper/2502.07299/) (2025)

## Abstract (arXiv)

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.