BioMatrix: Towards a Comprehensive Biological Foundation Model Spanning the Modality Matrix of Sequences, Structures, and Language
We present BioMatrix, the first multimodal foundation model that natively integrates sequences, structures, and natural language for both molecules and proteins within a single decoder-only architecture. Existing biological foundation models pursue native multimodality and broad entity coverage separately: those that fuse multiple modalities under a shared objective remain confined to a single entity type, while those spanning multiple entity types either omit explicit structural modeling or rely on adapter-based designs in which the model cannot natively generate the very modalities it can read. BioMatrix closes this gap by mapping molecular sequences (supporting both SMILES and SELFIES ...
| Authors | Qizhi Pei, Zhimeng Zhou, Yi Duan et al. |
|---|---|
| Primary category | cs.CL |
| Published | 20 June 2026 |
| Last updated at source | 20 June 2026 |
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- introvoyz043/BioMatrix-1.7B-BaseModel · cited by
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