# FishCaduceus

**FishCaduceus** is a family of single-nucleotide DNA language models developed for cyprinid and comparative fish genomics.

The project provides:

- pretrained FishCaduceus models with 512-bp and 1,024-bp context lengths
- pretraining datasets from seven major cyprinid aquaculture fishes and zebrafish
- cross-species benchmarks for translation initiation, translation termination, splice donor and splice acceptor prediction
- evolutionary constraint benchmarks derived from a 26-fish whole-genome alignment

FishCaduceus is designed for fish genome annotation, cross-species transfer, evolutionary constraint analysis and zero-shot variant prioritization.

## Resources

- Models: [FishCaduceus organization](https://huggingface.co/FishCaduceus)
- Functional-site benchmark: [FishCaduceus-Functional-Site-Benchmark](https://huggingface.co/datasets/FishCaduceus/FishCaduceus-Functional-Site-Benchmark)
- Evolutionary-constraint benchmark: [FishCaduceus-Evolutionary-Constraint-Benchmark](https://huggingface.co/datasets/FishCaduceus/FishCaduceus-Evolutionary-Constraint-Benchmark)

## Manuscript

**FishCaduceus: A DNA Language Model for Cyprinid Genomics at Single-Nucleotide Resolution**

The manuscript is in preparation.

## Contact

Xiao-Qin Xia  
Institute of Hydrobiology, Chinese Academy of Sciences  
Email: xqxia@ihb.ac.cn