| --- |
| pretty_name: FishCaduceus Pretraining Dataset 1024 |
| language: |
| - en |
| tags: |
| - genomics |
| - fish |
| - DNA |
| - pretraining |
| - DNA-language-model |
| - FishCaduceus |
| - cyprinid |
| - single-nucleotide |
| - masked-language-modeling |
| --- |
| |
| # FishCaduceus Pretraining Dataset 1024 |
|
|
| ## Dataset description |
|
|
| This dataset contains fixed-length 1,024-bp genomic sequence windows prepared for pretraining FishCaduceus DNA language models. It uses single-nucleotide tokenization and is intended for masked language modeling. |
|
|
| ## Dataset summary |
|
|
| The dataset contains 2,709,306 JSON Lines records. Each record contains genomic coordinates and a `seq` field. The six files were audited by streaming line-by-line parsing; all records were valid JSON and all observed sequences were 1,024 bp long. |
|
|
| ## Source genomes |
|
|
| The sequences were derived from eight fish reference genomes, including seven cyprinid aquaculture fishes and zebrafish: |
|
|
| - *Hypophthalmichthys nobilis* |
| - *Hypophthalmichthys molitrix* |
| - *Mylopharyngodon piceus* |
| - *Cyprinus carpio* |
| - *Megalobrama amblycephala* |
| - *Ctenopharyngodon idella* |
| - *Carassius gibelio* |
| - *Danio rerio* |
|
|
| ## Dataset construction |
|
|
| The corpus consists of fixed-length 1,024-bp genomic sequence windows with species-aware and repeat-content-aware stratified sampling. Sequences are represented with single-nucleotide tokens for masked language modeling. |
|
|
| ## Dataset structure |
|
|
| Each JSONL record includes fields such as `assembly`, `chrom`, `start`, `end`, `strand`, and `seq`. The `seq` field is the nucleotide sequence used for pretraining. |
|
|
| ## Dataset splits |
|
|
| | Split | Number of sequences | Sequence length | |
| |---|---:|---:| |
| | Train | 2,573,595 | 1,024 bp | |
| | Validation | 68,081 | 1,024 bp | |
| | Test | 67,630 | 1,024 bp | |
|
|
| ## Data characteristics |
|
|
| All final files in this repository were non-empty and readable as UTF-8 JSONL. The audit found no blank lines, invalid JSON records, missing `seq` fields, or non-ACGTN sequence characters. File sizes are recorded in `FILE_MANIFEST.tsv` at the upload-preparation root. |
|
|
| ## Intended uses |
|
|
| The dataset is intended for research on DNA language modeling, representation learning, and downstream analysis of fish genomes. Users should evaluate whether the sampling strategy and reference assemblies are appropriate for their application. |
|
|
| ## Limitations |
|
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| The data represent selected reference genomes and sampled genomic windows; they do not constitute a complete representation of fish genetic diversity. Coordinate conventions, assembly versions, and sampling strata should be considered when interpreting results. |
|
|
| ## Related models |
|
|
| - [FishCaduceus-28L-1024](https://huggingface.co/FishCaduceus/FishCaduceus-28L-1024) |
|
|
| ## Citation |
|
|
| The FishCaduceus manuscript is in preparation. Citation information will be added after publication. |
|
|
| ## Acknowledgements |
|
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| FishCaduceus was developed for research on fish genomes at the Institute of Hydrobiology, Chinese Academy of Sciences. |
|
|
| ## Contact |
|
|
| Xiao-Qin Xia |
| Institute of Hydrobiology, Chinese Academy of Sciences |
| Email: xqxia@ihb.ac.cn |
|
|
