| --- |
| license: cc-by-nc-4.0 |
| task_categories: |
| - text-classification |
| language: |
| - en |
| tags: |
| - genomics |
| - fish |
| - DNA |
| - benchmark |
| - promoter |
| - splice-site |
| - transcription-factor-binding-site |
| - histone-mark |
| size_categories: |
| - 100K<n<1M |
| pretty_name: FishGUE |
| --- |
| |
| # FishGUE |
|
|
| **FishGUE** is a unified fish genomics benchmark developed for evaluating DNA foundation models and other sequence models on fish genomic prediction tasks. |
|
|
| It was introduced in the FishNALM study, where it was used to systematically benchmark fish-specific and general DNA language models across diverse regulatory sequence prediction tasks. |
|
|
| ## Dataset summary |
|
|
| FishGUE contains **17 supervised prediction tasks** spanning four task groups: |
|
|
| - **Histone mark prediction** |
| - **Transcription factor binding-site prediction** |
| - **Promoter prediction** |
| - **Splice-site prediction** |
|
|
| The benchmark covers input sequence lengths from **300 bp to 2500 bp** and includes both **zebrafish-based datasets** and **multi-species cyprinid splice datasets**. |
|
|
| ## Why FishGUE? |
|
|
| Fish genomic benchmarks remain limited compared with those available for human, plant, or broad multi-species genomic modeling. FishGUE was constructed to provide a unified benchmark for evaluating model performance on representative fish genomic sequence prediction problems, especially those relevant to regulatory sequence recognition and gene structure annotation. |
|
|
| ## Benchmark composition |
|
|
| The FishGUE benchmark includes the following 17 tasks. |
|
|
| | Category | Task | Species | Sequence length (bp) | Train / Val / Test | |
| |---|---|---|---:|---:| |
| | Histone mark prediction | H3K4me1 | *Danio rerio* | variable (≤2500) | 48815 / 6102 / 6102 | |
| | Histone mark prediction | H3K4me3 | *Danio rerio* | variable (≤2500) | 47482 / 5935 / 5936 | |
| | Histone mark prediction | H3K9me3 | *Danio rerio* | variable (≤2500) | 40125 / 5016 / 5016 | |
| | Histone mark prediction | H3K27ac | *Danio rerio* | variable (≤2500) | 27611 / 3451 / 3452 | |
| | Histone mark prediction | H3K27me3 | *Danio rerio* | variable (≤2500) | 27017 / 3377 / 3378 | |
| | TF binding-site prediction | CTCF | *Danio rerio* | 800 | 28526 / 3566 / 3566 | |
| | TF binding-site prediction | Pou5f1 | *Danio rerio* | 800 | 11128 / 1391 / 1391 | |
| | TF binding-site prediction | Sox2 | *Danio rerio* | 800 | 9717 / 1215 / 1215 | |
| | Promoter prediction | Core promoter | *Danio rerio* | 300 | 17222 / 2153 / 2153 | |
| | Promoter prediction | Core promoter (TATA) | *Danio rerio* | 300 | 3464 / 433 / 434 | |
| | Promoter prediction | Core promoter (non-TATA) | *Danio rerio* | 300 | 13757 / 1720 / 1720 | |
| | Promoter prediction | Promoter | *Danio rerio* | 1000 | 17222 / 2153 / 2153 | |
| | Promoter prediction | Promoter (TATA) | *Danio rerio* | 1000 | 3464 / 433 / 434 | |
| | Promoter prediction | Promoter (non-TATA) | *Danio rerio* | 1000 | 13757 / 1720 / 1720 | |
| | Splice-site prediction | Splicing (acceptor) | Cyprinidae (5 species) | 600 | 17200 / 2150 / 2150 | |
| | Splice-site prediction | Splicing (donor) | Cyprinidae (5 species) | 600 | 27600 / 3450 / 3450 | |
| | Splice-site prediction | Splicing (both) | Cyprinidae (5 species) | 600 | 1720 / 2150 / 2105 | |
|
|
| ## Data sources and construction overview |
|
|
| According to the FishNALM manuscript, FishGUE was assembled from the following sources: |
|
|
| - **Histone mark datasets** were derived from public zebrafish ChIP-seq peak datasets. |
| - **Transcription factor binding-site datasets** were built from public ChIP-seq peaks for **CTCF**, **Pou5f1**, and **Sox2**. |
| - **Promoter datasets** were constructed from zebrafish promoter annotations from the **Eukaryotic Promoter Database (EPD)**. |
| - **Splice-site datasets** were compiled from annotated genomes of **five cyprinid fish species**. |
|
|
| For all tasks, positive and negative examples were constructed through task-specific processing, then split into **training**, **validation**, and **test** sets using an **8:1:1** ratio. |
|
|
| ## Suggested repository organization |
|
|
| If you plan to upload FishGUE as a single Hugging Face dataset repository, a clean structure is: |
|
|
| ```text |
| FishGUE/ |
| ├── README.md |
| ├── histone/ |
| │ ├── H3K4me1_train.tsv |
| │ ├── H3K4me1_val.tsv |
| │ ├── H3K4me1_test.tsv |
| │ └── ... |
| ├── tfbs/ |
| │ ├── CTCF_train.tsv |
| │ ├── CTCF_val.tsv |
| │ ├── CTCF_test.tsv |
| │ └── ... |
| ├── promoter/ |
| │ ├── core_promoter_300_train.tsv |
| │ └── ... |
| └── splice/ |
| ├── splice_acceptor_train.tsv |
| └── ... |
| ``` |
|
|
| If your files are already packaged in another layout, you can keep that layout and simply explain it in this README. |
|
|
| ## Intended uses |
|
|
| FishGUE is intended for: |
|
|
| - benchmarking DNA foundation models on fish genomic sequence prediction tasks |
| - evaluating transfer learning performance in fish genomics |
| - comparing task robustness across promoter, chromatin, TFBS, and splice-site prediction settings |
| - developing new fish-specific sequence models and downstream classifiers |
|
|
| ## Limitations |
|
|
| - Most non-splice tasks are based on **zebrafish** data. |
| - The splice-site benchmark uses **five cyprinid species**, so broader phylogenetic coverage remains limited. |
| - FishGUE is designed as a **research benchmark** and should not be interpreted as a clinical or diagnostic dataset. |
| - Performance on FishGUE does not guarantee performance on all fish species or all regulatory genomics tasks. |
|
|
| ## Citation |
|
|
| If you use FishGUE in your work, please cite the FishNALM manuscript. |
|
|
| **Manuscript:** |
|
|
| > FishNALM: A Foundation DNA Language Model for Fish Genomes |
|
|
| ## Project links |
|
|
| - **GitHub**: [bioinfoihb/FishNALM](https://github.com/bioinfoihb/FishNALM) |
|
|
| ## Contact |
|
|
| **Xiao-Qin Xia** |
| Institute of Hydrobiology, Chinese Academy of Sciences |
| Email: xqxia@ihb.ac.cn |
| Email: bioinfoihb@ihb.ac.cn |
|
|
