Add functional site benchmark datasets

Add the FishCaduceus benchmark datasets for translation initiation sites, translation termination sites, splice donor sites, and splice acceptor sites.

.gitattributes

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 # Video files - compressed
 *.mp4 filter=lfs diff=lfs merge=lfs -text
 *.webm filter=lfs diff=lfs merge=lfs -text
+acceptor/carassius_gibelio_test.csv filter=lfs diff=lfs merge=lfs -text
+acceptor/ctenopharyngodon_idella_test.csv filter=lfs diff=lfs merge=lfs -text
+acceptor/danio_rerio_test.csv filter=lfs diff=lfs merge=lfs -text
+acceptor/danio_rerio_train.csv filter=lfs diff=lfs merge=lfs -text
+acceptor/danio_rerio_validation.csv filter=lfs diff=lfs merge=lfs -text
+acceptor/larimichthys_crocea_test.csv filter=lfs diff=lfs merge=lfs -text
+acceptor/micropterus_salmoides_test.csv filter=lfs diff=lfs merge=lfs -text
+acceptor/pelteobagrus_fulvidraco_test.csv filter=lfs diff=lfs merge=lfs -text
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+tis/carassius_gibelio_test.csv filter=lfs diff=lfs merge=lfs -text
+tis/ctenopharyngodon_idella_test.csv filter=lfs diff=lfs merge=lfs -text
+tis/culter_alburnus_test.csv filter=lfs diff=lfs merge=lfs -text
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README.md

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 ---
-license: cc-by-nc-sa-4.0
+pretty_name: FishCaduceus Functional Site Benchmark
+language:
+- en
+tags:
+- genomics
+- fish
+- DNA
+- FishCaduceus
+- cyprinid
+- functional-annotation
+- translation-initiation-site
+- translation-termination-site
+- splice-donor
+- splice-acceptor
+- cross-species-transfer
+- sequence-classification
 ---
+
+# FishCaduceus Functional Site Benchmark
+
+## Dataset description
+
+This dataset contains sequence-based benchmarks for four gene-annotation tasks used to evaluate FishCaduceus:
+
+- translation initiation site (TIS) prediction
+- translation termination site (TTS) prediction
+- splice donor site prediction
+- splice acceptor site prediction
+
+The benchmark was designed to evaluate both within-species performance and cross-species transfer. Models are trained and selected only with labeled zebrafish (*Danio rerio*) data, then evaluated on a held-out zebrafish test set and six additional fish species without target-species retraining or parameter adjustment.
+
+## Dataset summary
+
+The repository contains four task directories:
+
+```text
+.
+├── acceptor/
+├── donor/
+├── tis/
+└── tts/
+```
+
+Each task directory contains:
+
+- zebrafish training, validation, and held-out test files
+- one cross-species test file for each of six additional fish species
+
+The original CSV structure generated by the FishCaduceus benchmark pipeline has been preserved. Files were renamed and organized by task, species, and split without altering their internal contents.
+
+## Tasks
+
+### Translation initiation sites
+
+Positive TIS examples correspond to annotated `ATG` translation initiation sites.
+
+### Translation termination sites
+
+Positive TTS examples correspond to annotated `TAA`, `TAG`, or `TGA` translation termination sites.
+
+### Splice donor and acceptor sites
+
+Positive splice-site examples correspond to annotated canonical `GT-AG` intron boundaries. The benchmark construction retained introns meeting the annotation-support and length criteria used in the FishCaduceus study.
+
+For each task, negative examples were constructed from motif-matched and motif-free genomic positions while excluding annotated functional sites and their surrounding regions. The final benchmark uses a 1:6 positive-to-negative design. Sequences were standardized to the functional orientation before downstream modeling.
+
+## Species and evaluation splits
+
+| Species | Repository split | Role in the benchmark | Included in FishCaduceus pretraining |
+|---|---|---|---|
+| *Danio rerio* | train / validation / test | source species for training, model selection, and held-out evaluation | Yes |
+| *Ctenopharyngodon idella* | test | cross-species evaluation | Yes |
+| *Carassius gibelio* | test | cross-species evaluation | Yes |
+| *Culter alburnus* | test | cross-species evaluation | No |
+| *Pelteobagrus fulvidraco* | test | cross-species evaluation | No |
+| *Micropterus salmoides* | test | cross-species evaluation | No |
+| *Larimichthys crocea* | test | cross-species evaluation | No |
+
+*Pelteobagrus fulvidraco* is also referred to as *Tachysurus fulvidraco* in parts of the literature. Repository filenames follow `pelteobagrus_fulvidraco`.
+
+## Repository structure
+
+```text
+.
+├── acceptor/
+│   ├── carassius_gibelio_test.csv
+│   ├── ctenopharyngodon_idella_test.csv
+│   ├── culter_alburnus_test.csv
+│   ├── danio_rerio_test.csv
+│   ├── danio_rerio_train.csv
+│   ├── danio_rerio_validation.csv
+│   ├── larimichthys_crocea_test.csv
+│   ├── micropterus_salmoides_test.csv
+│   └── pelteobagrus_fulvidraco_test.csv
+├── donor/
+│   └── [the same species and split organization]
+├── tis/
+│   └── [the same species and split organization]
+└── tts/
+    └── [the same species and split organization]
+```
+
+## Dataset structure
+
+Each CSV file contains the sequence examples and labels used in the corresponding FishCaduceus analysis. Column names and column order are retained exactly as generated by the original data-preparation pipeline.
+
+The central fields used for model training are:
+
+- a nucleotide sequence
+- a binary class label indicating a positive or negative functional site
+
+Depending on the task file, additional genomic-position or annotation fields may also be present. Users should inspect the CSV header before adapting the dataset to a new pipeline.
+
+## Sequence representation
+
+The benchmark was constructed from 1,024-bp genomic sequence windows centered on candidate functional sites. Sequences are represented at single-nucleotide resolution and oriented consistently with the annotated functional strand.
+
+Users applying models with a shorter context length should use a consistent centered truncation strategy.
+
+## Loading the data
+
+### With pandas
+
+```python
+import pandas as pd
+
+train = pd.read_csv("tis/danio_rerio_train.csv")
+validation = pd.read_csv("tis/danio_rerio_validation.csv")
+test = pd.read_csv("tis/danio_rerio_test.csv")
+
+cross_species_test = pd.read_csv(
+    "tis/ctenopharyngodon_idella_test.csv"
+)
+
+print(train.columns.tolist())
+print(train.shape)
+```
+
+### With Hugging Face Datasets
+
+```python
+from datasets import load_dataset
+
+data_files = {
+    "train": "tis/danio_rerio_train.csv",
+    "validation": "tis/danio_rerio_validation.csv",
+    "test": "tis/danio_rerio_test.csv",
+}
+
+dataset = load_dataset("csv", data_files=data_files)
+print(dataset)
+```
+
+A cross-species test file can be loaded separately:
+
+```python
+from datasets import load_dataset
+
+dataset = load_dataset(
+    "csv",
+    data_files={
+        "test": "tis/larimichthys_crocea_test.csv",
+    },
+)
+```
+
+## Benchmark protocol
+
+The benchmark protocol used in the FishCaduceus study is:
+
+1. train downstream models only on the *Danio rerio* training split;
+2. select models and hyperparameters only on the *Danio rerio* validation split;
+3. report within-species performance on the held-out *Danio rerio* test split;
+4. evaluate the selected model directly on the other six species;
+5. do not use labels from the target species for retraining or parameter adjustment.
+
+The primary evaluation metric is area under the precision-recall curve (AUPRC), which is appropriate for the class-imbalanced test sets.
+
+## Intended uses
+
+This dataset is intended for research on:
+
+- fish genome annotation
+- functional-site prediction
+- transfer learning with DNA language models
+- frozen-embedding classification
+- full-model fine-tuning
+- cross-species generalization
+- comparative benchmarking of genomic sequence models
+
+## Limitations
+
+- Labels are derived from reference genome annotations and therefore depend on annotation completeness and accuracy.
+- The benchmark focuses on canonical TIS, TTS, and `GT-AG` splice-site definitions used in the FishCaduceus study.
+- Negative examples are computationally constructed and do not represent every possible genomic background.
+- Cross-species performance can be affected by genome assembly quality, annotation quality, phylogenetic distance, and sequence composition.
+- The benchmark does not establish biological causality and should not replace experimental validation.
+- The included species do not represent the full diversity of teleost fishes.
+
+## Related models
+
+- [FishCaduceus-20L-512](https://huggingface.co/FishCaduceus/FishCaduceus-20L-512)
+- [FishCaduceus-28L-512](https://huggingface.co/FishCaduceus/FishCaduceus-28L-512)
+- [FishCaduceus-28L-1024](https://huggingface.co/FishCaduceus/FishCaduceus-28L-1024)
+
+## Citation
+
+The FishCaduceus manuscript is in preparation. Citation information will be added after publication.
+
+When using this benchmark, please cite the FishCaduceus manuscript and the original genome and annotation resources used to construct the species-specific datasets.
+
+## Acknowledgements
+
+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

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