Upload evolutionary constraint benchmark dataset

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README.md

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 ---
-license: cc-by-nc-sa-4.0
+pretty_name: FishCaduceus Evolutionary Constraint Benchmark
+language:
+- en
+tags:
+- genomics
+- fish
+- DNA
+- FishCaduceus
+- cyprinid
+- evolutionary-constraint
+- conservation
+- whole-genome-alignment
+- progressive-cactus
+- cross-species-transfer
+- sequence-classification
 ---
+
+# FishCaduceus Evolutionary Constraint Benchmark
+
+## Dataset description
+
+This dataset contains sequence-based benchmarks for evaluating whether FishCaduceus representations capture evolutionary constraint in fish genomes.
+
+Constraint labels were derived from a 26-fish whole-genome alignment generated with Progressive Cactus. Grass carp (*Ctenopharyngodon idella*) was used as the primary reference genome for defining aligned and conserved positions. The resulting labeled sites were converted into fixed-length 512-bp sequence windows for zero-shot scoring, frozen-embedding classification, and cross-species evaluation.
+
+## Dataset summary
+
+The repository contains two complementary benchmark components:
+
+```text
+.
+├── region_specific/
+└── whole_genome/
+```
+
+- `whole_genome/` contains the main training, validation, and cross-species test datasets.
+- `region_specific/` contains balanced test sets stratified by CDS, intron, and intergenic regions.
+
+The original CSV structure generated by the FishCaduceus constraint pipeline has been preserved. Files were renamed and organized without altering their internal contents.
+
+## Constraint-label construction
+
+For each reference position, bases projected from the other genomes in the 26-fish alignment were summarized using:
+
+- `n_cov`: number of species with an informative aligned base
+- `n_match`: number of informative species matching the reference base
+
+The benchmark uses the following definitions:
+
+```text
+Highly conserved:
+n_cov >= 24 and n_match >= 24
+
+Low conservation:
+n_cov >= 24 and n_match <= 10
+```
+
+Positions that did not meet either definition were not used as positive or negative benchmark examples.
+
+When a species contributed multiple aligned copies, concordant copies were merged into one species-level vote. Conflicting copies were treated as ambiguous and were excluded from `n_cov` and `n_match`.
+
+## Sequence representation
+
+Each benchmark example is represented by a 512-bp genomic sequence window centered on the labeled position.
+
+The positive class represents highly conserved positions, whereas the negative class represents low-conservation positions. The distributed CSV files retain the label encoding used by the original FishCaduceus analysis pipeline.
+
+## Whole-genome benchmark
+
+The `whole_genome/` directory contains:
+
+| Species | Available splits | Role |
+|---|---|---|
+| *Ctenopharyngodon idella* | train / validation / test | reference species for downstream training and held-out evaluation |
+| *Barbodes kweichowensis* | test | cross-species evaluation |
+| *Danio rerio* | test | cross-species evaluation |
+| *Megalobrama amblycephala* | test | cross-species evaluation |
+
+The benchmark construction used:
+
+| Species and split | Number of examples |
+|---|---:|
+| *Ctenopharyngodon idella* train | 70,000 |
+| *Ctenopharyngodon idella* validation | 10,000 |
+| *Ctenopharyngodon idella* test | 20,000 |
+| Each cross-species test set | 20,000 |
+
+These files support training on grass carp and direct evaluation on other fish species without target-species retraining.
+
+## Region-specific benchmark
+
+The `region_specific/` directory contains CDS, intron, and intergenic test sets for:
+
+- *Ctenopharyngodon idella*
+- *Danio rerio*
+- *Megalobrama amblycephala*
+
+Each regional test file was constructed as a balanced dataset containing 5,000 highly conserved and 5,000 low-conservation examples.
+
+The regional benchmarks are intended to test whether constraint prediction performance differs among coding and noncoding genomic contexts.
+
+## Repository structure
+
+```text
+.
+├── region_specific/
+│   ├── ctenopharyngodon_idella/
+│   │   ├── cds_test.csv
+│   │   ├── intergenic_test.csv
+│   │   └── intron_test.csv
+│   ├── danio_rerio/
+│   │   ├── cds_test.csv
+│   │   ├── intergenic_test.csv
+│   │   └── intron_test.csv
+│   └── megalobrama_amblycephala/
+│       ├── cds_test.csv
+│       ├── intergenic_test.csv
+│       └── intron_test.csv
+└── whole_genome/
+    ├── barbodes_kweichowensis_test.csv
+    ├── ctenopharyngodon_idella_test.csv
+    ├── ctenopharyngodon_idella_train.csv
+    ├── ctenopharyngodon_idella_validation.csv
+    ├── danio_rerio_test.csv
+    └── megalobrama_amblycephala_test.csv
+```
+
+## Dataset structure
+
+Each CSV contains the sequence examples and binary labels used in the FishCaduceus evolutionary-constraint analyses. Column names and column order are retained exactly as generated by the original pipeline.
+
+The core fields used for modeling are:
+
+- a 512-bp nucleotide sequence
+- a binary constraint label
+
+Depending on the source file, additional fields related to genomic coordinates or alignment-derived statistics may also be present. Users should inspect the CSV header before adapting the dataset to a new workflow.
+
+## Loading the data
+
+### With pandas
+
+```python
+import pandas as pd
+
+train = pd.read_csv(
+    "whole_genome/ctenopharyngodon_idella_train.csv"
+)
+validation = pd.read_csv(
+    "whole_genome/ctenopharyngodon_idella_validation.csv"
+)
+test = pd.read_csv(
+    "whole_genome/ctenopharyngodon_idella_test.csv"
+)
+
+cross_species_test = pd.read_csv(
+    "whole_genome/danio_rerio_test.csv"
+)
+
+print(train.columns.tolist())
+print(train.shape)
+```
+
+### With Hugging Face Datasets
+
+```python
+from datasets import load_dataset
+
+data_files = {
+    "train": "whole_genome/ctenopharyngodon_idella_train.csv",
+    "validation": "whole_genome/ctenopharyngodon_idella_validation.csv",
+    "test": "whole_genome/ctenopharyngodon_idella_test.csv",
+}
+
+dataset = load_dataset("csv", data_files=data_files)
+print(dataset)
+```
+
+A region-specific dataset can be loaded separately:
+
+```python
+from datasets import load_dataset
+
+dataset = load_dataset(
+    "csv",
+    data_files={
+        "test": (
+            "region_specific/danio_rerio/"
+            "cds_test.csv"
+        ),
+    },
+)
+```
+
+## Benchmark protocol
+
+The supervised transfer protocol used in the FishCaduceus study is:
+
+1. train a classifier using only the *Ctenopharyngodon idella* training split;
+2. perform model selection using only the *Ctenopharyngodon idella* validation split;
+3. report held-out performance on the *Ctenopharyngodon idella* test split;
+4. evaluate the selected classifier directly on the other species;
+5. do not use target-species labels for retraining or parameter adjustment.
+
+The dataset can also be used for zero-shot scoring by masking or otherwise scoring the center nucleotide with a pretrained DNA language model.
+
+## Intended uses
+
+This dataset is intended for research on:
+
+- evolutionary constraint prediction
+- conservation-aware genomic representation learning
+- frozen-embedding classification
+- zero-shot nucleotide scoring
+- cross-species transfer
+- comparative genomics
+- evaluation across CDS, intronic, and intergenic regions
+
+## Limitations
+
+- Constraint classes are computational labels derived from a specific 26-fish whole-genome alignment and fixed thresholds.
+- The labels are not equivalent to experimentally validated functional annotations.
+- Results depend on genome assembly quality, alignment quality, reference choice, species sampling, and multi-copy handling.
+- Repetitive, duplicated, poorly assembled, or rapidly evolving regions may be underrepresented or more difficult to align.
+- The highly conserved and low-conservation classes represent the two ends of the alignment-based conservation spectrum and do not cover all genomic positions.
+- The included test species and genomic regions do not represent the full diversity of fish genomes.
+
+## 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 resources used in the 26-fish whole-genome alignment.
+
+## 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

whole_genome/ctenopharyngodon_idella_train.csv

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