Datasets:
File size: 4,307 Bytes
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license: apache-2.0
tags:
- biology
- genomics
- dna
size_categories:
- 10K<n<100K
---
# evals_dart_task3
Cell-type-specific **chromatin-accessibility peak** dataset from
[DART-Eval](https://github.com/kundajelab/DART-Eval) **Task 3** ("Discriminating
Cell-Type-Specific Elements"). Each row is a **500 bp** ATAC-seq consensus-peak
window (±250 bp around the summit, GRCh38), labeled by the **cell type** it is
differentially accessible in. The benchmark question: can a model embedding
distinguish cell types from the sequence alone?
**Interval dataset, not variants** — no ref/alt, no consequence annotation, **no
matching and no subsampling**. The window set is DART-Eval's
`input_data/top_5000_deseq_peaks.tsv` — the **top 5,000 DESeq2
differentially-accessible peaks per cell type** (the subset they feed their
zero-shot clustering / UMAP), **25,000 windows, 5,000 balanced per cell type**,
with unique peak coordinates.
## Description
| | |
|---|---|
| Element | 500 bp ATAC-seq consensus peak (±250 bp around the summit; window midpoint = summit) |
| Label | One of 5 cell lines: `GM12878`, `H1ESC`, `HEPG2`, `IMR90`, `K562` |
| Selection | Top 5,000 DESeq2 differentially-accessible peaks per cell type (25,000 total, balanced) |
| Assay | ATAC-seq chromatin accessibility (ENCODE) |
| Source data | DART-Eval, Synapse [`syn62161401`](https://www.synapse.org/Synapse:syn62161401) (`top_5000_deseq_peaks.tsv`), project `syn60581042` |
| Genome build | GRCh38 |
| Coordinates | **0-based, half-open** (`end - start == 500`) |
| Matching | none (no subsampling) |
The full 500 bp peak is stored (never pre-cropped to a model's context window),
so the embedding context / pooling choice stays an open downstream decision.
## Splits
DART-Eval's canonical **3-way** chromosome holdout (verbatim from their Task-3
training scripts), shipped one file per split. Per-split counts follow the
peaks' genomic distribution.
| File | Windows | Chromosomes |
|---|---:|---|
| `train.parquet` | 17,965 | 1, 2, 3, 4, 7, 8, 9, 11, 12, 13, 15, 16, 17, 19, X, Y |
| `validation.parquet` | 1,958 | 6, 21 |
| `test.parquet` | 5,077 | 5, 10, 14, 18, 20, 22 |
| **total** | **25,000** | |
### Windows per cell type
| Cell type | train | validation | test | total |
|---|---:|---:|---:|---:|
| `GM12878` | 3,569 | 382 | 1,049 | 5,000 |
| `H1ESC` | 3,699 | 318 | 983 | 5,000 |
| `HEPG2` | 3,484 | 376 | 1,140 | 5,000 |
| `IMR90` | 3,572 | 325 | 1,103 | 5,000 |
| `K562` | 3,641 | 557 | 802 | 5,000 |
## Columns
| Column | Type | Description |
|---|---|---|
| `chrom` | str | Chromosome (no `chr` prefix), GRCh38 |
| `start` | int | Window start — 0-based, inclusive |
| `end` | int | Window end — 0-based, exclusive (`end - start == 500`) |
| `label` | str | Cell type the peak is differentially accessible in |
## Provenance
Built by the [`marin-dna`](https://github.com/Open-Athena/marin-dna) eval pipeline at commit
[`e3bccd1`](https://github.com/Open-Athena/marin-dna/tree/e3bccd17f960df1ef81a845df101299c135819e0/snakemake/evals).
- Curation pipeline: [`snakemake/evals`](https://github.com/Open-Athena/marin-dna/tree/e3bccd17f960df1ef81a845df101299c135819e0/snakemake/evals)
- Rules: [`snakemake/evals/workflow/rules/dart_task3.smk`](https://github.com/Open-Athena/marin-dna/blob/e3bccd17f960df1ef81a845df101299c135819e0/snakemake/evals/workflow/rules/dart_task3.smk)
- Parsing + splitting: [`src/marin_dna/pipelines/evals/dart_task3.py`](https://github.com/Open-Athena/marin-dna/blob/e3bccd17f960df1ef81a845df101299c135819e0/src/marin_dna/pipelines/evals/dart_task3.py)
## License
Released under the terms of its upstream sources. The peak set is redistributed
from [DART-Eval](https://github.com/kundajelab/DART-Eval) (Task 3) and derives
from **ENCODE** ATAC-seq in the 5 cell lines (freely redistributable under the
[ENCODE data-use policy](https://www.encodeproject.org/help/citing-encode/));
DART-Eval ships no explicit license, so consult it and ENCODE for redistribution
and commercial-use terms.
## Citation
If you use this benchmark, please cite the upstream sources:
- DART-Eval — Patel *et al.* 2024, [arXiv 2412.05430](https://arxiv.org/abs/2412.05430) (NeurIPS D&B 2024)
- ENCODE Project Consortium — the ATAC-seq data for GM12878, H1ESC, HEPG2, IMR90, K562
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