Datasets:
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 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 (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 eval pipeline at commit
e3bccd1.
- Curation pipeline:
snakemake/evals - Rules:
snakemake/evals/workflow/rules/dart_task3.smk - Parsing + splitting:
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 (Task 3) and derives from ENCODE ATAC-seq in the 5 cell lines (freely redistributable under the ENCODE data-use policy); 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 (NeurIPS D&B 2024)
- ENCODE Project Consortium — the ATAC-seq data for GM12878, H1ESC, HEPG2, IMR90, K562