| --- |
| 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 |
|
|
