| # File guide |
|
|
| All data files are under `data/`. They are byte-identical to the source assets |
| used by the BEND 2.0 evaluation package at revision |
| `bca34753d2993f6f23c7de25cc41fb8523656bbd`. |
|
|
| The files have different schemas. Download them individually with |
| `hf_hub_download`, or together with `snapshot_download`. The dataset viewer |
| provides separate previews of the five Parquet tables; its `data` split is only |
| a display grouping. Use each task's stored assignments and evaluation rules. |
|
|
| ## Source archives |
|
|
| | File | Size | Contents | |
| | --- | ---: | --- | |
| | `opensplice.tsv.gz` | 425.5 MB | Unchanged OpenSplice version-5 experimental table. BEND prepares 590,104 variants in 466 genes, retaining reference and variant sequences, measured effects, uncertainties and gene identifiers. | |
| | `siraj.zip` | 93.3 MB | Unchanged Siraj saturation-mutagenesis archive. BEND prepares 340,584 mutation/cell records in 128 elements; pairing HepG2 and K562 gives 170,292 cell contrasts. | |
| | `hg38.2bit` | 835.4 MB | Unchanged UCSC hg38 reference genome, used to extract the long GTEx sequence windows. | |
|
|
| The archives are inputs to the benchmark's preparation code. They are not a |
| single training table. Preserve the original filenames when using |
| `BEND2_ASSET_DIR`. |
|
|
| ## Atlas |
|
|
| | File | Contents | |
| | --- | --- | |
| | `atlas-population.parquet` | 7,684 rows: 4,223 training, 1,023 validation, 2,411 candidate and 27 excluded sequences. Columns include `id`, `sequence`, `family_id`, `population`, `split`, `eligible_calibration` and `program_annotations`. All sequences are 145 bases. | |
| | `atlas-programs.csv` | Sixteen activity patterns, with `program`, `on_cells` and `off_cells`. Cell names are separated by `\|`. | |
| | `atlas-source-activities.parquet` | Two measured activities in each of twelve cells for the 5,246 fitting sequences. | |
| | `atlas-candidate-activities.parquet` | The corresponding measurements for the 2,411 candidates, kept separately from fitting data. | |
|
|
| The activity columns start with `r1_` and `r2_`; `id` joins them to the sequence |
| table. Pandas reads `id` as the index, while Arrow exposes it as a column. |
| Activities are float64 values calculated from UMI-deduplicated RNA and DNA counts, |
| with a pseudocount of 0.5 and normalization to the median of 35 negative controls. |
| No measurement values were changed for this mirror. |
|
|
| Sequences belonging to families that overlap the candidates are excluded from |
| fitting. The 27 excluded rows are retained in the population table to document |
| that separation. BEND uses 7,657 sequences in total. |
|
|
| ## Sequence-prior panel |
|
|
| `prior-panel.parquet` contains 1,536 fixed-strand, 1,200-base GRCh38 windows: |
| 1,024 for baseline fitting and 512 for evaluation, separated by genomic blocks. |
| Columns include sequence, genomic coordinates, `reference_base`, |
| `recovery_position` and `split`. The hidden position is index 600 in zero-based |
| coordinates. |
|
|
| `prior-query-seeds.json` stores the two masking seeds per evaluation window used |
| by the NTv3 paper-prior adapter. It contains no sequences, hidden bases or |
| measurement outcomes. These reference-genome sequences may have appeared in |
| model pretraining. |
|
|
| ## Additional Siraj measurements |
|
|
| `siraj-numeric-reference.npz` preserves exact float64 values for all 340,584 |
| mutation/cell records. Its arrays are `record_id_bytes`, `columns` and `values`; |
| the numeric columns are `y_ref`, `y_alt`, `delta_y` and `sigma`. |
|
|
| `siraj_selective.parquet` contains 181,458 mutation and no-edit identifiers with |
| columns `ID`, `truth_hepg2` and `truth_k562`. These effects average the per-repeat |
| `log2((RNA + 0.5) / (DNA + 0.5))` difference from the unmutated parent across |
| five repeats. They are separate from the posterior effect estimates in the |
| Siraj archive. The cell-selective task uses 167,958 eligible substitutions |
| across 127 loci; the table also retains the identifiers needed for preparation. |
|
|
| ## GTEx |
|
|
| `gtex-targets.npz` contains `truth` (19,282 genes × 51 tissues), `gene_ids`, |
| `tissues`, and training, validation and test index arrays. Targets are |
| `log1p(TPM)` from the public GTEx v10 median-expression summary. |
|
|
| `gtex-genes.tsv` records gene identifiers and GENCODE v39 transcription-start |
| coordinates for reference-forward 131,072-base hg38 windows. It preserves the |
| target matrix's row order. |
|
|
| There are 12,146 training and 1,350 validation genes. The stored test set has |
| 5,786 genes; the four exclusions listed in `assets.json` leave the same |
| 5,782-gene evaluation set used in the paper. They lack complete predictions in |
| the paper's common model/reference comparison. |
|
|
| These are frozen GTEx v10 files and do not necessarily reflect the most current |
| or accurate data from the GTEx Portal. They contain public aggregate expression |
| only. No individual donor records or genotypes are included. |
|
|
| ## Provenance and checksums |
|
|
| - `assets.json` is an unchanged copy of the benchmark's source manifest. Its |
| `distribution: bundled` entries describe how the Python package ships those |
| assets, rather than their location in this Hugging Face repository. |
| - `checksums.json` lists the local `data/` paths, byte counts and SHA-256 values |
| for this release. The original MD5 checksums remain in `assets.json` where used |
| by the benchmark. |
| - `LICENSE.md` maps files to their source terms and acknowledgements. |
|
|
| The checksum manifest identifies file contents independently of the download |
| host. Rehosting does not change candidate sets, fold assignments, measurements |
| or scoring. |
|
|
