| # evo3 eval subsets — `standard` and `hard` |
|
|
| The exact rows the evo3 `standard` and `hard` eval suites score, one parquet |
| per dataset. Exported so these subsets can be scored elsewhere without running |
| the evo3 eval or reimplementing its selection logic. |
|
|
| - Exported: 2026-07-24T19:52:15.198474+00:00 |
| - evo3 commit: `48089c9b12ce559086bfa4a0d0f77f332cf1e378` |
| - pandas: 3.0.3 |
|
|
| ## Layout |
|
|
| ``` |
| standard/<dataset>.parquet |
| hard/<dataset>.parquet |
| manifest.json # full per-dataset provenance (source path, seed, sha256, columns) |
| ``` |
|
|
| ## Contents |
|
|
| | suite | dataset | rows | pos | neg | selection | source rows | |
| | --- | --- | ---: | ---: | ---: | --- | ---: | |
| | standard | clinvar | 5000 | 1675 | 3325 | `stratified_representative` n=5000 seed=1234 | 200036 | |
| | standard | splicevar | 5000 | 2979 | 2021 | `stratified_representative` n=5000 seed=1234 | 11978 | |
| | standard | gnomad_balanced | 5000 | 2500 | 2500 | `stratified_representative` n=5000 seed=1234 | 11992284 | |
| | standard | cosmic | 2000 | 183 | 1817 | `stratified_representative` n=2000 seed=1234 | 18903 | |
| | standard | traitgym_mendelian | 3380 | 338 | 3042 | full dataset (no subsampling) | 3380 | |
| | hard | traitgym_complex | 6840 | 1140 | 5700 | `matched_group_representative` n=None seed=1234 | 11400 | |
| | hard | denovodb | 4999 | 2569 | 2430 | `stratified_representative` n=5000 seed=1234 | 68669 | |
| | hard | causal_mpra | 5000 | 1024 | 3976 | `stratified_representative` n=5000 seed=1234 | 12256 | |
|
|
| ## Columns |
|
|
| Each parquet carries its source dataset's own columns plus what the evo3 eval |
| loader derives: |
|
|
| - **`_label`** — 1 = positive, 0 = negative. Use this rather than the raw label |
| column; the per-dataset positive/negative values are in `manifest.json`. |
| - **`chrom`** — normalized *without* a `chr` prefix (`1`, not `chr1`). |
| - **`strand`** — present where the dataset declares strand annotations (ClinVar); |
| minus-strand windows are meant to be reverse-complemented before scoring. |
| - **`_subset_stratum`** — audit key naming the stratum a row was drawn from. |
| |
| ## Notes |
| |
| - Selection is seeded and order-invariant: rows are sorted into a canonical |
| `(chrom, pos, ref, alt)` order before sampling, so the same seed picks the same |
| variants regardless of the source parquet's on-disk row order. Every subset here |
| was built twice and compared on the variant key before being written. |
| - `traitgym_mendelian` carries no subset and is exported in full (~3.4k rows). |
| - `traitgym_complex` keeps every positive with its matched controls, so its size is |
| `n_pos * (1 + negs_per_pos)` rather than a round `n`. |
| - `cosmic` keeps all 183 positives and fills the rest of n=2000 with negatives. |
| - `denovodb` holds 4999 rows, not 5000: the subset draws 5000 but one row has a |
| null `group_tag`, which the eval loader drops when deriving `_label`. The eval |
| scores 4999 too. |
| |
| Regenerate with: |
| |
| ```bash |
| PYTHONPATH=src python scripts/eval/export_subset_parquets.py \ |
| --suites standard hard --out /mnt/weka/shared_datasets/nvidia_subset_parquets |
| ``` |
| |
