| # Frozen protocol files |
|
|
| These files are the authoritative definition of the benchmark. The CSV tables in |
| `splits/`, `queries/` and `libraries/` are a human-readable view of them; if the two ever |
| disagree, the protocol files win. |
|
|
| ## Files |
|
|
| | file | content | |
| | --- | --- | |
| | `manifest_summary.json` | the frozen manifest of the historical Figure 3h producer: counts, seeds, per-split sizes, ordered-SMILES and source-row SHA-256 values, vocabulary sizes, artifact hashes, input CSV/h5 hashes | |
| | `protocol_pos.npz` | row-index arrays of the `[M+H]+` task | |
| | `protocol_neg.npz` | row-index arrays of the `[M-H]-` task | |
| | `smiles_pos.json` | list of canonical isomeric SMILES of the 41,348 positive compounds; a row's compound is `smiles_pos.json[smiles_index]` | |
| | `smiles_neg.json` | same for the 21,293 negative compounds | |
| | `adducts_pos.json`, `adducts_neg.json` | `["[M+H]+"]`, `["[M-H]-"]` — the strict adduct of each task | |
| | `derived/row_metadata_pos.npz`, `derived/row_metadata_neg.npz` | per-preprocessed-row metadata extracted from the (not redistributed) preprocessed-spectra HDF5 file | |
|
|
| ## `protocol_*.npz` arrays |
| |
| Each archive has five 1-D `int64` arrays. Their indices are **frozen preprocessed row |
| ids**: `0 … 301,635` for `pos`, `0 … 140,192` for `neg`. Row ids follow the source order of |
| `MSnLib.csv` after the strict-adduct filter and the peak preprocessing; `derived/row_metadata_*.npz` |
| maps them to `MSnLib.csv` data rows. |
| |
| | array | content | length (`pos` / `neg`) | |
| | --- | --- | --- | |
| | `train_rows` | training spectra, ordered "sorted train compound, then source order" | 211,745 / 98,401 | |
| | `val_query_rows` | the validation queries, ordered by sorted validation compound | 6,202 / 3,193 | |
| | `val_library_rows` | validation library, canonical-compound insertion order minus the validation queries | 250,424 / 116,135 | |
| | `test_query_rows` | the test queries, ordered by sorted test compound | 6,202 / 3,193 | |
| | `test_library_rows` | test library, canonical-compound insertion order minus the test queries | 295,434 / 137,000 | |
|
|
| Invariants (all checked by `rebuild/verify_release.py`): |
|
|
| * `test_query_rows` and `test_library_rows` are disjoint and together are exactly |
| `0 … N-1`: the test library is every preprocessed spectrum of the polarity minus the |
| selected test queries. |
| * `val_query_rows` and `val_library_rows` are disjoint and only contain compounds of the |
| train or validation fold; test compounds never appear in the validation task. |
| * The compound sets behind `train_rows`, `val_query_rows` and `test_query_rows` are the |
| pairwise-disjoint train / validation / test compound sets. |
|
|
| ## `derived/row_metadata_*.npz` arrays |
| |
| | array | dtype | meaning | |
| | --- | --- | --- | |
| | `source_row` | int64 | 0-based data row in `MSnLib.csv` (physical line = `source_row + 2`) | |
| | `smiles_index` | int32 | index into `smiles_*.json` | |
| | `adduct_index` | int16 | index into `adducts_*.json` (always 0 here) | |
| | `n_peaks` | uint16 | peaks kept by the preprocessing (≤ 150) | |
| | `precursor_mz` | float32 | precursor m/z as stored by the frozen protocol | |
|
|
| These arrays are *derived* from the historical preprocessed-spectra file and are not part |
| of the original manifest; they are included so that the package can be joined back to |
| `MSnLib.csv` and to the row-index arrays without that file. Their hashes are in |
| `../SHA256SUMS` like every other file. |
|
|
| ## `manifest_summary.json` redaction |
| |
| The frozen file recorded the absolute path of the original data-preparation workspace in |
| its `csv` field. The released copy replaces only that string with |
| `<original data-preparation workspace>/datasets/MSnLib/MSnLib.csv`; every count, seed, hash |
| and identity field is byte-identical. Original file SHA-256 |
| `b83656b2b4d265d1d4ea49df30372e844e207863a7ab768f44f241bd68b8186e`; released copy SHA-256 |
| `6129ed094df59265a684f436da146ef554d9c774e01768363bf58704f87ec237`. See `../VERIFY.md`. |
| |
| ## Ordered-list hashes |
| |
| `ordered_query_smiles_sha256`, `ordered_library_smiles_sha256` (validation and test), |
| `query_source_row_sha256` and `library_source_row_sha256` (test) are SHA-256 digests of the |
| corresponding sequence joined with `"\n"` (no trailing newline), computed over the strings |
| in frozen order. They can be recomputed directly from the CSV tables — see |
| `rebuild/verify_release.py`, which does exactly that and compares against |
| `manifest_summary.json`. |
|
|
