# 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`.