protocol/README.md

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.