VERIFY — verification record for ultrams_msnlib_benchmark_v1
Every number, ordering and overlap statement in this package was re-derived from the frozen protocol artifacts and checked against the CSV tables shipped here. No discrepancy was found. This file records what was checked, how, and with which exact values, including the checks that can only be performed against the original data-preparation-side artifacts.
The package consists of two independent splits. Split-A-specific evidence (counts,
cross-checks against the MSnLib original JSON formula fields, the repository voting
table, and the read-only replay of all six split-A tables) is recorded in
split_A_full_msnlib/VERIFY.md; this file summarises it
and covers the split-B payload, the cross-split statistics, and the release integrity.
1. Environments
| side | runtime |
|---|---|
| frozen split-B manifest producer / split-A table producer (isolated data-preparation environment, read-only) | Linux, Python 3.10.12, NumPy 2.2.6, h5py 3.16.0, RDKit 2026.03.5 |
| this verification run (local) | macOS, Python 3.13.11, NumPy 2.4.4, pandas 3.0.3, RDKit 2026.03.3 |
Access to the data-preparation environment was read-only: MSnLib.csv and small metadata files
were streamed out; nothing was written or modified on the remote side.
2. Inputs actually used
| input | identity |
|---|---|
MSnLib.csv |
560,084 data rows, 560,085 physical lines (no embedded newlines), 752,707,651 bytes, SHA-256 be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07 |
| frozen split-B manifest | fig3h_manifest_strict_adduct_v4, original SHA-256 b83656b2b4d265d1d4ea49df30372e844e207863a7ab768f44f241bd68b8186e; shipped copy redacted in one path field, SHA-256 6129ed094df59265a684f436da146ef554d9c774e01768363bf58704f87ec237 |
| frozen preprocessed spectra (not redistributed) | 110,091,598 bytes, SHA-256 9296d42e060e7019604e16b20ba80ae13128e03b3e8ee912ee2efeb60bafdf59; only its small metadata columns are shipped in protocol/derived/ |
| MSnLib original release (formula cross-check) | 18 per-file MS2 JSONL record lists, 560,084 records total, Zenodo 10.5281/zenodo.11163380, CC BY 4.0 |
| repository multiple-spectrum voting table (voting-unit cross-check) | benchmarks/molecular_identification/data/multiple_spectrum_voting_per_group.csv.gz (5,002 groups, 57,436 spectra) |
| hosted candidate file (not part of this manifest) | MSnLib_candidates.json, 1,368,264,026 bytes, SHA-256 125a1cdcc57a3fcef8cc76d5322ac0c434cd09b0bfb9e0c9d28bddf052f45fcc; candidate SMILES lists for the single-spectrum candidate-ranking task |
| retention-time source | MSnLib_with_rt.csv, 755,984,910 bytes, SHA-256 a5b7c38228287c5c1de401050445319b331ee9a5f17993d6e104e9a734fe2964, columns mzs,intensities,smiles,precursor_mz,adduct,collision_energy,fold,rt |
| retention-time table (shipped) | split_A_full_msnlib/msnlib_rt.csv.gz, 1,483,069 bytes, SHA-256 994053612db874f7ac7985f278e04cc3463f3b93cd649a195bd167c4c6c7d3d8, 560,084 rows |
3. Split A — formula-level split (summary)
Read-only replay in the isolated data-preparation environment with RDKit 2026.03.5 (split_A_full_msnlib/build_split_a.py)
reproduced every count and all six table SHA-256 values byte-for-byte:
| quantity | observed |
|---|---|
| data rows | 560,084 |
| unique molecular formulas | 21,107 |
| formulas train / validation / test | 16,885 / 2,110 / 2,112 |
| spectra train / validation / test | 446,667 / 55,980 / 57,437 |
| formulas occurring in more than one fold | 0 |
| RDKit SMILES parse failures | 0 (48,597 distinct source SMILES) |
| test spectra | 57,437 (2,112 formulas, 5,003 source SMILES, 4,889 canonical molecules) |
| official voting units — MSnLib source SMILES | 5,002 groups / 57,436 spectra |
| alternative canonical view — RDKit canonical isomeric SMILES | 4,888 groups / 57,436 spectra |
Cross-checks: the test and validation spectra tables match the historical MSnLib_test.csv /
MSnLib_val.csv row by row on smiles, precursor_mz, adduct, collision_energy
(0 mismatches); the RDKit formula agrees with the recorded formula field of the MSnLib
original JSON records (18/18 first records, 0 mismatches over 37,177 streamed records, and
all three located C10H10BrN5O2 records); the MSnLib-source-SMILES voting table is
member-for-member identical to the repository voting table. Details:
split_A_full_msnlib/VERIFY.md.
4. Split B — strict-adduct molecule-level split
rebuild/verify_release.py re-derived from the shipped CSV tables and the frozen
protocol/ arrays:
- counts against
protocol/manifest_summary.json(compounds, spectra, queries, libraries, valid/dropped rows, per-query exact-adduct library positives 6,201 / 3,160); - ordered query / library SMILES SHA-256 and source-row SHA-256 values for both polarities and both folds;
- table row order equals the frozen
query_index/library_index; - query↔library row disjointness, the test partition of all preprocessed rows, one query per validation/test compound, library fold scope;
- table ↔
protocol_*.npzrow-id mapping andprecursor_mz/n_peaksagreement with the frozen row metadata; - compound-level disjointness of the train / validation / test sets per polarity, and the
cross-polarity relation recorded in
stats.json(354 shared positive/negative test compounds).
All 97 split-B checks passed. The ordered-sequence hashes for both test tasks are:
| task | queries | library |
|---|---|---|
[M+H]+ test |
356f355727380d1df02abbb0aaa3391b180a5c7b93b2103058ba54e8dfae51f0 |
4d69c6f65f8c3ed84df54fc2aa6addd7b28fd1c28909386f4e4ced88d31aacce |
[M-H]- test |
db0aa2c39a1e5bc3c4463f97166c9d3e3ac150cba323f44bd29b636ccbd6553b |
00dd373d9e175b070c2bd39595ee9532fdbd94f02a344897e81480e4b7784bc2 |
5. Cross-split A × B
Rebuilt from the shipped tables (rebuild/verify_release.py) and reproduced exactly in
stats.json → cross_split:
- all 441,829 preprocessed split-B rows exist in
row_formula_fold.csv, each mapped to exactly one split-A fold; - compound-level cross-tab (per polarity), spectra-level cross-tab (per split-B table and role) and row-level cross-tab all reproduce the published matrices;
- the split-A test-fold overlap counts (31,570
[M+H]+rows and 13,413[M-H]-rows) are reproduced; - every split-B compound maps to a single formula and therefore a single split-A fold.
Key numbers (see figures_mapping.md §2 for the full matrices):
| quantity | [M+H]+ |
[M-H]- |
|---|---|---|
| split-B compounds | 41,348 | 21,293 |
| split-B compounds in the same split-A fold | 24,360 (58.9 %) | 12,645 (59.4 %) |
| split-B test compounds that are split-A test compounds | 654 / 6,202 | 303 / 3,193 |
| split-A test spectra inside the split-B tables | 31,570 / 57,437 | 13,413 / 57,437 |
5.4 Retention times (split A row metadata)
split_A_full_msnlib/msnlib_rt.csv.gz was exported from MSnLib_with_rt.csv after reading
both files in parallel and comparing them row by row:
| check | result |
|---|---|
| header prefix | 7-column MSnLib.csv header equals the first seven columns of the 8-column with-RT header |
| rows compared | 560,084 / 560,084 |
| first seven columns identical at every row | 0 mismatches |
| extra rows at the end of either file | 0 / 0 |
| unparsable RT values | 0 / 560,084 |
| distinct RT strings | 8,369 (RT is not constant) |
Shipped table: row_index,rt, 560,084 rows, 1,483,069 bytes, SHA-256
994053612db874f7ac7985f278e04cc3463f3b93cd649a195bd167c4c6c7d3d8; gzipped only (no
plain twin) to keep the package compact, and recorded in stats.json →
splits.A.retention_times and verification.rt_export.
6. Release integrity
rebuild/verify_release.py also verifies:
- every plain
.csvis byte-identical to its.csv.gztwin (16 pairs); stats.jsondocuments exactly the shipped files (exceptstats.jsonandSHA256SUMS) and every recorded byte size and SHA-256 matches;SHA256SUMSlists every shipped file except itself and every digest matches;- no retired legacy project naming appears anywhere in the shipped text files (the check itself is written so that the verifier does not contain the forbidden string);
- no internal absolute paths (data-preparation workspaces, cluster scratch directories, user home directories) and no private keys appear in the shipped text files.
Package size: 58 shipped data/document files (plus stats.json and SHA256SUMS);
192,701,913 bytes. The .csv.gz-only upload subset is ≈ 23.0 MiB; the full upload is
≈ 183.8 MiB.
7. Voting units: official 5,002 source-SMILES groups and 4,888 canonical groups
The published multiple-spectrum voting task reports n_molecules = 5002. Verified
member-for-member: those 5,002 groups are the test spectra grouped by the MSnLib source
SMILES string (5,003 distinct strings, one occurring in a single spectrum → 5,002 groups
covering 57,436 spectra). This is the official voting unit and is shipped as
split_A_full_msnlib/test_molecules_voting.csv.
An alternative chemical-deduplication view groups the same test spectra by RDKit
canonical isomeric SMILES: 114 source-string groups merge into chemically identical
molecules, giving 4,888 groups covering the same 57,436 spectra (the single excluded
molecule is CC(C)(C)OC(=O)NCC1(CC(=O)O)CCCCC1). It is shipped as
split_A_full_msnlib/test_molecules_voting_canonical_view.csv and is not the official
voting unit.
No data was altered to force either count. Details: split_A_full_msnlib/VERIFY.md §7 and
stats.json → splits.A.anomaly.
8. What could not be verified from this package alone
- The peak arrays themselves (
mzs/intensities) are not part of this manifest; they are hosted in the same Hugging Face dataset (dsadd4/UltraMS-MSnLib-Benchmark) asMSnLib.csv(752,707,651 bytes, SHA-256be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07), together withMSnLib_candidates.json(1,368,264,026 bytes, SHA-256125a1cdcc57a3fcef8cc76d5322ac0c434cd09b0bfb9e0c9d28bddf052f45fcc). The row pointers androw_formula_fold.csvare the authoritative link back to the spectra. - The historical Figure-3 analysis artifacts themselves; only the published repository voting-group table and the frozen protocol arrays were cross-checked.
- The exact physical row order of
MSnLib.csvbeyond what the shipped tables encode; the package depends on the row pointers, not on reconstructing the file order.
9. Reproduce this verification
python3 rebuild/verify_release.py # 140 checks, exit 0
shasum -a 256 -c SHA256SUMS # macOS; sha256sum -c SHA256SUMS on Linux
10. Transcript of rebuild/verify_release.py
Unedited output against the final package contents (140 checks, exit status 0):
[PASS] csv.gz twins byte-identical to plain csv
[PASS] B/pos: protocol adduct vocabulary == [M+H]+ :: ['[M+H]+']
[PASS] B/pos: preprocessed row metadata covers all 301,636 rows uniquely
[PASS] B/pos: compound split counts match manifest :: {'train': 28944, 'val': 6202, 'test': 6202} vs {'test': 6202, 'train': 28944, 'val': 6202}
[PASS] B/pos: compound vocabulary is exactly the frozen smiles vocabulary :: 41348 vs 41348
[PASS] B/pos: compound_ids unique
[PASS] B/pos: spectra per compound sum to manifest valid rows :: 301636
[PASS] B/pos: split table columns are the released schema :: ['polarity', 'compound_id', 'canonical_isomeric_smiles', 'split', 'n_spectra', 'n_frozen_queries', 'n_raw_smiles_variants', 'first_msnlib_csv_data_row']
[PASS] B/pos: train/val/test compound sets pairwise disjoint
[PASS] B/pos: the three compound sets cover the whole vocabulary
[PASS] B/pos/val: query count 6,202 matches manifest :: 6202 vs 6202
[PASS] B/pos/val: library count 250,424 matches manifest :: 250424 vs 250424
[PASS] B/pos/val: ordered query SMILES sha256 matches manifest
[PASS] B/pos/val: ordered library SMILES sha256 matches manifest
[PASS] B/pos/val: table row order == frozen query_index/library_index
[PASS] B/pos/val: query rows and library rows are disjoint :: 0 shared rows
[PASS] B/pos/val: queries are one spectrum per compound in this fold
[PASS] B/pos/val: library compounds respect the fold scope
[PASS] B/pos/val: query table maps to protocol_pos.npz query rows
[PASS] B/pos/val: library table maps to protocol_pos.npz library rows
[PASS] B/pos/val: source rows unique in each table
[PASS] B/pos/val: n_library_positives column reproduces from the library table
(pos/val queries with a library positive: 6,194 / 6,202)
[PASS] B/pos/val: adduct column is strict [M+H]+ everywhere
[PASS] B/pos/val: csv line = data row + 2 (header offset, no embedded newlines)
[PASS] B/pos/val: precursor_mz/n_peaks agree with frozen row metadata (queries)
[PASS] B/pos/val: query/library table columns are the released schema
[PASS] B/pos/test: query count 6,202 matches manifest :: 6202 vs 6202
[PASS] B/pos/test: library count 295,434 matches manifest :: 295434 vs 295434
[PASS] B/pos/test: ordered query SMILES sha256 matches manifest
[PASS] B/pos/test: ordered library SMILES sha256 matches manifest
[PASS] B/pos/test: table row order == frozen query_index/library_index
[PASS] B/pos/test: query rows and library rows are disjoint :: 0 shared rows
[PASS] B/pos/test: queries are one spectrum per compound in this fold
[PASS] B/pos/test: library compounds respect the fold scope
[PASS] B/pos/test: query table maps to protocol_pos.npz query rows
[PASS] B/pos/test: library table maps to protocol_pos.npz library rows
[PASS] B/pos/test: source rows unique in each table
[PASS] B/pos/test: n_library_positives column reproduces from the library table
[PASS] B/pos/test: queries with an exact-adduct library positive == manifest (6,201) :: 6201
[PASS] B/pos/test: source-row hashes match manifest
[PASS] B/pos/test: adduct column is strict [M+H]+ everywhere
[PASS] B/pos/test: csv line = data row + 2 (header offset, no embedded newlines)
[PASS] B/pos/test: precursor_mz/n_peaks agree with frozen row metadata (queries)
[PASS] B/pos/test: query/library table columns are the released schema
[PASS] B/pos: test queries + test library partition all preprocessed rows
[PASS] B/pos: protocol train_rows all belong to train compounds
[PASS] B/pos: protocol val_query_rows all belong to val compounds
[PASS] B/pos: protocol test_query_rows all belong to test compounds
[PASS] B/pos: source MSnLib.csv sha256 recorded
[PASS] B/neg: protocol adduct vocabulary == [M-H]- :: ['[M-H]-']
[PASS] B/neg: preprocessed row metadata covers all 140,193 rows uniquely
[PASS] B/neg: compound split counts match manifest :: {'train': 14907, 'val': 3193, 'test': 3193} vs {'test': 3193, 'train': 14907, 'val': 3193}
[PASS] B/neg: compound vocabulary is exactly the frozen smiles vocabulary :: 21293 vs 21293
[PASS] B/neg: compound_ids unique
[PASS] B/neg: spectra per compound sum to manifest valid rows :: 140193
[PASS] B/neg: split table columns are the released schema :: ['polarity', 'compound_id', 'canonical_isomeric_smiles', 'split', 'n_spectra', 'n_frozen_queries', 'n_raw_smiles_variants', 'first_msnlib_csv_data_row']
[PASS] B/neg: train/val/test compound sets pairwise disjoint
[PASS] B/neg: the three compound sets cover the whole vocabulary
[PASS] B/neg/val: query count 3,193 matches manifest :: 3193 vs 3193
[PASS] B/neg/val: library count 116,135 matches manifest :: 116135 vs 116135
[PASS] B/neg/val: ordered query SMILES sha256 matches manifest
[PASS] B/neg/val: ordered library SMILES sha256 matches manifest
[PASS] B/neg/val: table row order == frozen query_index/library_index
[PASS] B/neg/val: query rows and library rows are disjoint :: 0 shared rows
[PASS] B/neg/val: queries are one spectrum per compound in this fold
[PASS] B/neg/val: library compounds respect the fold scope
[PASS] B/neg/val: query table maps to protocol_neg.npz query rows
[PASS] B/neg/val: library table maps to protocol_neg.npz library rows
[PASS] B/neg/val: source rows unique in each table
[PASS] B/neg/val: n_library_positives column reproduces from the library table
(neg/val queries with a library positive: 3,163 / 3,193)
[PASS] B/neg/val: adduct column is strict [M-H]- everywhere
[PASS] B/neg/val: csv line = data row + 2 (header offset, no embedded newlines)
[PASS] B/neg/val: precursor_mz/n_peaks agree with frozen row metadata (queries)
[PASS] B/neg/val: query/library table columns are the released schema
[PASS] B/neg/test: query count 3,193 matches manifest :: 3193 vs 3193
[PASS] B/neg/test: library count 137,000 matches manifest :: 137000 vs 137000
[PASS] B/neg/test: ordered query SMILES sha256 matches manifest
[PASS] B/neg/test: ordered library SMILES sha256 matches manifest
[PASS] B/neg/test: table row order == frozen query_index/library_index
[PASS] B/neg/test: query rows and library rows are disjoint :: 0 shared rows
[PASS] B/neg/test: queries are one spectrum per compound in this fold
[PASS] B/neg/test: library compounds respect the fold scope
[PASS] B/neg/test: query table maps to protocol_neg.npz query rows
[PASS] B/neg/test: library table maps to protocol_neg.npz library rows
[PASS] B/neg/test: source rows unique in each table
[PASS] B/neg/test: n_library_positives column reproduces from the library table
[PASS] B/neg/test: queries with an exact-adduct library positive == manifest (3,160) :: 3160
[PASS] B/neg/test: source-row hashes match manifest
[PASS] B/neg/test: adduct column is strict [M-H]- everywhere
[PASS] B/neg/test: csv line = data row + 2 (header offset, no embedded newlines)
[PASS] B/neg/test: precursor_mz/n_peaks agree with frozen row metadata (queries)
[PASS] B/neg/test: query/library table columns are the released schema
[PASS] B/neg: test queries + test library partition all preprocessed rows
[PASS] B/neg: protocol train_rows all belong to train compounds
[PASS] B/neg: protocol val_query_rows all belong to val compounds
[PASS] B/neg: protocol test_query_rows all belong to test compounds
[PASS] B/neg: source MSnLib.csv sha256 recorded
[PASS] B: cross-polarity pos-test x neg-test intersection reproduces stats.json :: 354 vs 354
[PASS] A: formula_split columns :: ['formula', 'fold', 'n_spectra']
[PASS] A: formula_split has 21,107 unique formulas
[PASS] A: formula fold values are train/val/test
[PASS] A: formula-level counts 16,885 / 2,110 / 2,112 :: {'train': 16885, 'val': 2110, 'test': 2112}
[PASS] A: spectra counts 446,667 / 55,980 / 57,437 :: {'train': 446667, 'val': 55980, 'test': 57437}
[PASS] A: total spectra = 560,084
[PASS] A: row_formula_fold covers rows 0..560,083 in order
[PASS] A: every formula occurs in exactly one fold
[PASS] A: row_formula_fold agrees with formula_split (fold and n_spectra)
[PASS] A: row-level fold totals match formula_split
[PASS] A: test_spectra columns are the released schema :: ['row_index', 'smiles', 'precursor_mz', 'adduct', 'collision_energy', 'fold', 'canonical_isomeric_smiles']
[PASS] A: test_spectra has 57,437 rows, all fold=test
[PASS] A: test_spectra row_index equals the rows marked test in row_formula_fold
[PASS] A: val_spectra has 55,980 rows, all fold=val
[PASS] A: val_spectra row_index equals the rows marked val in row_formula_fold
[PASS] A: official voting-unit table columns are group_id, smiles, n_spectra :: ['group_id', 'smiles', 'n_spectra']
[PASS] A: official voting-unit table (MSnLib source SMILES) reproduces from test_spectra
[PASS] A: official voting-unit table has 5,002 groups / 57,436 spectra
[PASS] A: canonical-view table columns are group_id, canonical_isomeric_smiles, n_spectra :: ['group_id', 'canonical_isomeric_smiles', 'n_spectra']
[PASS] A: canonical-view table reproduces from test_spectra
[PASS] A: canonical-view table has 4,888 groups / 57,436 spectra
[PASS] A: exactly one test spectrum lies outside the voting tables :: CC(C)(C)OC(=O)NCC1(CC(=O)O)CCCCC1
[PASS] A: retention-time companion table is shipped and matches stats.json :: split_A_full_msnlib/msnlib_rt.csv.gz
[PASS] A: retention-time table columns are row_index, rt :: ['row_index', 'rt']
[PASS] A: retention-time table has 560,084 rows in row order
[PASS] A: every retention time is present and numeric :: 0 empty, 0 non-numeric
[PASS] A/B: every split-B table row exists in row_formula_fold :: 0 missing
[PASS] A/B: split-B tables cover all 441,829 preprocessed spectra :: 441829
[PASS] A/B: compound-level cross tab reproduces stats.json
[PASS] A/B: spectra-level cross tab reproduces stats.json
[PASS] A/B: row-level split-B x split-A cross tab reproduces stats.json
[PASS] A/B: row-level split-B totals equal the manifest split-spectra counts
[PASS] A/B/pos: A-test rows inside the split-B tables reproduce stats.json :: 31570 vs 31570
[PASS] A/B/neg: A-test rows inside the split-B tables reproduce stats.json :: 13413 vs 13413
[PASS] A/B: every split-B compound has a single split-A fold (same formula)
[PASS] stats.json documents exactly the shipped files (except stats.json and SHA256SUMS) :: missing=[] extra=[]
[PASS] stats.json byte sizes and sha256 match every shipped file
[PASS] SHA256SUMS parses as '<sha256> <path>' lines
[PASS] SHA256SUMS covers every shipped file except itself :: 60 entries
[PASS] SHA256SUMS hashes match the files
[PASS] no retired legacy project naming anywhere in the shipped text files
[PASS] no internal absolute paths or private keys in the shipped text files
140/140 checks passed
11. Version
Release 1.0.0, generated 2026-11-04. Any change to the tables or protocol files
invalidates these hashes and requires a new version directory.