Datasets:

dsadd4
/

UltraMS-MSnLib-Benchmark

@@ -1,424 +1,207 @@
-# UltraMS MSnLib benchmark
-Version **1.0.0** · 2026-11-04 · license **CC BY 4.0** (see [NOTICE.md](NOTICE.md))
-Two frozen, independent benchmark splits of the [MSnLib](https://doi.org/10.1038/s41592-025-02813-0)
-tandem mass spectral library, built and released by UltraMS:
-* **Split A — UltraMS MSnLib formula-level split**: the complete library (560,084 spectra,
-  all adducts) split by molecular formula into train / validation / test
-  (16,885 / 2,110 / 2,112 formulas, 446,667 / 55,980 / 57,437 spectra). Formula-disjoint.
-  This is the population for single-spectrum candidate ranking, multiple-spectrum voting,
-  label-blind grouping and embedding analyses.
-* **Split B — strict-adduct molecule-level split**: the strict `[M+H]+` and `[M-H]-`
-  subsets (447,956 source rows) re-split 70 / 15 / 15 at the level of RDKit canonical
-  isomeric SMILES, separately per polarity, with frozen queries and libraries for
-  spectrum-to-spectrum library search. Molecule-disjoint within each polarity.
-Both splits are frozen benchmark definitions with published checksums; neither is a
-redistribution of the MSnLib spectra.
 ---
-## 1. At a glance
-| | Split A (formula-level, all adducts) | Split B `[M+H]+` | Split B `[M-H]-` |
 | --- | ---: | ---: | ---: |
-| compounds / molecules | — (21,107 formulas) | 41,348 | 21,293 |
-| spectra | 560,084 | 301,636 | 140,193 |
-| train | 16,885 formulas · 446,667 spectra | 28,944 compounds · 211,745 spectra | 14,907 · 98,401 |
-| validation | 2,110 formulas · 55,980 spectra | 6,202 compounds · 44,881 spectra | 3,193 · 20,927 |
-| test | 2,112 formulas · 57,437 spectra | 6,202 compounds · 45,010 spectra | 3,193 · 20,865 |
-| test task | candidate ranking / voting (57,437 queries) | 6,202 queries vs 295,434 library spectra | 3,193 vs 137,000 |
-| queries with an exact-adduct library positive | — | 6,201 | 3,160 |
-| validation task | — | 6,202 vs 250,424 | 3,193 vs 116,135 |
-Split A test fold: 57,437 spectra, 2,112 formulas, 5,003 distinct MSnLib source SMILES,
-4,889 distinct RDKit canonical isomeric SMILES. The **official** multiple-spectrum voting
-unit is the MSnLib source SMILES string: 5,002 groups covering 57,436 spectra (canonical
-view: 4,888 groups).
-Split B split seeds: 42 (`[M+H]+`) / 43 (`[M-H]-`); query seed 119. Split A has no seed:
-its fold assignment is frozen in the `fold` column of `MSnLib.csv` and replayed exactly by
-`split_A_full_msnlib/build_split_a.py`.
-## 2. Disjointness: what is claimed — and what is not
-| split | disjointness unit | claimed |
-| --- | --- | --- |
-| A | molecular formula | every spectrum of a formula lies in exactly one fold; no formula occurs in two folds (0 conflicts out of 21,107) |
-| B | RDKit canonical isomeric SMILES, per polarity | the train / validation / test compound sets of each polarity are pairwise disjoint |
-**A and B are different objects and must not be combined into a global-disjointness claim.**
-About 41 % of split-B compounds are in a *different* split-A fold, and a spectrum can be a
-split-A test spectrum while its compound is a split-B train compound. Concrete numbers:
-* split B `[M+H]+` test compounds: 654 are split-A test, 4,922 are split-A train, 626 are
-  split-A validation;
-* split B `[M-H]-` test compounds: 303 are split-A test, 2,541 are split-A train, 349 are
-  split-A validation;
-* 31,570 split-A test spectra are `[M+H]+` rows of split B and 13,413 are `[M-H]-` rows.
-The full cross-tabulation (compound level and spectra level, per polarity, plus the
-relation of the split-A test fold to split B) is in [figures_mapping.md](figures_mapping.md) §2.
-Never report a cross-split score as a held-out result: train and evaluate inside one split.
-## 3. Package layout
-```text
-ultrams_msnlib_benchmark_v1/
-├── README.md                     this file
-├── figures_mapping.md            which manuscript panel uses which split (+ cross-split statistics)
-├── VERIFY.md                     full verification record and reproducible commands
-├── NOTICE.md                     MSnLib attribution, provenance and licensing
-├── SHA256SUMS                    checksums of every file except itself
-├── stats.json                    machine-readable release summary (all counts + file hashes)
-├── split_A_full_msnlib/          split A (formula-level, full library)
-│   ├── README.md
-│   ├── VERIFY.md                 split-A verification record
-│   ├── REPORT.json               split-A machine-readable report
-│   ├── build_split_a.py          replay of split A from MSnLib.csv + hash check
-│   ├── formula_split.csv(.gz)                21,107 formulas → fold, n_spectra
-│   ├── row_formula_fold.csv(.gz)             560,084 rows → formula, fold
-│   ├── test_spectra.csv(.gz)                 57,437 test spectra
-│   ├── val_spectra.csv(.gz)                  55,980 validation spectra
-│   ├── test_molecules_voting.csv(.gz)        5,002 official source-SMILES voting units
-│   ├── test_molecules_voting_canonical_view.csv(.gz)  4,888 canonical-SMILES alternative view
-│   └── msnlib_rt.csv.gz                      560,084 row_index → retention time (seconds)
-├── splits/                       split B compound tables (70/15/15, per polarity)
-│   ├── pos_compound_split.csv(.gz)           41,348 compounds
-│   └── neg_compound_split.csv(.gz)           21,293 compounds
-├── queries/                      split B query spectra
-│   ├── pos_val_queries.csv(.gz)              6,202
-│   ├── pos_test_queries.csv(.gz)             6,202
-│   ├── neg_val_queries.csv(.gz)              3,193
-│   └── neg_test_queries.csv(.gz)             3,193
-├── libraries/                    split B library spectra
-│   ├── pos_val_library.csv(.gz)              250,424
-│   ├── pos_test_library.csv(.gz)             295,434
-│   ├── neg_val_library.csv(.gz)              116,135
-│   └── neg_test_library.csv(.gz)             137,000
-├── protocol/                     frozen split-B protocol arrays and manifest
-│   ├── manifest_summary.json
-│   ├── protocol_{pos,neg}.npz
-│   ├── smiles_{pos,neg}.json
-│   ├── adducts_{pos,neg}.json
-│   ├── derived/row_metadata_{pos,neg}.npz
-│   └── README.md
-├── rebuild/
-│   ├── build_library_manifest.py the split-B producer (replays MSnLib.csv)
-│   ├── baseline_common.py        its helper module
-│   ├── verify_release.py         self-contained verifier for the whole package
-│   ├── LICENSE-APACHE-2.0.txt
-│   └── README.md
-├── hf_dataset_card.md            Hugging Face dataset card draft
-├── hf_upload_commands.sh         upload commands, dry-run by default, not executed
-└── zenodo_metadata.json          Zenodo deposition metadata draft
 ```
-Every plain `.csv` has a byte-identical `.csv.gz` twin; `rebuild/verify_release.py` checks
-this, all counts, all orderings, the cross-split statistics and the checksums.
-## 4. Split A — UltraMS MSnLib formula-level split
-### 4.1 Definition
-For every MSnLib spectrum the neutral molecular formula is computed from the source SMILES
-with RDKit (`rdMolDescriptors.CalcMolFormula(Chem.MolFromSmiles(smiles))`). The frozen
-`fold` column of `MSnLib.csv` assigns each formula to exactly one fold; the split is the
-formula-grouped 80/10/10 partition that results. The rule was verified for all 560,084
-spectra: 21,107 formulas, none in more than one fold. This is the frozen benchmark
-definition; `build_split_a.py` replays it from `MSnLib.csv` and reproduces every table
-byte-for-byte.
-### 4.2 Tables
-| file | rows | columns |
-| --- | ---: | --- |
-| `formula_split.csv` | 21,107 | `formula, fold, n_spectra` — ordered by fold (train, valid, test) then formula |
-| `row_formula_fold.csv` | 560,084 | `row_index, formula, fold` — 0-based `MSnLib.csv` data row → formula → fold |
-| `test_spectra.csv` | 57,437 | `row_index, smiles, precursor_mz, adduct, collision_energy, fold, canonical_isomeric_smiles` |
-| `val_spectra.csv` | 55,980 | same schema for the validation fold |
-| `test_molecules_voting.csv` | 5,002 | `group_id, smiles, n_spectra` — **official** voting units (MSnLib source SMILES) |
-| `test_molecules_voting_canonical_view.csv` | 4,888 | `group_id, canonical_isomeric_smiles, n_spectra` — alternative canonical view |
-| `msnlib_rt.csv.gz` | 560,084 | `row_index, rt` — per-spectrum retention time in seconds (gzipped only, see §4.5) |
-`row_index` is the 0-based data row of `MSnLib.csv` (physical line = data row + 2). The
-tables do not carry peak data; join on `row_index` against `MSnLib.csv` (see §8).
-### 4.3 Official voting units — read this before using the voting tables
-The **official multiple-spectrum voting units are the 5,002 MSnLib source-SMILES groups
-covering 57,436 spectra**, exactly the grouping used by the published multiple-spectrum
-voting task (Figure 3d and the Figure 3a voting readouts, `n_molecules = 5002`). The test
-fold contains 5,003 distinct source SMILES strings; one occurs in only one spectrum, hence
-5,002 groups. This table is `test_molecules_voting.csv` (columns `group_id, smiles,
-n_spectra`) and it is verified member-for-member against the repository voting table
-(`benchmarks/molecular_identification/data/multiple_spectrum_voting_per_group.csv.gz`).
-An **alternative canonical view** is provided as `test_molecules_voting_canonical_view.csv`:
-the same test spectra grouped by RDKit canonical isomeric SMILES give 4,888 groups covering
-the same 57,436 spectra (114 source-string groups merge into chemically identical
-molecules; the single excluded molecule is `CC(C)(C)OC(=O)NCC1(CC(=O)O)CCCCC1`). This view
-is not the official voting unit.
-No data was altered to force either count. See `split_A_full_msnlib/VERIFY.md` §7 and
-`REPORT.json` → `anomalies`.
-### 4.5 Retention times (RT)
-`split_A_full_msnlib/msnlib_rt.csv.gz` is a compact companion table needed by the
-label-blind grouping and multiple-spectrum voting analyses (Figure 3d): `row_index` is the
-0-based `MSnLib.csv` data row (0 … 560,083) and `rt` is the retention time in seconds, kept
-in the source text representation.
-RT is **source metadata from the MSnLib records** (CC BY 4.0, Zenodo
-10.5281/zenodo.11163380; see `NOTICE.md`). The table was exported from
-`MSnLib_with_rt.csv` (755,984,910 bytes, SHA-256
-`a5b7c38228287c5c1de401050445319b331ee9a5f17993d6e104e9a734fe2964`) after verifying
-row-by-row that its first seven columns are identical to `MSnLib.csv` in the same order
-(560,084/560,084 rows, 0 mismatches; see `split_A_full_msnlib/VERIFY.md` §5.4). The full
-756 MB CSV is not duplicated; only this 1.4 MB gzipped table is shipped.
 ```python
-import pandas as pd
-test = pd.read_csv("split_A_full_msnlib/test_spectra.csv")
-rt = pd.read_csv("split_A_full_msnlib/msnlib_rt.csv.gz")   # row_index, rt
-test_rt = test.merge(rt, on="row_index", how="left")
-assert test_rt["rt"].notna().all()
 ```
-The same `row_index` join works for every row of `row_formula_fold.csv`.
-#### Provenance of split A
-Source rows, formulas and folds were computed read-only in an isolated data-preparation
-environment with RDKit 2026.03.5. The split-A tables were frozen from that run; cross-checks against the
-historical per-fold CSV files, against the MSnLib original JSON `formula` fields, and
-against the repository voting table are recorded in `split_A_full_msnlib/VERIFY.md`.
-## 5. Split B — strict-adduct molecule-level split
-### 5.1 Definition
-Split B keeps only the strict `[M+H]+` (303,709 source rows) and `[M-H]-` (144,247 source
-rows) spectra. After the frozen spectrum preprocessing (drop `m/z ≤ 0` peaks, require at
-least 3 peaks, normalise to the base peak, keep the 150 most intense peaks and sort by m/z)
-2,073 positive and 4,054 negative rows are dropped, leaving **301,636** and **140,193**
-preprocessed spectra. Compound identity is RDKit canonical isomeric SMILES (frozen with
-RDKit 2026.03.5). Per polarity the sorted compound list is shuffled with
-`random.Random(42)` (`[M+H]+`) / `random.Random(43)` (`[M-H]-`) and split 70 / 15 / 15;
-one query spectrum per validation/test compound is drawn with a fresh `random.Random(119)`.
-### 5.2 Tables
-| table | schema |
-| --- | --- |
-| `splits/{pos,neg}_compound_split.csv` | `polarity, compound_id, canonical_isomeric_smiles, split, n_spectra, n_frozen_queries, n_raw_smiles_variants, first_msnlib_csv_data_row` |
-| `queries/{pos,neg}_{val,test}_queries.csv` | `polarity, split, query_index, compound_id, canonical_isomeric_smiles, adduct, msnlib_csv_data_row, msnlib_csv_line, precursor_mz, n_peaks, collision_energy, source_smiles_raw, n_library_positives` |
-| `libraries/{pos,neg}_{val,test}_library.csv` | same as queries with `library_index` and `compound_split` instead of `query_index`; row order is the frozen library order |
-### 5.3 Protocol
-1. Score every query against the **complete** library of its task (no candidate short list).
-2. A retrieved library spectrum is correct iff its canonical isomeric SMILES equals the
-   query's (exact same-adduct spectrum of the same molecule).
 3. Empirical FDR = `(accepted − correct) / accepted`; identification recall =
    `correct / n_queries_with_library_positive` (6,201 / 3,160 for the two test tasks).
    Queries without a library positive enter the FDR denominator but not the recall
-   denominator; `n_library_positives` is published per query.
-4. The **test library** is every preprocessed spectrum of the polarity except the selected
-   test queries (it therefore still contains further spectra of the test molecules; a query
-   never occurs in its own library). The **validation library** contains train and
-   validation compounds only, so test compounds never influence validation scores.
-5. Validation is for model selection only; the test fold is evaluated once.
-The split-B tables deliberately do **not** carry the formula-level fold of the spectra:
-that label belongs to split A. To obtain each split-B row's split-A fold, join
-`msnlib_csv_data_row` (queries/libraries) or `first_msnlib_csv_data_row` (compound split)
-against `split_A_full_msnlib/row_formula_fold.csv`; the packaged verifier does exactly this
-for the cross-split statistics.
-The frozen row-index arrays behind these tables are in `protocol/`; the CSV tables are a
-human-readable view. `rebuild/build_library_manifest.py` replays them bit-for-bit from
-`MSnLib.csv`, and `rebuild/verify_release.py` checks the tables against the arrays and the
-frozen manifest.
-### 5.4 Cross-collision-energy subtask
-The cross-collision-energy library-search task uses split B test queries that were measured
-at two or more collision energies: **6,161 positive** and **2,999 negative** queries (out of
-6,202 / 3,193 split-B test queries). The task pairs a low-energy query spectrum with a
-high-energy reference library (or vice versa) and asks for the same-molecule hit; the
-query identities are a subset of the split-B test queries published here. The CE values in
-MSnLib are 15, 20, 30, 45, 60 and 75 eV. The cross-CE pairing manifest and readouts are
-part of the UltraMS repository, not of this split package.
-## 6. Relation to split A
-Split A and split B are independent; see §2 for the disjointness statement and
-[figures_mapping.md](figures_mapping.md) §2 for the full cross-tabulation. Summary: 58.9 %
-positive and 59.4 % negative split-B compounds keep the same fold in split A; 654 positive
-and 303 negative split-B test compounds are also split-A test compounds; 31,570 / 13,413
-split-A test spectra are `[M+H]+` / `[M-H]-` rows of split B.
-## 7. Manuscript figures
-[figures_mapping.md](figures_mapping.md) maps every figure panel to the split it uses:
-* **A**: Figure 2b, Figure 2j, Figure 3a, 3b, 3d, 3g, 3a_sp_4, 3a_sp_5 and the
-  single-spectrum baselines Top-1 table;
-* **B**: Figure 3e, 3f, 3h, 3h_sp_1 and the cross-collision-energy task (6,161 / 2,999);
-* **not this dataset**: NPLIB1 and MassSpecGym comparison panels (independent external
-  benchmarks); Figure 3c / 3i case studies are not split-defined.
-Candidate-ranking tables (the per-formula candidate lists behind Figure 3a/3b/3d/3g) are
-part of the UltraMS repository, not of this split package; this package provides the frozen
-queries, identities and folds they are evaluated on.
-## 8. Data acquisition and rebuilding
-### 8.1 The spectra are not part of this manifest
-This package publishes splits and identifiers, not peak arrays. Every table is joined back
-to the spectra through `row_index` / `msnlib_csv_data_row`, which point into `MSnLib.csv`;
-both large files are hosted in the same Hugging Face dataset (see the managed-file table
-below) rather than duplicated in this manifest.
-| item | value |
-| --- | --- |
-| file | `MSnLib.csv` — one row per MSnLib spectrum |
-| rows | 560,084 data rows (560,085 physical lines, no embedded newlines) |
-| bytes | 752,707,651 |
-| SHA-256 | `be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07` |
-| columns | `mzs, intensities, smiles, precursor_mz, adduct, collision_energy, fold` |
-| CSV format | peaks stored as comma-separated strings (`mzs`, `intensities`), one spectrum per row |
-**Managed files on Hugging Face.** The dataset is planned for Hugging Face under the
-placeholder id **`dsadd4/UltraMS-MSnLib-Benchmark`** (dataset card and upload commands are
-drafted here as `hf_dataset_card.md` and `hf_upload_commands.sh`; the upload has **not**
-been executed). The repository will host:
 | hosted file | bytes | SHA-256 | purpose |
 | --- | ---: | --- | --- |
-| every file of this manifest (`split_A_full_msnlib/`, `splits/`, `queries/`, `libraries/`, `protocol/`, `rebuild/`, docs; 59 files) | ≈ 185.2 MiB total | see `SHA256SUMS` | the two benchmark splits, verifier, docs |
-| `split_A_full_msnlib/msnlib_rt.csv.gz` | 1,483,069 | `994053612db874f7ac7985f278e04cc3463f3b93cd649a195bd167c4c6c7d3d8` | compact per-spectrum retention time (`row_index, rt` in seconds); joins `MSnLib.csv` rows 1:1 and supplies the RT used by the label-blind grouping analysis (Figure 3d) |
-| `MSnLib.csv` | 752,707,651 | `be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07` | the full source CSV: one row per MSnLib spectrum; every `row_index` / `msnlib_csv_data_row` / `first_msnlib_csv_data_row` pointer resolves here |
 | `MSnLib_candidates.json` | 1,368,264,026 | `125a1cdcc57a3fcef8cc76d5322ac0c434cd09b0bfb9e0c9d28bddf052f45fcc` | candidate SMILES lists behind the single-spectrum candidate-ranking task: a JSON object mapping a query SMILES string to its candidate SMILES list (9,886 query entries) |
-The large files are hosted because every table points into them: spectra (`MSnLib.csv`) and
-candidate rankings (`MSnLib_candidates.json`). The upload script keeps them in a separate
-step and remains dry-run by default.
-It can also be rebuilt from the **MSnLib original release** (Brungs et al., Zenodo
-[10.5281/zenodo.11163380](https://doi.org/10.5281/zenodo.11163380), CC BY 4.0): the release
-provides 18 per-file MS2 JSONL record lists with exactly 560,084 records in total (equal to
-the CSV data-row count), each record carrying `peaks`, `smiles`, `precursor_mz`, `adduct`
-and `collision_energy`. The UltraMS CSV conversion writes one row per record in the frozen
-conversion order with the columns above and carries the frozen fold labels. The
-authoritative row → formula → fold mapping is shipped independently as
-`split_A_full_msnlib/row_formula_fold.csv`, so downstream work never depends on
-reconstructing the conversion order.
-### 8.2 Rebuilding split A
-```bash
-python3 split_A_full_msnlib/build_split_a.py \
-    --csv /path/to/MSnLib.csv \
-    --output-dir replay_split_a
-```
-Needs Python ≥ 3.10 and RDKit 2026.03.5 (the frozen canonicalisation runtime). The script
-verifies all counts and all six table SHA-256 values; with a different RDKit patch release
-the canonical-string tables can differ textually while every count still matches (the
-script reports that, or downgrades it to a warning with `--lenient-rdkit`).
-### 8.3 Rebuilding split B
-See [rebuild/README.md](rebuild/README.md). In short:
-```bash
-python3 rebuild/build_library_manifest.py \
-    --csv /path/to/MSnLib.csv --skip-reference-regression \
-    --output-dir replay_manifest
 ```
-This regenerates `protocol/*.npz`, `smiles_*.json`, `adducts_*.json` and
-`manifest_summary.json` (needs NumPy, h5py, RDKit). The CSV tables are then rebuilt from the
-protocol arrays through `protocol/derived/row_metadata_*.npz` (see `protocol/README.md`).
-## 9. Verification
-```bash
-python3 rebuild/verify_release.py     # self-contained; no network, no MSnLib download
-sha256sum -c SHA256SUMS              # or: shasum -a 256 -c SHA256SUMS (macOS)
-```
-`rebuild/verify_release.py` re-derives every published count, ordering hash, disjointness
-statement, query/library partition, per-query library positive, cross-split statistic and
-file checksum from the shipped files; the complete transcript is in [VERIFY.md](VERIFY.md).
-Split-A-specific evidence (including the read-only replay and the voting-unit check) is in
-`split_A_full_msnlib/VERIFY.md`.
-## 10. Known properties and caveats
-1. **Two splits, two disjointness units.** Split A is formula-disjoint; split B is
-   compound-disjoint within each polarity. Do not merge them into one global-disjointness
-   claim and do not reuse a fold label across splits (§2).
-2. **Voting units: official 5,002 source-SMILES groups / 57,436 spectra, alternative
-   canonical view 4,888 groups / 57,436 spectra.** The official unit is the one used by the
-   published `n_molecules = 5002` grouping; both tables are shipped (§4.3).
-3. **Retention times are split-A row metadata.** `split_A_full_msnlib/msnlib_rt.csv.gz`
-   (`row_index, rt` in seconds) is source metadata from the MSnLib release, verified
-   row-aligned to `MSnLib.csv`; it is not part of split B and carries no fold label of its
-   own.
-4. **Queries without a library positive are expected** in split B: 1 positive and 33
-   negative *test* queries (and 8 / 30 *validation* queries) are singleton compounds whose
-   only spectrum is the query. They enter the FDR denominator but not the recall
-   denominator; `n_library_positives` is published per query.
-5. **Singleton compounds are retained** in split B (39 positive and 202 negative compounds
-   have exactly one spectrum). Filtering them changes the benchmark.
-6. **Compound identity is frozen text** (RDKit 2026.03.5 canonical isomeric SMILES). Other
-   RDKit patch releases can serialise the same molecule differently; compare the published
-   strings, not freshly canonicalised ones. Molecular formulas are stable across RDKit
-   patch releases.
-7. **Precursor m/z** is the source CSV text value; the split-B protocol stores it as
-   float32 and all 441,829 preprocessed rows agree exactly after the cast.
-8. **Collision energy is source metadata**, not a selection criterion; all six values
-   (15, 20, 30, 45, 60, 75 eV) occur in both polarities.
-9. **Split B libraries are large by design** (≈47.6 positive / ≈42.9 negative spectra per
-   query on average); ranking must cover the full library, there is no candidate short list.
-10. **Split A includes all adducts** (11 distinct adducts in the test fold), not only the
-   strict `[M+H]+` / `[M-H]-` subset used by split B.
-## 11. Provenance and licensing
-The upstream MSnLib release (spectra and molecule metadata) is CC BY 4.0 (Brungs et al.,
-Zenodo 10.5281/zenodo.11163380). The split definitions, tables and scripts added by UltraMS
-are released under CC BY 4.0 as well. `rebuild/build_library_manifest.py` and
-`rebuild/baseline_common.py` are Apache-2.0 files copied from the UltraMS public release.
-See [NOTICE.md](NOTICE.md) for the full attribution and licensing statement, and
-`protocol/manifest_summary.json` for the frozen split-B manifest (one path field is
-redacted to a placeholder; every count, seed and hash is byte-identical).
-## 12. Citation
-If you use this benchmark, please cite MSnLib and UltraMS:
-* MSnLib: Brungs C., Schmid R., Pluskal T. *MSnLib: efficient generation of open
-  multi-stage fragmentation mass spectral libraries.* Nature Methods (2025),
-  doi:10.1038/s41592-025-02813-0; data: Zenodo 10.5281/zenodo.11163380 (CC BY 4.0).
-* UltraMS: Li Y., Zhong Y., Liu P., Xia J. *UltraMS* (manuscript in preparation;
-  code: <https://github.com/Dsadd4/UltraMS>).
-Machine-readable citation metadata is in [`zenodo_metadata.json`](zenodo_metadata.json) and
-[`hf_dataset_card.md`](hf_dataset_card.md).
-## 13. Versioning
-`1.0.0` is the first joint release of splits A and B. Its content is defined by
-`stats.json`, `SHA256SUMS` and the frozen `protocol/manifest_summary.json`. Any change to
-the splits, the compound/formula identity or the library scope requires a new version
-directory and new manifests — the frozen tables must stay frozen so that published
-FDR/recall/ranking numbers remain comparable.

+---
+pretty_name: UltraMS MSnLib benchmark (formula-level split A + strict-adduct molecule-level split B)
+license: cc-by-4.0
+language:
+  - en
+size_categories:
+  - 100K<n<1M
+task_categories:
+  - other
+configs:
+  - config_name: split_A_formula_split
+    data_files: split_A_full_msnlib/formula_split.csv
+  - config_name: split_A_row_formula_fold
+    data_files: split_A_full_msnlib/row_formula_fold.csv
+  - config_name: split_A_test_spectra
+    data_files: split_A_full_msnlib/test_spectra.csv
+  - config_name: split_A_val_spectra
+    data_files: split_A_full_msnlib/val_spectra.csv
+  - config_name: split_A_test_molecules_voting_official
+    data_files: split_A_full_msnlib/test_molecules_voting.csv
+  - config_name: split_A_test_molecules_voting_canonical_view
+    data_files: split_A_full_msnlib/test_molecules_voting_canonical_view.csv
+  - config_name: split_A_msnlib_rt
+    data_files: split_A_full_msnlib/msnlib_rt.csv.gz
+  - config_name: split_B_pos_compound_split
+    data_files: splits/pos_compound_split.csv
+  - config_name: split_B_neg_compound_split
+    data_files: splits/neg_compound_split.csv
+  - config_name: split_B_pos_val_queries
+    data_files: queries/pos_val_queries.csv
+  - config_name: split_B_pos_test_queries
+    data_files: queries/pos_test_queries.csv
+  - config_name: split_B_neg_val_queries
+    data_files: queries/neg_val_queries.csv
+  - config_name: split_B_neg_test_queries
+    data_files: queries/neg_test_queries.csv
+  - config_name: split_B_pos_val_library
+    data_files: libraries/pos_val_library.csv
+  - config_name: split_B_pos_test_library
+    data_files: libraries/pos_test_library.csv
+  - config_name: split_B_neg_val_library
+    data_files: libraries/neg_val_library.csv
+  - config_name: split_B_neg_test_library
+    data_files: libraries/neg_test_library.csv
+tags:
+  - chemistry
+  - mass-spectrometry
+  - metabolomics
+  - small-molecules
+  - tandem-ms
+  - spectrum-library-search
+  - molecule-retrieval
+  - benchmark
+  - ultraMS
 ---
+# UltraMS MSnLib benchmark
+Two frozen, independent benchmark splits of the [MSnLib](https://doi.org/10.1038/s41592-025-02813-0)
+tandem mass spectral library, released by UltraMS. The splits are different objects:
+* **Split A — UltraMS MSnLib formula-level split** (all 560,084 spectra, all adducts):
+  21,107 molecular formulas, split 16,885 / 2,110 / 2,112 formulas and
+  446,667 / 55,980 / 57,437 spectra into train / validation / test. Formula-disjoint. Test
+  fold: 57,437 spectra, 2,112 formulas, 5,003 source SMILES / 4,889 canonical molecules.
+  Population for single-spectrum candidate ranking, multiple-spectrum voting, label-blind
+  grouping, fingerprint prediction and embedding analyses (Figure 2b/2j, 3a/3b/3d/3g,
+  3a_sp_4, 3a_sp_5, single-spectrum baselines). The **official multiple-spectrum voting
+  units are the 5,002 MSnLib source-SMILES groups covering 57,436 spectra**
+  (`test_molecules_voting.csv`); a canonical-SMILES alternative view (4,888 groups) is also
+  provided (`test_molecules_voting_canonical_view.csv`). Per-spectrum retention times
+  (`row_index, rt` in seconds) are in `msnlib_rt.csv.gz` for the label-blind grouping and
+  multiple-spectrum voting analyses.
+* **Split B — strict-adduct molecule-level split** (`[M+H]+` and `[M-H]-` only): 41,348 /
+  21,293 compounds and 301,636 / 140,193 preprocessed spectra, split 70/15/15 per polarity
+  by RDKit canonical isomeric SMILES, with frozen queries and libraries for
+  spectrum-to-spectrum library search. Population for Figure 3e/3f/3h, 3h_sp_1 and the
+  cross-collision-energy task (6,161 positive / 2,999 negative queries).
+| split-B task | queries | library spectra | queries with an exact-adduct library positive |
 | --- | ---: | ---: | ---: |
+| `[M+H]+` test | 6,202 | 295,434 | 6,201 |
+| `[M+H]+` validation | 6,202 | 250,424 | 6,194 |
+| `[M-H]-` test | 3,193 | 137,000 | 3,160 |
+| `[M-H]-` validation | 3,193 | 116,135 | 3,163 |
+> **Disjointness.** Split A is formula-disjoint (no formula in two folds); split B is
+> molecule-disjoint within each polarity (the train / validation / test compound sets are
+> pairwise empty). The two splits must **not** be merged into a global-disjointness claim:
+> about 41 % of split-B compounds lie in a different split-A fold, and a spectrum can be
+> split-A test while its compound is split-B train. See the package
+> `figures_mapping.md` §2 for the full cross-tabulation.
+## Usage
+```python
+import pandas as pd
+base = "https://huggingface.co/datasets/dsadd4/UltraMS-MSnLib-Benchmark/resolve/main/"
+# split A — formula-level split of the full library
+formulas = pd.read_csv(base + "split_A_full_msnlib/formula_split.csv")
+rows = pd.read_csv(base + "split_A_full_msnlib/row_formula_fold.csv")      # 560,084 rows
+test = pd.read_csv(base + "split_A_full_msnlib/test_spectra.csv")          # 57,437 rows
+assert formulas.groupby("formula")["fold"].nunique().max() == 1
+# split B — strict-adduct molecule-level library search
+compound_split = pd.read_csv(base + "splits/pos_compound_split.csv")
+queries = pd.read_csv(base + "queries/pos_test_queries.csv")
+library = pd.read_csv(base + "libraries/pos_test_library.csv")
+positives = library.groupby("canonical_isomeric_smiles").size()
+n_pos = queries["canonical_isomeric_smiles"].map(positives).fillna(0).astype(int)
+denominator = int((n_pos > 0).sum())      # 6,201
 ```
+With `datasets` (one config per table, see the YAML header):
 ```python
+from datasets import load_dataset
+queries = load_dataset("dsadd4/UltraMS-MSnLib-Benchmark", "split_B_pos_test_queries", split="train")
 ```
+Peak data are **not** part of the split tables. Every row is joined back to the spectra by
+`row_index` / `msnlib_csv_data_row` / `first_msnlib_csv_data_row`, which point into
+`MSnLib.csv`. `MSnLib.csv` and `MSnLib_candidates.json` are hosted in the same dataset; see
+**Hosted files** below.
+## Columns
+* `split_A_full_msnlib/formula_split.csv`: `formula, fold, n_spectra`
+* `split_A_full_msnlib/row_formula_fold.csv`: `row_index, formula, fold`
+* `split_A_full_msnlib/{test,val}_spectra.csv`: `row_index, smiles, precursor_mz, adduct,
+  collision_energy, fold, canonical_isomeric_smiles`
+* `split_A_full_msnlib/test_molecules_voting.csv`: `group_id, smiles, n_spectra` —
+  **official** voting units: 5,002 MSnLib-source-SMILES groups covering 57,436 spectra, the
+  grouping of the published multiple-spectrum voting task (`n_molecules = 5002`)
+* `split_A_full_msnlib/test_molecules_voting_canonical_view.csv`: `group_id,
+  canonical_isomeric_smiles, n_spectra` — alternative canonical view: 4,888 groups covering
+  the same 57,436 spectra
+* `split_A_full_msnlib/msnlib_rt.csv.gz`: `row_index, rt` — per-spectrum retention time in
+  seconds, aligned 1:1 to the `MSnLib.csv` data rows (560,084 rows)
+* `splits/*_compound_split.csv`: `polarity, compound_id, canonical_isomeric_smiles, split,
+  n_spectra, n_frozen_queries, n_raw_smiles_variants, first_msnlib_csv_data_row`
+* `queries/*.csv`: `polarity, split, query_index, compound_id, canonical_isomeric_smiles,
+  adduct, msnlib_csv_data_row, msnlib_csv_line, precursor_mz, n_peaks, collision_energy,
+  source_smiles_raw, n_library_positives`
+* `libraries/*.csv`: same as queries with `library_index` and `compound_split` instead of
+  `query_index`; row order is the frozen library order
+## Split-B evaluation protocol
+1. Score every query against the complete library of its task (no candidate short list).
+2. Correct = the top-1 library spectrum has the same canonical compound identity.
 3. Empirical FDR = `(accepted − correct) / accepted`; identification recall =
    `correct / n_queries_with_library_positive` (6,201 / 3,160 for the two test tasks).
    Queries without a library positive enter the FDR denominator but not the recall
+   denominator; `n_library_positives` is provided per query.
+4. The test library contains all preprocessed spectra of the polarity except the selected
+   test queries; the validation library contains train and validation compounds only.
+5. Validation is for model selection only; evaluate the test fold once.
+## Hosted files
+The dataset hosts the complete manifest plus two large source files. Every file of the
+manifest is checksummed in `SHA256SUMS`; the two large files are kept in a separate upload
+step (see `hf_upload_commands.sh`, dry-run by default).
 | hosted file | bytes | SHA-256 | purpose |
 | --- | ---: | --- | --- |
+| manifest: `split_A_full_msnlib/`, `splits/`, `queries/`, `libraries/`, `protocol/`, `rebuild/`, docs (59 files) | ≈ 185.2 MiB | see `SHA256SUMS` | the two benchmark splits, verifier, docs |
+| `split_A_full_msnlib/msnlib_rt.csv.gz` | 1,483,069 | `994053612db874f7ac7985f278e04cc3463f3b93cd649a195bd167c4c6c7d3d8` | compact per-spectrum retention time (`row_index, rt` in seconds), aligned 1:1 to `MSnLib.csv`; used by the label-blind grouping analysis |
+| `MSnLib.csv` | 752,707,651 | `be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07` | full source CSV: one row per MSnLib spectrum (560,084 rows); every row pointer in the split tables resolves here |
 | `MSnLib_candidates.json` | 1,368,264,026 | `125a1cdcc57a3fcef8cc76d5322ac0c434cd09b0bfb9e0c9d28bddf052f45fcc` | candidate SMILES lists behind the single-spectrum candidate-ranking task: a JSON object mapping a query SMILES string to its candidate SMILES list (9,886 query entries) |
+`MSnLib.csv` is the UltraMS CSV conversion of the MSnLib original release (Zenodo
+10.5281/zenodo.11163380, CC BY 4.0), whose 18 per-file MS2 JSONL record lists contain the
+same 560,084 spectra. `MSnLib_candidates.json` contains candidate SMILES lists derived from
+the MSnLib compound set; both files carry the MSnLib attribution.
+## Provenance, verification, license
+* Source rows: `MSnLib.csv` (560,084 rows) converted from the MSnLib original release
+  (Brungs et al., CC BY 4.0; Zenodo 10.5281/zenodo.11163380).
+* Hosted source files: `MSnLib.csv` (752,707,651 bytes, SHA-256 `be54b330…`) and
+  `MSnLib_candidates.json` (1,368,264,026 bytes, SHA-256 `125a1cdc…`).
+* Frozen split-B manifest, seeds 42 / 43, query seed 119; frozen split-A fold assignment
+  from the `fold` column of `MSnLib.csv`.
+* `SHA256SUMS` covers every file; `rebuild/verify_release.py` is a self-contained verifier
+  that re-checks every count, ordering hash, disjointness statement, cross-split statistic
+  and checksum offline.
+* License **CC BY 4.0**, with attribution to MSnLib (CC BY 4.0); Apache-2.0 for the two
+  UltraMS producer scripts. See the package `NOTICE.md`.
+## Citation
+```bibtex
+@misc{ultrams_msnlib_benchmark_2026,
+  title  = {UltraMS MSnLib benchmark: full-library formula-level split and strict-adduct molecule-level library-search split},
+  author = {Li, Yifan and Zhong, Yunhua and Liu, Pan and Xia, Jun},
+  year   = {2026},
+  note   = {Derived from MSnLib (Brungs, Schmid, Pluskal; CC BY 4.0, Zenodo 10.5281/zenodo.11163380)},
+  howpublished = {Hugging Face / Zenodo dataset, version 1.0.0}
+}
 ```
+Please also cite MSnLib (doi:10.1038/s41592-025-02813-0) and the UltraMS manuscript.