Set dataset card

README.md

@@ -1,79 +1,59 @@
-# UltraMS SpectraVerse benchmark
+---
+pretty_name: UltraMS SpectraVerse benchmark (molecule-level 8:1:1 split)
+license: cc-by-4.0
+language:
+  - en
+size_categories:
+  - 100K<n<1M
+task_categories:
+  - other
+configs:
+  - config_name: spectraverse_split
+    data_files: splits/spectraverse_compound_split.csv
+  - config_name: spectraverse_spectra
+    data_files: Spectraverse.csv
+---
 
-Version **1.0.0** · 2026-11-04 · license **CC BY 4.0** (see [NOTICE.md](NOTICE.md))
+# UltraMS SpectraVerse benchmark
 
-A frozen, molecule-disjoint benchmark table built from the
-[SpectraVerse](https://doi.org/10.5281/zenodo.17870921) tandem mass spectral library and
-released by UltraMS. It is the negative-ion structure-family evaluation population of the
-UltraMS manuscript (Figure 2c) and the external test set of the ionization-polarity transfer
-experiment.
+A frozen, molecule-disjoint benchmark table built from the SpectraVerse tandem mass
+spectral library and released by UltraMS. It is the negative-ion structure-family
+evaluation population of the UltraMS manuscript (Figure 2c) and the external test set of
+the ionization-polarity transfer experiment.
 
-## 1. The table
+## Contents
 
-| item | value |
+| file | description |
 | --- | --- |
-| file | `Spectraverse.csv` |
-| rows | 464,346 spectra |
-| bytes | 707,447,509 |
-| SHA-256 | `06e084501e91f92cc642c3d60de2863266ff3d0db958354a011e32851bef3976` |
-| columns | `mzs, intensities, smiles, precursor_mz, adduct, collision_energy, fold` |
-| peak format | comma-separated strings, one spectrum per row |
+| `Spectraverse.csv` | 464,346 spectra; columns `mzs, intensities, smiles, precursor_mz, adduct, collision_energy, fold`; 707,447,509 B, SHA-256 `06e084501e91f92cc642c3d60de2863266ff3d0db958354a011e32851bef3976` |
+| `splits/spectraverse_compound_split.csv` | 42,308 exact SMILES → `fold` (train / validation / test) with `n_spectra` |
+| `README.md`, `NOTICE.md`, `VERIFY.md`, `stats.json`, `SHA256SUMS` | documentation, attribution, verification and checksums |
 
-The `fold` column is the frozen train / validation / test assignment of this benchmark:
+## Split
 
 | fold | spectra | unique exact SMILES |
 | --- | ---: | ---: |
 | train | 370,362 | 33,846 |
 | validation | 47,825 | 4,231 |
 | test | 46,159 | 4,231 |
-| total | 464,346 | 42,308 |
-
-## 2. Split definition
 
-- The split unit is the **exact SMILES string** (molecule level): every spectrum of a given
-  SMILES string falls in exactly one fold, and no exact SMILES occurs in more than one fold
-  (0 crossing strings out of 42,308).
-- The partition is 8:1:1 at the molecule (exact-SMILES) level: 33,846 / 4,231 / 4,231
-  unique SMILES.
-- **This split is not formula-disjoint.** Structural isomers share a molecular formula, and
-  molecular formulas do recur across folds in this library. Downstream work must describe
-  the partition as molecule/SMILES-disjoint, not as a formula-disjoint partition.
+The split unit is the exact SMILES string: every spectrum of a SMILES string lies in one
+fold and no string crosses folds (molecule/SMILES-disjoint 8:1:1). It is **not**
+formula-disjoint: structural isomers share a formula and formulas recur across folds.
 
-The frozen assignment is distributed as
-[`splits/spectraverse_compound_split.csv`](splits/spectraverse_compound_split.csv)
-(42,308 rows: `smiles, fold, n_spectra`), so the benchmark can be used without
-reconstructing the assignment.
-
-## 3. Usage
+## Usage
 
 ```python
 import pandas as pd
-
 base = "https://huggingface.co/datasets/dsadd4/UltraMS-Spectraverse-Benchmark/resolve/v1.0.0/"
 spectra = pd.read_csv(base + "Spectraverse.csv")
 split = pd.read_csv(base + "splits/spectraverse_compound_split.csv")
-
 test = spectra[spectra.fold == "test"]
-assert split.groupby("smiles").fold.nunique().max() == 1
 ```
 
-The UltraMS repository consumes this table in
-`benchmarks/spectral_properties/prepare_library_spectra.py --dataset spectraverse`
-(published size/SHA-256 and fold counts are verified before use).
-
-## 4. Provenance and licence
+## Provenance and licence
 
 The spectra are the public SpectraVerse library (SpectraVerse v1.0.1, Zenodo
-[10.5281/zenodo.17870921](https://doi.org/10.5281/zenodo.17870921), CC BY 4.0;
-Gupta, Qiang, Chung, Herbst and Skinnider). UltraMS contributed the CSV
-representation, the frozen molecule-level train / validation / test split and its
-distribution. See [NOTICE.md](NOTICE.md) for the full attribution.
-
-## 5. Files
-
-```text
-README.md, NOTICE.md, SHA256SUMS, VERIFY.md, stats.json
-Spectraverse.csv                          (hosted with the release; not duplicated in the archive)
-splits/spectraverse_compound_split.csv(.gz)
-hf_dataset_card.md, hf_upload_commands.sh, zenodo_metadata.json
-```
+doi:10.5281/zenodo.17870921, CC BY 4.0; Gupta, Qiang, Chung, Herbst and Skinnider).
+UltraMS contributed the CSV representation, the frozen molecule-level split and the release.
+Released under CC BY 4.0; attribution to the SpectraVerse authors is required.