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{
 "release": {
  "name": "ultrams_msnlib_benchmark_v1",
  "title": "UltraMS MSnLib benchmark: full-library formula-level split (A) and strict-adduct molecule-level library-search split (B)",
  "version": "1.0.0",
  "date": "2026-11-04",
  "license": "CC BY 4.0",
  "file_count_excluding_stats_and_sums": 59,
  "bytes_excluding_stats_and_sums": 194215545,
  "csv_and_csv_gz_pairs": 16,
  "documentation": [
   "README.md",
   "figures_mapping.md",
   "VERIFY.md",
   "NOTICE.md"
  ]
 },
 "source": {
  "msnlib_csv": {
   "data_rows": 560084,
   "physical_lines": 560085,
   "bytes": 752707651,
   "sha256": "be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07",
   "columns": [
    "mzs",
    "intensities",
    "smiles",
    "precursor_mz",
    "adduct",
    "collision_energy",
    "fold"
   ],
   "csv_line_to_data_row": "physical line = data row + 2 (header = line 1, no embedded newlines)",
   "distribution": "distributed with the Hugging Face dataset placeholder dsadd4/UltraMS-MSnLib-Benchmark"
  },
  "msnlib_original_release": {
   "citation": "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.",
   "zenodo_record": "10.5281/zenodo.11163380",
   "license": "CC BY 4.0",
   "format": "18 per-file MS2 JSONL record lists (*_ms2.json)",
   "n_files": 18,
   "n_records_total": 560084,
   "n_records_equals_csv_data_rows": true
  },
  "msnlib_candidates": {
   "file": "MSnLib_candidates.json",
   "bytes": 1368264026,
   "sha256": "125a1cdcc57a3fcef8cc76d5322ac0c434cd09b0bfb9e0c9d28bddf052f45fcc",
   "content": "JSON object mapping a query SMILES string to its candidate SMILES list (9,886 query entries)",
   "purpose": "candidate SMILES lists behind the single-spectrum candidate-ranking task (Figure 3a/3b/3d/3g)",
   "hosted": "Hugging Face dataset dsadd4/UltraMS-MSnLib-Benchmark (not part of this manifest)"
  },
  "msnlib_with_rt": {
   "file": "MSnLib_with_rt.csv",
   "bytes": 755984910,
   "sha256": "a5b7c38228287c5c1de401050445319b331ee9a5f17993d6e104e9a734fe2964",
   "columns": [
    "mzs",
    "intensities",
    "smiles",
    "precursor_mz",
    "adduct",
    "collision_energy",
    "fold",
    "rt"
   ],
   "role": "source of the compact retention-time table split_A_full_msnlib/msnlib_rt.csv.gz",
   "alignment": "first seven columns identical to MSnLib.csv row-by-row in the same order (560,084 rows, 0 mismatches, 0 unparsable RT values)"
  }
 },
 "hosted_files": {
  "note": "the manifest files are listed in stats.files; the two large source files are hosted alongside them in the Hugging Face dataset and are not duplicated here",
  "manifest": {
   "file_count": 59,
   "bytes": 194215545
  },
  "large_files": [
   {
    "file": "MSnLib.csv",
    "bytes": 752707651,
    "sha256": "be54b33039cf18675751ea3c6354b592177c899a0cd5df303ae616330133ec07",
    "purpose": "full source CSV: one row per MSnLib spectrum; all row_index / msnlib_csv_data_row pointers resolve here"
   },
   {
    "file": "MSnLib_candidates.json",
    "bytes": 1368264026,
    "sha256": "125a1cdcc57a3fcef8cc76d5322ac0c434cd09b0bfb9e0c9d28bddf052f45fcc",
    "purpose": "candidate SMILES lists for the single-spectrum candidate-ranking task"
   }
  ]
 },
 "splits": {
  "A": {
   "name": "UltraMS MSnLib formula-level split",
   "unit": "neutral molecular formula (RDKit CalcMolFormula from the source SMILES)",
   "disjointness": "formula-disjoint (every formula lies in exactly one fold; 0 conflicts)",
   "fold_source": "frozen `fold` column of MSnLib.csv",
   "all_adducts": true,
   "counts": {
    "n_formulas": 21107,
    "n_formulas_by_fold": {
     "train": 16885,
     "val": 2110,
     "test": 2112
    },
    "n_spectra_by_fold": {
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     "val": 55980,
     "test": 57437
    },
    "n_spectra_total": 560084,
    "n_test_spectra": 57437,
    "n_test_formulas": 2112,
    "n_test_source_smiles": 5003,
    "n_test_canonical_molecules": 4889,
    "n_voting_groups_official": 5002,
    "n_voting_groups_official_unit": "MSnLib source SMILES string (official; matches the published n_molecules = 5002 grouping)",
    "n_voting_spectra_official": 57436,
    "n_voting_groups_canonical_view": 4888,
    "n_voting_spectra_canonical_view": 57436
   },
   "tables": {
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     "bytes": 424350,
     "sha256": "fcc44d1996d25306c884a6f8da30c1447fbe74f93c6fa12a3f271c0475a704b8"
    },
    "row_formula_fold.csv": {
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     "bytes": 13351630,
     "sha256": "ac6113867fdda683304533f097fc7287c13271a2deac8e792d1316dcf00264ff"
    },
    "test_spectra.csv": {
     "rows": 57437,
     "bytes": 7751575,
     "sha256": "f2a870ba8ac9a54a36feaf1ecc12929ad9250ade2d082dc31454028c4b66b548"
    },
    "val_spectra.csv": {
     "rows": 55980,
     "bytes": 7421554,
     "sha256": "f4fa5e0f8875991bf9df2bcb67a05437271ee18c317f33d9108f3ec28a887a82"
    },
    "test_molecules_voting.csv": {
     "rows": 5002,
     "bytes": 276185,
     "sha256": "edad6ec7d6b6f9fc4763deac5245207aee767c78661532621c87acc5a9b1ee07"
    },
    "test_molecules_voting_canonical_view.csv": {
     "rows": 4888,
     "bytes": 269502,
     "sha256": "9fcd16ff4159e665833ea145848f94bee7c44115f4a858dd75fe486f15e92bd0"
    }
   },
   "retention_times": {
    "file": "split_A_full_msnlib/msnlib_rt.csv.gz",
    "columns": [
     "row_index",
     "rt"
    ],
    "n_rows": 560084,
    "bytes": 1483069,
    "sha256": "994053612db874f7ac7985f278e04cc3463f3b93cd649a195bd167c4c6c7d3d8",
    "unit": "seconds (source text representation)",
    "source": "MSnLib_with_rt.csv (755,984,910 bytes, SHA-256 a5b7c38228287c5c1de401050445319b331ee9a5f17993d6e104e9a734fe2964)",
    "alignment": "row_index = 0-based MSnLib.csv data row; first seven columns verified identical row-by-row (560,084 rows, 0 mismatches)",
    "used_by": "label-blind grouping / multiple-spectrum voting (Figure 3d)",
    "gzipped_only": true
   },
   "anomaly": "official voting units are the 5,002 MSnLib source-SMILES groups covering 57,436 spectra (test_molecules_voting.csv); the alternative canonical view merges 114 groups into 4,888 chemically identical molecules (test_molecules_voting_canonical_view.csv); both tables are shipped",
   "verification": "split_A_full_msnlib/VERIFY.md (incl. the read-only replay and byte-identical table hashes)"
  },
  "B": {
   "name": "UltraMS strict-adduct molecule-level split",
   "unit": "RDKit canonical isomeric SMILES, per polarity",
   "disjointness": "the train / validation / test compound sets of each polarity are pairwise disjoint",
   "seeds": {
    "split_pos": 42,
    "split_neg": 43,
    "query": 119
   },
   "modes": {
    "neg": {
     "collision_energy_values": {
      "15.0": 5442,
      "20.0": 75115,
      "30.0": 16784,
      "45.0": 10177,
      "60.0": 32573,
      "75.0": 102
     },
     "compounds_with_single_spectrum": 202,
     "invalid_preprocessing_rows": 4054,
     "n_compounds": 21293,
     "raw_strict_adduct_rows": 144247,
     "spectra_per_compound": {
      "max": 87,
      "mean": 6.584,
      "median": 5.0,
      "min": 1
     },
     "split_compound_counts": {
      "test": 3193,
      "train": 14907,
      "val": 3193
     },
     "split_spectra_counts": {
      "test": 20865,
      "train": 98401,
      "val": 20927
     },
     "test": {
      "library_msnlib_row_sha256": "99b8d480087a6e90a17cfa8d0653e785285fce1e60cfd3596b4d1cf6d5ca97a4",
      "library_smiles_sha256": "00dd373d9e175b070c2bd39595ee9532fdbd94f02a344897e81480e4b7784bc2",
      "n_library": 137000,
      "n_queries_with_library_positive": 3160,
      "n_query": 3193,
      "query_msnlib_row_sha256": "2c9e896b1a267295882f6658ad664d6aab1648c37c7d02dfe98248fab69c42c8",
      "query_smiles_sha256": "db0aa2c39a1e5bc3c4463f97166c9d3e3ac150cba323f44bd29b636ccbd6553b"
     },
     "val": {
      "library_smiles_sha256": "3fb782c8fbad923500cc392c5a080ad0718969519b5f69ae63adde0563cd955a",
      "n_library": 116135,
      "n_queries_with_library_positive": 3163,
      "n_query": 3193,
      "query_smiles_sha256": "3000c6a8bd24ae9dd082706d0ef3bcbd40939e1040f5ffe704a9923665f88412"
     },
     "valid_preprocessed_rows": 140193
    },
    "pos": {
     "collision_energy_values": {
      "15.0": 15194,
      "20.0": 157042,
      "30.0": 36530,
      "45.0": 19845,
      "60.0": 72758,
      "75.0": 267
     },
     "compounds_with_single_spectrum": 39,
     "invalid_preprocessing_rows": 2073,
     "n_compounds": 41348,
     "raw_strict_adduct_rows": 303709,
     "spectra_per_compound": {
      "max": 64,
      "mean": 7.2951,
      "median": 8.0,
      "min": 1
     },
     "split_compound_counts": {
      "test": 6202,
      "train": 28944,
      "val": 6202
     },
     "split_spectra_counts": {
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      "train": 211745,
      "val": 44881
     },
     "test": {
      "library_msnlib_row_sha256": "044dc90f6ff8a69a847b9a289a9225a701a907be84d5a14d854e732c9423e0d0",
      "library_smiles_sha256": "4d69c6f65f8c3ed84df54fc2aa6addd7b28fd1c28909386f4e4ced88d31aacce",
      "n_library": 295434,
      "n_queries_with_library_positive": 6201,
      "n_query": 6202,
      "query_msnlib_row_sha256": "6dd85e3f3ab28de89b5b3363314a7d84810cf7a53853e150e2160a712610bf9e",
      "query_smiles_sha256": "356f355727380d1df02abbb0aaa3391b180a5c7b93b2103058ba54e8dfae51f0"
     },
     "val": {
      "library_smiles_sha256": "fd4c3083f8930973ca7f1439284b5cec5dff35f4167f1d9da386ca26599b5500",
      "n_library": 250424,
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      "n_query": 6202,
      "query_smiles_sha256": "39ead3a4ce7f7bed717167cea96f5c929abacae13787db8dd018eb775cd74339"
     },
     "valid_preprocessed_rows": 301636
    }
   },
   "cross_polarity": {
    "neg_compounds": 21293,
    "neg_only": 4591,
    "pos_compounds": 41348,
    "pos_only": 24646,
    "pos_test_intersect_neg_test": 354,
    "pos_test_intersect_neg_vocab": 2425,
    "shared_compounds": 16702,
    "shared_same_split": 8999,
    "shared_split_pairs": {
     "pos=test/neg=test": 354,
     "pos=test/neg=train": 1694,
     "pos=test/neg=val": 377,
     "pos=train/neg=test": 1728,
     "pos=train/neg=train": 8265,
     "pos=train/neg=val": 1765,
     "pos=val/neg=test": 394,
     "pos=val/neg=train": 1745,
     "pos=val/neg=val": 380
    }
   },
   "manifest_redaction": {
    "original_sha256": "b83656b2b4d265d1d4ea49df30372e844e207863a7ab768f44f241bd68b8186e",
    "original_value_replaced": true,
    "redacted_field": "csv",
    "redacted_value": "<original data-preparation workspace>/datasets/MSnLib/MSnLib.csv",
    "redacted_sha256": "6129ed094df59265a684f436da146ef554d9c774e01768363bf58704f87ec237"
   },
   "rebuild_scripts": {
    "baseline_common.py": {
     "sha256": "72969bc51f39dc8ae044ebaf47cdd3546f90b32edfc2b467c356b10ff0232000"
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 },
 "cross_split": {
  "note": "split A and split B are different objects; their folds disagree for about 41% of split-B compounds and must not be merged into a global-disjointness claim",
  "compound_cross_tab": {
   "pos": {
    "test": {
     "test": 654,
     "train": 4922,
     "val": 626
    },
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     "val": 2901
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