Evidence claim
Evidence summary: Shortlist molecular identities from tandem mass spectra
Summary of Shortlist molecular identities from tandem mass spectra
Two preprints report formula-free retrieval of the true structure from mass-matched PubChem candidates for MassSpecGym spectra, and their values are not directly comparable. In the MSAlign preprint, MSAlign ranks first among the formula-free methods on every split the paper reports, but its top-1 recall falls from about half on the formula split to under a fifth on the MCES split. On the MassSpecGym formula split, Recall@1 was 47.5 for MSAlign and 58.2 with score fusion, against 42.7 for Emb-Cos, 13.9 for JESTR and 4.7 for DeepSet, with standard deviations of 0.5 to 3.4 over three random splitting seeds. On the MCES split the order is the same but the values are much lower: 19.0, 30.8, 12.6, 7.9 and 1.9; the table caption describes three splits there too, but the methods describe two swapped variants. Recall@20 reaches 87.0 for MSAlign and 92.8 with score fusion on the formula split, and 64.9 and 82.0 on MCES. An earlier version of the same paper reports Recall@1 of 53.8 for MSAlign and 41.2 for Emb-Cos on the formula split, so the two versions differ and are not independent measurements. These MSAlign values assume the true structure is among 256 mass-matched candidates and were scored by the MSAlign authors. MassSpecGym in the Wild, whose authors include the developers of MIST, MIST-CF and MassSpecGym, reports two formula-free configurations that it does not flag for formula leakage, on the MassSpecGym test fold with up to 256 mass-matched candidates per spectrum. MIST given the top formula predicted by MIST-CF found the true structure at rank 1 for 26.64 percent of test spectra and within the top 20 for 54.90 percent, against 0.43 and 7.99 percent for random ranking. Its candidate pool and split differ from MSAlign's, and the MIST score depends on the formula annotator as well as the retriever. All of these values are reported by the authors of preprints, and none measures open-world identification, because the true structure is always among the candidates.
Plain-language summary of what the reviewed evidence shows. Draft until reviewed.
Evidence
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Evidence table
Inspect claims, sources and review details
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
21 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Claimed field summary Context-only references | msalign: Primary paper PDF uc20260930-source-msalign-v2: Table 3 p7, massspecgym-formula, massspecgym-mces and spectraverse blocks, R@1 and R@20 rows; evidence-official-760ab2fa8c396aeb796c: Table 3, no-formula blocks, R@1 and R@20 rows; lit-otheromics-20261011-msgwild-source-liu2026: Table 2, rows 'Random' and 'MIST (MIST-CF top-1 formula)', columns 'Hit rate@1' and 'Hit rate@20'; Section 4.3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2605.19752v1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Claimed field summary Context-only references | MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery uc20260930-source-msalign-v2: Table 3 p7, massspecgym-formula, massspecgym-mces and spectraverse blocks, R@1 and R@20 rows; evidence-official-760ab2fa8c396aeb796c: Table 3, no-formula blocks, R@1 and R@20 rows; lit-otheromics-20261011-msgwild-source-liu2026: Table 2, rows 'Random' and 'MIST (MIST-CF top-1 formula)', columns 'Hit rate@1' and 'Hit rate@20'; Section 4.3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed field summary Context-only references | MSAlign arXiv v2 Table 3 uc20260930-source-msalign-v2: Table 3 p7, massspecgym-formula, massspecgym-mces and spectraverse blocks, R@1 and R@20 rows; evidence-official-760ab2fa8c396aeb796c: Table 3, no-formula blocks, R@1 and R@20 rows; lit-otheromics-20261011-msgwild-source-liu2026: Table 2, rows 'Random' and 'MIST (MIST-CF top-1 formula)', columns 'Hit rate@1' and 'Hit rate@20'; Section 4.3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2605.19752v2, 25 September 2026 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records120 values
| msalign: Primary paper PDF uc20260930-source-msalign-v2: Table 3 p7, massspecgym-formula, massspecgym-mces and spectraverse blocks, R@1 and R@20 rows; evidence-official-760ab2fa8c396aeb796c: Table 3, no-formula blocks, R@1 and R@20 rows; lit-otheromics-20261011-msgwild-source-liu2026: Table 2, rows 'Random' and 'MIST (MIST-CF top-1 formula)', columns 'Hit rate@1' and 'Hit rate@20'; Section 4.3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2605.19752v1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Pinned records120 values
| MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery uc20260930-source-msalign-v2: Table 3 p7, massspecgym-formula, massspecgym-mces and spectraverse blocks, R@1 and R@20 rows; evidence-official-760ab2fa8c396aeb796c: Table 3, no-formula blocks, R@1 and R@20 rows; lit-otheromics-20261011-msgwild-source-liu2026: Table 2, rows 'Random' and 'MIST (MIST-CF top-1 formula)', columns 'Hit rate@1' and 'Hit rate@20'; Section 4.3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Pinned records120 values
| MSAlign arXiv v2 Table 3 uc20260930-source-msalign-v2: Table 3 p7, massspecgym-formula, massspecgym-mces and spectraverse blocks, R@1 and R@20 rows; evidence-official-760ab2fa8c396aeb796c: Table 3, no-formula blocks, R@1 and R@20 rows; lit-otheromics-20261011-msgwild-source-liu2026: Table 2, rows 'Random' and 'MIST (MIST-CF top-1 formula)', columns 'Hit rate@1' and 'Hit rate@20'; Section 4.3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2605.19752v2, 25 September 2026 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Source location uc20260930-source-msalign-v2: Table 3 p7, massspecgym-formula, massspecgym-mces and spectraverse blocks, R@1 and R@20 rows; evidence-official-760ab2fa8c396aeb796c: Table 3, no-formula blocks, R@1 and R@20 rows; lit-otheromics-20261011-msgwild-source-liu2026: Table 2, rows 'Random' and 'MIST (MIST-CF top-1 formula)', columns 'Hit rate@1' and 'Hit rate@20'; Section 4.3 Context-only references | msalign: Primary paper PDF uc20260930-source-msalign-v2: Table 3 p7, massspecgym-formula, massspecgym-mces and spectraverse blocks, R@1 and R@20 rows; evidence-official-760ab2fa8c396aeb796c: Table 3, no-formula blocks, R@1 and R@20 rows; lit-otheromics-20261011-msgwild-source-liu2026: Table 2, rows 'Random' and 'MIST (MIST-CF top-1 formula)', columns 'Hit rate@1' and 'Hit rate@20'; Section 4.3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2605.19752v1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| Source location uc20260930-source-msalign-v2: Table 3 p7, massspecgym-formula, massspecgym-mces and spectraverse blocks, R@1 and R@20 rows; evidence-official-760ab2fa8c396aeb796c: Table 3, no-formula blocks, R@1 and R@20 rows; lit-otheromics-20261011-msgwild-source-liu2026: Table 2, rows 'Random' and 'MIST (MIST-CF top-1 formula)', columns 'Hit rate@1' and 'Hit rate@20'; Section 4.3 Context-only references | MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery uc20260930-source-msalign-v2: Table 3 p7, massspecgym-formula, massspecgym-mces and spectraverse blocks, R@1 and R@20 rows; evidence-official-760ab2fa8c396aeb796c: Table 3, no-formula blocks, R@1 and R@20 rows; lit-otheromics-20261011-msgwild-source-liu2026: Table 2, rows 'Random' and 'MIST (MIST-CF top-1 formula)', columns 'Hit rate@1' and 'Hit rate@20'; Section 4.3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Source location uc20260930-source-msalign-v2: Table 3 p7, massspecgym-formula, massspecgym-mces and spectraverse blocks, R@1 and R@20 rows; evidence-official-760ab2fa8c396aeb796c: Table 3, no-formula blocks, R@1 and R@20 rows; lit-otheromics-20261011-msgwild-source-liu2026: Table 2, rows 'Random' and 'MIST (MIST-CF top-1 formula)', columns 'Hit rate@1' and 'Hit rate@20'; Section 4.3 Context-only references | MSAlign arXiv v2 Table 3 uc20260930-source-msalign-v2: Table 3 p7, massspecgym-formula, massspecgym-mces and spectraverse blocks, R@1 and R@20 rows; evidence-official-760ab2fa8c396aeb796c: Table 3, no-formula blocks, R@1 and R@20 rows; lit-otheromics-20261011-msgwild-source-liu2026: Table 2, rows 'Random' and 'MIST (MIST-CF top-1 formula)', columns 'Hit rate@1' and 'Hit rate@20'; Section 4.3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2605.19752v2, 25 September 2026 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| Claimed value Two preprints report formula-free retrieval of the true structure from mass-matched PubChem candidates for MassSpecGym spectra, and their values are not directly comparable. In the MSAlign preprint, MSAlign ranks first among the formula-free methods on every split the paper reports, but its top-1 recall falls from about half on the formula split to under a fifth on the MCES split. On the MassSpecGym formula split, Recall@1 was 47.5 for MSAlign and 58.2 with score fusion, against 42.7 for Emb-Cos, 13.9 for JESTR and 4.7 for DeepSet, with standard deviations of 0.5 to 3.4 over three random splitting seeds. On the MCES split the order is the same but the values are much lower: 19.0, 30.8, 12.6, 7.9 and 1.9; the table caption describes three splits there too, but the methods describe two swapped variants. Recall@20 reaches 87.0 for MSAlign and 92.8 with score fusion on the formula split, and 64.9 and 82.0 on MCES. An earlier version of the same paper reports Recall@1 of 53.8 for MSAlign and 41.2 for Emb-Cos on the formula split, so the two versions differ and are not independent measurements. These MSAlign values assume the true structure is among 256 mass-matched candidates and were scored by the MSAlign authors. MassSpecGym in the Wild, whose authors include the developers of MIST, MIST-CF and MassSpecGym, reports two formula-free configurations that it does not flag for formula leakage, on the MassSpecGym test fold with up to 256 mass-matched candidates per spectrum. MIST given the top formula predicted by MIST-CF found the true structure at rank 1 for 26.64 percent of test spectra and within the top 20 for 54.90 percent, against 0.43 and 7.99 percent for random ranking. Its candidate pool and split differ from MSAlign's, and the MIST score depends on the formula annotator as well as the retriever. All of these values are reported by the authors of preprints, and none measures open-world identification, because the true structure is always among the candidates. Context-only references | msalign: Primary paper PDF uc20260930-source-msalign-v2: Table 3 p7, massspecgym-formula, massspecgym-mces and spectraverse blocks, R@1 and R@20 rows; evidence-official-760ab2fa8c396aeb796c: Table 3, no-formula blocks, R@1 and R@20 rows; lit-otheromics-20261011-msgwild-source-liu2026: Table 2, rows 'Random' and 'MIST (MIST-CF top-1 formula)', columns 'Hit rate@1' and 'Hit rate@20'; Section 4.3 Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2605.19752v1 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
Sources and history
Release 2026-10-23-5347695500ed · Record review: source checked
3 source records and release history
- msalign: Primary paper PDF · Original source · 2605.19752v1
- MSAlign arXiv v2 Table 3 · Original source · 2605.19752v2, 25 September 2026
- MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Original source · arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering
Technical metadata and extraction receipts
Stable ID: use-case-summary-mass-spectrum-molecule-shortlisting
- field
- summary
- value
- Two preprints report formula-free retrieval of the true structure from mass-matched PubChem candidates for MassSpecGym spectra, and their values are not directly comparable. In the MSAlign preprint, MSAlign ranks first among the formula-free methods on every split the paper reports, but its top-1 recall falls from about half on the formula split to under a fifth on the MCES split. On the MassSpecGym formula split, Recall@1 was 47.5 for MSAlign and 58.2 with score fusion, against 42.7 for Emb-Cos, 13.9 for JESTR and 4.7 for DeepSet, with standard deviations of 0.5 to 3.4 over three random splitting seeds. On the MCES split the order is the same but the values are much lower: 19.0, 30.8, 12.6, 7.9 and 1.9; the table caption describes three splits there too, but the methods describe two swapped variants. Recall@20 reaches 87.0 for MSAlign and 92.8 with score fusion on the formula split, and 64.9 and 82.0 on MCES. An earlier version of the same paper reports Recall@1 of 53.8 for MSAlign and 41.2 for Emb-Cos on the formula split, so the two versions differ and are not independent measurements. These MSAlign values assume the true structure is among 256 mass-matched candidates and were scored by the MSAlign authors. MassSpecGym in the Wild, whose authors include the developers of MIST, MIST-CF and MassSpecGym, reports two formula-free configurations that it does not flag for formula leakage, on the MassSpecGym test fold with up to 256 mass-matched candidates per spectrum. MIST given the top formula predicted by MIST-CF found the true structure at rank 1 for 26.64 percent of test spectra and within the top 20 for 54.90 percent, against 0.43 and 7.99 percent for random ranking. Its candidate pool and split differ from MSAlign's, and the MIST score depends on the formula annotator as well as the retriever. All of these values are reported by the authors of preprints, and none measures open-world identification, because the true structure is always among the candidates.
- source locator
- uc20260930-source-msalign-v2: Table 3 p7, massspecgym-formula, massspecgym-mces and spectraverse blocks, R@1 and R@20 rows; evidence-official-760ab2fa8c396aeb796c: Table 3, no-formula blocks, R@1 and R@20 rows; lit-otheromics-20261011-msgwild-source-liu2026: Table 2, rows 'Random' and 'MIST (MIST-CF top-1 formula)', columns 'Hit rate@1' and 'Hit rate@20'; Section 4.3
- review
- method: independent-cell-check; scope-review; method note: Rebuilt the use case's judgements with deriveUseCaseInputs and compared every number with the printed_value of the stored source_checked result it comes from, on an evaluation of an active judgement, including rounding, tool, dataset and split. Checked each range and ranking against every active evaluation on the protocol, not only the cited rows. Checked origin, publication status, truth-set and leakage limits against the judgement, protocol, dataset and source records, that each cited source is source_checked with no evidence_concerns, that no withheld judgement is described, and that nothing is recommended.; reviewer: claude; reviewer note: Separate Claude review agent, independent of the agent that drafted the summary; the reviewer corrected the text; no human review claimed; reviewed at: 2026-10-12T15:00:00Z; note: Drafted in data/omics/use-case-followups-20261012/summary-drafts.md and corrected in this review: named the formula-leakage exclusion for MassSpecGym in the Wild, said the MSAlign values were scored by the MSAlign authors, and restored the Spectraverse block to the locator. Descriptive summary only; no execution, human scientific review or clinical validation. See docs/reviews/use-cases/use-case-summaries-2026-10-12.md.
- pins
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