MassFormer predictor with Transformer embedder (FlexMS)
MassFormer predictor with Transformer embedder; no settings beyond its name are recorded.
Overview
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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
1 evaluation · 2 results. Different protocols are not a single leaderboard.
Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2) · Dataset: MassSpecGym (FlexMS spectrum prediction)
Sorted by Jensen shannon similarity (test split; bin resolution not stated in the caption) (higher is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
| Tested configuration | Jensen shannon similarity (test split; bin resolution not stated in the caption) | Spectrum cosine similarity (test split; bin resolution not stated in the caption) |
|---|---|---|
| MassFormer predictor with Transformer embedder (FlexMS)Evaluation | 0.471 | 0.31 |
All 2 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: MassFormer predictor with Transformer embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2) Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.471 Jensen shannon similarity (test split; bin resolution not stated in the caption) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceMassFormer with Transformer on MassSpecGym spectrum prediction lit20261011-zhong2026-protocol-t2-massspecgym Aggregation: Not reported FlexMS: A Unified Public Benchmark for Molecule Tandem Mass Spectrum Prediction · Table 2 section 'Jensen-Shannon Similarity (JS Sim)', row 'Mass', column 'Trans' |
| Configuration: MassFormer predictor with Transformer embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2) Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.31 Spectrum cosine similarity (test split; bin resolution not stated in the caption) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceMassFormer with Transformer on MassSpecGym spectrum prediction lit20261011-zhong2026-protocol-t2-massspecgym Aggregation: Not reported FlexMS: A Unified Public Benchmark for Molecule Tandem Mass Spectrum Prediction · Table 2 section 'Cosine Similarity (Cos Sim)', row 'Mass', column 'Trans' |
Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.
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How it works, versions and access
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Evidence
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Evidence table
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Sources and history
Release 2026-10-23-5347695500ed · Record review: source checked
1 source record and release history
- FlexMS: A Unified Public Benchmark for Molecule Tandem Mass Spectrum Prediction · Original source · arXiv 2602.22822v4 (v1 submitted 2026-02-26; v4 dated 2026-06-24 on the PDF)
Technical metadata and extraction receipts
Stable ID: lit20261011-zhong2026-config-mass-trans
- areas
- metabolomics
- contexts
- research
- method types
- supervised_machine_learning
- reported name
- MassFormer predictor with Transformer embedder (FlexMS)
- foundation model eligible
- false
- version
- Trained by the benchmark authors in FlexMS
- configuration
- embedder: Transformer; predictor: MassFormer
- source locator
- Table 2 row 'Mass', column 'Trans'; caption abbreviations
- missing metadata
- checkpoint: reason: unreported
- provenance note
- MassFormer predictor with Transformer embedder (FlexMS) as run in the cited comparison.
Related records
- configuration of: MassFormer
- system: MassFormer with Transformer on MassSpecGym spectrum prediction