| Configuration: MassFormer predictor with All-Descriptors MLP embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.491 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 All-Descriptors MLP 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 'AllDes' |
|---|
| Configuration: MassFormer predictor with All-Descriptors MLP embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.332 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 All-Descriptors MLP 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 'AllDes' |
|---|
| Configuration: MassFormer predictor with AttentiveFP embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.489 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 AttentiveFP 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 'Attn' |
|---|
| Configuration: MassFormer predictor with AttentiveFP embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.323 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 AttentiveFP 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 'Attn' |
|---|
| Configuration: MassFormer predictor with ChemBERTa embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.48 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 ChemBERTa 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 'CBTa' |
|---|
| Configuration: MassFormer predictor with ChemBERTa embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.317 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 ChemBERTa 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 'CBTa' |
|---|
| Configuration: MassFormer predictor with CNN embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.477 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 CNN 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 'CNN' |
|---|
| Configuration: MassFormer predictor with CNN embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.316 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 CNN 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 'CNN' |
|---|
| Configuration: MassFormer predictor with Daylight fingerprint embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.481 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 Daylight fingerprint 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 'DL' |
|---|
| Configuration: MassFormer predictor with Daylight fingerprint embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.324 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 Daylight fingerprint 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 'DL' |
|---|
| Configuration: MassFormer predictor with ESPF embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.475 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 ESPF 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 'ESPF' |
|---|
| Configuration: MassFormer predictor with ESPF 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 ESPF 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 'ESPF' |
|---|
| Configuration: MassFormer predictor with GAT embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.483 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 GAT 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 'GAT' |
|---|
| Configuration: MassFormer predictor with GAT embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.317 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 GAT 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 'GAT' |
|---|
| Configuration: MassFormer predictor with GCN embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.484 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 GCN 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 'GCN' |
|---|
| Configuration: MassFormer predictor with GCN embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.306 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 GCN 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 'GCN' |
|---|
| Configuration: MassFormer predictor with GraphormerV2 embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.516 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 GraphormerV2 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 'GFv2' |
|---|
| Configuration: MassFormer predictor with GraphormerV2 embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.357 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 GraphormerV2 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 'GFv2' |
|---|
| Configuration: MassFormer predictor with GIN embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.494 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 GIN 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 'GIN' |
|---|
| Configuration: MassFormer predictor with GIN embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.329 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 GIN 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 'GIN' |
|---|
| 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' |
|---|
| Configuration: MolMS predictor with All-Descriptors MLP embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.446 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 sourceMolMS with All-Descriptors MLP 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 'MolMS', column 'AllDes' |
|---|
| Configuration: MolMS predictor with All-Descriptors MLP embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.241 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 sourceMolMS with All-Descriptors MLP 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 'MolMS', column 'AllDes' |
|---|
| Configuration: MolMS predictor with AttentiveFP embedder (FlexMS) | Protocol: FlexMS molecule-to-spectrum prediction on MassSpecGym, embedder-predictor grid (Table 2)
Dataset: MassSpecGym (FlexMS spectrum prediction) | 0.442 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 sourceMolMS with AttentiveFP 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 'MolMS', column 'Attn' |
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