FFN contrastive | configuration

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Evaluations and results

1 evaluation · 7 results. Different protocols are not a single leaderboard.

Dataset subset: MIST CANOPUS benchmark test set used in DreaMS Extended Data Table 1 (MIST CANOPUS retrieval split)

Sorted by Top-1 accuracy (retrieval) (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	Protocol and dataset	Top-1 accuracy (retrieval)	Top-10 accuracy (retrieval)	Top-100 accuracy (retrieval)	Top-20 accuracy (retrieval)	Top-200 accuracy (retrieval)	Top-5 accuracy (retrieval)	Top-50 accuracy (retrieval)
FFN contrastiveEvaluation	MIST CANOPUS retrieval Top 1: MIST CANOPUS fingerprint retrieval: Top 1	20.6%	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported
FFN contrastiveEvaluation	MIST CANOPUS retrieval Top 10: MIST CANOPUS fingerprint retrieval: Top 10	Not reported	54.4%	Not reported	Not reported	Not reported	Not reported	Not reported
FFN contrastiveEvaluation	MIST CANOPUS retrieval Top 100: MIST CANOPUS fingerprint retrieval: Top 100	Not reported	Not reported	80.6%	Not reported	Not reported	Not reported	Not reported
FFN contrastiveEvaluation	MIST CANOPUS retrieval Top 20: MIST CANOPUS fingerprint retrieval: Top 20	Not reported	Not reported	Not reported	63.5%	Not reported	Not reported	Not reported
FFN contrastiveEvaluation	MIST CANOPUS retrieval Top 200: MIST CANOPUS fingerprint retrieval: Top 200	Not reported	Not reported	Not reported	Not reported	86.1%	Not reported	Not reported
FFN contrastiveEvaluation	MIST CANOPUS retrieval Top 5: MIST CANOPUS fingerprint retrieval: Top 5	Not reported	Not reported	Not reported	Not reported	Not reported	45%	Not reported
FFN contrastiveEvaluation	MIST CANOPUS retrieval Top 50: MIST CANOPUS fingerprint retrieval: Top 50	Not reported	Not reported	Not reported	Not reported	Not reported	Not reported	75.1%

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: FFN contrastive	Protocol: MIST CANOPUS retrieval Top 1: MIST CANOPUS fingerprint retrieval: Top 1 Dataset subset: MIST CANOPUS benchmark test set used in DreaMS Extended Data Table 1 (MIST CANOPUS retrieval split)	20.6% Top-1 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source FFN contrastive on MIST CANOPUS retrieval Top 1: MIST CANOPUS fingerprint retrieval: Top 1 MIST CANOPUS PubChem candidate retrieval; candidate positives share true molecule InChIKey first14 characters, negatives share molecular formula; rank cosine similarity of predicted and candidate fingerprints; accuracy@k is fraction of spectra with positive candidate in top k, printed as percent. Full test set named in Extended Data Table 1; exact split version/hash unextracted; 8000 spectra/7000 molecules describes total benchmark, not confirmed test denominator. Aggregation: Not reported dreams: Journal full-text XML · Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 1
Configuration: FFN contrastive	Protocol: MIST CANOPUS retrieval Top 10: MIST CANOPUS fingerprint retrieval: Top 10 Dataset subset: MIST CANOPUS benchmark test set used in DreaMS Extended Data Table 1 (MIST CANOPUS retrieval split)	54.4% Top-10 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source FFN contrastive on MIST CANOPUS retrieval Top 10: MIST CANOPUS fingerprint retrieval: Top 10 MIST CANOPUS PubChem candidate retrieval; candidate positives share true molecule InChIKey first14 characters, negatives share molecular formula; rank cosine similarity of predicted and candidate fingerprints; accuracy@k is fraction of spectra with positive candidate in top k, printed as percent. Full test set named in Extended Data Table 1; exact split version/hash unextracted; 8000 spectra/7000 molecules describes total benchmark, not confirmed test denominator. Aggregation: Not reported dreams: Journal full-text XML · Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 10
Configuration: FFN contrastive	Protocol: MIST CANOPUS retrieval Top 100: MIST CANOPUS fingerprint retrieval: Top 100 Dataset subset: MIST CANOPUS benchmark test set used in DreaMS Extended Data Table 1 (MIST CANOPUS retrieval split)	80.6% Top-100 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source FFN contrastive on MIST CANOPUS retrieval Top 100: MIST CANOPUS fingerprint retrieval: Top 100 MIST CANOPUS PubChem candidate retrieval; candidate positives share true molecule InChIKey first14 characters, negatives share molecular formula; rank cosine similarity of predicted and candidate fingerprints; accuracy@k is fraction of spectra with positive candidate in top k, printed as percent. Full test set named in Extended Data Table 1; exact split version/hash unextracted; 8000 spectra/7000 molecules describes total benchmark, not confirmed test denominator. Aggregation: Not reported dreams: Journal full-text XML · Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 100
Configuration: FFN contrastive	Protocol: MIST CANOPUS retrieval Top 20: MIST CANOPUS fingerprint retrieval: Top 20 Dataset subset: MIST CANOPUS benchmark test set used in DreaMS Extended Data Table 1 (MIST CANOPUS retrieval split)	63.5% Top-20 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source FFN contrastive on MIST CANOPUS retrieval Top 20: MIST CANOPUS fingerprint retrieval: Top 20 MIST CANOPUS PubChem candidate retrieval; candidate positives share true molecule InChIKey first14 characters, negatives share molecular formula; rank cosine similarity of predicted and candidate fingerprints; accuracy@k is fraction of spectra with positive candidate in top k, printed as percent. Full test set named in Extended Data Table 1; exact split version/hash unextracted; 8000 spectra/7000 molecules describes total benchmark, not confirmed test denominator. Aggregation: Not reported dreams: Journal full-text XML · Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 20
Configuration: FFN contrastive	Protocol: MIST CANOPUS retrieval Top 200: MIST CANOPUS fingerprint retrieval: Top 200 Dataset subset: MIST CANOPUS benchmark test set used in DreaMS Extended Data Table 1 (MIST CANOPUS retrieval split)	86.1% Top-200 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source FFN contrastive on MIST CANOPUS retrieval Top 200: MIST CANOPUS fingerprint retrieval: Top 200 MIST CANOPUS PubChem candidate retrieval; candidate positives share true molecule InChIKey first14 characters, negatives share molecular formula; rank cosine similarity of predicted and candidate fingerprints; accuracy@k is fraction of spectra with positive candidate in top k, printed as percent. Full test set named in Extended Data Table 1; exact split version/hash unextracted; 8000 spectra/7000 molecules describes total benchmark, not confirmed test denominator. Aggregation: Not reported dreams: Journal full-text XML · Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 200
Configuration: FFN contrastive	Protocol: MIST CANOPUS retrieval Top 5: MIST CANOPUS fingerprint retrieval: Top 5 Dataset subset: MIST CANOPUS benchmark test set used in DreaMS Extended Data Table 1 (MIST CANOPUS retrieval split)	45% Top-5 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source FFN contrastive on MIST CANOPUS retrieval Top 5: MIST CANOPUS fingerprint retrieval: Top 5 MIST CANOPUS PubChem candidate retrieval; candidate positives share true molecule InChIKey first14 characters, negatives share molecular formula; rank cosine similarity of predicted and candidate fingerprints; accuracy@k is fraction of spectra with positive candidate in top k, printed as percent. Full test set named in Extended Data Table 1; exact split version/hash unextracted; 8000 spectra/7000 molecules describes total benchmark, not confirmed test denominator. Aggregation: Not reported dreams: Journal full-text XML · Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 5
Configuration: FFN contrastive	Protocol: MIST CANOPUS retrieval Top 50: MIST CANOPUS fingerprint retrieval: Top 50 Dataset subset: MIST CANOPUS benchmark test set used in DreaMS Extended Data Table 1 (MIST CANOPUS retrieval split)	75.1% Top-50 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Evaluation origin not reported · Source checked Methods, coverage and source FFN contrastive on MIST CANOPUS retrieval Top 50: MIST CANOPUS fingerprint retrieval: Top 50 MIST CANOPUS PubChem candidate retrieval; candidate positives share true molecule InChIKey first14 characters, negatives share molecular formula; rank cosine similarity of predicted and candidate fingerprints; accuracy@k is fraction of spectra with positive candidate in top k, printed as percent. Full test set named in Extended Data Table 1; exact split version/hash unextracted; 8000 spectra/7000 molecules describes total benchmark, not confirmed test denominator. Aggregation: Not reported dreams: Journal full-text XML · Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 50

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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dreams: Journal full-text XML · Original source · Retrieved page snapshot; no immutable publisher revision supplied

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Technical metadata and extraction receipts

Stable ID: dreams-mist-retrieval-method-ffn-contrastive

areas: metabolomics
source locator: Extended Data Table 1 (XML Tab1), FFN contrastive row
missing metadata: checkpoint revision: reason: unreported; parameters: reason: unextracted
provenance note: Comparator configuration as reported in the DreaMS paper; original execution provenance is unresolved.

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