rewirebio.iobenchmarks
Evaluation

FFN contrastive on MIST CANOPUS retrieval Top 5: MIST CANOPUS fingerprint retrieval: Top 5

MIST CANOPUS retrieval evaluation of FFN contrastive on MIST CANOPUS fingerprint retrieval: Top 5, scored with Retrieval accuracy@5.

Evaluation results

1 evaluation · 1 result. Different protocols are not a single leaderboard.

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: FFN contrastiveProtocol: 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

Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

Release 2026-11-02-a7f03c9e55a5 · Evidence verified: Not verified

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Metrics are recomputed from the saved predictions: not yet verified
  • Sample annotations are recorded: not yet verified
  • Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • A pinned run recipe exists: not yet verified
  • Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

  • No verified artifact manifest is linked to this exact record.
  • File checksums match the recorded files: not yet verified
  • Predictions are matched to the right samples: not yet verified
  • Score meaning and direction are confirmed: not yet verified
  • Independent validation data exist: not yet verified
  • Overlap with training data is checked: not yet verified

Verified: Not verified

Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.

Artifacts and reproduction

No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.

Evaluation procedure

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.

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)
origin
Evaluation origin not reported
configuration
Not reported
protocol id
dreams-mist-retrieval-task-top-5
metric implementation
Retrieval accuracy@5

Metadata review: source checked. Unreported conditions prevent automatic comparisons.

Reproduction

Split
Not reported
Adaptation
Not reported
Scoring implementation
Retrieval accuracy@5

No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.

Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.

Evidence

Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

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.

13 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-11-02-a7f03c9e55a5
Property and statementOriginal source and locationReview and provenance
Adaptation
Supervised fingerprint prediction; contrastive comparators use additional PubChem candidates. Model-specific inputs and training differ.
Context-only references
dreams: Journal full-text XML

Original source ↗

Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 5

Version: Retrieved page snapshot; no immutable publisher revision supplied
Retrieved: 2026-09-16T19:53:03.200000+00:00

not individually reviewed

No individual claim review recorded

unreported

Audit details

Field: attributes.adaptation

Source artifact SHA-256: 4bbe2ecff0ad75944b3aec5131369c1b2f75ff6f4b5dc257487a274fdd7b0fef

Hash scope: SHA-256 of retrieved original artifact bytes

Format: original_artifact

Inspected artifact

Comparison: metric implementation
Retrieval accuracy@5
Context-only references
dreams: Journal full-text XML

Original source ↗

Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 5

Version: Retrieved page snapshot; no immutable publisher revision supplied
Retrieved: 2026-09-16T19:53:03.200000+00:00

not individually reviewed

No individual claim review recorded

unreported

Audit details

Field: attributes.comparison.metric_implementation

Source artifact SHA-256: 4bbe2ecff0ad75944b3aec5131369c1b2f75ff6f4b5dc257487a274fdd7b0fef

Hash scope: SHA-256 of retrieved original artifact bytes

Format: original_artifact

Inspected artifact

Comparison: protocol id
dreams-mist-retrieval-task-top-5
Context-only references
dreams: Journal full-text XML

Original source ↗

Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 5

Version: Retrieved page snapshot; no immutable publisher revision supplied
Retrieved: 2026-09-16T19:53:03.200000+00:00

not individually reviewed

No individual claim review recorded

unreported

Audit details

Field: attributes.comparison.protocol_id

Source artifact SHA-256: 4bbe2ecff0ad75944b3aec5131369c1b2f75ff6f4b5dc257487a274fdd7b0fef

Hash scope: SHA-256 of retrieved original artifact bytes

Format: original_artifact

Inspected artifact

Evaluation group id
dreams-mist-retrieval-method-ffn-contrastive-dreams-mist-retrieval-dataset-mist-canopus-benchmark-test-set-used-in-dreams-extended-data-table-1-evaluation-setup
Context-only references
dreams: Journal full-text XML

Original source ↗

Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 5

Version: Retrieved page snapshot; no immutable publisher revision supplied
Retrieved: 2026-09-16T19:53:03.200000+00:00

not individually reviewed

No individual claim review recorded

unreported

Audit details

Field: attributes.evaluation_group_id

Source artifact SHA-256: 4bbe2ecff0ad75944b3aec5131369c1b2f75ff6f4b5dc257487a274fdd7b0fef

Hash scope: SHA-256 of retrieved original artifact bytes

Format: original_artifact

Inspected artifact

Evidence overlap
Complete Extended Data Table 1 from one paper. Comparator execution provenance is unresolved; do not treat quoted comparisons as additional independent experiments.
Context-only references
dreams: Journal full-text XML

Original source ↗

Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 5

Version: Retrieved page snapshot; no immutable publisher revision supplied
Retrieved: 2026-09-16T19:53:03.200000+00:00

not individually reviewed

No individual claim review recorded

unreported

Audit details

Field: attributes.evidence_overlap

Source artifact SHA-256: 4bbe2ecff0ad75944b3aec5131369c1b2f75ff6f4b5dc257487a274fdd7b0fef

Hash scope: SHA-256 of retrieved original artifact bytes

Format: original_artifact

Inspected artifact

Origin
unreported
Context-only references
dreams: Journal full-text XML

Original source ↗

Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 5

Version: Retrieved page snapshot; no immutable publisher revision supplied
Retrieved: 2026-09-16T19:53:03.200000+00:00

missing or unspecified

No individual claim review recorded

unreported

Audit details

Field: attributes.origin

Source artifact SHA-256: 4bbe2ecff0ad75944b3aec5131369c1b2f75ff6f4b5dc257487a274fdd7b0fef

Hash scope: SHA-256 of retrieved original artifact bytes

Format: original_artifact

Inspected artifact

Protocol
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.
Context-only references
dreams: Journal full-text XML

Original source ↗

Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 5

Version: Retrieved page snapshot; no immutable publisher revision supplied
Retrieved: 2026-09-16T19:53:03.200000+00:00

not individually reviewed

No individual claim review recorded

unreported

Audit details

Field: attributes.protocol

Source artifact SHA-256: 4bbe2ecff0ad75944b3aec5131369c1b2f75ff6f4b5dc257487a274fdd7b0fef

Hash scope: SHA-256 of retrieved original artifact bytes

Format: original_artifact

Inspected artifact

Source location
Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 5
Context-only references
dreams: Journal full-text XML

Original source ↗

Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 5

Version: Retrieved page snapshot; no immutable publisher revision supplied
Retrieved: 2026-09-16T19:53:03.200000+00:00

not individually reviewed

No individual claim review recorded

unreported

Audit details

Field: attributes.source_locator

Source artifact SHA-256: 4bbe2ecff0ad75944b3aec5131369c1b2f75ff6f4b5dc257487a274fdd7b0fef

Hash scope: SHA-256 of retrieved original artifact bytes

Format: original_artifact

Inspected artifact

Description
MIST CANOPUS retrieval evaluation of FFN contrastive on MIST CANOPUS fingerprint retrieval: Top 5, scored with Retrieval accuracy@5.
Context-only references
dreams: Journal full-text XML

Original source ↗

Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 5

Version: Retrieved page snapshot; no immutable publisher revision supplied
Retrieved: 2026-09-16T19:53:03.200000+00:00

not individually reviewed

No individual claim review recorded

unreported

Audit details

Field: description

Source artifact SHA-256: 4bbe2ecff0ad75944b3aec5131369c1b2f75ff6f4b5dc257487a274fdd7b0fef

Hash scope: SHA-256 of retrieved original artifact bytes

Format: original_artifact

Inspected artifact

Relationship: assessment
dreams-mist-retrieval-task-top-5
Context-only references
dreams: Journal full-text XML

Original source ↗

Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 5

Version: Retrieved page snapshot; no immutable publisher revision supplied
Retrieved: 2026-09-16T19:53:03.200000+00:00

not individually reviewed

No individual claim review recorded

unreported

Audit details

Field: links:assessment:dreams-mist-retrieval-task-top-5

Source artifact SHA-256: 4bbe2ecff0ad75944b3aec5131369c1b2f75ff6f4b5dc257487a274fdd7b0fef

Hash scope: SHA-256 of retrieved original artifact bytes

Format: original_artifact

Inspected artifact

How to read the evidence

Sources and history

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

1 source record and release historyDownload this release (gzip)
Technical metadata and extraction receipts

Stable ID: dreams-mist-retrieval-evaluation-ffn-contrastive-top-5

areas
metabolomics
tasks
MIST CANOPUS fingerprint retrieval: Top 5
origin
unreported
protocol
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.
comparison
protocol id: dreams-mist-retrieval-task-top-5; metric implementation: Retrieval accuracy@5
missing metadata
budget: reason: unreported; checkpoint revision: reason: unreported; seeds: reason: unreported; split manifest: reason: unextracted
source locator
Extended Data Table 1 (XML Tab1), row FFN contrastive, column Top 5
adaptation
Supervised fingerprint prediction; contrastive comparators use additional PubChem candidates. Model-specific inputs and training differ.
evidence overlap
Complete Extended Data Table 1 from one paper. Comparator execution provenance is unresolved; do not treat quoted comparisons as additional independent experiments.
evaluation group id
dreams-mist-retrieval-method-ffn-contrastive-dreams-mist-retrieval-dataset-mist-canopus-benchmark-test-set-used-in-dreams-extended-data-table-1-evaluation-setup
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