rewirebio.iobenchmarks
Evaluation

ICEBERG forward-model retrieval with imputed collision energies on MassSpecGym formula-retrieval (Hit rate@20)

Published comparison transcribed from the pinned source; not reproduced.

Evaluation results

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Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: ICEBERG forward-model retrieval with imputed collision energies (MassSpecGym in the Wild)Protocol: MassSpecGym formula-known retrieval (bonus), Hit rate@20 (MassSpecGym in the Wild Table 3)
Dataset: MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)
78.83 (77.74–79.78)% Top-20 accuracy (retrieval)
percent · higher

Uncertainty: 99.9% CI 77.74 to 79.78. Range printed in parentheses after the mean. Appendix 'Confidence Intervals': 99.9% bootstrap interval over 20,000 resamples of the test set.

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

ICEBERG forward-model retrieval with imputed collision energies on MassSpecGym formula-retrieval (Hit rate@20)

lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-20

Aggregation: Not reported

MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery · Table 3, section 'Reported Performance in Retrieval Task w/ Bonus (i.e., Formula Known)', row 'ICEBERG (forward model retrieval)', column 'Hit rate@20'

Source checking is not independent reproduction. Release 2026-10-23-5347695500ed.

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Release 2026-10-23-5347695500ed · Evidence verified: Not verified

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Verified: Not verified

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Verified: Not verified

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Verified: Not verified

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Evaluation procedure

MassSpecGym formula-known retrieval (bonus), Hit rate@20 (MassSpecGym in the Wild Table 3)

Configuration
ICEBERG forward-model retrieval with imputed collision energies (MassSpecGym in the Wild)
Protocol
MassSpecGym formula-known retrieval (bonus), Hit rate@20 (MassSpecGym in the Wild Table 3)
Dataset
MassSpecGym test fold, formula-known retrieval candidates (bonus) (MassSpecGym in the Wild)
origin
Author-reported evaluation
configuration
Primary source as retrieved 2026-10-11
protocol id
lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-20
dataset version
Not reported
split
MassSpecGym test fold
population
Not reported
inputs
MS/MS spectrum, precursor mass and ground-truth formula (bonus)
adaptation
Not reported
metric implementation
Not reported
aggregation
Mean over test spectra
budget
Not reported

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

Reproduction

Split
MassSpecGym test fold
Adaptation
Not reported
Scoring implementation
Not reported

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

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Evidence table

Inspect claims, sources and review details

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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

19 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-10-23-5347695500ed
Property and statementOriginal source and locationReview and provenance
Comparison: adaptation
Not reported
Context-only references
MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

Original source ↗

Table 3 row 'ICEBERG (forward model retrieval)', column 'Hit rate@20'

Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.adaptation

Source artifact SHA-256: 47f329399853bdd2a513707b97271dfd8875271be383168effde1b0f13efb0d2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: aggregation
Mean over test spectra
Context-only references
MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

Original source ↗

Table 3 row 'ICEBERG (forward model retrieval)', column 'Hit rate@20'

Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.aggregation

Source artifact SHA-256: 47f329399853bdd2a513707b97271dfd8875271be383168effde1b0f13efb0d2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: budget
Not reported
Context-only references
MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

Original source ↗

Table 3 row 'ICEBERG (forward model retrieval)', column 'Hit rate@20'

Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.budget

Source artifact SHA-256: 47f329399853bdd2a513707b97271dfd8875271be383168effde1b0f13efb0d2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: dataset version
Not reported
Context-only references
MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

Original source ↗

Table 3 row 'ICEBERG (forward model retrieval)', column 'Hit rate@20'

Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.dataset_version

Source artifact SHA-256: 47f329399853bdd2a513707b97271dfd8875271be383168effde1b0f13efb0d2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: inputs
MS/MS spectrum, precursor mass and ground-truth formula (bonus)
Context-only references
MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

Original source ↗

Table 3 row 'ICEBERG (forward model retrieval)', column 'Hit rate@20'

Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.inputs

Source artifact SHA-256: 47f329399853bdd2a513707b97271dfd8875271be383168effde1b0f13efb0d2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: metric implementation
Not reported
Context-only references
MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

Original source ↗

Table 3 row 'ICEBERG (forward model retrieval)', column 'Hit rate@20'

Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.metric_implementation

Source artifact SHA-256: 47f329399853bdd2a513707b97271dfd8875271be383168effde1b0f13efb0d2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: population
Not reported
Context-only references
MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

Original source ↗

Table 3 row 'ICEBERG (forward model retrieval)', column 'Hit rate@20'

Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

missing or unspecified

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.population

Source artifact SHA-256: 47f329399853bdd2a513707b97271dfd8875271be383168effde1b0f13efb0d2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: protocol id
lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-20
Context-only references
MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

Original source ↗

Table 3 row 'ICEBERG (forward model retrieval)', column 'Hit rate@20'

Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.protocol_id

Source artifact SHA-256: 47f329399853bdd2a513707b97271dfd8875271be383168effde1b0f13efb0d2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Comparison: split
MassSpecGym test fold
Context-only references
MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

Original source ↗

Table 3 row 'ICEBERG (forward model retrieval)', column 'Hit rate@20'

Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.comparison.split

Source artifact SHA-256: 47f329399853bdd2a513707b97271dfd8875271be383168effde1b0f13efb0d2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Limitations
1 values
  • Run by the MassSpecGym in the Wild authors on a method or baseline from their own groups.
Context-only references
MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

Original source ↗

Table 3 row 'ICEBERG (forward model retrieval)', column 'Hit rate@20'

Version: arXiv:2606.19624v1 (submitted 2026-06-17), arXiv HTML rendering
Retrieved: 2026-10-11T21:27:08Z

not individually reviewed

No individual claim review recorded

author reported

Audit details

Field: attributes.limitations

Source artifact SHA-256: 47f329399853bdd2a513707b97271dfd8875271be383168effde1b0f13efb0d2

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

How to read the evidence

Sources and history

Release 2026-10-23-5347695500ed · Record review: source checked

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

Stable ID: lit-otheromics-20261011-msgwild-eval-iceberg-forward-model-retrieval-with-imputed-collision-energies-formula-retrieval-hit-rate-20

areas
metabolomics
contexts
research
origin
author_reported
protocol
lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-20
version
Primary source as retrieved 2026-10-11
comparison
protocol id: lit-otheromics-20261011-msgwild-protocol-formula-retrieval-hit-rate-20; dataset version: Not reported; split: MassSpecGym test fold; population: Not reported; inputs: MS/MS spectrum, precursor mass and ground-truth formula (bonus); adaptation: Not reported; metric implementation: Not reported; aggregation: Mean over test spectra; budget: Not reported
source locator
Table 3 row 'ICEBERG (forward model retrieval)', column 'Hit rate@20'
missing metadata
comparison.adaptation: reason: unreported; comparison.budget: reason: unreported; comparison.dataset version: reason: unreported; comparison.metric implementation: reason: unreported; note: Section 6.2 recommends the MassSpecGym v1.5 reference metrics; the tables do not state which implementation produced these values; comparison.population: reason: unreported
limitations
Run by the MassSpecGym in the Wild authors on a method or baseline from their own groups.
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