Protocol

MSAlign v2 retrieval: massspecgym-formula-formula-free

Recall@1, @5 and @20, preserving split and formula access.

Overview

Recall@1, @5 and @20, preserving split and formula access.

Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

5 recorded evaluations, 15 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

View coverage and remaining gaps across all benchmarks

Results

Results are available, but no reviewed comparison panel is linked in this release.

All evaluations

5 evaluations · 15 results. Different protocols are not a single leaderboard.

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: DeepSet [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	4.7 ± 0.6% recall_at_1 percent · higher Uncertainty: type: standard_deviation; reported spread: 0.6; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSet massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@1 row, DeepSet column
Configuration: DeepSet [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	27.5 ± 2.0% recall_at_20 percent · higher Uncertainty: type: standard_deviation; reported spread: 2.0; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSet massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@20 row, DeepSet column
Configuration: DeepSet [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	13.0 ± 1.3% recall_at_5 percent · higher Uncertainty: type: standard_deviation; reported spread: 1.3; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSet massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@5 row, DeepSet column
Configuration: Emb-Cos [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	42.7 ± 3.0% recall_at_1 percent · higher Uncertainty: type: standard_deviation; reported spread: 3.0; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Emb-Cos massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@1 row, Emb-Cos column
Configuration: Emb-Cos [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	80.4 ± 1.6% recall_at_20 percent · higher Uncertainty: type: standard_deviation; reported spread: 1.6; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Emb-Cos massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@20 row, Emb-Cos column
Configuration: Emb-Cos [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	65.2 ± 2.8% recall_at_5 percent · higher Uncertainty: type: standard_deviation; reported spread: 2.8; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Emb-Cos massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@5 row, Emb-Cos column
Configuration: JESTR [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	13.9 ± 0.5% recall_at_1 percent · higher Uncertainty: type: standard_deviation; reported spread: 0.5; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source JESTR massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@1 row, JESTR column
Configuration: JESTR [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	57.0 ± 0.7% recall_at_20 percent · higher Uncertainty: type: standard_deviation; reported spread: 0.7; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source JESTR massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@20 row, JESTR column
Configuration: JESTR [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	32.5 ± 0.8% recall_at_5 percent · higher Uncertainty: type: standard_deviation; reported spread: 0.8; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source JESTR massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@5 row, JESTR column
Configuration: MSAlign [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	47.5 ± 3.4% recall_at_1 percent · higher Uncertainty: type: standard_deviation; reported spread: 3.4; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSAlign massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@1 row, MSAlign column
Configuration: MSAlign [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	87.0 ± 1.1% recall_at_20 percent · higher Uncertainty: type: standard_deviation; reported spread: 1.1; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSAlign massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@20 row, MSAlign column
Configuration: MSAlign [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	71.3 ± 2.6% recall_at_5 percent · higher Uncertainty: type: standard_deviation; reported spread: 2.6; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSAlign massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@5 row, MSAlign column
Configuration: MSAlign score fusion (overbar) [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	58.2 ± 3.4% recall_at_1 percent · higher Uncertainty: type: standard_deviation; reported spread: 3.4; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSAlign score fusion (overbar) massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@1 row, MSAlign score fusion (overbar) column
Configuration: MSAlign score fusion (overbar) [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	92.8 ± 1.1% recall_at_20 percent · higher Uncertainty: type: standard_deviation; reported spread: 1.1; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSAlign score fusion (overbar) massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@20 row, MSAlign score fusion (overbar) column
Configuration: MSAlign score fusion (overbar) [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-formula-formula-free Dataset subset: MSAlign v2 massspecgym-formula-formula-free	80.7 ± 3.0% recall_at_5 percent · higher Uncertainty: type: standard_deviation; reported spread: 3.0; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MSAlign score fusion (overbar) massspecgym-formula-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-formula block, R@5 row, MSAlign score fusion (overbar) column

Source checking is not independent reproduction. Release 2026-09-30-e37e3ab1284d.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

Benchmarks

MSAlign molecular retrieval evaluations

These source-backed links do not make different protocols or scores interchangeable.

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.

No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.

Author-reported evaluations: 5

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Select a task-valid null control after reviewing inputs and metric

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Select an upstream conventional reference after reviewing the full protocol

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-09-30-e37e3ab1284d. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.

Run instructions

No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.

Strengths, limitations and unresolved questions

Applicable tests and references

Applicability is distinct from a completed evaluation.

DeepSet fingerprint baseline: massspecgym-formula-formula-free · source_supported

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.

1 evidence row matching the loaded filters

Claims, original sources and review scope · Release 2026-09-30-e37e3ab1284d
Property and statement	Original source and location	Review and provenance
Relationship: part of msalign-2026-molecular-retrieval Individual claims	MSAlign arXiv v2 Table 3 Original source ↗ MSAlign 2605.19752v2 Table 3; Section 5.1 Version: 2605.19752v2, 25 September 2026 Retrieved: 2026-09-30	source checked automated source review · 2026-09-30T21:44:09.612264+00:00 Audit details Field: `links:part_of:msalign-2026-molecular-retrieval` Claim: uc20260930-protocol-parent-b1e55d78e4a89bae Source artifact SHA-256: `a31d1167b0ded72f64717881dd6cba0946a56b495d76f169d8e44115c3266fda` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

View linked audit checks and correction history

Release 2026-09-30-e37e3ab1284d · Record review: source checked

1 source records and release history

MSAlign arXiv v2 Table 3 · Original source · 2605.19752v2, 25 September 2026

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Technical metadata and extraction receipts

Stable ID: uc20260930-msalign-v2-protocol-massspecgym-formula-formula-free

areas: metabolomics
version: 2605.19752v2
source locator: Table 3; Section 5.1 Data Splitting and seeds
review: method: automated_source_review; reviewer: Codex experimental-use-case curation; date: 2026-09-30; reviewed at: 2026-09-30T21:40:59.576893+00:00; scope: Primary-source transcription and catalogue applicability audit; not human scientific review or independent experimental reproduction.
split replicates: 3
limitations: None recorded

Related records

part of: MSAlign molecular retrieval evaluations
applicable to: DeepSet fingerprint baseline: massspecgym-formula-formula-free
protocol: DeepSet massspecgym-formula-formula-free
protocol: Emb-Cos massspecgym-formula-formula-free
protocol: JESTR massspecgym-formula-formula-free
protocol: MSAlign massspecgym-formula-formula-free
protocol: MSAlign score fusion (overbar) massspecgym-formula-formula-free
subject: MSAlign v2 retrieval: massspecgym-formula-formula-free study membership

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