Configuration

DeepSet [MSAlign v2]

Exact Table 3 source implementation. Formula-free retrieval; neutral mass is still used.

Overview

Exact Table 3 source implementation. Formula-free retrieval; neutral mass is still used.

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

Evaluations and results

3 evaluations · 9 results. Different protocols are not a single leaderboard.

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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: DeepSet [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-mces-formula-free Dataset subset: MSAlign v2 massspecgym-mces-formula-free	1.9 ± 0.5% recall_at_1 percent · higher Uncertainty: type: standard_deviation; reported spread: 0.5; scope: Two MCES validation/test-swapped variants per methods, despite blanket three-split table caption. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSet massspecgym-mces-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-mces block, R@1 row, DeepSet column
Configuration: DeepSet [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-mces-formula-free Dataset subset: MSAlign v2 massspecgym-mces-formula-free	21.8 ± 1.4% recall_at_20 percent · higher Uncertainty: type: standard_deviation; reported spread: 1.4; scope: Two MCES validation/test-swapped variants per methods, despite blanket three-split table caption. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSet massspecgym-mces-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-mces block, R@20 row, DeepSet column
Configuration: DeepSet [MSAlign v2]	Protocol: MSAlign v2 retrieval: massspecgym-mces-formula-free Dataset subset: MSAlign v2 massspecgym-mces-formula-free	8.4 ± 0.6% recall_at_5 percent · higher Uncertainty: type: standard_deviation; reported spread: 0.6; scope: Two MCES validation/test-swapped variants per methods, despite blanket three-split table caption. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSet massspecgym-mces-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; massspecgym-mces block, R@5 row, DeepSet column
Configuration: DeepSet [MSAlign v2]	Protocol: MSAlign v2 retrieval: spectraverse-formula-free Dataset subset: MSAlign v2 spectraverse-formula-free	2.0 ± 0.4% recall_at_1 percent · higher Uncertainty: type: standard_deviation; reported spread: 0.4; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSet spectraverse-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; spectraverse block, R@1 row, DeepSet column
Configuration: DeepSet [MSAlign v2]	Protocol: MSAlign v2 retrieval: spectraverse-formula-free Dataset subset: MSAlign v2 spectraverse-formula-free	22.9 ± 0.9% recall_at_20 percent · higher Uncertainty: type: standard_deviation; reported spread: 0.9; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSet spectraverse-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; spectraverse block, R@20 row, DeepSet column
Configuration: DeepSet [MSAlign v2]	Protocol: MSAlign v2 retrieval: spectraverse-formula-free Dataset subset: MSAlign v2 spectraverse-formula-free	8.4 ± 1.0% recall_at_5 percent · higher Uncertainty: type: standard_deviation; reported spread: 1.0; scope: Three random splitting seeds. Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSet spectraverse-formula-free Not reported Aggregation: Not reported MSAlign arXiv v2 Table 3 · Table 3 p7; spectraverse block, R@5 row, DeepSet column

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

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How it works, versions and access

Related profile: MassSpecGym DeepSets fingerprint predictor. This page retains the exact record and its evaluation context.

Strengths, limitations and unresolved questions

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: variant of uc20260930-model-massspecgym-deepsets-fingerprint-predictor Individual claims	MSAlign arXiv v2 Table 3 Original source ↗ Table 3 source column DeepSet; Section 5.1 Baselines Version: 2605.19752v2, 25 September 2026 Retrieved: 2026-09-30	source checked automated source review · 2026-09-30T21:40:59.576893+00:00 Audit details Field: `links:variant_of:uc20260930-model-massspecgym-deepsets-fingerprint-predictor` Claim: uc20260930-config-family-1f5f4e84667b5253 Source artifact SHA-256: `a31d1167b0ded72f64717881dd6cba0946a56b495d76f169d8e44115c3266fda` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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Sources and history

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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-config-deepset

areas: metabolomics
source locator: Table 3 column DeepSet; Sections 3 and 5.1
missing metadata: checkpoint hash: unextracted
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.
reported name: DeepSet

Related records

variant of: MassSpecGym DeepSets fingerprint predictor
subject: DeepSet [MSAlign v2] family identity
configuration: DeepSet fingerprint baseline: massspecgym-formula-formula-free
configuration: DeepSet fingerprint baseline: massspecgym-mces-formula-free
configuration: DeepSet fingerprint baseline: spectraverse-formula-free
configuration: DeepSet massspecgym-formula-formula-free
configuration: DeepSet massspecgym-mces-formula-free
configuration: DeepSet spectraverse-formula-free

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