FFN
Evaluated retrieval configuration from MSAlign Table 3; model-specific inputs and training are retained in the protocol.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
4 evaluations · 12 results. Different protocols are not a single leaderboard.
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.
All 12 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: FFN | Protocol: MSAlign molecular retrieval MassSpecGym formula split: no formula, R@1: MassSpecGym formula split retrieval with no formula Dataset subset: MassSpecGym formula split, no formula candidate pool (MSAlign molecular retrieval split) | 16.9% Top-1 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSection 5.1 candidate retrieval: 256 mass-matched PubChem candidates per spectrum without formula; formula-conditioned methods can exploit true formula and MSAlign+Filter reduces the pool to about 100. Preserve the named source split; exact original split hashes remain unextracted. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym formula split, row R@1, column 3 (FFN) |
| Configuration: FFN | Protocol: MSAlign molecular retrieval MassSpecGym formula split: no formula, R@20: MassSpecGym formula split retrieval with no formula Dataset subset: MassSpecGym formula split, no formula candidate pool (MSAlign molecular retrieval split) | 40.4% Top-20 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSection 5.1 candidate retrieval: 256 mass-matched PubChem candidates per spectrum without formula; formula-conditioned methods can exploit true formula and MSAlign+Filter reduces the pool to about 100. Preserve the named source split; exact original split hashes remain unextracted. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym formula split, row R@20, column 3 (FFN) |
| Configuration: FFN | Protocol: MSAlign molecular retrieval MassSpecGym formula split: no formula, R@5: MassSpecGym formula split retrieval with no formula Dataset subset: MassSpecGym formula split, no formula candidate pool (MSAlign molecular retrieval split) | 27.8% Top-5 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSection 5.1 candidate retrieval: 256 mass-matched PubChem candidates per spectrum without formula; formula-conditioned methods can exploit true formula and MSAlign+Filter reduces the pool to about 100. Preserve the named source split; exact original split hashes remain unextracted. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym formula split, row R@5, column 3 (FFN) |
| Configuration: FFN | Protocol: MSAlign molecular retrieval MassSpecGym MCES split: no formula, R@1: MassSpecGym MCES split retrieval with no formula Dataset subset: MassSpecGym MCES split, no formula candidate pool (MSAlign molecular retrieval split) | 2.54% Top-1 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSection 5.1 candidate retrieval: 256 mass-matched PubChem candidates per spectrum without formula; formula-conditioned methods can exploit true formula and MSAlign+Filter reduces the pool to about 100. Preserve the named source split; exact original split hashes remain unextracted. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym MCES split, row R@1, column 3 (FFN) |
| Configuration: FFN | Protocol: MSAlign molecular retrieval MassSpecGym MCES split: no formula, R@20: MassSpecGym MCES split retrieval with no formula Dataset subset: MassSpecGym MCES split, no formula candidate pool (MSAlign molecular retrieval split) | 20% Top-20 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSection 5.1 candidate retrieval: 256 mass-matched PubChem candidates per spectrum without formula; formula-conditioned methods can exploit true formula and MSAlign+Filter reduces the pool to about 100. Preserve the named source split; exact original split hashes remain unextracted. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym MCES split, row R@20, column 3 (FFN) |
| Configuration: FFN | Protocol: MSAlign molecular retrieval MassSpecGym MCES split: no formula, R@5: MassSpecGym MCES split retrieval with no formula Dataset subset: MassSpecGym MCES split, no formula candidate pool (MSAlign molecular retrieval split) | 7.59% Top-5 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSection 5.1 candidate retrieval: 256 mass-matched PubChem candidates per spectrum without formula; formula-conditioned methods can exploit true formula and MSAlign+Filter reduces the pool to about 100. Preserve the named source split; exact original split hashes remain unextracted. Aggregation: Not reported msalign: Primary paper PDF · Table 3, MassSpecGym MCES split, row R@5, column 3 (FFN) |
| Configuration: FFN | Protocol: MSAlign molecular retrieval NPLIB1: no formula, R@1: NPLIB1 retrieval with no formula Dataset subset: NPLIB1, no formula candidate pool (MSAlign molecular retrieval split) | 8.9% Top-1 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceFFN on MSAlign molecular retrieval NPLIB1: no formula, R@1: NPLIB1 retrieval with no formula Section 5.1 candidate retrieval: 256 mass-matched PubChem candidates per spectrum without formula; formula-conditioned methods can exploit true formula and MSAlign+Filter reduces the pool to about 100. Preserve the named source split; exact original split hashes remain unextracted. Aggregation: Not reported msalign: Primary paper PDF · Table 3, NPLIB1, row R@1, column 3 (FFN) |
| Configuration: FFN | Protocol: MSAlign molecular retrieval NPLIB1: no formula, R@20: NPLIB1 retrieval with no formula Dataset subset: NPLIB1, no formula candidate pool (MSAlign molecular retrieval split) | 44.4% Top-20 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceFFN on MSAlign molecular retrieval NPLIB1: no formula, R@20: NPLIB1 retrieval with no formula Section 5.1 candidate retrieval: 256 mass-matched PubChem candidates per spectrum without formula; formula-conditioned methods can exploit true formula and MSAlign+Filter reduces the pool to about 100. Preserve the named source split; exact original split hashes remain unextracted. Aggregation: Not reported msalign: Primary paper PDF · Table 3, NPLIB1, row R@20, column 3 (FFN) |
| Configuration: FFN | Protocol: MSAlign molecular retrieval NPLIB1: no formula, R@5: NPLIB1 retrieval with no formula Dataset subset: NPLIB1, no formula candidate pool (MSAlign molecular retrieval split) | 22% Top-5 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceFFN on MSAlign molecular retrieval NPLIB1: no formula, R@5: NPLIB1 retrieval with no formula Section 5.1 candidate retrieval: 256 mass-matched PubChem candidates per spectrum without formula; formula-conditioned methods can exploit true formula and MSAlign+Filter reduces the pool to about 100. Preserve the named source split; exact original split hashes remain unextracted. Aggregation: Not reported msalign: Primary paper PDF · Table 3, NPLIB1, row R@5, column 3 (FFN) |
| Configuration: FFN | Protocol: MSAlign molecular retrieval Spectraverse: no formula, R@1: Spectraverse retrieval with no formula Dataset subset: Spectraverse, no formula candidate pool (MSAlign molecular retrieval split) | 9.5% Top-1 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSection 5.1 candidate retrieval: 256 mass-matched PubChem candidates per spectrum without formula; formula-conditioned methods can exploit true formula and MSAlign+Filter reduces the pool to about 100. Preserve the named source split; exact original split hashes remain unextracted. Aggregation: Not reported msalign: Primary paper PDF · Table 3, Spectraverse, row R@1, column 3 (FFN) |
| Configuration: FFN | Protocol: MSAlign molecular retrieval Spectraverse: no formula, R@20: Spectraverse retrieval with no formula Dataset subset: Spectraverse, no formula candidate pool (MSAlign molecular retrieval split) | 34.7% Top-20 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSection 5.1 candidate retrieval: 256 mass-matched PubChem candidates per spectrum without formula; formula-conditioned methods can exploit true formula and MSAlign+Filter reduces the pool to about 100. Preserve the named source split; exact original split hashes remain unextracted. Aggregation: Not reported msalign: Primary paper PDF · Table 3, Spectraverse, row R@20, column 3 (FFN) |
| Configuration: FFN | Protocol: MSAlign molecular retrieval Spectraverse: no formula, R@5: Spectraverse retrieval with no formula Dataset subset: Spectraverse, no formula candidate pool (MSAlign molecular retrieval split) | 18.9% Top-5 accuracy (retrieval) percent · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible | Independent external evaluation · Source checkedMethods, coverage and sourceSection 5.1 candidate retrieval: 256 mass-matched PubChem candidates per spectrum without formula; formula-conditioned methods can exploit true formula and MSAlign+Filter reduces the pool to about 100. Preserve the named source split; exact original split hashes remain unextracted. Aggregation: Not reported msalign: Primary paper PDF · Table 3, Spectraverse, row R@5, column 3 (FFN) |
Source checking is not independent reproduction. Release 2026-11-02-a7f03c9e55a5.
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How it works, versions and access
Additional methodological details, versions and access terms have not yet been extracted into a structured profile for this configuration. Consult the linked sources and evaluation records below.
Evidence
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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.
3 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
Facets: method types1 values
| msalign: Primary paper PDF MassSpecGym Section 4.1: Fingerprint FFN "employs a feedforward neural network to predict the Morgan fingerprint", and DeepSets; MSAlign arXiv 2605.19752 Table 1 and "Baselines" (v1 and v2): JESTR "pretrains with batch InfoNCE", Emb-Cos "uses candidates InfoNCE to learn a shared space", SAIL is trained with the batch loss Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2605.19752v1 | conflicting claim ["source-hash-verification","automated-source-review"] · 2026-10-12 Audit detailsCorrect the method type from none to supervised_machine_learning (use-case baseline review 2026-10-12, table 1). Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. MSAlign v1 Section 5.1 "Baselines" and Table 1: FFN and DeepSets are fingerprint predictors from MassSpecGym; JESTR, Emb-Cos and SAIL are trained with InfoNCE losses; MSAlign aligns two frozen foundation models. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: Field: Claim: metadata-correction-tags-20261012-575618aa73d2eeccadde Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact Extraction artifact SHA-256: |
Facets: method types1 values
| MassSpecGym: A benchmark for the discovery and identification of molecules MassSpecGym Section 4.1: Fingerprint FFN "employs a feedforward neural network to predict the Morgan fingerprint", and DeepSets; MSAlign arXiv 2605.19752 Table 1 and "Baselines" (v1 and v2): JESTR "pretrains with batch InfoNCE", Emb-Cos "uses candidates InfoNCE to learn a shared space", SAIL is trained with the batch loss Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2410.23326v1 | conflicting claim ["source-hash-verification","automated-source-review"] · 2026-10-12 Audit detailsCorrect the method type from none to supervised_machine_learning (use-case baseline review 2026-10-12, table 1). Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. MSAlign v1 Section 5.1 "Baselines" and Table 1: FFN and DeepSets are fingerprint predictors from MassSpecGym; JESTR, Emb-Cos and SAIL are trained with InfoNCE losses; MSAlign aligns two frozen foundation models. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: Field: Claim: metadata-correction-tags-20261012-575618aa73d2eeccadde Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. Extraction artifact SHA-256: |
Facets: method types1 values
| MSAlign arXiv v2 Table 3 MassSpecGym Section 4.1: Fingerprint FFN "employs a feedforward neural network to predict the Morgan fingerprint", and DeepSets; MSAlign arXiv 2605.19752 Table 1 and "Baselines" (v1 and v2): JESTR "pretrains with batch InfoNCE", Emb-Cos "uses candidates InfoNCE to learn a shared space", SAIL is trained with the batch loss Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: 2605.19752v2, 25 September 2026 | conflicting claim ["source-hash-verification","automated-source-review"] · 2026-10-12 Audit detailsCorrect the method type from none to supervised_machine_learning (use-case baseline review 2026-10-12, table 1). Evidence from docs/reviews/use-cases/baselines-2026-10-12.md. Independent review 2026-10-12: approved. MSAlign v1 Section 5.1 "Baselines" and Table 1: FFN and DeepSets are fingerprint predictors from MassSpecGym; JESTR, Emb-Cos and SAIL are trained with InfoNCE losses; MSAlign aligns two frozen foundation models. See docs/reviews/2026-10-12-method-type-corrections.md. Conflicting source claim: Field: Claim: metadata-correction-tags-20261012-575618aa73d2eeccadde Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record Extraction artifact SHA-256: |
Sources and history
Release 2026-11-02-a7f03c9e55a5 · Record review: source checked
1 source record and release history
- msalign: Primary paper PDF · Original source · 2605.19752v1
Technical metadata and extraction receipts
Stable ID: msalign-2026-table3-method-ffn
- areas
- metabolomics
- method types
- supervised_machine_learning
- source locator
- Table 3, column FFN; Section 5.1
- missing metadata
- checkpoint revision: reason: unreported; parameters: reason: unextracted
Related records
- subject: FFN: facets.method_types
- system: FFN on MSAlign molecular retrieval MassSpecGym formula split: no formula, R@1: MassSpecGym formula split retrieval with no formula
- system: FFN on MSAlign molecular retrieval MassSpecGym formula split: no formula, R@20: MassSpecGym formula split retrieval with no formula
- system: FFN on MSAlign molecular retrieval MassSpecGym formula split: no formula, R@5: MassSpecGym formula split retrieval with no formula
- system: FFN on MSAlign molecular retrieval MassSpecGym MCES split: no formula, R@1: MassSpecGym MCES split retrieval with no formula
- system: FFN on MSAlign molecular retrieval MassSpecGym MCES split: no formula, R@20: MassSpecGym MCES split retrieval with no formula
- system: FFN on MSAlign molecular retrieval MassSpecGym MCES split: no formula, R@5: MassSpecGym MCES split retrieval with no formula
- system: FFN on MSAlign molecular retrieval NPLIB1: no formula, R@1: NPLIB1 retrieval with no formula
- system: FFN on MSAlign molecular retrieval NPLIB1: no formula, R@20: NPLIB1 retrieval with no formula
- system: FFN on MSAlign molecular retrieval NPLIB1: no formula, R@5: NPLIB1 retrieval with no formula
- system: FFN on MSAlign molecular retrieval Spectraverse: no formula, R@1: Spectraverse retrieval with no formula
- system: FFN on MSAlign molecular retrieval Spectraverse: no formula, R@20: Spectraverse retrieval with no formula
- system: FFN on MSAlign molecular retrieval Spectraverse: no formula, R@5: Spectraverse retrieval with no formula
- implemented by: FFN comparator role