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MassSpecGym · formula

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Evaluation results

5 evaluations · 20 results. Different protocols are not a single leaderboard.

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Random (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	27.74 (26.52-28.84)% Hit rate @20 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 26.52; upper: 28.84 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Random (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, Random, Hit rate @20
Configuration: DeepSets (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	4.42 (3.92-4.97)% Hit rate @1 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 3.92; upper: 4.97 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSets (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, DeepSets, Hit rate @1
Configuration: DeepSets (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	14.46 (13.58-15.36)% Hit rate @5 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 13.58; upper: 15.36 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSets (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, DeepSets, Hit rate @5
Configuration: MIST (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	41.12 (39.98-42.34)% Hit rate @20 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 39.98; upper: 42.34 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MIST (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, MIST, Hit rate @20
Configuration: DeepSets + Fourier features (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	33.46 (32.39-34.59)% Hit rate @20 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 32.39; upper: 34.59 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSets + Fourier features (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, DeepSets + Fourier features, Hit rate @20
Configuration: DeepSets (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	15.04 (14.89-15.19) MCES @1 edge-edit distance · lower Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 14.89; upper: 15.19 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSets (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, DeepSets, MCES @1
Configuration: Random (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	11.35 (10.60-12.12)% Hit rate @5 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 10.60; upper: 12.12 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Random (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, Random, Hit rate @5
Configuration: Fingerprint FFN (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	5.09 (4.57-5.66)% Hit rate @1 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 4.57; upper: 5.66 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Fingerprint FFN (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, Fingerprint FFN, Hit rate @1
Configuration: MIST (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	9.57 (8.88-10.30)% Hit rate @1 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 8.88; upper: 10.30 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MIST (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, MIST, Hit rate @1
Configuration: Fingerprint FFN (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	14.69 (13.83-15.56)% Hit rate @5 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 13.83; upper: 15.56 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Fingerprint FFN (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, Fingerprint FFN, Hit rate @5
Configuration: MIST (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	22.11 (21.10-23.13)% Hit rate @5 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 21.10; upper: 23.13 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MIST (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, MIST, Hit rate @5
Configuration: DeepSets + Fourier features (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	6.56 (5.95-7.16)% Hit rate @1 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 5.95; upper: 7.16 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSets + Fourier features (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, DeepSets + Fourier features, Hit rate @1
Configuration: Fingerprint FFN (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	14.94 (14.79-15.09) MCES @1 edge-edit distance · lower Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 14.79; upper: 15.09 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Fingerprint FFN (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, Fingerprint FFN, MCES @1
Configuration: Random (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	13.87 (13.70-14.03) MCES @1 edge-edit distance · lower Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 13.70; upper: 14.03 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Random (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, Random, MCES @1
Configuration: DeepSets + Fourier features (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	14.14 (13.98-14.31) MCES @1 edge-edit distance · lower Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 13.98; upper: 14.31 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSets + Fourier features (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, DeepSets + Fourier features, MCES @1
Configuration: Random (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	3.06 (2.64-3.52)% Hit rate @1 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 2.64; upper: 3.52 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Random (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, Random, Hit rate @1
Configuration: DeepSets + Fourier features (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	16.46 (15.58-17.35)% Hit rate @5 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 15.58; upper: 17.35 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSets + Fourier features (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, DeepSets + Fourier features, Hit rate @5
Configuration: DeepSets (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	30.76 (29.67-31.93)% Hit rate @20 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 29.67; upper: 31.93 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source DeepSets (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, DeepSets, Hit rate @20
Configuration: Fingerprint FFN (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	31.97 (30.86-33.10)% Hit rate @20 percent · higher Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 30.86; upper: 33.10 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Fingerprint FFN (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, Fingerprint FFN, Hit rate @20
Configuration: MIST (formula)	Protocol: MassSpecGym · formula (MassSpecGym Molecule retrieval) Dataset: MassSpecGym · formula	12.75 (12.59-12.91) MCES @1 edge-edit distance · lower Uncertainty: type: bootstrap confidence interval; level: 0.999; resamples: 20000; lower: 12.59; upper: 12.91 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MIST (formula): MassSpecGym · formula Retrieve the correct molecule from up to 256 candidates using an input spectrum; compare separately within the main challenge and molecular-formula challenge. MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Aggregation: Not reported MassSpecGym: A benchmark for the discovery and identification of molecules · Table 3, bonus formula challenge, MIST, MCES @1

Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.

Dataset and evaluation context

A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.

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Evidence table

Inspect claims, sources and review details

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6 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
attributes.reported_population Not reported Context-only references	MassSpecGym: A benchmark for the discovery and identification of molecules Original source ↗ Table 3: Hit rate @1, formula Version: 2410.23326v1 Retrieved: 2026-09-17T07:56:11.146650+00:00	missing or unspecified No individual claim review recorded Audit details Field: `attributes.reported_population` Source artifact SHA-256: `82176d50e8947c8b9baa2a0d91493f5680c0e4c7e25a2266ff7879f48a58c40c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
attributes.source_locator Table 3: Hit rate @1, formula Context-only references	MassSpecGym: A benchmark for the discovery and identification of molecules Original source ↗ Table 3: Hit rate @1, formula Version: 2410.23326v1 Retrieved: 2026-09-17T07:56:11.146650+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.source_locator` Source artifact SHA-256: `82176d50e8947c8b9baa2a0d91493f5680c0e4c7e25a2266ff7879f48a58c40c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
attributes.split MCES single-linkage molecular clustering at threshold 10; fixed held-out test split Context-only references	MassSpecGym: A benchmark for the discovery and identification of molecules Original source ↗ Table 3: Hit rate @1, formula Version: 2410.23326v1 Retrieved: 2026-09-17T07:56:11.146650+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.split` Source artifact SHA-256: `82176d50e8947c8b9baa2a0d91493f5680c0e4c7e25a2266ff7879f48a58c40c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
attributes.subset formula Context-only references	MassSpecGym: A benchmark for the discovery and identification of molecules Original source ↗ Table 3: Hit rate @1, formula Version: 2410.23326v1 Retrieved: 2026-09-17T07:56:11.146650+00:00	not individually reviewed No individual claim review recorded Audit details Field: `attributes.subset` Source artifact SHA-256: `82176d50e8947c8b9baa2a0d91493f5680c0e4c7e25a2266ff7879f48a58c40c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
description Dataset and cohort used in the cited comparison. Dataset population counts do not establish successful prediction coverage. Context-only references	MassSpecGym: A benchmark for the discovery and identification of molecules Original source ↗ Table 3: Hit rate @1, formula Version: 2410.23326v1 Retrieved: 2026-09-17T07:56:11.146650+00:00	not individually reviewed No individual claim review recorded Audit details Field: `description` Source artifact SHA-256: `82176d50e8947c8b9baa2a0d91493f5680c0e4c7e25a2266ff7879f48a58c40c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
name MassSpecGym · formula Context-only references	MassSpecGym: A benchmark for the discovery and identification of molecules Original source ↗ Table 3: Hit rate @1, formula Version: 2410.23326v1 Retrieved: 2026-09-17T07:56:11.146650+00:00	not individually reviewed No individual claim review recorded Audit details Field: `name` Source artifact SHA-256: `82176d50e8947c8b9baa2a0d91493f5680c0e4c7e25a2266ff7879f48a58c40c` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

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Release 2026-09-29-06401fd5b220 · Record review: needs review

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MassSpecGym: A benchmark for the discovery and identification of molecules · Original source · 2410.23326v1

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Technical metadata and extraction receipts

Stable ID: paper-dataset-e3dee7ae24615eecfb

areas: metabolomics
split: MCES single-linkage molecular clustering at threshold 10; fixed held-out test split
subset: formula
reported population: Not reported
source locator: Table 3: Hit rate @1, formula
missing metadata: manifest: unextracted; scored count: unreported
entity classification: review date: 2026-09-17; rationale: This record identifies a biological data collection or source-labelled evaluation cohort. Keep its dataset identity; split, assay, taxonomic level, candidate restrictions and comparison context remain attributes rather than automatically becoming new entity kinds.; source ids: part2-massspecgym-arxiv-v1; source locator: Table 3: Hit rate @1, formula; ambiguities: The formula/main label describes task input or candidate constraints in some MassSpecGym tables, not necessarily a different biological population. Preserve the paper-specific data identity and do not infer subset equivalence.

Related records

dataset: DeepSets (formula): MassSpecGym · formula
dataset: DeepSets + Fourier features (formula): MassSpecGym · formula
dataset: MIST (formula): MassSpecGym · formula
dataset: Random (formula): MassSpecGym · formula
dataset: Fingerprint FFN (formula): MassSpecGym · formula

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