Configuration

MPNN

MPNN as evaluated in the cited study. MPNN architecture in Table 2; single-task supervised encoder plus MLP; interaction additionally uses ESM-1b protein embeddings

Sources

GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Domain

11 evaluations · 11 results

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Evaluations and results

11 evaluations · 11 results. Different protocols are not a single leaderboard.

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: MPNN	Protocol: GlyConnect glycosylation · Glycos (GlycanML glycosylation type prediction) Dataset: GlyConnect glycosylation · Glycos	97.41(0.90)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.9; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MPNN: GlyConnect glycosylation · Glycos Author-reported single-task models on the same held-out task; not a cross-paper ranking. Taxonomy, immunogenicity and glycosylation: motif-frequency K-means cluster allocation 8:1:1. Interaction: MMseqs2 protein clusters at minimum identity 0.5 allocated 8:1:1. Exact counts are attached to each column. Aggregation: Not reported GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Glycos
Configuration: MPNN	Protocol: SugarBase taxonomy · Phylum (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Phylum	82.48(0.94)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.94; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MPNN: SugarBase taxonomy · Phylum Author-reported single-task models on the same held-out task; not a cross-paper ranking. SugarBase taxonomy: motif-frequency K-means cluster allocation 8:1:1. Aggregation: Not reported GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Phylum
Configuration: MPNN	Protocol: SugarBase taxonomy · Kingdom (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Kingdom	90.39(0.94)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.94; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MPNN: SugarBase taxonomy · Kingdom Author-reported single-task models on the same held-out task; not a cross-paper ranking. SugarBase taxonomy: motif-frequency K-means cluster allocation 8:1:1. Aggregation: Not reported GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Kingdom
Configuration: MPNN	Protocol: SugarBase taxonomy · Family (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Family	41.60(0.64)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.64; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MPNN: SugarBase taxonomy · Family Author-reported single-task models on the same held-out task; not a cross-paper ranking. SugarBase taxonomy: motif-frequency K-means cluster allocation 8:1:1. Aggregation: Not reported GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Family
Configuration: MPNN	Protocol: SugarBase taxonomy · Domain (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Domain	93.83(0.17)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.17; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MPNN: SugarBase taxonomy · Domain Author-reported single-task models on the same held-out task; not a cross-paper ranking. SugarBase taxonomy: motif-frequency K-means cluster allocation 8:1:1. Aggregation: Not reported GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Domain
Configuration: MPNN	Protocol: SugarBase immunogenicity · Immuno (GlycanML immunogenicity prediction) Dataset: SugarBase immunogenicity · Immuno	0.674(0.119) AUPRC dimensionless · higher Uncertainty: type: standard_deviation; value: 0.119; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MPNN: SugarBase immunogenicity · Immuno Author-reported single-task models on the same held-out task; not a cross-paper ranking. Taxonomy, immunogenicity and glycosylation: motif-frequency K-means cluster allocation 8:1:1. Interaction: MMseqs2 protein clusters at minimum identity 0.5 allocated 8:1:1. Exact counts are attached to each column. Aggregation: Not reported GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Immuno
Configuration: MPNN	Protocol: SugarBase taxonomy · Species (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Species	33.80(1.87)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 1.87; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MPNN: SugarBase taxonomy · Species Author-reported single-task models on the same held-out task; not a cross-paper ranking. SugarBase taxonomy: motif-frequency K-means cluster allocation 8:1:1. Aggregation: Not reported GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Species
Configuration: MPNN	Protocol: SugarBase taxonomy · Order (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Order	45.85(0.87)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.87; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MPNN: SugarBase taxonomy · Order Author-reported single-task models on the same held-out task; not a cross-paper ranking. SugarBase taxonomy: motif-frequency K-means cluster allocation 8:1:1. Aggregation: Not reported GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Order
Configuration: MPNN	Protocol: SugarBase taxonomy · Class (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Class	66.52(1.76)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 1.76; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MPNN: SugarBase taxonomy · Class Author-reported single-task models on the same held-out task; not a cross-paper ranking. SugarBase taxonomy: motif-frequency K-means cluster allocation 8:1:1. Aggregation: Not reported GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Class
Configuration: MPNN	Protocol: SugarBase taxonomy · Genus (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Genus	37.69(2.02)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 2.02; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MPNN: SugarBase taxonomy · Genus Author-reported single-task models on the same held-out task; not a cross-paper ranking. SugarBase taxonomy: motif-frequency K-means cluster allocation 8:1:1. Aggregation: Not reported GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Genus
Configuration: MPNN	Protocol: LectinOracle interaction · Interaction (GlycanML protein-glycan interaction prediction) Dataset: LectinOracle interaction · Interaction	0.217(0.002) Spearman rho dimensionless · higher Uncertainty: type: standard_deviation; value: 0.002; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source MPNN: LectinOracle interaction · Interaction Author-reported single-task models on the same held-out task; not a cross-paper ranking. Taxonomy, immunogenicity and glycosylation: motif-frequency K-means cluster allocation 8:1:1. Interaction: MMseqs2 protein clusters at minimum identity 0.5 allocated 8:1:1. Exact counts are attached to each column. Aggregation: Not reported GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Interaction

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MPNN architecture in Table 2; single-task supervised encoder plus MLP; interaction additionally uses ESM-1b protein embeddings

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GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Domain

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Stable record: paper-model-5b1f3a82b020f49ebe

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Claims, original sources and review scope · Release 2026-09-29-06401fd5b220
Property and statement	Original source and location	Review and provenance
Evaluation in this paper MPNN architecture in Table 2; single-task supervised encoder plus MLP; interaction additionally uses ESM-1b protein embeddings Individual claims	GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning Original source ↗ Table 3, row MPNN, column Domain Version: arXiv:2405.16206v1, 2024-05-25 Retrieved: 2026-09-16T21:04:56.017006+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.sections.0.body` Source artifact SHA-256: `9ba3db678b4550898a612b42e8832bf9dee40935090fc4d969ba8f6ac5106979` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact
Introduction MPNN as evaluated in the cited study. MPNN architecture in Table 2; single-task supervised encoder plus MLP; interaction additionally uses ESM-1b protein embeddings Individual claims	GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning Original source ↗ Table 3, row MPNN, column Domain Version: arXiv:2405.16206v1, 2024-05-25 Retrieved: 2026-09-16T21:04:56.017006+00:00	source checked automated source review · 2026-09-17 Audit details Primary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: `attributes.profile.summary` Source artifact SHA-256: `9ba3db678b4550898a612b42e8832bf9dee40935090fc4d969ba8f6ac5106979` Hash scope: Exact retrieved primary paper artifact bytes. Inspected artifact

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GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Original source · arXiv:2405.16206v1, 2024-05-25

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Stable ID: paper-model-5b1f3a82b020f49ebe

areas: glycomics
entity level: method
configuration type: reported_configuration
version: MPNN architecture in Table 2; single-task supervised encoder plus MLP; interaction additionally uses ESM-1b protein embeddings
legacy kinds: model
entity classification: review date: 2026-09-17; rationale: This source-scoped entry preserves the method/configuration actually named in an evaluation. It is neither a global family identity nor proof of an immutable checkpoint; the linked evaluation retains adaptation, fitting and scoring details.; source ids: expansion-p3-glycanml-2405-16206v1; source locator: Table 3, row MPNN, column Domain; ambiguities: Configuration means the source-labelled evaluated identity. It does not establish missing checkpoint hashes, default settings or equivalence to same-named records in other papers.

Related records

model: MPNN: SugarBase taxonomy · Family
model: MPNN: SugarBase taxonomy · Phylum
model: MPNN: SugarBase taxonomy · Domain
model: MPNN: LectinOracle interaction · Interaction
model: MPNN: SugarBase taxonomy · Order
model: MPNN: SugarBase taxonomy · Kingdom
model: MPNN: GlyConnect glycosylation · Glycos
model: MPNN: SugarBase taxonomy · Class
model: MPNN: SugarBase taxonomy · Species
model: MPNN: SugarBase taxonomy · Genus
model: MPNN: SugarBase immunogenicity · Immuno

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