Configuration

GIN

GIN as evaluated in the cited study. GIN 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 GIN, column Domain

11 evaluations · 11 results

Overview

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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: GIN	Protocol: GlyConnect glycosylation · Glycos (GlycanML glycosylation type prediction) Dataset: GlyConnect glycosylation · Glycos	97.16(0.19)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.19; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GIN: 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 GIN, column Glycos
Configuration: GIN	Protocol: SugarBase taxonomy · Phylum (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Phylum	84.04(1.07)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 1.07; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GIN: 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 GIN, column Phylum
Configuration: GIN	Protocol: SugarBase taxonomy · Order (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Order	35.40(1.92)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 1.92; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GIN: 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 GIN, column Order
Configuration: GIN	Protocol: SugarBase taxonomy · Class (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Class	67.54(0.31)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.31; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GIN: 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 GIN, column Class
Configuration: GIN	Protocol: LectinOracle interaction · Interaction (GlycanML protein-glycan interaction prediction) Dataset: LectinOracle interaction · Interaction	0.249(0.004) Spearman rho dimensionless · higher Uncertainty: type: standard_deviation; value: 0.004; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GIN: 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 GIN, column Interaction
Configuration: GIN	Protocol: SugarBase taxonomy · Family (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Family	40.04(0.86)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.86; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GIN: 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 GIN, column Family
Configuration: GIN	Protocol: SugarBase taxonomy · Kingdom (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Kingdom	92.35(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 GIN: 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 GIN, column Kingdom
Configuration: GIN	Protocol: SugarBase immunogenicity · Immuno (GlycanML immunogenicity prediction) Dataset: SugarBase immunogenicity · Immuno	0.716(0.051) AUPRC dimensionless · higher Uncertainty: type: standard_deviation; value: 0.051; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GIN: 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 GIN, column Immuno
Configuration: GIN	Protocol: SugarBase taxonomy · Domain (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Domain	94.41(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 GIN: 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 GIN, column Domain
Configuration: GIN	Protocol: SugarBase taxonomy · Genus (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Genus	34.28(0.44)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 0.44; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GIN: 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 GIN, column Genus
Configuration: GIN	Protocol: SugarBase taxonomy · Species (GlycanML taxonomy prediction) Dataset: SugarBase taxonomy · Species	31.85(2.19)% accuracy percent · higher Uncertainty: type: standard_deviation; value: 2.19; n: 3; unit: same_as_metric Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source GIN: 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 GIN, column Species

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GIN 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 GIN, column Domain

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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 GIN 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 GIN, 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 GIN as evaluated in the cited study. GIN 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 GIN, 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-6fafc268816dbf275d

areas: glycomics
entity level: method
configuration type: reported_configuration
version: GIN 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 GIN, 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: GIN: SugarBase immunogenicity · Immuno
model: GIN: SugarBase taxonomy · Genus
model: GIN: GlyConnect glycosylation · Glycos
model: GIN: SugarBase taxonomy · Phylum
model: GIN: SugarBase taxonomy · Family
model: GIN: LectinOracle interaction · Interaction
model: GIN: SugarBase taxonomy · Species
model: GIN: SugarBase taxonomy · Domain
model: GIN: SugarBase taxonomy · Kingdom
model: GIN: SugarBase taxonomy · Order
model: GIN: SugarBase taxonomy · Class

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