SugarBase taxonomy class; GlycanML official motif split (GlycanML split)
Dataset subset reported in GlycanGT published supplementary archive, Table S4. Exact split manifest remains unextracted; source-table identity is retained.
Evaluation results
10 evaluations · 10 metric rows. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: GlycanAA | Protocol: GlycanML class Accuracy: GlycanGT study: class Accuracy Dataset subset: SugarBase taxonomy class; GlycanML official motif split (GlycanML split) | 0.74646666666666595 ± 0.0136313364470742 accuracy fraction · higher Uncertainty: type: standard_deviation; value: 0.0136313364470742 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceGlycanAA on GlycanML class Accuracy: GlycanGT study: class Accuracy Taxonomy: 13,209 glycans total across eight levels, 4–1,737 classes per level. Official fixed GlycanML motif-based train/validation/test splits (8:1:1). Section 2.5 reports class-balanced classifiers, train ∪ validation hyperparameter selection by randomized search with 3-fold cross-validation, followed by one evaluation on the held-out test set; complete procedure repeated with three random seeds, reporting mean and standard deviation. GlycanGT large model pretrained with 35% masking provides [Graph] embeddings to SVM/LightGBM; the selected classifier for each S4 row is not identified. Section 2.6 states that all four graph baselines were trained and evaluated on the same datasets/splits; it does not establish that each baseline used the GlycanGT downstream classifier search. SVM search: 10 iterations, RBF/linear, C logU(1e-3,1e2), gamma logU(1e-4,1e-1); LightGBM: 15 randomized iterations. Do not combine with separate original GlycanML-paper protocols. Aggregation: Not reported GlycanGT published supplementary archive, Table S4; glycangt: Journal full-text XML · btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A24:E24 (mean D24, SD E24) |
| Configuration: GlycanAA | Protocol: GlycanML class Macro-F1: GlycanGT study: class Macro-F1 Dataset subset: SugarBase taxonomy class; GlycanML official motif split (GlycanML split) | 0.41666666666666602 ± 0.0177798575172393 macro_f1 dimensionless · higher Uncertainty: type: standard_deviation; value: 0.0177798575172393 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceGlycanAA on GlycanML class Macro-F1: GlycanGT study: class Macro-F1 Taxonomy: 13,209 glycans total across eight levels, 4–1,737 classes per level. Official fixed GlycanML motif-based train/validation/test splits (8:1:1). Section 2.5 reports class-balanced classifiers, train ∪ validation hyperparameter selection by randomized search with 3-fold cross-validation, followed by one evaluation on the held-out test set; complete procedure repeated with three random seeds, reporting mean and standard deviation. GlycanGT large model pretrained with 35% masking provides [Graph] embeddings to SVM/LightGBM; the selected classifier for each S4 row is not identified. Section 2.6 states that all four graph baselines were trained and evaluated on the same datasets/splits; it does not establish that each baseline used the GlycanGT downstream classifier search. SVM search: 10 iterations, RBF/linear, C logU(1e-3,1e2), gamma logU(1e-4,1e-1); LightGBM: 15 randomized iterations. Do not combine with separate original GlycanML-paper protocols. Aggregation: Not reported GlycanGT published supplementary archive, Table S4; glycangt: Journal full-text XML · btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A25:E25 (mean D25, SD E25) |
| Pipeline: GlycanGT | Protocol: GlycanML class Accuracy: GlycanGT study: class Accuracy Dataset subset: SugarBase taxonomy class; GlycanML official motif split (GlycanML split) | 0.69350743561842498 ± 0.0072451883770178003 accuracy fraction · higher Uncertainty: type: standard_deviation; value: 0.0072451883770178003 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceGlycanGT on GlycanML class Accuracy: GlycanGT study: class Accuracy Taxonomy: 13,209 glycans total across eight levels, 4–1,737 classes per level. Official fixed GlycanML motif-based train/validation/test splits (8:1:1). Section 2.5 reports class-balanced classifiers, train ∪ validation hyperparameter selection by randomized search with 3-fold cross-validation, followed by one evaluation on the held-out test set; complete procedure repeated with three random seeds, reporting mean and standard deviation. GlycanGT large model pretrained with 35% masking provides [Graph] embeddings to SVM/LightGBM; the selected classifier for each S4 row is not identified. Section 2.6 states that all four graph baselines were trained and evaluated on the same datasets/splits; it does not establish that each baseline used the GlycanGT downstream classifier search. SVM search: 10 iterations, RBF/linear, C logU(1e-3,1e2), gamma logU(1e-4,1e-1); LightGBM: 15 randomized iterations. Do not combine with separate original GlycanML-paper protocols. Aggregation: Not reported GlycanGT published supplementary archive, Table S4; glycangt: Journal full-text XML · btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A71:E71 (mean D71, SD E71) |
| Pipeline: GlycanGT | Protocol: GlycanML class Macro-F1: GlycanGT study: class Macro-F1 Dataset subset: SugarBase taxonomy class; GlycanML official motif split (GlycanML split) | 0.39715349769695701 ± 0.0084870172846663004 macro_f1 dimensionless · higher Uncertainty: type: standard_deviation; value: 0.0084870172846663004 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceGlycanGT on GlycanML class Macro-F1: GlycanGT study: class Macro-F1 Taxonomy: 13,209 glycans total across eight levels, 4–1,737 classes per level. Official fixed GlycanML motif-based train/validation/test splits (8:1:1). Section 2.5 reports class-balanced classifiers, train ∪ validation hyperparameter selection by randomized search with 3-fold cross-validation, followed by one evaluation on the held-out test set; complete procedure repeated with three random seeds, reporting mean and standard deviation. GlycanGT large model pretrained with 35% masking provides [Graph] embeddings to SVM/LightGBM; the selected classifier for each S4 row is not identified. Section 2.6 states that all four graph baselines were trained and evaluated on the same datasets/splits; it does not establish that each baseline used the GlycanGT downstream classifier search. SVM search: 10 iterations, RBF/linear, C logU(1e-3,1e2), gamma logU(1e-4,1e-1); LightGBM: 15 randomized iterations. Do not combine with separate original GlycanML-paper protocols. Aggregation: Not reported GlycanGT published supplementary archive, Table S4; glycangt: Journal full-text XML · btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A72:E72 (mean D72, SD E72) |
| Configuration: Graphormer | Protocol: GlycanML class Accuracy: GlycanGT study: class Accuracy Dataset subset: SugarBase taxonomy class; GlycanML official motif split (GlycanML split) | 0.66340200000000005 ± 0.013518000000000001 accuracy fraction · higher Uncertainty: type: standard_deviation; value: 0.013518000000000001 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceGraphormer on GlycanML class Accuracy: GlycanGT study: class Accuracy Taxonomy: 13,209 glycans total across eight levels, 4–1,737 classes per level. Official fixed GlycanML motif-based train/validation/test splits (8:1:1). Section 2.5 reports class-balanced classifiers, train ∪ validation hyperparameter selection by randomized search with 3-fold cross-validation, followed by one evaluation on the held-out test set; complete procedure repeated with three random seeds, reporting mean and standard deviation. GlycanGT large model pretrained with 35% masking provides [Graph] embeddings to SVM/LightGBM; the selected classifier for each S4 row is not identified. Section 2.6 states that all four graph baselines were trained and evaluated on the same datasets/splits; it does not establish that each baseline used the GlycanGT downstream classifier search. SVM search: 10 iterations, RBF/linear, C logU(1e-3,1e2), gamma logU(1e-4,1e-1); LightGBM: 15 randomized iterations. Do not combine with separate original GlycanML-paper protocols. Aggregation: Not reported GlycanGT published supplementary archive, Table S4; glycangt: Journal full-text XML · btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A86:E86 (mean D86, SD E86) |
| Configuration: Graphormer | Protocol: GlycanML class Macro-F1: GlycanGT study: class Macro-F1 Dataset subset: SugarBase taxonomy class; GlycanML official motif split (GlycanML split) | 0.275447 ± 0.017925 macro_f1 dimensionless · higher Uncertainty: type: standard_deviation; value: 0.017925 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceGraphormer on GlycanML class Macro-F1: GlycanGT study: class Macro-F1 Taxonomy: 13,209 glycans total across eight levels, 4–1,737 classes per level. Official fixed GlycanML motif-based train/validation/test splits (8:1:1). Section 2.5 reports class-balanced classifiers, train ∪ validation hyperparameter selection by randomized search with 3-fold cross-validation, followed by one evaluation on the held-out test set; complete procedure repeated with three random seeds, reporting mean and standard deviation. GlycanGT large model pretrained with 35% masking provides [Graph] embeddings to SVM/LightGBM; the selected classifier for each S4 row is not identified. Section 2.6 states that all four graph baselines were trained and evaluated on the same datasets/splits; it does not establish that each baseline used the GlycanGT downstream classifier search. SVM search: 10 iterations, RBF/linear, C logU(1e-3,1e2), gamma logU(1e-4,1e-1); LightGBM: 15 randomized iterations. Do not combine with separate original GlycanML-paper protocols. Aggregation: Not reported GlycanGT published supplementary archive, Table S4; glycangt: Journal full-text XML · btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A87:E87 (mean D87, SD E87) |
| Configuration: RGCN | Protocol: GlycanML class Accuracy: GlycanGT study: class Accuracy Dataset subset: SugarBase taxonomy class; GlycanML official motif split (GlycanML split) | 0.10518679724338 ± 0.0041196288326443 accuracy fraction · higher Uncertainty: type: standard_deviation; value: 0.0041196288326443 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceRGCN on GlycanML class Accuracy: GlycanGT study: class Accuracy Taxonomy: 13,209 glycans total across eight levels, 4–1,737 classes per level. Official fixed GlycanML motif-based train/validation/test splits (8:1:1). Section 2.5 reports class-balanced classifiers, train ∪ validation hyperparameter selection by randomized search with 3-fold cross-validation, followed by one evaluation on the held-out test set; complete procedure repeated with three random seeds, reporting mean and standard deviation. GlycanGT large model pretrained with 35% masking provides [Graph] embeddings to SVM/LightGBM; the selected classifier for each S4 row is not identified. Section 2.6 states that all four graph baselines were trained and evaluated on the same datasets/splits; it does not establish that each baseline used the GlycanGT downstream classifier search. SVM search: 10 iterations, RBF/linear, C logU(1e-3,1e2), gamma logU(1e-4,1e-1); LightGBM: 15 randomized iterations. Do not combine with separate original GlycanML-paper protocols. Aggregation: Not reported GlycanGT published supplementary archive, Table S4; glycangt: Journal full-text XML · btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A9:E9 (mean D9, SD E9) |
| Configuration: RGCN | Protocol: GlycanML class Macro-F1: GlycanGT study: class Macro-F1 Dataset subset: SugarBase taxonomy class; GlycanML official motif split (GlycanML split) | 0.0260332801336721 ± 0.0019212473071402001 macro_f1 dimensionless · higher Uncertainty: type: standard_deviation; value: 0.0019212473071402001 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceRGCN on GlycanML class Macro-F1: GlycanGT study: class Macro-F1 Taxonomy: 13,209 glycans total across eight levels, 4–1,737 classes per level. Official fixed GlycanML motif-based train/validation/test splits (8:1:1). Section 2.5 reports class-balanced classifiers, train ∪ validation hyperparameter selection by randomized search with 3-fold cross-validation, followed by one evaluation on the held-out test set; complete procedure repeated with three random seeds, reporting mean and standard deviation. GlycanGT large model pretrained with 35% masking provides [Graph] embeddings to SVM/LightGBM; the selected classifier for each S4 row is not identified. Section 2.6 states that all four graph baselines were trained and evaluated on the same datasets/splits; it does not establish that each baseline used the GlycanGT downstream classifier search. SVM search: 10 iterations, RBF/linear, C logU(1e-3,1e2), gamma logU(1e-4,1e-1); LightGBM: 15 randomized iterations. Do not combine with separate original GlycanML-paper protocols. Aggregation: Not reported GlycanGT published supplementary archive, Table S4; glycangt: Journal full-text XML · btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A10:E10 (mean D10, SD E10) |
| Configuration: SweetNet | Protocol: GlycanML class Accuracy: GlycanGT study: class Accuracy Dataset subset: SugarBase taxonomy class; GlycanML official motif split (GlycanML split) | 0.66376496191512502 ± 0.0116181482611874 accuracy fraction · higher Uncertainty: type: standard_deviation; value: 0.0116181482611874 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceSweetNet on GlycanML class Accuracy: GlycanGT study: class Accuracy Taxonomy: 13,209 glycans total across eight levels, 4–1,737 classes per level. Official fixed GlycanML motif-based train/validation/test splits (8:1:1). Section 2.5 reports class-balanced classifiers, train ∪ validation hyperparameter selection by randomized search with 3-fold cross-validation, followed by one evaluation on the held-out test set; complete procedure repeated with three random seeds, reporting mean and standard deviation. GlycanGT large model pretrained with 35% masking provides [Graph] embeddings to SVM/LightGBM; the selected classifier for each S4 row is not identified. Section 2.6 states that all four graph baselines were trained and evaluated on the same datasets/splits; it does not establish that each baseline used the GlycanGT downstream classifier search. SVM search: 10 iterations, RBF/linear, C logU(1e-3,1e2), gamma logU(1e-4,1e-1); LightGBM: 15 randomized iterations. Do not combine with separate original GlycanML-paper protocols. Aggregation: Not reported GlycanGT published supplementary archive, Table S4; glycangt: Journal full-text XML · btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A47:E47 (mean D47, SD E47) |
| Configuration: SweetNet | Protocol: GlycanML class Macro-F1: GlycanGT study: class Macro-F1 Dataset subset: SugarBase taxonomy class; GlycanML official motif split (GlycanML split) | 0.27351444034146899 ± 0.035852517550952402 macro_f1 dimensionless · higher Uncertainty: type: standard_deviation; value: 0.035852517550952402 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceSweetNet on GlycanML class Macro-F1: GlycanGT study: class Macro-F1 Taxonomy: 13,209 glycans total across eight levels, 4–1,737 classes per level. Official fixed GlycanML motif-based train/validation/test splits (8:1:1). Section 2.5 reports class-balanced classifiers, train ∪ validation hyperparameter selection by randomized search with 3-fold cross-validation, followed by one evaluation on the held-out test set; complete procedure repeated with three random seeds, reporting mean and standard deviation. GlycanGT large model pretrained with 35% masking provides [Graph] embeddings to SVM/LightGBM; the selected classifier for each S4 row is not identified. Section 2.6 states that all four graph baselines were trained and evaluated on the same datasets/splits; it does not establish that each baseline used the GlycanGT downstream classifier search. SVM search: 10 iterations, RBF/linear, C logU(1e-3,1e2), gamma logU(1e-4,1e-1); LightGBM: 15 randomized iterations. Do not combine with separate original GlycanML-paper protocols. Aggregation: Not reported GlycanGT published supplementary archive, Table S4; glycangt: Journal full-text XML · btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A57:E57 (mean D57, SD E57) |
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4 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| description Dataset subset reported in GlycanGT published supplementary archive, Table S4. Exact split manifest remains unextracted; source-table identity is retained. Context-only references | glycangt: Journal full-text XML No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Primary article XML snapshot | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| description Dataset subset reported in GlycanGT published supplementary archive, Table S4. Exact split manifest remains unextracted; source-table identity is retained. Context-only references | GlycanGT published supplementary archive, Table S4 No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Published Bioinformatics btag147 supplementary archive, retrieved 2026-09-23; Table_S4.xlsx SHA-256 d7c35909bac6bcb78ca8fdb32c0463f05e692f15861a8184e65e415e7216f493 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| name SugarBase taxonomy class; GlycanML official motif split (GlycanML split) Context-only references | glycangt: Journal full-text XML No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Primary article XML snapshot | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| name SugarBase taxonomy class; GlycanML official motif split (GlycanML split) Context-only references | GlycanGT published supplementary archive, Table S4 No field-specific location recorded Shared locator for this statement’s cited sources; not a separate locator for each citation. Version: Published Bioinformatics btag147 supplementary archive, retrieved 2026-09-23; Table_S4.xlsx SHA-256 d7c35909bac6bcb78ca8fdb32c0463f05e692f15861a8184e65e415e7216f493 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
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Release 2026-09-23-2b89723c6dd9 · Record review: source checked
2 source records and release history
- GlycanGT published supplementary archive, Table S4 · Original source · Published Bioinformatics btag147 supplementary archive, retrieved 2026-09-23; Table_S4.xlsx SHA-256 d7c35909bac6bcb78ca8fdb32c0463f05e692f15861a8184e65e415e7216f493
- glycangt: Journal full-text XML · Original source · Primary article XML snapshot
Technical metadata and extraction receipts
Stable ID: glycangt-2026-table-s4-dataset-sugarbase-taxonomy-class-glycanml-official-motif-split
- areas
- glycans
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- version: unreported; url: unextracted
Related records
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