Dataset subset reported in GlycanGT published supplementary archive, Table S4. Exact split manifest remains unextracted; source-table identity is retained.
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10 evaluations · 10 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: GlycanAA | Protocol: GlycanML phylum Accuracy: GlycanGT study: phylum Accuracy Dataset subset: SugarBase taxonomy phylum; GlycanML official motif split (GlycanML split) | 0.86686666666666601 ± 0.0142043420591498 accuracy fraction · higher Uncertainty: type: standard_deviation; value: 0.0142043420591498 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGlycanAA on GlycanML phylum Accuracy: GlycanGT study: phylum 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!A40:E40 (mean D40, SD E40) |
| Configuration: GlycanAA | Protocol: GlycanML phylum Macro-F1: GlycanGT study: phylum Macro-F1 Dataset subset: SugarBase taxonomy phylum; GlycanML official motif split (GlycanML split) | 0.440066666666666 ± 0.0041428653530296202 macro_f1 dimensionless · higher Uncertainty: type: standard_deviation; value: 0.0041428653530296202 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGlycanAA on GlycanML phylum Macro-F1: GlycanGT study: phylum 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!A41:E41 (mean D41, SD E41) |
| Pipeline: GlycanGT | Protocol: GlycanML phylum Accuracy: GlycanGT study: phylum Accuracy Dataset subset: SugarBase taxonomy phylum; GlycanML official motif split (GlycanML split) | 0.84149437794704296 ± 0.003324320417088 accuracy fraction · higher Uncertainty: type: standard_deviation; value: 0.003324320417088 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGlycanGT on GlycanML phylum Accuracy: GlycanGT study: phylum 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!A69:E69 (mean D69, SD E69) |
| Pipeline: GlycanGT | Protocol: GlycanML phylum Macro-F1: GlycanGT study: phylum Macro-F1 Dataset subset: SugarBase taxonomy phylum; GlycanML official motif split (GlycanML split) | 0.49333063993822701 ± 0.080739293560509295 macro_f1 dimensionless · higher Uncertainty: type: standard_deviation; value: 0.080739293560509295 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGlycanGT on GlycanML phylum Macro-F1: GlycanGT study: phylum 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!A70:E70 (mean D70, SD E70) |
| Configuration: Graphormer | Protocol: GlycanML phylum Accuracy: GlycanGT study: phylum Accuracy Dataset subset: SugarBase taxonomy phylum; GlycanML official motif split (GlycanML split) | 0.81936900000000001 ± 0.025911 accuracy fraction · higher Uncertainty: type: standard_deviation; value: 0.025911 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGraphormer on GlycanML phylum Accuracy: GlycanGT study: phylum 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!A102:E102 (mean D102, SD E102) |
| Configuration: Graphormer | Protocol: GlycanML phylum Macro-F1: GlycanGT study: phylum Macro-F1 Dataset subset: SugarBase taxonomy phylum; GlycanML official motif split (GlycanML split) | 0.38569900000000001 ± 0.015233 macro_f1 dimensionless · higher Uncertainty: type: standard_deviation; value: 0.015233 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGraphormer on GlycanML phylum Macro-F1: GlycanGT study: phylum 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!A103:E103 (mean D103, SD E103) |
| Configuration: RGCN | Protocol: GlycanML phylum Accuracy: GlycanGT study: phylum Accuracy Dataset subset: SugarBase taxonomy phylum; GlycanML official motif split (GlycanML split) | 0.51323902792890796 ± 0.001662160208544 accuracy fraction · higher Uncertainty: type: standard_deviation; value: 0.001662160208544 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRGCN on GlycanML phylum Accuracy: GlycanGT study: phylum 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!A7:E7 (mean D7, SD E7) |
| Configuration: RGCN | Protocol: GlycanML phylum Macro-F1: GlycanGT study: phylum Macro-F1 Dataset subset: SugarBase taxonomy phylum; GlycanML official motif split (GlycanML split) | 0.090538684791431095 ± 0.0011545811568653001 macro_f1 dimensionless · higher Uncertainty: type: standard_deviation; value: 0.0011545811568653001 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRGCN on GlycanML phylum Macro-F1: GlycanGT study: phylum 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!A8:E8 (mean D8, SD E8) |
| Configuration: SweetNet | Protocol: GlycanML phylum Accuracy: GlycanGT study: phylum Accuracy Dataset subset: SugarBase taxonomy phylum; GlycanML official motif split (GlycanML split) | 0.82988755894087696 ± 0.019793636053162401 accuracy fraction · higher Uncertainty: type: standard_deviation; value: 0.019793636053162401 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSweetNet on GlycanML phylum Accuracy: GlycanGT study: phylum 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!A46:E46 (mean D46, SD E46) |
| Configuration: SweetNet | Protocol: GlycanML phylum Macro-F1: GlycanGT study: phylum Macro-F1 Dataset subset: SugarBase taxonomy phylum; GlycanML official motif split (GlycanML split) | 0.37055186011768798 ± 0.065574251495964103 macro_f1 dimensionless · higher Uncertainty: type: standard_deviation; value: 0.065574251495964103 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSweetNet on GlycanML phylum Macro-F1: GlycanGT study: phylum 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!A56:E56 (mean D56, SD E56) |
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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 phylum; 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 phylum; 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 2026-09-29-06401fd5b220 · Record review: source checked
Stable ID: glycangt-2026-table-s4-dataset-sugarbase-taxonomy-phylum-glycanml-official-motif-split