Dataset subset reported in GlycanGT published supplementary archive, Table S4. Exact split manifest remains unextracted; source-table identity is retained.
These checks assess whether the evidence supports a reproducible investigation. A source-checked score alone does not meet these requirements.
Release 2026-09-29-06401fd5b220 · Evidence verified: Not verified
Exact outcomes, predictions, identifiers and evaluator are connected.
Missing or unresolved evidence
Verified: Not verified
Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.
Missing or unresolved evidence
Verified: Not verified
A pinned recipe describes the inputs, environment and resource requirements.
Missing or unresolved evidence
Verified: Not verified
Separate data and exposure records support an independent test.
Missing or unresolved evidence
Verified: Not verified
Readiness describes the evidence in this release. Availability on your computer is checked separately when an investigation runs. Existing data exposure can prevent independent validation even when files are available.
No verified artifact manifest is connected to this record yet. The gaps above identify what is needed before analysis can begin.
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 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) |
Source checking is not independent reproduction. Release 2026-09-29-06401fd5b220.
This record describes a particular subset or cohort used in an evaluation. Its results do not describe the full dataset.
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.
One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
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 |
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: source checked
Stable ID: glycangt-2026-table-s4-dataset-sugarbase-taxonomy-class-glycanml-official-motif-split