Graphormer on GlycanML class Accuracy: GlycanGT study: class Accuracy
GlycanML evaluation of Graphormer on GlycanGT study: class Accuracy, scored with Accuracy.
Evaluation results
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| 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) |
Source checking is not independent reproduction. Release 2026-09-23-2b89723c6dd9.
Evaluation procedure
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.
- Configuration
- Graphormer
- Protocol
- GlycanML class Accuracy: GlycanGT study: class Accuracy
- Dataset subset
- SugarBase taxonomy class; GlycanML official motif split (GlycanML split)
- origin
- Author-reported evaluation
- configuration
- Not reported
- protocol id
- glycangt-2026-table-s4-task-class-accuracy
- metric implementation
- Accuracy
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
Reproduction
- Split
- Not reported
- Adaptation
- Not reported
- Scoring implementation
- Accuracy
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Reproducing this published result requires matching its model configuration, data, split and scorer. Source checking or a successful smoke test does not establish score reproduction.
Evidence
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Evidence table
Inspect claims, sources and review details
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One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.
34 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.adaptation Task-specific supervised prediction as described in primary paper Sections 2.5–2.6; three random seeds; not a frozen zero-shot evaluation. Context-only references | glycangt: Journal full-text XML btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A86:E86 (mean D86, SD E86) 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 author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.adaptation Task-specific supervised prediction as described in primary paper Sections 2.5–2.6; three random seeds; not a frozen zero-shot evaluation. Context-only references | GlycanGT published supplementary archive, Table S4 btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A86:E86 (mean D86, SD E86) 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 author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.metric_implementation Accuracy Context-only references | glycangt: Journal full-text XML btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A86:E86 (mean D86, SD E86) 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 author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.comparison.metric_implementation Accuracy Context-only references | GlycanGT published supplementary archive, Table S4 btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A86:E86 (mean D86, SD E86) 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 author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.comparison.protocol_id glycangt-2026-table-s4-task-class-accuracy Context-only references | glycangt: Journal full-text XML btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A86:E86 (mean D86, SD E86) 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 author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.comparison.protocol_id glycangt-2026-table-s4-task-class-accuracy Context-only references | GlycanGT published supplementary archive, Table S4 btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A86:E86 (mean D86, SD E86) 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 author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.evidence_overlap Same-study reported cells, not independent new experimental evidence. Keep distinct from original GlycanML tables and reused descriptions. Context-only references | glycangt: Journal full-text XML btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A86:E86 (mean D86, SD E86) 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 author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.evidence_overlap Same-study reported cells, not independent new experimental evidence. Keep distinct from original GlycanML tables and reused descriptions. Context-only references | GlycanGT published supplementary archive, Table S4 btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A86:E86 (mean D86, SD E86) 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 author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
| attributes.origin author_reported Context-only references | glycangt: Journal full-text XML btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A86:E86 (mean D86, SD E86) 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 author reported Audit detailsField: Source artifact SHA-256: Hash scope: SHA-256 of retrieved original artifact bytes Format: original_artifact |
| attributes.origin author_reported Context-only references | GlycanGT published supplementary archive, Table S4 btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A86:E86 (mean D86, SD E86) 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 author reported Audit detailsField: Source artifact SHA-256: Hash scope: Hash scope not separately documented; inspect source record |
Sources and history
View linked audit checks and correction history
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-evaluation-graphormer-class-accuracy
- areas
- glycans
- tasks
- GlycanGT study: class Accuracy
- origin
- author_reported
- protocol
- 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.
- comparison
- protocol id: glycangt-2026-table-s4-task-class-accuracy; metric implementation: Accuracy
- missing metadata
- checkpoint revision: unreported; seeds: unreported; budget: unreported; split manifest: unextracted
- source locator
- btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A86:E86 (mean D86, SD E86)
- replicate count
- 3
- replicate type
- random seed
- primary protocol source id
- evidence-official-87c70bddba97a72a5e5d
- adaptation
- Task-specific supervised prediction as described in primary paper Sections 2.5–2.6; three random seeds; not a frozen zero-shot evaluation.
- evidence overlap
- Same-study reported cells, not independent new experimental evidence. Keep distinct from original GlycanML tables and reused descriptions.
- published score reproduction
- false
- suite complete
- false