GlycanGT on GlycanML immunogenicity AUPRC: GlycanGT study: immunogenicity AUPRC
GlycanML evaluation of GlycanGT on GlycanGT study: immunogenicity AUPRC, scored with AUPRC.
Evaluation results
1 evaluation · 1 metric rows. Different protocols are not a single leaderboard.
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| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Pipeline: GlycanGT | Protocol: GlycanML immunogenicity AUPRC: GlycanGT study: immunogenicity AUPRC Dataset subset: SugarBase immunogenicity; GlycanML official motif split (GlycanML split) | 0.84419033765294005 ± 0.0036259797661145998 auprc dimensionless · higher Uncertainty: type: standard_deviation; value: 0.0036259797661145998 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · source checkedMethods, coverage and sourceGlycanGT on GlycanML immunogenicity AUPRC: GlycanGT study: immunogenicity AUPRC Immunogenicity: 1,320 glycans total; binary immune activity. 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!A83:E83 (mean D83, SD E83) |
Source checking is not independent reproduction. Release 2026-09-23-2b89723c6dd9.
Evaluation procedure
Immunogenicity: 1,320 glycans total; binary immune activity. 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.
- Pipeline
- GlycanGT
- Protocol
- GlycanML immunogenicity AUPRC: GlycanGT study: immunogenicity AUPRC
- Dataset subset
- SugarBase immunogenicity; GlycanML official motif split (GlycanML split)
- origin
- Author-reported evaluation
- configuration
- Not reported
- protocol id
- glycangt-2026-table-s4-task-immunogenicity-auprc
- metric implementation
- AUPRC
Metadata review: source checked. Unreported conditions prevent automatic comparisons.
Reproduction
- Split
- Not reported
- Adaptation
- Not reported
- Scoring implementation
- AUPRC
No execution recipe has been verified for this exact configuration and evaluation. A benchmark's general instructions may use different inputs, splits or model settings.
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
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Evidence table
Inspect claims, sources and review details
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.
34 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| attributes.adaptation Pretrained large/35%-masked encoder embeddings with supervised SVM/LightGBM downstream classification; per-task classifier choice unreported. Context-only references | glycangt: Journal full-text XML btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A83:E83 (mean D83, SD E83) 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 Pretrained large/35%-masked encoder embeddings with supervised SVM/LightGBM downstream classification; per-task classifier choice unreported. Context-only references | GlycanGT published supplementary archive, Table S4 btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A83:E83 (mean D83, SD E83) 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 AUPRC Context-only references | glycangt: Journal full-text XML btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A83:E83 (mean D83, SD E83) 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 AUPRC Context-only references | GlycanGT published supplementary archive, Table S4 btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A83:E83 (mean D83, SD E83) 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-immunogenicity-auprc Context-only references | glycangt: Journal full-text XML btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A83:E83 (mean D83, SD E83) 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-immunogenicity-auprc Context-only references | GlycanGT published supplementary archive, Table S4 btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A83:E83 (mean D83, SD E83) 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!A83:E83 (mean D83, SD E83) 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!A83:E83 (mean D83, SD E83) 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!A83:E83 (mean D83, SD E83) 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!A83:E83 (mean D83, SD E83) 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-glycangt-immunogenicity-auprc
- areas
- glycans
- tasks
- GlycanGT study: immunogenicity AUPRC
- origin
- author_reported
- protocol
- Immunogenicity: 1,320 glycans total; binary immune activity. 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-immunogenicity-auprc; metric implementation: AUPRC
- missing metadata
- checkpoint revision: unreported; seeds: unreported; budget: unreported; split manifest: unextracted
- source locator
- btag147_supplementary_data.zip / Table_S4.xlsx / Sheet1!A83:E83 (mean D83, SD E83)
- replicate count
- 3
- replicate type
- random seed
- primary protocol source id
- evidence-official-87c70bddba97a72a5e5d
- adaptation
- Pretrained large/35%-masked encoder embeddings with supervised SVM/LightGBM downstream classification; per-task classifier choice unreported.
- 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