Strengths and considerations
No source-reviewed explanatory claims are recorded here yet.
Protocol
GlyConnect glycosylation · Glycos (GlycanML glycosylation type prediction)
GlycanML Glycos · Table 3, p. 8. Author-reported single-task models on the same held-out task; not a cross-paper ranking. Taxonomy, immunogenicity and glycosylation: motif-frequency K-means cluster allocation 8:1:1. Interaction: MMseqs2 protein clusters at minimum identity 0.5 allocated 8:1:1. Exact counts are attached to each column.
Sources
GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, p. 8, GlycosOverview
Key specifications have not been extracted for this record. See the linked evaluation and sources for the reported setup.
limited source coverage · Automated source review, 2026-09-17. All specifications and missing details
Results
Each comparison retains its reviewed evaluation scope, dataset and metric. Results are shown without a pooled ranking.
GlycanML Glycos · Table 3, p. 8
accuracy (percent) · Higher values are better.
GlyConnect glycosylation · Glycos (GlycanML glycosylation type prediction) · GlyConnect glycosylation · Glycos
Evidence origin: Author-reported evaluation.
GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, p. 8, Glycos- Taxonomic levels are distinct tasks; do not combine raw accuracy across levels.
- Protein–glycan scores evaluate combined glycan encoders plus ESM-1b/MLP, not an ESM-1b standalone checkpoint.
- Cluster manifests and trained checkpoint hashes are not enumerated in the paper table.
Comparison details and limitations
Author-reported single-task models on the same held-out task; not a cross-paper ranking. Taxonomy, immunogenicity and glycosylation: motif-frequency K-means cluster allocation 8:1:1. Interaction: MMseqs2 protein clusters at minimum identity 0.5 allocated 8:1:1. Exact counts are attached to each column.
Automated source review: 2026-09-17. Numerical source review does not establish independent reproduction.
Dots show point estimates. Whiskers show only explicitly defined uncertainty (standard deviation, standard error or a labelled interval); their definitions remain in Table. Unresolved uncertainty is not plotted. Differences do not establish statistical significance.
Showing 10 of 10 matching rows.
Tested configuration
0255075100
Reported scoreMethods and evaluation design
Procedure, tasks and evaluated configurations
How it works
Evaluation in this paper
Author-reported single-task models on the same held-out task; not a cross-paper ranking. Taxonomy, immunogenicity and glycosylation: motif-frequency K-means cluster allocation 8:1:1. Interaction: MMseqs2 protein clusters at minimum identity 0.5 allocated 8:1:1. Exact counts are attached to each column.
Sources
GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, p. 8, GlycosEvaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
Tasks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- GIN: GlyConnect glycosylation · Glycos
- LSTM: GlyConnect glycosylation · Glycos
- GCN: GlyConnect glycosylation · Glycos
- MPNN: GlyConnect glycosylation · Glycos
- RGCN: GlyConnect glycosylation · Glycos
- Shallow CNN: GlyConnect glycosylation · Glycos
- CompGCN: GlyConnect glycosylation · Glycos
- Transformer: GlyConnect glycosylation · Glycos
- GAT: GlyConnect glycosylation · Glycos
- ResNet: GlyConnect glycosylation · Glycos
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
No reviewed evaluations with results linked in this release.
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Select a task-valid null control after reviewing inputs and metric
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Select an upstream conventional reference after reviewing the full protocol
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV · Model evaluation matrix · Source table · Release and checksums
Coverage is derived from release 2026-09-29-06401fd5b220. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Strengths and limitations
Limitations and conditions
No source-reviewed explanatory claims are recorded here yet.
Profile review details
Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.
Stable record: paper-protocol-1e0e586e8edab0dc26Specifications
Inputs, training, access and other details
Explanatory profile: limited source coverage · Automated source review, 2026-09-17. Review applies to the cited claims; unresolved fields are listed below. Numerical results retain their own review status.
| Property | Description and evidence |
|---|---|
| Datasets | Not extracted or verified for this record. |
| Organisms | Not extracted or verified for this record. |
| Assays | Not extracted or verified for this record. |
| Splits | Not extracted or verified for this record. |
| Allowed inputs | Not extracted or verified for this record. |
| Adaptation | Not extracted or verified for this record. |
| Metrics | Not extracted or verified for this record. |
| Baselines | Not extracted or verified for this record. |
Evidence
Source checking verifies the cited claim or transcription. It does not establish independent reproduction.
Papers and result coverage
Last literature check: 2026-09-17. Primary-paper within-study comparison; numerical results not independently reproduced.
| Paper or primary resource | Version | Reference |
|---|---|---|
| GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning | arXiv:2405.16206v1, 2024-05-25 | Read source |
Historical gaps recorded on 2026-09-17
The catalogue now holds 10 result rows for this benchmark. A note below about pending extraction describes the state on 2026-09-17 and may since have been answered by a later batch. The result rows and their sources are the current record.
- Paper table does not enumerate trained checkpoint hashes; source configuration names retained.
Search and extraction details
complete comparison extracted
Searches
- GlycanML benchmark 2405.16206
Evidence locations
- Table 3, p. 8, Glycos
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.
4 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Evaluation in this paper Author-reported single-task models on the same held-out task; not a cross-paper ranking. Taxonomy, immunogenicity and glycosylation: motif-frequency K-means cluster allocation 8:1:1. Interaction: MMseqs2 protein clusters at minimum identity 0.5 allocated 8:1:1. Exact counts are attached to each column. Individual claims | GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning Table 3, p. 8, Glycos Version: arXiv:2405.16206v1, 2024-05-25 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Introduction GlycanML Glycos · Table 3, p. 8. Author-reported single-task models on the same held-out task; not a cross-paper ranking. Taxonomy, immunogenicity and glycosylation: motif-frequency K-means cluster allocation 8:1:1. Interaction: MMseqs2 protein clusters at minimum identity 0.5 allocated 8:1:1. Exact counts are attached to each column. Individual claims | GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning Table 3, p. 8, Glycos Version: arXiv:2405.16206v1, 2024-05-25 | source checked automated source review · 2026-09-17 Audit detailsPrimary-source transcription and separate automated review. No human sign-off or experimental reproduction. Field: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: evaluates task discovery-benchmark-glycanml-glycosylation-type-prediction Individual claims | GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning Table 3, p. 8, Glycos Version: arXiv:2405.16206v1, 2024-05-25 | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-0b9d3bbf2ac04ab720 Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| Relationship: part of discovery-benchmark-glycanml Individual claims | GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning Table 3, p. 8, Glycos Version: arXiv:2405.16206v1, 2024-05-25 | source checked automated source review · 2026-09-17 Audit detailsField: Claim: paper-claim-accb34acc7592660b4 Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
View linked audit checks and correction history
Release 2026-09-29-06401fd5b220 · Record review: needs review
1 source records and release history
- GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Original source · arXiv:2405.16206v1, 2024-05-25
Technical metadata and extraction receipts
Stable ID: paper-protocol-1e0e586e8edab0dc26
- areas
- glycomics
- entity level
- protocol
- protocol
- Author-reported single-task models on the same held-out task; not a cross-paper ranking. Taxonomy, immunogenicity and glycosylation: motif-frequency K-means cluster allocation 8:1:1. Interaction: MMseqs2 protein clusters at minimum identity 0.5 allocated 8:1:1. Exact counts are attached to each column.
- comparison panels
- id: glycanml-v1-single-glycos; title: GlycanML Glycos · Table 3, p. 8; protocol id: paper-protocol-1e0e586e8edab0dc26; dataset id: paper-dataset-e797e17c76c1278706; metric: accuracy; unit: percent; direction: higher; result ids: paper-result-ee2fc7d3f24c74d26a; paper-result-cd7d5e177d170e4ce3; paper-result-c7fcf3af8b768565b7; paper-result-e2f3edb52244aed4ea; paper-result-edb19c124f6d9e2398; paper-result-ebfebb353d4b0a9e5a; paper-result-04b741864eefb0125e; paper-result-00ca74108e1dd8a295; paper-result-7ef41afc692b853ffd; paper-result-c4ba6aef76ee19b8d5; source ids: expansion-p3-glycanml-2405-16206v1; source locator: Table 3, p. 8, Glycos; context: Author-reported single-task models on the same held-out task; not a cross-paper ranking. Taxonomy, immunogenicity and glycosylation: motif-frequency K-means cluster allocation 8:1:1. Interaction: MMseqs2 protein clusters at minimum identity 0.5 allocated 8:1:1. Exact counts are attached to each column.; caveats: Taxonomic levels are distinct tasks; do not combine raw accuracy across levels.; Protein–glycan scores evaluate combined glycan encoders plus ESM-1b/MLP, not an ESM-1b standalone checkpoint.; Cluster manifests and trained checkpoint hashes are not enumerated in the paper table.; review: method: automated_source_review; date: 2026-09-17
- benchmark research
- review date: 2026-09-17; status: complete_comparison_extracted; primary sources: expansion-p3-glycanml-2405-16206v1; inspected locators: Table 3, p. 8, Glycos; searched queries: GlycanML benchmark 2405.16206; gaps: Paper table does not enumerate trained checkpoint hashes; source configuration names retained.; claim scope: Primary-paper within-study comparison; numerical results not independently reproduced.
- legacy kinds
- benchmark
- entity classification
- review date: 2026-09-17; rationale: The source-backed record identifies a specified evaluated procedure and its dataset/split/scoring context. Classify it as a protocol while preserving version and comparison restrictions.; source ids: expansion-p3-glycanml-2405-16206v1; source locator: Table 3, p. 8, Glycos; ambiguities: None recorded
Related records
- evaluates task: GlycanML glycosylation type prediction
- part of: GlycanML
- subject: GlyConnect glycosylation · Glycos (GlycanML glycosylation type prediction): links:evaluates_task:discovery-benchmark-glycanml-glycosylation-type-prediction
- subject: GlyConnect glycosylation · Glycos (GlycanML glycosylation type prediction): links:part_of:discovery-benchmark-glycanml
- benchmark: GIN: GlyConnect glycosylation · Glycos
- benchmark: LSTM: GlyConnect glycosylation · Glycos
- benchmark: GCN: GlyConnect glycosylation · Glycos
- benchmark: MPNN: GlyConnect glycosylation · Glycos
- benchmark: RGCN: GlyConnect glycosylation · Glycos
- benchmark: Shallow CNN: GlyConnect glycosylation · Glycos
- benchmark: CompGCN: GlyConnect glycosylation · Glycos
- benchmark: Transformer: GlyConnect glycosylation · Glycos
- benchmark: GAT: GlyConnect glycosylation · Glycos
- benchmark: ResNet: GlyConnect glycosylation · Glycos