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Protocol

LectinOracle interaction · Interaction (GlycanML protein-glycan interaction prediction)

GlycanML Interaction · 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.

SourcesGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, p. 8, Interaction

10 evaluations · 10 metric rows

At a glance

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.

Data, procedure and scoring
PropertyDescription and evidence
DatasetsNot extracted or verified for this record.
OrganismsNot extracted or verified for this record.
AssaysNot extracted or verified for this record.
SplitsNot extracted or verified for this record.
Allowed inputsNot extracted or verified for this record.
AdaptationNot extracted or verified for this record.
MetricsNot extracted or verified for this record.
BaselinesNot extracted or verified for this record.

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.

SourcesGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, p. 8, Interaction

Evaluation design

Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.

These source-backed links do not make different protocols or scores interchangeable.

Recorded evaluations

Each evaluation records what was tested and under which conditions.

Published comparisons

Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies.

GlycanML Interaction · Table 3, p. 8

Spearman rho (dimensionless) · Higher values are better for this metric.

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.

Evaluation protocol · LectinOracle interaction · Interaction

  1. Shallow CNN · Configuration · Author-reported evaluation0.261(0.008)
  2. ResNet · Configuration · Author-reported evaluation0.273(0.004)
  3. LSTM · Configuration · Author-reported evaluation0.280(0.001)
  4. Transformer · Configuration · Author-reported evaluation0.244(0.009)
  5. GCN · Configuration · Author-reported evaluation0.233(0.009)
  6. GAT · Configuration · Author-reported evaluation0.229(0.002)
  7. GIN · Configuration · Author-reported evaluation0.249(0.004)
  8. MPNN · Configuration · Author-reported evaluation0.217(0.002)
  9. RGCN · Configuration · Author-reported evaluation0.262(0.005)
  10. CompGCN · Configuration · Author-reported evaluation0.257(0.004)

Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.

GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, p. 8, Interaction
Values, uncertainty and evidence
Spearman rho: original source values
Tested entityPrinted valueUncertaintyEvidence
Shallow CNN · Configuration0.261(0.008) dimensionlesstype: standard_deviation; value: 0.008; n: 3; unit: same_as_metricAuthor-reported evaluation · source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row Shallow CNN, column Interaction
ResNet · Configuration0.273(0.004) dimensionlesstype: standard_deviation; value: 0.004; n: 3; unit: same_as_metricAuthor-reported evaluation · source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row ResNet, column Interaction
LSTM · Configuration0.280(0.001) dimensionlesstype: standard_deviation; value: 0.001; n: 3; unit: same_as_metricAuthor-reported evaluation · source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row LSTM, column Interaction
Transformer · Configuration0.244(0.009) dimensionlesstype: standard_deviation; value: 0.009; n: 3; unit: same_as_metricAuthor-reported evaluation · source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row Transformer, column Interaction
GCN · Configuration0.233(0.009) dimensionlesstype: standard_deviation; value: 0.009; n: 3; unit: same_as_metricAuthor-reported evaluation · source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row GCN, column Interaction
GAT · Configuration0.229(0.002) dimensionlesstype: standard_deviation; value: 0.002; n: 3; unit: same_as_metricAuthor-reported evaluation · source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row GAT, column Interaction
GIN · Configuration0.249(0.004) dimensionlesstype: standard_deviation; value: 0.004; n: 3; unit: same_as_metricAuthor-reported evaluation · source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row GIN, column Interaction
MPNN · Configuration0.217(0.002) dimensionlesstype: standard_deviation; value: 0.002; n: 3; unit: same_as_metricAuthor-reported evaluation · source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Interaction
RGCN · Configuration0.262(0.005) dimensionlesstype: standard_deviation; value: 0.005; n: 3; unit: same_as_metricAuthor-reported evaluation · source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row RGCN, column Interaction
CompGCN · Configuration0.257(0.004) dimensionlesstype: standard_deviation; value: 0.004; n: 3; unit: same_as_metricAuthor-reported evaluation · source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row CompGCN, column Interaction
Scope and limitations
  • 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.

Source transcription and grouping reviewed by automated source review on 2026-09-17. These experiments were not independently reproduced by rewire.

Tested entities and results

Release 2026-09-17-d277315f7d76 · 10 evaluations · 10 metric rows. Different protocols are not a single leaderboard.

Results grouped by the exact reported evaluation
Metric and findingCoverage and uncertaintyEvidence
Shallow CNN: LectinOracle interaction · Interaction

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.

Author-reported evaluation · Evaluation metadata: needs review

0.261(0.008) Spearman rho

Unit: dimensionless · Direction: higher

Uncertainty: type: standard deviation; value: 0.008; n: 3; unit: same as metric

Scored: Not reported · Eligible: Not reported

source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row Shallow CNN, column Interaction

Source checking is not independent reproduction.

GAT: LectinOracle interaction · Interaction

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.

Author-reported evaluation · Evaluation metadata: needs review

0.229(0.002) Spearman rho

Unit: dimensionless · Direction: higher

Uncertainty: type: standard deviation; value: 0.002; n: 3; unit: same as metric

Scored: Not reported · Eligible: Not reported

source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row GAT, column Interaction

Source checking is not independent reproduction.

GIN: LectinOracle interaction · Interaction

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.

Author-reported evaluation · Evaluation metadata: needs review

0.249(0.004) Spearman rho

Unit: dimensionless · Direction: higher

Uncertainty: type: standard deviation; value: 0.004; n: 3; unit: same as metric

Scored: Not reported · Eligible: Not reported

source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row GIN, column Interaction

Source checking is not independent reproduction.

LSTM: LectinOracle interaction · Interaction

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.

Author-reported evaluation · Evaluation metadata: needs review

0.280(0.001) Spearman rho

Unit: dimensionless · Direction: higher

Uncertainty: type: standard deviation; value: 0.001; n: 3; unit: same as metric

Scored: Not reported · Eligible: Not reported

source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row LSTM, column Interaction

Source checking is not independent reproduction.

CompGCN: LectinOracle interaction · Interaction

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.

Author-reported evaluation · Evaluation metadata: needs review

0.257(0.004) Spearman rho

Unit: dimensionless · Direction: higher

Uncertainty: type: standard deviation; value: 0.004; n: 3; unit: same as metric

Scored: Not reported · Eligible: Not reported

source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row CompGCN, column Interaction

Source checking is not independent reproduction.

ResNet: LectinOracle interaction · Interaction

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.

Author-reported evaluation · Evaluation metadata: needs review

0.273(0.004) Spearman rho

Unit: dimensionless · Direction: higher

Uncertainty: type: standard deviation; value: 0.004; n: 3; unit: same as metric

Scored: Not reported · Eligible: Not reported

source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row ResNet, column Interaction

Source checking is not independent reproduction.

Transformer: LectinOracle interaction · Interaction

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.

Author-reported evaluation · Evaluation metadata: needs review

0.244(0.009) Spearman rho

Unit: dimensionless · Direction: higher

Uncertainty: type: standard deviation; value: 0.009; n: 3; unit: same as metric

Scored: Not reported · Eligible: Not reported

source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row Transformer, column Interaction

Source checking is not independent reproduction.

GCN: LectinOracle interaction · Interaction

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.

Author-reported evaluation · Evaluation metadata: needs review

0.233(0.009) Spearman rho

Unit: dimensionless · Direction: higher

Uncertainty: type: standard deviation; value: 0.009; n: 3; unit: same as metric

Scored: Not reported · Eligible: Not reported

source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row GCN, column Interaction

Source checking is not independent reproduction.

MPNN: LectinOracle interaction · Interaction

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.

Author-reported evaluation · Evaluation metadata: needs review

0.217(0.002) Spearman rho

Unit: dimensionless · Direction: higher

Uncertainty: type: standard deviation; value: 0.002; n: 3; unit: same as metric

Scored: Not reported · Eligible: Not reported

source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row MPNN, column Interaction

Source checking is not independent reproduction.

RGCN: LectinOracle interaction · Interaction

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.

Author-reported evaluation · Evaluation metadata: needs review

0.262(0.005) Spearman rho

Unit: dimensionless · Direction: higher

Uncertainty: type: standard deviation; value: 0.005; n: 3; unit: same as metric

Scored: Not reported · Eligible: Not reported

source checkedGlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning · Table 3, row RGCN, column Interaction

Source checking is not 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 resourceVersionReference
GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine LearningarXiv:2405.16206v1, 2024-05-25Read source

What is still missing

  • 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, Interaction

Strengths and limitations

Strengths and considerations

No source-reviewed explanatory claims are recorded here yet.

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-e914e4149f3b3c8185

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

Claims, original sources and review scope · Release 2026-09-17-d277315f7d76
Property and statementOriginal source and locationReview 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

Original source ↗

Table 3, p. 8, Interaction

Version: arXiv:2405.16206v1, 2024-05-25
Retrieved: 2026-09-16T21:04:56.017006+00:00

source checked

automated source review · 2026-09-17

Audit details

Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.

Field: attributes.profile.sections.0.body

Source artifact SHA-256: 9ba3db678b4550898a612b42e8832bf9dee40935090fc4d969ba8f6ac5106979

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Introduction

GlycanML Interaction · 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

Original source ↗

Table 3, p. 8, Interaction

Version: arXiv:2405.16206v1, 2024-05-25
Retrieved: 2026-09-16T21:04:56.017006+00:00

source checked

automated source review · 2026-09-17

Audit details

Primary-source transcription and separate automated review. No human sign-off or experimental reproduction.

Field: attributes.profile.summary

Source artifact SHA-256: 9ba3db678b4550898a612b42e8832bf9dee40935090fc4d969ba8f6ac5106979

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Relationship: evaluates task

discovery-benchmark-glycanml-protein-glycan-interaction-prediction

Individual claims
GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning

Original source ↗

Table 3, p. 8, Interaction

Version: arXiv:2405.16206v1, 2024-05-25
Retrieved: 2026-09-16T21:04:56.017006+00:00

source checked

automated source review · 2026-09-17

Audit details

Field: links:evaluates_task:discovery-benchmark-glycanml-protein-glycan-interaction-prediction

Claim: paper-claim-3cb2e3444588089bc1

Source artifact SHA-256: 9ba3db678b4550898a612b42e8832bf9dee40935090fc4d969ba8f6ac5106979

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Relationship: part of

discovery-benchmark-glycanml

Individual claims
GlycanML: A Multi-Task and Multi-Structure Benchmark for Glycan Machine Learning

Original source ↗

Table 3, p. 8, Interaction

Version: arXiv:2405.16206v1, 2024-05-25
Retrieved: 2026-09-16T21:04:56.017006+00:00

source checked

automated source review · 2026-09-17

Audit details

Field: links:part_of:discovery-benchmark-glycanml

Claim: paper-claim-638042e029c2400c15

Source artifact SHA-256: 9ba3db678b4550898a612b42e8832bf9dee40935090fc4d969ba8f6ac5106979

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Sources and history

Release 2026-09-17-d277315f7d76 · Record review: needs review

1 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: paper-protocol-e914e4149f3b3c8185

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-interaction; title: GlycanML Interaction · Table 3, p. 8; protocol id: paper-protocol-e914e4149f3b3c8185; dataset id: paper-dataset-cc0cb44a535d3e0e7a; metric: Spearman rho; unit: dimensionless; direction: higher; result ids: paper-result-16108af1186bb07643; paper-result-b40c9e0218e574eca5; paper-result-9284b039f056e2a302; paper-result-cc74f69913e5a2aaa7; paper-result-cd20816595a9f309d0; paper-result-37e29e684dddd82a16; paper-result-6bc53e8c78556b6241; paper-result-e3e3952c325b6ef0a2; paper-result-f5c722997fa24f0560; paper-result-9865abcc65a28a6bed; source ids: expansion-p3-glycanml-2405-16206v1; source locator: Table 3, p. 8, Interaction; 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, Interaction; 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, Interaction; ambiguities: None recorded
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