GCN (DeepProtein benchmark)
Configuration of GCN: graph model; default DeepProtein configuration.
Overview
An explanatory profile has not yet been reviewed for this record.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluations and results
52 evaluations · 52 results. Different protocols are not a single leaderboard.
Sorted by Peak memory (peak GPU memory) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.
All 52 result rows with coverage, uncertainty and sources
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Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein beta-lactamase (PEER): MAE ↓ Dataset: beta-lactamase (PEER) | 0.225 ± 0.001 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.001 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN on DeepProtein beta-lactamase (PEER) (MAE ↓) lit-protein-20261011-deepprotein-protocol-beta-lactamase-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'GCN', column group 'β-lactamase', column 'MAE ↓' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein beta-lactamase (PEER): GPU Memory (GB) Dataset: beta-lactamase (PEER) | 1.07 Peak memory (peak GPU memory) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN resource usage on DeepProtein beta-lactamase (PEER) (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-beta-lactamase-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'Beta' / 'GCN', column 'GPU Memory (GB)' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein beta-lactamase (PEER): ρ ↑ Dataset: beta-lactamase (PEER) | 0.450±0.006 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.006 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN on DeepProtein beta-lactamase (PEER) (ρ ↑) lit-protein-20261011-deepprotein-protocol-beta-lactamase-rho Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'GCN', column group 'β-lactamase', column 'ρ ↑' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein beta-lactamase (PEER): Time (hour) Dataset: beta-lactamase (PEER) | 0.14 Runtime (training wall-clock time) hour · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN resource usage on DeepProtein beta-lactamase (PEER) (Time (hour)) lit-protein-20261011-deepprotein-protocol-beta-lactamase-time Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'Beta' / 'GCN', column 'Time (hour)' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Binary localization (PEER): Averaged F1 ↑ Dataset: Binary localization (PEER) | 81.80 ± 0.07% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.07 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN on DeepProtein Binary localization (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-binary-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 3. row 'GCN', column group 'Binary', column 'Averaged F1 ↑' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Binary localization (PEER): GPU Memory (GB) Dataset: Binary localization (PEER) | 10.8 Peak memory (peak GPU memory) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN resource usage on DeepProtein Binary localization (PEER) (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-binary-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'SubCellular-Bin' / 'GCN', column 'GPU Memory (GB)' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Binary localization (PEER): PR-AUC ↑ Dataset: Binary localization (PEER) | 83.43±0.10% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.10 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN on DeepProtein Binary localization (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-binary-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 3. row 'GCN', column group 'Binary', column 'PR-AUC ↑' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Binary localization (PEER): Time (hour) Dataset: Binary localization (PEER) | 0.052 Runtime (training wall-clock time) hour · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN resource usage on DeepProtein Binary localization (PEER) (Time (hour)) lit-protein-20261011-deepprotein-protocol-binary-time Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'SubCellular-Bin' / 'GCN', column 'Time (hour)' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein CRISPR-Leenay repair outcome: MAE ↓ Dataset: CRISPR-Leenay repair outcome | 0.1274±0.0019 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.0019 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN on DeepProtein CRISPR-Leenay repair outcome (MAE ↓) lit-protein-20261011-deepprotein-protocol-crispr-leenay-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'GCN', column group 'CRISPR-Leenay', column 'MAE ↓' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein CRISPR-Leenay repair outcome: GPU Memory (GB) Dataset: CRISPR-Leenay repair outcome | 0.538 Peak memory (peak GPU memory) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN resource usage on DeepProtein CRISPR-Leenay repair outcome (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-crispr-leenay-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'CRISPR' / 'GCN', column 'GPU Memory (GB)' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein CRISPR-Leenay repair outcome: R2 ↑ Dataset: CRISPR-Leenay repair outcome | 0.066 ± 0.010 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.010 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN on DeepProtein CRISPR-Leenay repair outcome (R2 ↑) lit-protein-20261011-deepprotein-protocol-crispr-leenay-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'GCN', column group 'CRISPR-Leenay', column 'R2 ↑' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein CRISPR-Leenay repair outcome: Time (hour) Dataset: CRISPR-Leenay repair outcome | 0.001 Runtime (training wall-clock time) hour · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN resource usage on DeepProtein CRISPR-Leenay repair outcome (Time (hour)) lit-protein-20261011-deepprotein-protocol-crispr-leenay-time Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'CRISPR' / 'GCN', column 'Time (hour)' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Fluorescence (TAPE): MAE ↓ Dataset: Fluorescence (TAPE) | 0.864 ± 0.018 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.018 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN on DeepProtein Fluorescence (TAPE) (MAE ↓) lit-protein-20261011-deepprotein-protocol-fluorescence-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'GCN', column group 'Fluorescence', column 'MAE ↓' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Fluorescence (TAPE): GPU Memory (GB) Dataset: Fluorescence (TAPE) | 1 Peak memory (peak GPU memory) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN resource usage on DeepProtein Fluorescence (TAPE) (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-fluorescence-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'Fluorescence' / 'GCN', column 'GPU Memory (GB)' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Fluorescence (TAPE): ρ ↑ Dataset: Fluorescence (TAPE) | 0.397±0.002 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.002 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN on DeepProtein Fluorescence (TAPE) (ρ ↑) lit-protein-20261011-deepprotein-protocol-fluorescence-rho Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'GCN', column group 'Fluorescence', column 'ρ ↑' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Fluorescence (TAPE): Time (hour) Dataset: Fluorescence (TAPE) | 0.132 Runtime (training wall-clock time) hour · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN resource usage on DeepProtein Fluorescence (TAPE) (Time (hour)) lit-protein-20261011-deepprotein-protocol-fluorescence-time Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'Fluorescence' / 'GCN', column 'Time (hour)' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Fold classification (TAPE): Acc ↑ Dataset: Fold classification (TAPE) | 8.09 ± 0.36% Accuracy (accuracy, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.36 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN on DeepProtein Fold classification (TAPE) (Acc ↑) lit-protein-20261011-deepprotein-protocol-fold-acc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 7. row 'GCN', column group 'Fold', column 'Acc ↑' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Fold classification (TAPE): Averaged F1 ↑ Dataset: Fold classification (TAPE) | 2.34 ± 0.15% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.15 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN on DeepProtein Fold classification (TAPE) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-fold-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 7. row 'GCN', column group 'Fold', column 'Averaged F1 ↑' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Fold classification (TAPE): GPU Memory (GB) Dataset: Fold classification (TAPE) | 1.81 Peak memory (peak GPU memory) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN resource usage on DeepProtein Fold classification (TAPE) (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-fold-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'Fold' / 'GCN', column 'GPU Memory (GB)' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Fold classification (TAPE): Time (hour) Dataset: Fold classification (TAPE) | 0.06 Runtime (training wall-clock time) hour · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN resource usage on DeepProtein Fold classification (TAPE) (Time (hour)) lit-protein-20261011-deepprotein-protocol-fold-time Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'Fold' / 'GCN', column 'Time (hour)' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER) | 71.05 ± 2.90% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 2.90 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN on DeepProtein Human PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'GCN', column group 'Human PPI', column 'Averaged F1 ↑' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Human PPI (PEER): GPU Memory (GB) Dataset: Human PPI (PEER) | 2.13 Peak memory (peak GPU memory) gigabyte · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN resource usage on DeepProtein Human PPI (PEER) (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-human-ppi-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'Human-PPI' / 'GCN', column 'GPU Memory (GB)' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER) | 82.21 ± 1.13% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.13 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN on DeepProtein Human PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'GCN', column group 'Human PPI', column 'PR-AUC ↑' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Human PPI (PEER): Time (hour) Dataset: Human PPI (PEER) | 1.1 Runtime (training wall-clock time) hour · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN resource usage on DeepProtein Human PPI (PEER) (Time (hour)) lit-protein-20261011-deepprotein-protocol-human-ppi-time Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'Human-PPI' / 'GCN', column 'Time (hour)' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein PPI affinity (PEER): MAE ↓ Dataset: PPI affinity (PEER) | 2.443 ± 0.036 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.036 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN on DeepProtein PPI affinity (PEER) (MAE ↓) lit-protein-20261011-deepprotein-protocol-ppi-affinity-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'GCN', column group 'PPI Affinity', column 'MAE ↓' |
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- DeepProtein: deep learning library and benchmark for protein sequence learning · Original source · Version of record, Bioinformatics 2025 (PMC12553333 JATS full text)
Technical metadata and extraction receipts
Stable ID: lit-protein-20261011-deepprotein-config-gcn
- areas
- protein-function
- contexts
- research
- method types
- specialist
- reported name
- GCN
- reported configuration
- graph model; default DeepProtein configuration (Table 9)
- foundation model eligible
- false
- source locator
- Tables 2 to 8, row 'GCN'; Table 9 for the default configuration
- missing metadata
- version: reason: unreported; note: The tables name the model without a release version
- provenance note
- GCN as trained and evaluated in the DeepProtein benchmark (graph model).
Related records
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- system: GCN on DeepProtein Solubility (PEER) (PR-AUC ↑)
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- system: GCN on DeepProtein Stability (TAPE) (MAE ↓)
- system: GCN resource usage on DeepProtein Stability (TAPE) (GPU Memory (GB))
- system: GCN on DeepProtein Stability (TAPE) (ρ ↑)
- system: GCN resource usage on DeepProtein Stability (TAPE) (Time (hour))
- system: GCN on DeepProtein Subcellular localization (PEER) (Acc ↑)
- system: GCN on DeepProtein Subcellular localization (PEER) (Averaged F1 ↑)
- system: GCN resource usage on DeepProtein Subcellular localization (PEER) (GPU Memory (GB))
- system: GCN resource usage on DeepProtein Subcellular localization (PEER) (Time (hour))
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