rewirebio.iobenchmarks
Configuration

CNN (DeepProtein benchmark)

Configuration of CNN: sequence model; default DeepProtein configuration.

60 evaluations · 60 results

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

60 evaluations · 60 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.

Tested configurationProtocol and datasetPeak memory (peak GPU memory)Runtime (training wall-clock time)Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale)MAE (mean absolute error)AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale)R² (coefficient of determination)Accuracy (accuracy, printed on a 0 to 100 scale)AUROC (area under the ROC curve, printed on a 0 to 100 scale)Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split)
CNN (DeepProtein benchmark)EvaluationDeepProtein CRISPR-Leenay repair outcome: GPU Memory (GB), CRISPR-Leenay repair outcome0.629 (best in column)Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein SAbDab-Chen antibody developability: GPU Memory (GB), SAbDab-Chen antibody developability0.65Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Fluorescence (TAPE): GPU Memory (GB), Fluorescence (TAPE)0.78Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Stability (TAPE): GPU Memory (GB), Stability (TAPE)0.845Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein beta-lactamase (PEER): GPU Memory (GB), beta-lactamase (PEER)0.847Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Solubility (PEER): GPU Memory (GB), Solubility (PEER)0.847Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Fold classification (TAPE): GPU Memory (GB), Fold classification (TAPE)0.922Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Human PPI (PEER): GPU Memory (GB), Human PPI (PEER)0.96Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein PPI affinity (PEER): GPU Memory (GB), PPI affinity (PEER)1.37Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Binary localization (PEER): GPU Memory (GB), Binary localization (PEER)1.83Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein TAP antibody developability: GPU Memory (GB), TAP antibody developability1.95Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Yeast PPI (PEER): GPU Memory (GB), Yeast PPI (PEER)2.69Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Subcellular localization (PEER): GPU Memory (GB), Subcellular localization (PEER)2.94Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein beta-lactamase (PEER): MAE ↓, beta-lactamase (PEER)Not reportedNot reportedNot reported0.152 ± 0.001Not reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein beta-lactamase (PEER): ρ ↑, beta-lactamase (PEER)Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported0.721 ± 0.020 (best in column)
CNN (DeepProtein benchmark)EvaluationDeepProtein beta-lactamase (PEER): Time (hour), beta-lactamase (PEER)Not reported0.0015Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Binary localization (PEER): Averaged F1 ↑, Binary localization (PEER)Not reportedNot reported87.74 ± 0.08%Not reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Binary localization (PEER): PR-AUC ↑, Binary localization (PEER)Not reportedNot reportedNot reportedNot reported90.88±0.31% (best in column)Not reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Binary localization (PEER): Time (hour), Binary localization (PEER)Not reported0.0011Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein CRISPR-Leenay repair outcome: MAE ↓, CRISPR-Leenay repair outcomeNot reportedNot reportedNot reported0.0745 ± 0.0005 (best in column)Not reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein CRISPR-Leenay repair outcome: R2 ↑, CRISPR-Leenay repair outcomeNot reportedNot reportedNot reportedNot reportedNot reported0.781 ± 0.009 (best in column)Not reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein CRISPR-Leenay repair outcome: Time (hour), CRISPR-Leenay repair outcomeNot reported0.0002 (best in column)Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Fluorescence (TAPE): MAE ↓, Fluorescence (TAPE)Not reportedNot reportedNot reported0.194 ± 0.001Not reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Fluorescence (TAPE): ρ ↑, Fluorescence (TAPE)Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported0.680 ± 0.001
CNN (DeepProtein benchmark)EvaluationDeepProtein Fluorescence (TAPE): Time (hour), Fluorescence (TAPE)Not reported0.01Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Fold classification (TAPE): Acc ↑, Fold classification (TAPE)Not reportedNot reportedNot reportedNot reportedNot reportedNot reported8.01 ± 0.44%Not reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Fold classification (TAPE): Averaged F1 ↑, Fold classification (TAPE)Not reportedNot reported0.47 ± 0.11%Not reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Fold classification (TAPE): Time (hour), Fold classification (TAPE)Not reported0.01Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Human PPI (PEER): Averaged F1 ↑, Human PPI (PEER)Not reportedNot reported69.65 ± 1.63%Not reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Human PPI (PEER): PR-AUC ↑, Human PPI (PEER)Not reportedNot reportedNot reportedNot reported70.37±1.22%Not reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Human PPI (PEER): Time (hour), Human PPI (PEER)Not reported0.14Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein IEDB epitope prediction: Averaged F1 ↑, IEDB epitope predictionNot reportedNot reported10.34 ± 0.02%Not reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein IEDB epitope prediction: ROC-AUC ↑, IEDB epitope predictionNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported54.03±0.02%Not reported
CNN (DeepProtein benchmark)EvaluationDeepProtein PDB-Jespersen epitope prediction: Averaged F1 ↑, PDB-Jespersen epitope predictionNot reportedNot reported52.43 ± 0.35%Not reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein PDB-Jespersen epitope prediction: ROC-AUC ↑, PDB-Jespersen epitope predictionNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported74.46 ± 0.21**%Not reported
CNN (DeepProtein benchmark)EvaluationDeepProtein PPI affinity (PEER): MAE ↓, PPI affinity (PEER)Not reportedNot reportedNot reported1.764 ± 0.051Not reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein PPI affinity (PEER): R2 ↑, PPI affinity (PEER)Not reportedNot reportedNot reportedNot reportedNot reported0.646±0.003Not reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein PPI affinity (PEER): Time (hour), PPI affinity (PEER)Not reported0.004Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein SAbDab-Chen antibody developability: MAE ↓, SAbDab-Chen antibody developabilityNot reportedNot reportedNot reported0.219 ± 0.006Not reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein SAbDab-Chen antibody developability: R2 ↑, SAbDab-Chen antibody developabilityNot reportedNot reportedNot reportedNot reportedNot reported0.547 ± 0.014Not reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein SAbDab-Chen antibody developability: Time (hour), SAbDab-Chen antibody developabilityNot reported0.003Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein SAbDab-Liberis paratope prediction: Averaged F1 ↑, SAbDab-Liberis paratope predictionNot reportedNot reported61.51 ± 0.11%Not reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein SAbDab-Liberis paratope prediction: ROC-AUC ↑, SAbDab-Liberis paratope predictionNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported90.85 ± 0.08% (best in column)Not reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Secondary structure prediction (TAPE): Acc ↑, Secondary structure prediction (TAPE)Not reportedNot reportedNot reportedNot reportedNot reportedNot reported99.44 ± 0.00% (best in column)Not reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Secondary structure prediction (TAPE): Averaged F1 ↑, Secondary structure prediction (TAPE)Not reportedNot reported87.76 ± 0.06% (best in column)Not reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Solubility (PEER): Averaged F1 ↑, Solubility (PEER)Not reportedNot reported62.50 ± 2.69%Not reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Solubility (PEER): PR-AUC ↑, Solubility (PEER)Not reportedNot reportedNot reportedNot reported74.61±0.55%Not reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Solubility (PEER): Time (hour), Solubility (PEER)Not reported0.013Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Stability (TAPE): MAE ↓, Stability (TAPE)Not reportedNot reportedNot reported0.312 ± 0.008Not reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Stability (TAPE): ρ ↑, Stability (TAPE)Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported0.715 ± 0.025
CNN (DeepProtein benchmark)EvaluationDeepProtein Stability (TAPE): Time (hour), Stability (TAPE)Not reported0.016Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Subcellular localization (PEER): Acc ↑, Subcellular localization (PEER)Not reportedNot reportedNot reportedNot reportedNot reportedNot reported50.18 ± 1.21%Not reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Subcellular localization (PEER): Averaged F1 ↑, Subcellular localization (PEER)Not reportedNot reported30.44 ± 0.28%Not reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Subcellular localization (PEER): Time (hour), Subcellular localization (PEER)Not reported0.006Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein TAP antibody developability: MAE ↓, TAP antibody developabilityNot reportedNot reportedNot reported3.217±0.026Not reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein TAP antibody developability: R2 ↑, TAP antibody developabilityNot reportedNot reportedNot reportedNot reportedNot reported0.469 ± 0.066Not reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein TAP antibody developability: Time (hour), TAP antibody developabilityNot reported0.01Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Yeast PPI (PEER): Averaged F1 ↑, Yeast PPI (PEER)Not reportedNot reported25.90 ± 0.10%Not reportedNot reportedNot reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Yeast PPI (PEER): PR-AUC ↑, Yeast PPI (PEER)Not reportedNot reportedNot reportedNot reported51.93±0.92%Not reportedNot reportedNot reportedNot reported
CNN (DeepProtein benchmark)EvaluationDeepProtein Yeast PPI (PEER): Time (hour), Yeast PPI (PEER)Not reported0.01Not reportedNot reportedNot reportedNot reportedNot reportedNot reportedNot reported
All 60 result rows with coverage, uncertainty and sources
Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein beta-lactamase (PEER): MAE ↓
Dataset: beta-lactamase (PEER)
0.152 ± 0.001 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.001

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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 'CNN', column group 'β-lactamase', column 'MAE ↓'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein beta-lactamase (PEER): GPU Memory (GB)
Dataset: beta-lactamase (PEER)
0.847 Peak memory (peak GPU memory)
gigabyte · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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' / 'CNN', column 'GPU Memory (GB)'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein beta-lactamase (PEER): ρ ↑
Dataset: beta-lactamase (PEER)
0.721 ± 0.020 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split)
unitless · higher

Uncertainty: SD 0.020

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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 'CNN', column group 'β-lactamase', column 'ρ ↑'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein beta-lactamase (PEER): Time (hour)
Dataset: beta-lactamase (PEER)
0.0015 Runtime (training wall-clock time)
hour · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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' / 'CNN', column 'Time (hour)'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Binary localization (PEER): Averaged F1 ↑
Dataset: Binary localization (PEER)
87.74 ± 0.08% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale)
percent · higher

Uncertainty: SD 0.08

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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 'CNN', column group 'Binary', column 'Averaged F1 ↑'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Binary localization (PEER): GPU Memory (GB)
Dataset: Binary localization (PEER)
1.83 Peak memory (peak GPU memory)
gigabyte · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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' / 'CNN', column 'GPU Memory (GB)'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Binary localization (PEER): PR-AUC ↑
Dataset: Binary localization (PEER)
90.88±0.31% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale)
percent · higher

Uncertainty: SD 0.31

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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 'CNN', column group 'Binary', column 'PR-AUC ↑'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Binary localization (PEER): Time (hour)
Dataset: Binary localization (PEER)
0.0011 Runtime (training wall-clock time)
hour · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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' / 'CNN', column 'Time (hour)'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein CRISPR-Leenay repair outcome: MAE ↓
Dataset: CRISPR-Leenay repair outcome
0.0745 ± 0.0005 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.0005

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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 'CNN', column group 'CRISPR-Leenay', column 'MAE ↓'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein CRISPR-Leenay repair outcome: GPU Memory (GB)
Dataset: CRISPR-Leenay repair outcome
0.629 Peak memory (peak GPU memory)
gigabyte · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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' / 'CNN', column 'GPU Memory (GB)'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein CRISPR-Leenay repair outcome: R2 ↑
Dataset: CRISPR-Leenay repair outcome
0.781 ± 0.009 R² (coefficient of determination)
unitless · higher

Uncertainty: SD 0.009

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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 'CNN', column group 'CRISPR-Leenay', column 'R2 ↑'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein CRISPR-Leenay repair outcome: Time (hour)
Dataset: CRISPR-Leenay repair outcome
0.0002 Runtime (training wall-clock time)
hour · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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' / 'CNN', column 'Time (hour)'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
0.194 ± 0.001 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.001

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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 'CNN', column group 'Fluorescence', column 'MAE ↓'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): GPU Memory (GB)
Dataset: Fluorescence (TAPE)
0.78 Peak memory (peak GPU memory)
gigabyte · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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' / 'CNN', column 'GPU Memory (GB)'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): ρ ↑
Dataset: Fluorescence (TAPE)
0.680 ± 0.001 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split)
unitless · higher

Uncertainty: SD 0.001

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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 'CNN', column group 'Fluorescence', column 'ρ ↑'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): Time (hour)
Dataset: Fluorescence (TAPE)
0.01 Runtime (training wall-clock time)
hour · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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' / 'CNN', column 'Time (hour)'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Fold classification (TAPE): Acc ↑
Dataset: Fold classification (TAPE)
8.01 ± 0.44% Accuracy (accuracy, printed on a 0 to 100 scale)
percent · higher

Uncertainty: SD 0.44

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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 'CNN', column group 'Fold', column 'Acc ↑'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Fold classification (TAPE): Averaged F1 ↑
Dataset: Fold classification (TAPE)
0.47 ± 0.11% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale)
percent · higher

Uncertainty: SD 0.11

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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 'CNN', column group 'Fold', column 'Averaged F1 ↑'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Fold classification (TAPE): GPU Memory (GB)
Dataset: Fold classification (TAPE)
0.922 Peak memory (peak GPU memory)
gigabyte · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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' / 'CNN', column 'GPU Memory (GB)'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Fold classification (TAPE): Time (hour)
Dataset: Fold classification (TAPE)
0.01 Runtime (training wall-clock time)
hour · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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' / 'CNN', column 'Time (hour)'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑
Dataset: Human PPI (PEER)
69.65 ± 1.63% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale)
percent · higher

Uncertainty: SD 1.63

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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 'CNN', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Human PPI (PEER): GPU Memory (GB)
Dataset: Human PPI (PEER)
0.96 Peak memory (peak GPU memory)
gigabyte · lower

Uncertainty: Not reported by the source

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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' / 'CNN', column 'GPU Memory (GB)'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑
Dataset: Human PPI (PEER)
70.37±1.22% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale)
percent · higher

Uncertainty: SD 1.22

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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 'CNN', column group 'Human PPI', column 'PR-AUC ↑'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein Human PPI (PEER): Time (hour)
Dataset: Human PPI (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 checked
Methods, coverage and source

CNN 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' / 'CNN', column 'Time (hour)'
Configuration: CNN (DeepProtein benchmark)Protocol: DeepProtein IEDB epitope prediction: Averaged F1 ↑
Dataset: IEDB epitope prediction
10.34 ± 0.02% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale)
percent · higher

Uncertainty: SD 0.02

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN on DeepProtein IEDB epitope prediction (Averaged F1 ↑)

lit-protein-20261011-deepprotein-protocol-iedb-avg-f1

Aggregation: Not reported

DeepProtein: deep learning library and benchmark for protein sequence learning · Table 5. row 'CNN', column group 'IEDB', column 'Averaged F1 ↑'

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
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Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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Stable ID: lit-protein-20261011-deepprotein-config-cnn

areas
protein-function
contexts
research
method types
specialist
reported name
CNN
reported configuration
sequence model; default DeepProtein configuration (Table 9)
foundation model eligible
false
source locator
Tables 2 to 8, row 'CNN'; Table 9 for the default configuration
missing metadata
version: reason: unreported; note: The tables name the model without a release version
provenance note
CNN as trained and evaluated in the DeepProtein benchmark (sequence model).
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