Configuration

Deep Prot-T5 (DeepProtein benchmark)

Configuration of Deep Prot-T5: fine-tuned protein language model introduced by this paper; default DeepProtein configuration.

26 evaluations · 26 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

26 evaluations · 26 results. Different protocols are not a single leaderboard.

Sorted by MAE (mean absolute error) (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 configuration	Protocol and dataset	MAE (mean absolute error)	Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale)	AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale)	R² (coefficient of determination)	Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split)	Accuracy (accuracy, printed on a 0 to 100 scale)
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein CRISPR-Leenay repair outcome: MAE ↓, CRISPR-Leenay repair outcome	0.078 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein beta-lactamase (PEER): MAE ↓, beta-lactamase (PEER)	0.084**	Not reported	Not reported	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein SAbDab-Chen antibody developability: MAE ↓, SAbDab-Chen antibody developability	0.186	Not reported	Not reported	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Stability (TAPE): MAE ↓, Stability (TAPE)	0.551	Not reported	Not reported	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Fluorescence (TAPE): MAE ↓, Fluorescence (TAPE)	0.642	Not reported	Not reported	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein PPI affinity (PEER): MAE ↓, PPI affinity (PEER)	1.87	Not reported	Not reported	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein TAP antibody developability: MAE ↓, TAP antibody developability	2.92	Not reported	Not reported	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein beta-lactamase (PEER): ρ ↑, beta-lactamase (PEER)	Not reported	Not reported	Not reported	Not reported	0.874** (best in column)	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Binary localization (PEER): Averaged F1 ↑, Binary localization (PEER)	Not reported	92.2% (best in column)	Not reported	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Binary localization (PEER): PR-AUC ↑, Binary localization (PEER)	Not reported	Not reported	92.2% (best in column)	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein CRISPR-Leenay repair outcome: R2 ↑, CRISPR-Leenay repair outcome	Not reported	Not reported	Not reported	0.753	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Fluorescence (TAPE): ρ ↑, Fluorescence (TAPE)	Not reported	Not reported	Not reported	Not reported	0.614	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Fold classification (TAPE): Acc ↑, Fold classification (TAPE)	Not reported	Not reported	Not reported	Not reported	Not reported	74.00**%
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Fold classification (TAPE): Averaged F1 ↑, Fold classification (TAPE)	Not reported	73.61**%	Not reported	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Human PPI (PEER): Averaged F1 ↑, Human PPI (PEER)	Not reported	80.3%	Not reported	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Human PPI (PEER): PR-AUC ↑, Human PPI (PEER)	Not reported	Not reported	76.4%	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein PPI affinity (PEER): R2 ↑, PPI affinity (PEER)	Not reported	Not reported	Not reported	0.643	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein SAbDab-Chen antibody developability: R2 ↑, SAbDab-Chen antibody developability	Not reported	Not reported	Not reported	0.536	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Solubility (PEER): Averaged F1 ↑, Solubility (PEER)	Not reported	68.25**%	Not reported	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Solubility (PEER): PR-AUC ↑, Solubility (PEER)	Not reported	Not reported	77%	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Stability (TAPE): ρ ↑, Stability (TAPE)	Not reported	Not reported	Not reported	Not reported	0.725	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Subcellular localization (PEER): Acc ↑, Subcellular localization (PEER)	Not reported	Not reported	Not reported	Not reported	Not reported	82.7% (best in column)
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Subcellular localization (PEER): Averaged F1 ↑, Subcellular localization (PEER)	Not reported	82.5%	Not reported	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein TAP antibody developability: R2 ↑, TAP antibody developability	Not reported	Not reported	Not reported	0.758 (best in column)	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Yeast PPI (PEER): Averaged F1 ↑, Yeast PPI (PEER)	Not reported	66.7%	Not reported	Not reported	Not reported	Not reported
Deep Prot-T5 (DeepProtein benchmark)Evaluation	DeepProtein Yeast PPI (PEER): PR-AUC ↑, Yeast PPI (PEER)	Not reported	Not reported	63.2%	Not reported	Not reported	Not reported

All 26 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): MAE ↓ Dataset: beta-lactamase (PEER)	0.084** MAE (mean absolute error) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 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 'Deep Prot-T5', column group 'β-lactamase', column 'MAE ↓'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): ρ ↑ Dataset: beta-lactamase (PEER)	0.874** Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 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 'Deep Prot-T5', column group 'β-lactamase', column 'ρ ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Binary localization (PEER): Averaged F1 ↑ Dataset: Binary localization (PEER)	92.2% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 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 'Deep Prot-T5', column group 'Binary', column 'Averaged F1 ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Binary localization (PEER): PR-AUC ↑ Dataset: Binary localization (PEER)	92.2% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 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 'Deep Prot-T5', column group 'Binary', column 'PR-AUC ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein CRISPR-Leenay repair outcome: MAE ↓ Dataset: CRISPR-Leenay repair outcome	0.078 MAE (mean absolute error) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 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 'Deep Prot-T5', column group 'CRISPR-Leenay', column 'MAE ↓'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein CRISPR-Leenay repair outcome: R2 ↑ Dataset: CRISPR-Leenay repair outcome	0.753 R² (coefficient of determination) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 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 'Deep Prot-T5', column group 'CRISPR-Leenay', column 'R2 ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Fluorescence (TAPE): MAE ↓ Dataset: Fluorescence (TAPE)	0.642 MAE (mean absolute error) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 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 'Deep Prot-T5', column group 'Fluorescence', column 'MAE ↓'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Fluorescence (TAPE): ρ ↑ Dataset: Fluorescence (TAPE)	0.614 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 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 'Deep Prot-T5', column group 'Fluorescence', column 'ρ ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Fold classification (TAPE): Acc ↑ Dataset: Fold classification (TAPE)	74.00%** Accuracy (accuracy, printed on a 0 to 100 scale) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 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 'Deep Prot-T5', column group 'Fold', column 'Acc ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Fold classification (TAPE): Averaged F1 ↑ Dataset: Fold classification (TAPE)	73.61%** Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 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 'Deep Prot-T5', column group 'Fold', column 'Averaged F1 ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER)	80.3% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 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 'Deep Prot-T5', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER)	76.4% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 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 'Deep Prot-T5', column group 'Human PPI', column 'PR-AUC ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): MAE ↓ Dataset: PPI affinity (PEER)	1.87 MAE (mean absolute error) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 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 'Deep Prot-T5', column group 'PPI Affinity', column 'MAE ↓'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.643 R² (coefficient of determination) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 on DeepProtein PPI affinity (PEER) (R2 ↑) lit-protein-20261011-deepprotein-protocol-ppi-affinity-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Deep Prot-T5', column group 'PPI Affinity', column 'R2 ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein SAbDab-Chen antibody developability: MAE ↓ Dataset: SAbDab-Chen antibody developability	0.186 MAE (mean absolute error) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 on DeepProtein SAbDab-Chen antibody developability (MAE ↓) lit-protein-20261011-deepprotein-protocol-sabdab-chen-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'Deep Prot-T5', column group 'SAbDab-Chen', column 'MAE ↓'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein SAbDab-Chen antibody developability: R2 ↑ Dataset: SAbDab-Chen antibody developability	0.536 R² (coefficient of determination) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 on DeepProtein SAbDab-Chen antibody developability (R2 ↑) lit-protein-20261011-deepprotein-protocol-sabdab-chen-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'Deep Prot-T5', column group 'SAbDab-Chen', column 'R2 ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Solubility (PEER): Averaged F1 ↑ Dataset: Solubility (PEER)	68.25%** Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 on DeepProtein Solubility (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-solubility-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Deep Prot-T5', column group 'Solubility', column 'Averaged F1 ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Solubility (PEER): PR-AUC ↑ Dataset: Solubility (PEER)	77% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 on DeepProtein Solubility (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-solubility-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Deep Prot-T5', column group 'Solubility', column 'PR-AUC ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Stability (TAPE): MAE ↓ Dataset: Stability (TAPE)	0.551 MAE (mean absolute error) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 on DeepProtein Stability (TAPE) (MAE ↓) lit-protein-20261011-deepprotein-protocol-stability-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Deep Prot-T5', column group 'Stability', column 'MAE ↓'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE)	0.725 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 on DeepProtein Stability (TAPE) (ρ ↑) lit-protein-20261011-deepprotein-protocol-stability-rho Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'Deep Prot-T5', column group 'Stability', column 'ρ ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Subcellular localization (PEER): Acc ↑ Dataset: Subcellular localization (PEER)	82.7% Accuracy (accuracy, printed on a 0 to 100 scale) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 on DeepProtein Subcellular localization (PEER) (Acc ↑) lit-protein-20261011-deepprotein-protocol-subcellular-acc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 3. row 'Deep Prot-T5', column group 'Subcellular', column 'Acc ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Subcellular localization (PEER): Averaged F1 ↑ Dataset: Subcellular localization (PEER)	82.5% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 on DeepProtein Subcellular localization (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-subcellular-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 3. row 'Deep Prot-T5', column group 'Subcellular', column 'Averaged F1 ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein TAP antibody developability: MAE ↓ Dataset: TAP antibody developability	2.92 MAE (mean absolute error) unit-unreported · lower Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 on DeepProtein TAP antibody developability (MAE ↓) lit-protein-20261011-deepprotein-protocol-tap-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'Deep Prot-T5', column group 'TAP', column 'MAE ↓'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein TAP antibody developability: R2 ↑ Dataset: TAP antibody developability	0.758 R² (coefficient of determination) unitless · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 on DeepProtein TAP antibody developability (R2 ↑) lit-protein-20261011-deepprotein-protocol-tap-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'Deep Prot-T5', column group 'TAP', column 'R2 ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): Averaged F1 ↑ Dataset: Yeast PPI (PEER)	66.7% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: Not reported by the source Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Evidence concern: excluded from comparisons Figure 3's caption calls the regression metric 'Spearman (Pearson) Coefficient' while the Evaluation metrics section defines rho as Spearman rank correlation and R2 separately. The section's definition is taken as authoritative and the rho columns are recorded as Spearman; the caption wording is noted so a reader of the figure is not surprised.DeepProtein: deep learning library and benchmark for protein sequence learning · Tables 2, 4 and 6 column headings 'rho' and 'R2'; Figure 3 caption Methods, coverage and source Deep Prot-T5 on DeepProtein Yeast PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Deep Prot-T5', column group 'Yeast PPI', column 'Averaged F1 ↑'

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DeepProtein: deep learning library and benchmark for protein sequence learning · Original source · Version of record, Bioinformatics 2025 (PMC12553333 JATS full text)

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Stable ID: lit-protein-20261011-deepprotein-config-deep-prot-t5

areas: protein-function
contexts: research
method types: foundation_model
reported name: Deep Prot-T5
reported configuration: fine-tuned protein language model introduced by this paper; default DeepProtein configuration (Table 9)
foundation model eligible: true
source locator: Tables 2 to 8, row 'Deep Prot-T5'; Table 9 for the default configuration
missing metadata: version: reason: unreported; note: The tables name the model without a release version
provenance note: Deep Prot-T5 as trained and evaluated in the DeepProtein benchmark (fine-tuned protein language model introduced by this paper).

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