Configuration

NeuralFP (DeepProtein benchmark)

Configuration of NeuralFP: 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

24 evaluations · 24 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)
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein CRISPR-Leenay repair outcome: MAE ↓, CRISPR-Leenay repair outcome	0.1243±0.0001 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein SAbDab-Chen antibody developability: MAE ↓, SAbDab-Chen antibody developability	0.253±0.011	Not reported	Not reported	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein beta-lactamase (PEER): MAE ↓, beta-lactamase (PEER)	0.263 ± 0.001	Not reported	Not reported	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein Stability (TAPE): MAE ↓, Stability (TAPE)	0.484 ± 0.020	Not reported	Not reported	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein Fluorescence (TAPE): MAE ↓, Fluorescence (TAPE)	1.016 ± 0.081	Not reported	Not reported	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein PPI affinity (PEER): MAE ↓, PPI affinity (PEER)	2.555 ± 0.040	Not reported	Not reported	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein TAP antibody developability: MAE ↓, TAP antibody developability	3.436±0.015	Not reported	Not reported	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein beta-lactamase (PEER): ρ ↑, beta-lactamase (PEER)	Not reported	Not reported	Not reported	Not reported	0.171±0.007	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein Binary localization (PEER): Averaged F1 ↑, Binary localization (PEER)	Not reported	79.95 ± 0.09% (best in column)	Not reported	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein Binary localization (PEER): PR-AUC ↑, Binary localization (PEER)	Not reported	Not reported	81.14±0.06% (best in column)	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein CRISPR-Leenay repair outcome: R2 ↑, CRISPR-Leenay repair outcome	Not reported	Not reported	Not reported	0.177 ± 0.029	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein Fluorescence (TAPE): ρ ↑, Fluorescence (TAPE)	Not reported	Not reported	Not reported	Not reported	0.349±0.049	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein Human PPI (PEER): Averaged F1 ↑, Human PPI (PEER)	Not reported	67.62 ± 1.03%	Not reported	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein Human PPI (PEER): PR-AUC ↑, Human PPI (PEER)	Not reported	Not reported	80.11±1.25%	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein PPI affinity (PEER): R2 ↑, PPI affinity (PEER)	Not reported	Not reported	Not reported	0.100±0.054	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein SAbDab-Chen antibody developability: R2 ↑, SAbDab-Chen antibody developability	Not reported	Not reported	Not reported	0.452 ± 0.027 (best in column)	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein Solubility (PEER): Averaged F1 ↑, Solubility (PEER)	Not reported	62.72 ± 1.91%	Not reported	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein Solubility (PEER): PR-AUC ↑, Solubility (PEER)	Not reported	Not reported	78.74±0.24%	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein Stability (TAPE): ρ ↑, Stability (TAPE)	Not reported	Not reported	Not reported	Not reported	0.373±0.023 (best in column)	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein Subcellular localization (PEER): Acc ↑, Subcellular localization (PEER)	Not reported	Not reported	Not reported	Not reported	Not reported	45.20±0.49%
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein Subcellular localization (PEER): Averaged F1 ↑, Subcellular localization (PEER)	Not reported	27.07 ± 0.93%	Not reported	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein TAP antibody developability: R2 ↑, TAP antibody developability	Not reported	Not reported	Not reported	0.205 ± 0.035	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein Yeast PPI (PEER): Averaged F1 ↑, Yeast PPI (PEER)	Not reported	58.94 ± 4.74%	Not reported	Not reported	Not reported	Not reported
NeuralFP (DeepProtein benchmark)Evaluation	DeepProtein Yeast PPI (PEER): PR-AUC ↑, Yeast PPI (PEER)	Not reported	Not reported	57.00±1.51%	Not reported	Not reported	Not reported

All 24 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): MAE ↓ Dataset: beta-lactamase (PEER)	0.263 ± 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 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 NeuralFP 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 'NeuralFP', column group 'β-lactamase', column 'MAE ↓'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): ρ ↑ Dataset: beta-lactamase (PEER)	0.171±0.007 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.007 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 NeuralFP 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 'NeuralFP', column group 'β-lactamase', column 'ρ ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Binary localization (PEER): Averaged F1 ↑ Dataset: Binary localization (PEER)	79.95 ± 0.09% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.09 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 NeuralFP 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 'NeuralFP', column group 'Binary', column 'Averaged F1 ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Binary localization (PEER): PR-AUC ↑ Dataset: Binary localization (PEER)	81.14±0.06% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.06 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 NeuralFP 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 'NeuralFP', column group 'Binary', column 'PR-AUC ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein CRISPR-Leenay repair outcome: MAE ↓ Dataset: CRISPR-Leenay repair outcome	0.1243±0.0001 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.0001 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 NeuralFP 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 'NeuralFP', column group 'CRISPR-Leenay', column 'MAE ↓'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein CRISPR-Leenay repair outcome: R2 ↑ Dataset: CRISPR-Leenay repair outcome	0.177 ± 0.029 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.029 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 NeuralFP 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 'NeuralFP', column group 'CRISPR-Leenay', column 'R2 ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Fluorescence (TAPE): MAE ↓ Dataset: Fluorescence (TAPE)	1.016 ± 0.081 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.081 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 NeuralFP 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 'NeuralFP', column group 'Fluorescence', column 'MAE ↓'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Fluorescence (TAPE): ρ ↑ Dataset: Fluorescence (TAPE)	0.349±0.049 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.049 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 NeuralFP 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 'NeuralFP', column group 'Fluorescence', column 'ρ ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER)	67.62 ± 1.03% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.03 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 NeuralFP 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 'NeuralFP', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER)	80.11±1.25% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.25 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 NeuralFP 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 'NeuralFP', column group 'Human PPI', column 'PR-AUC ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): MAE ↓ Dataset: PPI affinity (PEER)	2.555 ± 0.040 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.040 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 NeuralFP 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 'NeuralFP', column group 'PPI Affinity', column 'MAE ↓'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.100±0.054 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.054 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 NeuralFP 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 'NeuralFP', column group 'PPI Affinity', column 'R2 ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein SAbDab-Chen antibody developability: MAE ↓ Dataset: SAbDab-Chen antibody developability	0.253±0.011 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.011 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 NeuralFP 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 'NeuralFP', column group 'SAbDab-Chen', column 'MAE ↓'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein SAbDab-Chen antibody developability: R2 ↑ Dataset: SAbDab-Chen antibody developability	0.452 ± 0.027 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.027 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 NeuralFP 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 'NeuralFP', column group 'SAbDab-Chen', column 'R2 ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Solubility (PEER): Averaged F1 ↑ Dataset: Solubility (PEER)	62.72 ± 1.91% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.91 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 NeuralFP 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 'NeuralFP', column group 'Solubility', column 'Averaged F1 ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Solubility (PEER): PR-AUC ↑ Dataset: Solubility (PEER)	78.74±0.24% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.24 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 NeuralFP 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 'NeuralFP', column group 'Solubility', column 'PR-AUC ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Stability (TAPE): MAE ↓ Dataset: Stability (TAPE)	0.484 ± 0.020 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.020 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 NeuralFP 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 'NeuralFP', column group 'Stability', column 'MAE ↓'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE)	0.373±0.023 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.023 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 NeuralFP 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 'NeuralFP', column group 'Stability', column 'ρ ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Subcellular localization (PEER): Acc ↑ Dataset: Subcellular localization (PEER)	45.20±0.49% Accuracy (accuracy, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.49 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 NeuralFP 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 'NeuralFP', column group 'Subcellular', column 'Acc ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Subcellular localization (PEER): Averaged F1 ↑ Dataset: Subcellular localization (PEER)	27.07 ± 0.93% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.93 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 NeuralFP 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 'NeuralFP', column group 'Subcellular', column 'Averaged F1 ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein TAP antibody developability: MAE ↓ Dataset: TAP antibody developability	3.436±0.015 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.015 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 NeuralFP 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 'NeuralFP', column group 'TAP', column 'MAE ↓'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein TAP antibody developability: R2 ↑ Dataset: TAP antibody developability	0.205 ± 0.035 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.035 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 NeuralFP 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 'NeuralFP', column group 'TAP', column 'R2 ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): Averaged F1 ↑ Dataset: Yeast PPI (PEER)	58.94 ± 4.74% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 4.74 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 NeuralFP 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 'NeuralFP', column group 'Yeast PPI', column 'Averaged F1 ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): PR-AUC ↑ Dataset: Yeast PPI (PEER)	57.00±1.51% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.51 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 NeuralFP on DeepProtein Yeast PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'NeuralFP', column group 'Yeast PPI', column 'PR-AUC ↑'

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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-neuralfp

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

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