Configuration

MPNN (DeepProtein benchmark)

Configuration of MPNN: graph model; default DeepProtein configuration.

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Evaluations and results

8 evaluations · 8 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)	Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split)	AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale)	Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale)
MPNN (DeepProtein benchmark)Evaluation	DeepProtein beta-lactamase (PEER): MAE ↓, beta-lactamase (PEER)	0.262 ± 0.003 (best in column)	Not reported	Not reported	Not reported
MPNN (DeepProtein benchmark)Evaluation	DeepProtein Stability (TAPE): MAE ↓, Stability (TAPE)	0.732 ± 0.006	Not reported	Not reported	Not reported
MPNN (DeepProtein benchmark)Evaluation	DeepProtein Fluorescence (TAPE): MAE ↓, Fluorescence (TAPE)	1.275 ± 0.011	Not reported	Not reported	Not reported
MPNN (DeepProtein benchmark)Evaluation	DeepProtein beta-lactamase (PEER): ρ ↑, beta-lactamase (PEER)	Not reported	0.068±0.015	Not reported	Not reported
MPNN (DeepProtein benchmark)Evaluation	DeepProtein Fluorescence (TAPE): ρ ↑, Fluorescence (TAPE)	Not reported	0.249±0.002 (best in column)	Not reported	Not reported
MPNN (DeepProtein benchmark)Evaluation	DeepProtein Solubility (PEER): Averaged F1 ↑, Solubility (PEER)	Not reported	Not reported	Not reported	40.56 ± 5.46%
MPNN (DeepProtein benchmark)Evaluation	DeepProtein Solubility (PEER): PR-AUC ↑, Solubility (PEER)	Not reported	Not reported	62.53±0.31%	Not reported
MPNN (DeepProtein benchmark)Evaluation	DeepProtein Stability (TAPE): ρ ↑, Stability (TAPE)	Not reported	0.118±0.061	Not reported	Not reported

All 8 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: MPNN (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): MAE ↓ Dataset: beta-lactamase (PEER)	0.262 ± 0.003 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.003 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 MPNN 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 'MPNN', column group 'β-lactamase', column 'MAE ↓'
Configuration: MPNN (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): ρ ↑ Dataset: beta-lactamase (PEER)	0.068±0.015 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher 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 MPNN 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 'MPNN', column group 'β-lactamase', column 'ρ ↑'
Configuration: MPNN (DeepProtein benchmark)	Protocol: DeepProtein Fluorescence (TAPE): MAE ↓ Dataset: Fluorescence (TAPE)	1.275 ± 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 MPNN 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 'MPNN', column group 'Fluorescence', column 'MAE ↓'
Configuration: MPNN (DeepProtein benchmark)	Protocol: DeepProtein Fluorescence (TAPE): ρ ↑ Dataset: Fluorescence (TAPE)	0.249±0.002 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.002 Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source 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 MPNN 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 'MPNN', column group 'Fluorescence', column 'ρ ↑'
Configuration: MPNN (DeepProtein benchmark)	Protocol: DeepProtein Solubility (PEER): Averaged F1 ↑ Dataset: Solubility (PEER)	40.56 ± 5.46% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 5.46 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 MPNN 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 'MPNN', column group 'Solubility', column 'Averaged F1 ↑'
Configuration: MPNN (DeepProtein benchmark)	Protocol: DeepProtein Solubility (PEER): PR-AUC ↑ Dataset: Solubility (PEER)	62.53±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 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 MPNN 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 'MPNN', column group 'Solubility', column 'PR-AUC ↑'
Configuration: MPNN (DeepProtein benchmark)	Protocol: DeepProtein Stability (TAPE): MAE ↓ Dataset: Stability (TAPE)	0.732 ± 0.006 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.006 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 MPNN 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 'MPNN', column group 'Stability', column 'MAE ↓'
Configuration: MPNN (DeepProtein benchmark)	Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE)	0.118±0.061 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.061 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 MPNN 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 'MPNN', column group 'Stability', column 'ρ ↑'

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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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Technical metadata and extraction receipts

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

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

Related records

configuration of: MPNN
system: MPNN on DeepProtein beta-lactamase (PEER) (MAE ↓)
system: MPNN on DeepProtein beta-lactamase (PEER) (ρ ↑)
system: MPNN on DeepProtein Fluorescence (TAPE) (MAE ↓)
system: MPNN on DeepProtein Fluorescence (TAPE) (ρ ↑)
system: MPNN on DeepProtein Solubility (PEER) (Averaged F1 ↑)
system: MPNN on DeepProtein Solubility (PEER) (PR-AUC ↑)
system: MPNN on DeepProtein Stability (TAPE) (MAE ↓)
system: MPNN on DeepProtein Stability (TAPE) (ρ ↑)

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