Configuration

ESM-1b (DeepProtein benchmark)

Configuration of ESM-1b: protein language model; default DeepProtein configuration.

Overview

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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)
ESM-1b (DeepProtein benchmark)Evaluation	DeepProtein beta-lactamase (PEER): MAE ↓, beta-lactamase (PEER)	0.171 ± 0.001 (best in column)	Not reported	Not reported	Not reported
ESM-1b (DeepProtein benchmark)Evaluation	DeepProtein Stability (TAPE): MAE ↓, Stability (TAPE)	0.282 ± 0.010	Not reported	Not reported	Not reported
ESM-1b (DeepProtein benchmark)Evaluation	DeepProtein Fluorescence (TAPE): MAE ↓, Fluorescence (TAPE)	0.548 ± 0.004	Not reported	Not reported	Not reported
ESM-1b (DeepProtein benchmark)Evaluation	DeepProtein beta-lactamase (PEER): ρ ↑, beta-lactamase (PEER)	Not reported	0.664 ± 0.002	Not reported	Not reported
ESM-1b (DeepProtein benchmark)Evaluation	DeepProtein Fluorescence (TAPE): ρ ↑, Fluorescence (TAPE)	Not reported	0.562 ± 0.003	Not reported	Not reported
ESM-1b (DeepProtein benchmark)Evaluation	DeepProtein Solubility (PEER): Averaged F1 ↑, Solubility (PEER)	Not reported	Not reported	Not reported	Length Exceeded%
ESM-1b (DeepProtein benchmark)Evaluation	DeepProtein Solubility (PEER): PR-AUC ↑, Solubility (PEER)	Not reported	Not reported	Length Exceeded%	Not reported
ESM-1b (DeepProtein benchmark)Evaluation	DeepProtein Stability (TAPE): ρ ↑, Stability (TAPE)	Not reported	0.682 ± 0.077 (best in column)	Not reported	Not reported

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ESM-1b (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): MAE ↓ Dataset: beta-lactamase (PEER)	0.171 ± 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 ESM-1b 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 'ESM-1b', column group 'β-lactamase', column 'MAE ↓'
Configuration: ESM-1b (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): ρ ↑ Dataset: beta-lactamase (PEER)	0.664 ± 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 ESM-1b 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 'ESM-1b', column group 'β-lactamase', column 'ρ ↑'
Configuration: ESM-1b (DeepProtein benchmark)	Protocol: DeepProtein Fluorescence (TAPE): MAE ↓ Dataset: Fluorescence (TAPE)	0.548 ± 0.004 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.004 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 ESM-1b 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 'ESM-1b', column group 'Fluorescence', column 'MAE ↓'
Configuration: ESM-1b (DeepProtein benchmark)	Protocol: DeepProtein Fluorescence (TAPE): ρ ↑ Dataset: Fluorescence (TAPE)	0.562 ± 0.003 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher 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 ESM-1b 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 'ESM-1b', column group 'Fluorescence', column 'ρ ↑'
Configuration: ESM-1b (DeepProtein benchmark)	Protocol: DeepProtein Solubility (PEER): Averaged F1 ↑ Dataset: Solubility (PEER)	Length Exceeded% 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 ESM-1b 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 'ESM-1b', column group 'Solubility', column 'Averaged F1 ↑'
Configuration: ESM-1b (DeepProtein benchmark)	Protocol: DeepProtein Solubility (PEER): PR-AUC ↑ Dataset: Solubility (PEER)	Length Exceeded% 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 ESM-1b 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 'ESM-1b', column group 'Solubility', column 'PR-AUC ↑'
Configuration: ESM-1b (DeepProtein benchmark)	Protocol: DeepProtein Stability (TAPE): MAE ↓ Dataset: Stability (TAPE)	0.282 ± 0.010 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.010 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 ESM-1b 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 'ESM-1b', column group 'Stability', column 'MAE ↓'
Configuration: ESM-1b (DeepProtein benchmark)	Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE)	0.682 ± 0.077 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.077 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 ESM-1b 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 'ESM-1b', 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-esm-1b

areas: protein-function
contexts: research
method types: foundation_model
reported name: ESM-1b
reported configuration: protein language model; default DeepProtein configuration (Table 9)
foundation model eligible: true
source locator: Tables 2 to 8, row 'ESM-1b'; Table 9 for the default configuration
missing metadata: version: reason: unreported; note: The tables name the model without a release version
provenance note: ESM-1b as trained and evaluated in the DeepProtein benchmark (protein language model).

Related records

configuration of: ESM-1b
system: ESM-1b on DeepProtein beta-lactamase (PEER) (MAE ↓)
system: ESM-1b on DeepProtein beta-lactamase (PEER) (ρ ↑)
system: ESM-1b on DeepProtein Fluorescence (TAPE) (MAE ↓)
system: ESM-1b on DeepProtein Fluorescence (TAPE) (ρ ↑)
system: ESM-1b on DeepProtein Solubility (PEER) (Averaged F1 ↑)
system: ESM-1b on DeepProtein Solubility (PEER) (PR-AUC ↑)
system: ESM-1b on DeepProtein Stability (TAPE) (MAE ↓)
system: ESM-1b on DeepProtein Stability (TAPE) (ρ ↑)

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