Protocol

DeepProtein PDB-Jespersen epitope prediction: Averaged F1 ↑

Residue-level epitope prediction on the Jespersen PDB dataset. Scored by averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale.

3 evaluations · 3 results

Overview

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3 recorded evaluations, 3 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.

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Results

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All evaluations

3 evaluations · 3 results. Different protocols are not a single leaderboard.

Protocol: DeepProtein PDB-Jespersen epitope prediction: Averaged F1 ↑ · Dataset: PDB-Jespersen epitope prediction

Sorted by Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) (higher 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	Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale)
CNN (DeepProtein benchmark)Evaluation	52.43 ± 0.35% (best in column)
CNN-RNN (DeepProtein benchmark)Evaluation	44.82 ± 1.69%
Transformer (DeepProtein benchmark)Evaluation	27.31 ± 0.56%

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: CNN (DeepProtein benchmark)	Protocol: DeepProtein PDB-Jespersen epitope prediction: Averaged F1 ↑ Dataset: PDB-Jespersen epitope prediction	52.43 ± 0.35% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.35 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 CNN on DeepProtein PDB-Jespersen epitope prediction (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-pdb-jespersen-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 5. row 'CNN', column group 'PDB-Jespersen', column 'Averaged F1 ↑'
Configuration: CNN-RNN (DeepProtein benchmark)	Protocol: DeepProtein PDB-Jespersen epitope prediction: Averaged F1 ↑ Dataset: PDB-Jespersen epitope prediction	44.82 ± 1.69% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.69 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 CNN-RNN on DeepProtein PDB-Jespersen epitope prediction (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-pdb-jespersen-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 5. row 'CNN-RNN', column group 'PDB-Jespersen', column 'Averaged F1 ↑'
Configuration: Transformer (DeepProtein benchmark)	Protocol: DeepProtein PDB-Jespersen epitope prediction: Averaged F1 ↑ Dataset: PDB-Jespersen epitope prediction	27.31 ± 0.56% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.56 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 Transformer on DeepProtein PDB-Jespersen epitope prediction (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-pdb-jespersen-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 5. row 'Transformer', column group 'PDB-Jespersen', column 'Averaged F1 ↑'

Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.

Methods and evaluation design

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Author-reported evaluations: 3

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Evidence table

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

1 source record and release history

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-protocol-pdb-jespersen-avg-f1

areas: protein-function
contexts: research
protocol: Train on the task's training split and score PDB-Jespersen epitope prediction on its test split; five random seeds per method, mean and standard deviation reported.
metric: macro-f1
metric direction: higher
unit: percent
metric qualifier: averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale
version: As published 2025
source locator: PDB-Jespersen epitope prediction: column 'Averaged F1 ↑' of its table in Tables 2 to 8
replicates: Five random seeds (table footnote a: 'we used five different random seeds to perform independent runs, reporting the average results along with their standard deviations')
limitations: Author-reported results: the DeepProtein authors ran every method.
dataset: PDB-Jespersen epitope prediction; train/valid/test 313/45/89

Related records

part of: DeepProtein benchmark
uses data: PDB-Jespersen epitope prediction
assessment: CNN on DeepProtein PDB-Jespersen epitope prediction (Averaged F1 ↑)
assessment: CNN-RNN on DeepProtein PDB-Jespersen epitope prediction (Averaged F1 ↑)
assessment: Transformer on DeepProtein PDB-Jespersen epitope prediction (Averaged F1 ↑)

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