Protocol

DeepProtein Secondary structure prediction (TAPE): Averaged F1 ↑

Per-residue secondary structure prediction. 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 Secondary structure prediction (TAPE): Averaged F1 ↑ · Dataset: Secondary structure prediction (TAPE)

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-RNN (DeepProtein benchmark)Evaluation	98.80 ± 0.00% (best in column)
CNN (DeepProtein benchmark)Evaluation	87.76 ± 0.06%
Transformer (DeepProtein benchmark)Evaluation	49.66 ± 0.00%

All 3 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: CNN (DeepProtein benchmark)	Protocol: DeepProtein Secondary structure prediction (TAPE): Averaged F1 ↑ Dataset: Secondary structure prediction (TAPE)	87.76 ± 0.06% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), 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 CNN on DeepProtein Secondary structure prediction (TAPE) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-secondary-structure-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 7. row 'CNN', column group 'Secondary Structure', column 'Averaged F1 ↑'
Configuration: CNN-RNN (DeepProtein benchmark)	Protocol: DeepProtein Secondary structure prediction (TAPE): Averaged F1 ↑ Dataset: Secondary structure prediction (TAPE)	98.80 ± 0.00% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.00 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 Secondary structure prediction (TAPE) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-secondary-structure-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 7. row 'CNN-RNN', column group 'Secondary Structure', column 'Averaged F1 ↑'
Configuration: Transformer (DeepProtein benchmark)	Protocol: DeepProtein Secondary structure prediction (TAPE): Averaged F1 ↑ Dataset: Secondary structure prediction (TAPE)	49.66 ± 0.00% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.00 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 Secondary structure prediction (TAPE) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-secondary-structure-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 7. row 'Transformer', column group 'Secondary Structure', column 'Averaged F1 ↑'

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

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

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Baseline coverage

Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.

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Author-reported evaluations: 3

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Null control

Proposed control: requires review

Protocol-specific valid geometric or structural control

Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.

This is a suggested selection rule, not a validated method or a measured score.

Conventional reference

Proposed control: requires review

Upstream conventional structural reference with matched templates and cutoffs

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This is a suggested selection rule, not a validated method or a measured score.

Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)

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Strengths, limitations and unresolved questions

Evidence

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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-secondary-structure-avg-f1

areas: protein-structure
contexts: research
protocol: Train on the task's training split and score Secondary structure prediction (TAPE) 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: Secondary structure prediction (TAPE): 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: Secondary structure prediction (TAPE); train/valid/test 8678/2170/513

Related records

part of: DeepProtein benchmark
uses data: Secondary structure prediction (TAPE)
assessment: CNN on DeepProtein Secondary structure prediction (TAPE) (Averaged F1 ↑)
assessment: CNN-RNN on DeepProtein Secondary structure prediction (TAPE) (Averaged F1 ↑)
assessment: Transformer on DeepProtein Secondary structure prediction (TAPE) (Averaged F1 ↑)

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