Protocol

DeepProtein PPI affinity (PEER): MAE ↓

Protein-protein binding affinity regression. Scored by mean absolute error.

Overview

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Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.

11 recorded evaluations, 11 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

11 evaluations · 11 results. Different protocols are not a single leaderboard.

Protocol: DeepProtein PPI affinity (PEER): MAE ↓ · Dataset: PPI affinity (PEER)

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	MAE (mean absolute error)
CNN (DeepProtein benchmark)Evaluation	1.764 ± 0.051 (best in column)
Deep Prot-T5 (DeepProtein benchmark)Evaluation	1.87
CNN-RNN (DeepProtein benchmark)Evaluation	1.886 ± 0.108
ESM-2-650M (DeepProtein benchmark)Evaluation	1.893 ± 0.005
Prot-T5-XL (DeepProtein benchmark)Evaluation	1.979 ± 0.007
Transformer (DeepProtein benchmark)Evaluation	2.081 ± 0.133
GCN (DeepProtein benchmark)Evaluation	2.443 ± 0.036
GAT (DeepProtein benchmark)Evaluation	2.463 ± 0.015
NeuralFP (DeepProtein benchmark)Evaluation	2.555 ± 0.040
LlaSMol-Mistral-7B (DeepProtein benchmark)Evaluation	20.3
ChemLLM-7B (DeepProtein benchmark)Evaluation	28.8

All 11 result rows with coverage, uncertainty and sources

Filter evaluations

Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): MAE ↓ Dataset: PPI affinity (PEER)	28.8 MAE (mean absolute error) unit-unreported · lower 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 ChemLLM-7B 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 'ChemLLM-7B', column group 'PPI Affinity', column 'MAE ↓'
Configuration: CNN (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): MAE ↓ Dataset: PPI affinity (PEER)	1.764 ± 0.051 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.051 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 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 'CNN', column group 'PPI Affinity', column 'MAE ↓'
Configuration: CNN-RNN (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): MAE ↓ Dataset: PPI affinity (PEER)	1.886 ± 0.108 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.108 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 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 'CNN-RNN', column group 'PPI Affinity', column 'MAE ↓'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): MAE ↓ Dataset: PPI affinity (PEER)	1.87 MAE (mean absolute error) unit-unreported · lower 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 Deep Prot-T5 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 'Deep Prot-T5', column group 'PPI Affinity', column 'MAE ↓'
Configuration: ESM-2-650M (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): MAE ↓ Dataset: PPI affinity (PEER)	1.893 ± 0.005 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.005 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-2-650M 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 'ESM-2-650M', column group 'PPI Affinity', column 'MAE ↓'
Configuration: GAT (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): MAE ↓ Dataset: PPI affinity (PEER)	2.463 ± 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 GAT 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 'GAT', column group 'PPI Affinity', column 'MAE ↓'
Configuration: GCN (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): MAE ↓ Dataset: PPI affinity (PEER)	2.443 ± 0.036 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.036 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 GCN 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 'GCN', column group 'PPI Affinity', column 'MAE ↓'
Configuration: LlaSMol-Mistral-7B (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): MAE ↓ Dataset: PPI affinity (PEER)	20.3 MAE (mean absolute error) unit-unreported · lower 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 LlaSMol-Mistral-7B 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 'LlaSMol-Mistral-7B', column group 'PPI Affinity', column 'MAE ↓'
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: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): MAE ↓ Dataset: PPI affinity (PEER)	1.979 ± 0.007 MAE (mean absolute error) unit-unreported · lower 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 Prot-T5-XL 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 'Prot-T5-XL', column group 'PPI Affinity', column 'MAE ↓'
Configuration: Transformer (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): MAE ↓ Dataset: PPI affinity (PEER)	2.081 ± 0.133 MAE (mean absolute error) unit-unreported · lower Uncertainty: SD 0.133 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 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 'Transformer', column group 'PPI Affinity', column 'MAE ↓'

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

Methods and evaluation design

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Recorded evaluations

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Baseline coverage

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Author-reported evaluations: 11

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Conventional reference

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Simple features with train-only ridge regression

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

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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-ppi-affinity-mae

areas: protein-function
contexts: research
protocol: Train on the task's training split and score PPI affinity (PEER) on its test split; five random seeds per method, mean and standard deviation reported.
metric: mean-absolute-error
metric direction: lower
unit: unit-unreported
metric qualifier: mean absolute error
version: As published 2025
source locator: PPI affinity (PEER): column 'MAE ↓' 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.
unit detail: error in the task's own measurement units
dataset: PPI affinity (PEER); train/valid/test 2127/212/343

Related records

part of: DeepProtein benchmark
uses data: PPI affinity (PEER)
assessment: ChemLLM-7B on DeepProtein PPI affinity (PEER) (MAE ↓)
assessment: CNN on DeepProtein PPI affinity (PEER) (MAE ↓)
assessment: CNN-RNN on DeepProtein PPI affinity (PEER) (MAE ↓)
assessment: Deep Prot-T5 on DeepProtein PPI affinity (PEER) (MAE ↓)
assessment: ESM-2-650M on DeepProtein PPI affinity (PEER) (MAE ↓)
assessment: GAT on DeepProtein PPI affinity (PEER) (MAE ↓)
assessment: GCN on DeepProtein PPI affinity (PEER) (MAE ↓)
assessment: LlaSMol-Mistral-7B on DeepProtein PPI affinity (PEER) (MAE ↓)
assessment: NeuralFP on DeepProtein PPI affinity (PEER) (MAE ↓)
assessment: Prot-T5-XL on DeepProtein PPI affinity (PEER) (MAE ↓)
assessment: Transformer on DeepProtein PPI affinity (PEER) (MAE ↓)

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