Dataset

PPI affinity (PEER)

Protein-protein binding affinity regression.

Evaluation results

28 evaluations · 28 results. Different protocols are not a single leaderboard.

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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 ↓'
Configuration: CNN (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): GPU Memory (GB) Dataset: PPI affinity (PEER)	1.37 Peak memory (peak GPU memory) gigabyte · 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 CNN resource usage on DeepProtein PPI affinity (PEER) (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-ppi-affinity-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'PPI_Affinity' / 'CNN', column 'GPU Memory (GB)'
Configuration: GCN (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): GPU Memory (GB) Dataset: PPI affinity (PEER)	1.65 Peak memory (peak GPU memory) gigabyte · 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 GCN resource usage on DeepProtein PPI affinity (PEER) (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-ppi-affinity-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'PPI_Affinity' / 'GCN', column 'GPU Memory (GB)'
Configuration: Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): GPU Memory (GB) Dataset: PPI affinity (PEER)	5.16 Peak memory (peak GPU memory) gigabyte · 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 Prot-T5 resource usage on DeepProtein PPI affinity (PEER) (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-ppi-affinity-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'PPI_Affinity' / 'Prot-T5', column 'GPU Memory (GB)'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.082 R² (coefficient of determination) unitless · 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 ChemLLM-7B on DeepProtein PPI affinity (PEER) (R2 ↑) lit-protein-20261011-deepprotein-protocol-ppi-affinity-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'ChemLLM-7B', column group 'PPI Affinity', column 'R2 ↑'
Configuration: CNN (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.646±0.003 R² (coefficient of determination) 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 CNN on DeepProtein PPI affinity (PEER) (R2 ↑) lit-protein-20261011-deepprotein-protocol-ppi-affinity-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'CNN', column group 'PPI Affinity', column 'R2 ↑'
Configuration: CNN-RNN (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.584 ± 0.026 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.026 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) (R2 ↑) lit-protein-20261011-deepprotein-protocol-ppi-affinity-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'CNN-RNN', column group 'PPI Affinity', column 'R2 ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.643 R² (coefficient of determination) unitless · 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 Deep Prot-T5 on DeepProtein PPI affinity (PEER) (R2 ↑) lit-protein-20261011-deepprotein-protocol-ppi-affinity-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Deep Prot-T5', column group 'PPI Affinity', column 'R2 ↑'
Configuration: ESM-2-650M (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.592 ± 0.001 R² (coefficient of determination) unitless · higher 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-2-650M on DeepProtein PPI affinity (PEER) (R2 ↑) lit-protein-20261011-deepprotein-protocol-ppi-affinity-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'ESM-2-650M', column group 'PPI Affinity', column 'R2 ↑'
Configuration: GAT (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.230±0.001 R² (coefficient of determination) unitless · higher 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 GAT on DeepProtein PPI affinity (PEER) (R2 ↑) lit-protein-20261011-deepprotein-protocol-ppi-affinity-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'GAT', column group 'PPI Affinity', column 'R2 ↑'
Configuration: GCN (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.366±0.034 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.034 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) (R2 ↑) lit-protein-20261011-deepprotein-protocol-ppi-affinity-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'GCN', column group 'PPI Affinity', column 'R2 ↑'
Configuration: LlaSMol-Mistral-7B (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	−0.008 R² (coefficient of determination) unitless · 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 LlaSMol-Mistral-7B on DeepProtein PPI affinity (PEER) (R2 ↑) lit-protein-20261011-deepprotein-protocol-ppi-affinity-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'LlaSMol-Mistral-7B', column group 'PPI Affinity', column 'R2 ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.100±0.054 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.054 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) (R2 ↑) lit-protein-20261011-deepprotein-protocol-ppi-affinity-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'NeuralFP', column group 'PPI Affinity', column 'R2 ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.573 ± 0.011 R² (coefficient of determination) unitless · higher 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 Prot-T5-XL on DeepProtein PPI affinity (PEER) (R2 ↑) lit-protein-20261011-deepprotein-protocol-ppi-affinity-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Prot-T5-XL', column group 'PPI Affinity', column 'R2 ↑'
Configuration: Transformer (DeepProtein benchmark)	Protocol: DeepProtein PPI affinity (PEER): R2 ↑ Dataset: PPI affinity (PEER)	0.425±0.021 R² (coefficient of determination) unitless · higher Uncertainty: SD 0.021 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) (R2 ↑) lit-protein-20261011-deepprotein-protocol-ppi-affinity-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Transformer', column group 'PPI Affinity', column 'R2 ↑'

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Claims, original sources and review scope · Release 2026-10-22-1b7cf027e4f6
Property and statement	Original source and location	Review and provenance
Population train/valid/test 2127/212/343 Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Tables 2 to 7, column group 'PPI Affinity'; the train/valid/test row of its table Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.population` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Source location Tables 2 to 7, column group 'PPI Affinity'; the train/valid/test row of its table Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Tables 2 to 7, column group 'PPI Affinity'; the train/valid/test row of its table Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.source_locator` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Split 2127/212/343 Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Tables 2 to 7, column group 'PPI Affinity'; the train/valid/test row of its table Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `attributes.split` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Description Protein-protein binding affinity regression. Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Tables 2 to 7, column group 'PPI Affinity'; the train/valid/test row of its table Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `description` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact
Name PPI affinity (PEER) Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Tables 2 to 7, column group 'PPI Affinity'; the train/valid/test row of its table Version: Version of record, Bioinformatics 2025 (PMC12553333 JATS full text) Retrieved: 2026-10-11T21:30:00Z	not individually reviewed No individual claim review recorded Source has a recorded evidence concern. Consult its source page before using the claim. Audit details Field: `name` Source artifact SHA-256: `b586921363170806d9f332afb37762ea61f464da6067a3ef0ab8853281964b7f` Hash scope: Hash scope not separately documented; inspect source record Inspected artifact

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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-data-ppi-affinity

areas: protein-function
contexts: research
split: 2127/212/343
source locator: Tables 2 to 7, column group 'PPI Affinity'; the train/valid/test row of its table
missing metadata: version: reason: unreported; note: The article names the source benchmark without a dataset version
population: train/valid/test 2127/212/343

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