Dataset

Human PPI (PEER)

Human protein-protein interaction classification.

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 Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER)	15.5% 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 ChemLLM-7B on DeepProtein Human PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'ChemLLM-7B', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: CNN (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER)	69.65 ± 1.63% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.63 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 Human PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'CNN', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: CNN-RNN (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER)	69.87 ± 2.59% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 2.59 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 Human PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'CNN-RNN', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER)	80.3% 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 Deep Prot-T5 on DeepProtein Human PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Deep Prot-T5', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: ESM-2-650M (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER)	87.63 ± 0.60% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.60 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 Human PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'ESM-2-650M', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: GAT (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER)	73.92 ± 3.50% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 3.50 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 Human PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'GAT', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: GCN (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER)	71.05 ± 2.90% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 2.90 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 Human PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'GCN', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: LlaSMol-Mistral-7B (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER)	49.1% 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 LlaSMol-Mistral-7B on DeepProtein Human PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'LlaSMol-Mistral-7B', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER)	67.62 ± 1.03% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.03 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 Human PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'NeuralFP', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER)	87.64 ± 0.98% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.98 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 Human PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Prot-T5-XL', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: Transformer (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): Averaged F1 ↑ Dataset: Human PPI (PEER)	68.64 ± 1.06% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.06 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 Transformer on DeepProtein Human PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Transformer', column group 'Human PPI', column 'Averaged F1 ↑'
Configuration: CNN (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): GPU Memory (GB) Dataset: Human PPI (PEER)	0.96 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 Human PPI (PEER) (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-human-ppi-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'Human-PPI' / 'CNN', column 'GPU Memory (GB)'
Configuration: GCN (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): GPU Memory (GB) Dataset: Human PPI (PEER)	2.13 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 Human PPI (PEER) (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-human-ppi-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'Human-PPI' / 'GCN', column 'GPU Memory (GB)'
Configuration: Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): GPU Memory (GB) Dataset: Human PPI (PEER)	9.38 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 Human PPI (PEER) (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-human-ppi-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'Human-PPI' / 'Prot-T5', column 'GPU Memory (GB)'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER)	47.1% 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 ChemLLM-7B on DeepProtein Human PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'ChemLLM-7B', column group 'Human PPI', column 'PR-AUC ↑'
Configuration: CNN (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER)	70.37±1.22% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.22 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 Human PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'CNN', column group 'Human PPI', column 'PR-AUC ↑'
Configuration: CNN-RNN (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER)	70.45±2.68% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 2.68 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 Human PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'CNN-RNN', column group 'Human PPI', column 'PR-AUC ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER)	76.4% 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 Deep Prot-T5 on DeepProtein Human PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Deep Prot-T5', column group 'Human PPI', column 'PR-AUC ↑'
Configuration: ESM-2-650M (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER)	96.17 ± 0.18% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.18 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 Human PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'ESM-2-650M', column group 'Human PPI', column 'PR-AUC ↑'
Configuration: GAT (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER)	77.63±3.13% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 3.13 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 Human PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'GAT', column group 'Human PPI', column 'PR-AUC ↑'
Configuration: GCN (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER)	82.21 ± 1.13% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.13 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 Human PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'GCN', column group 'Human PPI', column 'PR-AUC ↑'
Configuration: LlaSMol-Mistral-7B (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER)	49.5% 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 LlaSMol-Mistral-7B on DeepProtein Human PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'LlaSMol-Mistral-7B', column group 'Human PPI', column 'PR-AUC ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER)	80.11±1.25% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.25 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 Human PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'NeuralFP', column group 'Human PPI', column 'PR-AUC ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER)	95.36 ± 0.07% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.07 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 Human PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Prot-T5-XL', column group 'Human PPI', column 'PR-AUC ↑'
Configuration: Transformer (DeepProtein benchmark)	Protocol: DeepProtein Human PPI (PEER): PR-AUC ↑ Dataset: Human PPI (PEER)	59.36±4.00% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 4.00 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 Human PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-human-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Transformer', column group 'Human PPI', column 'PR-AUC ↑'

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Release 2026-10-22-1b7cf027e4f6 · Evidence verified: Not verified

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Source checking verifies the cited claim or transcription. It does not establish independent reproduction.

Evidence table

Inspect claims, sources and review details

Trace each statement to its source and review. A context-only reference supports the record generally; it does not verify an individual field. Source checking does not reproduce an experiment.

One row per statement and cited source. Multiple citations are not independent evaluations. Shared locators are labelled explicitly.

5 evidence rows matching the loaded filters

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 6844/277/227 Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Tables 2 to 7, column group 'Human PPI'; 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 'Human PPI'; 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 'Human PPI'; 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 6844/277/227 Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Tables 2 to 7, column group 'Human PPI'; 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 Human protein-protein interaction classification. Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Tables 2 to 7, column group 'Human PPI'; 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 Human PPI (PEER) Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Tables 2 to 7, column group 'Human PPI'; 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

How to read the evidence

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-human-ppi

areas: protein-function
contexts: research
split: 6844/277/227
source locator: Tables 2 to 7, column group 'Human PPI'; 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 6844/277/227

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