Dataset

Yeast PPI (PEER)

Yeast 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 Yeast PPI (PEER): Averaged F1 ↑ Dataset: Yeast PPI (PEER)	15.4% 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 Yeast PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'ChemLLM-7B', column group 'Yeast PPI', column 'Averaged F1 ↑'
Configuration: CNN (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): Averaged F1 ↑ Dataset: Yeast PPI (PEER)	25.90 ± 0.10% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.10 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 Yeast PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'CNN', column group 'Yeast PPI', column 'Averaged F1 ↑'
Configuration: CNN-RNN (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): Averaged F1 ↑ Dataset: Yeast PPI (PEER)	47.20 ± 3.62% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 3.62 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 Yeast PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'CNN-RNN', column group 'Yeast PPI', column 'Averaged F1 ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): Averaged F1 ↑ Dataset: Yeast PPI (PEER)	66.7% 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 Yeast PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Deep Prot-T5', column group 'Yeast PPI', column 'Averaged F1 ↑'
Configuration: ESM-2-650M (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): Averaged F1 ↑ Dataset: Yeast PPI (PEER)	63.99 ± 1.00% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.00 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 ESM-2-650M on DeepProtein Yeast PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'ESM-2-650M', column group 'Yeast PPI', column 'Averaged F1 ↑'
Configuration: GAT (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): Averaged F1 ↑ Dataset: Yeast PPI (PEER)	57.00 ± 3.83% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 3.83 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 Yeast PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'GAT', column group 'Yeast PPI', column 'Averaged F1 ↑'
Configuration: GCN (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): Averaged F1 ↑ Dataset: Yeast PPI (PEER)	48.13 ± 3.88% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 3.88 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 Yeast PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'GCN', column group 'Yeast PPI', column 'Averaged F1 ↑'
Configuration: LlaSMol-Mistral-7B (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): Averaged F1 ↑ Dataset: Yeast PPI (PEER)	51.4% 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 Yeast PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'LlaSMol-Mistral-7B', column group 'Yeast PPI', column 'Averaged F1 ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): Averaged F1 ↑ Dataset: Yeast PPI (PEER)	58.94 ± 4.74% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 4.74 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 Yeast PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'NeuralFP', column group 'Yeast PPI', column 'Averaged F1 ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): Averaged F1 ↑ Dataset: Yeast PPI (PEER)	66.97 ± 0.01% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.01 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 Yeast PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Prot-T5-XL', column group 'Yeast PPI', column 'Averaged F1 ↑'
Configuration: Transformer (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): Averaged F1 ↑ Dataset: Yeast PPI (PEER)	51.93 ± 0.40% Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.40 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 Yeast PPI (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Transformer', column group 'Yeast PPI', column 'Averaged F1 ↑'
Configuration: CNN (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): GPU Memory (GB) Dataset: Yeast PPI (PEER)	2.69 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 Yeast PPI (PEER) (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-yeast-ppi-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'Yeast-PPI' / 'CNN', column 'GPU Memory (GB)'
Configuration: GCN (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): GPU Memory (GB) Dataset: Yeast PPI (PEER)	12.6 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 Yeast PPI (PEER) (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-yeast-ppi-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'Yeast-PPI' / 'GCN', column 'GPU Memory (GB)'
Configuration: Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): GPU Memory (GB) Dataset: Yeast PPI (PEER)	9.04 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 Yeast PPI (PEER) (GPU Memory (GB)) lit-protein-20261011-deepprotein-protocol-yeast-ppi-memory Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 8 row 'Yeast-PPI' / 'Prot-T5', column 'GPU Memory (GB)'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): PR-AUC ↑ Dataset: Yeast PPI (PEER)	53.6% 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 Yeast PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'ChemLLM-7B', column group 'Yeast PPI', column 'PR-AUC ↑'
Configuration: CNN (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): PR-AUC ↑ Dataset: Yeast PPI (PEER)	51.93±0.92% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.92 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 Yeast PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'CNN', column group 'Yeast PPI', column 'PR-AUC ↑'
Configuration: CNN-RNN (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): PR-AUC ↑ Dataset: Yeast PPI (PEER)	53.28±0.85% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.85 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 Yeast PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'CNN-RNN', column group 'Yeast PPI', column 'PR-AUC ↑'
Configuration: Deep Prot-T5 (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): PR-AUC ↑ Dataset: Yeast PPI (PEER)	63.2% 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 Yeast PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Deep Prot-T5', column group 'Yeast PPI', column 'PR-AUC ↑'
Configuration: ESM-2-650M (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): PR-AUC ↑ Dataset: Yeast PPI (PEER)	67.36 ± 0.80% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.80 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 Yeast PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'ESM-2-650M', column group 'Yeast PPI', column 'PR-AUC ↑'
Configuration: GAT (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): PR-AUC ↑ Dataset: Yeast PPI (PEER)	53.72±0.39% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.39 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 Yeast PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'GAT', column group 'Yeast PPI', column 'PR-AUC ↑'
Configuration: GCN (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): PR-AUC ↑ Dataset: Yeast PPI (PEER)	58.98 ± 0.72% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.72 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 Yeast PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'GCN', column group 'Yeast PPI', column 'PR-AUC ↑'
Configuration: LlaSMol-Mistral-7B (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): PR-AUC ↑ Dataset: Yeast PPI (PEER)	53.6% 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 Yeast PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'LlaSMol-Mistral-7B', column group 'Yeast PPI', column 'PR-AUC ↑'
Configuration: NeuralFP (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): PR-AUC ↑ Dataset: Yeast PPI (PEER)	57.00±1.51% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.51 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 Yeast PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'NeuralFP', column group 'Yeast PPI', column 'PR-AUC ↑'
Configuration: Prot-T5-XL (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): PR-AUC ↑ Dataset: Yeast PPI (PEER)	69.84 ± 0.46% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 0.46 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 Yeast PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Prot-T5-XL', column group 'Yeast PPI', column 'PR-AUC ↑'
Configuration: Transformer (DeepProtein benchmark)	Protocol: DeepProtein Yeast PPI (PEER): PR-AUC ↑ Dataset: Yeast PPI (PEER)	53.79±1.07% AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale) percent · higher Uncertainty: SD 1.07 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 Transformer on DeepProtein Yeast PPI (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-yeast-ppi-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 4. row 'Transformer', column group 'Yeast PPI', column 'PR-AUC ↑'

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

Research readiness

0 of 4 readiness checks met. These checks assess whether the evidence supports a reproducible investigation; a source-checked score alone does not meet them.

Readiness checks, gaps and artifacts

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

Evidence incomplete

Replay metrics

Exact outcomes, predictions, identifiers and evaluator are connected.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Metrics are recomputed from the saved predictions: not yet verified

Verified: Not verified

Evidence incomplete

Investigate discrepancies

Replay evidence includes annotations and an assessment of dependence. Unknown independence permits descriptive analysis only.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Metrics are recomputed from the saved predictions: not yet verified
Sample annotations are recorded: not yet verified
Dependence between samples is assessed: not yet verified

Verified: Not verified

Evidence incomplete

Run locally

A pinned recipe describes the inputs, environment and resource requirements.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
A pinned run recipe exists: not yet verified
Compute requirements are estimated: not yet verified

Verified: Not verified

Evidence incomplete

Validate independently

Separate data and exposure records support an independent test.

Missing or unresolved evidence

No verified artifact manifest is linked to this exact record.
File checksums match the recorded files: not yet verified
Predictions are matched to the right samples: not yet verified
Score meaning and direction are confirmed: not yet verified
Independent validation data exist: not yet verified
Overlap with training data is checked: not yet verified

Verified: Not verified

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Dataset and evaluation context

A dataset supplies biological observations. The evaluation protocol defines how those observations are split, used and scored.

Evidence

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 1668/131/373 Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Tables 2 to 7, column group 'Yeast 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 'Yeast 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 'Yeast 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 1668/131/373 Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Tables 2 to 7, column group 'Yeast 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 Yeast 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 'Yeast 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 Yeast PPI (PEER) Context-only references	DeepProtein: deep learning library and benchmark for protein sequence learning Original source ↗ Tables 2 to 7, column group 'Yeast 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-yeast-ppi

areas: protein-function
contexts: research
split: 1668/131/373
source locator: Tables 2 to 7, column group 'Yeast 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 1668/131/373

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