Configuration

ChemLLM-7B (DeepProtein benchmark)

Configuration of ChemLLM-7B: chemistry large language model prompted for the task; default DeepProtein configuration.

Overview

An explanatory profile has not yet been reviewed for this record.

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

Evaluations and results

26 evaluations · 26 results. Different protocols are not a single leaderboard.

Sorted by MAE (mean absolute error) (lower is better). The best value in each column is highlighted. Decimals are rounded for display; each value links to the printed value and its source.

Tested configuration	Protocol and dataset	MAE (mean absolute error)	Macro F1 (averaged macro F1 (Figure 3 caption: 'averaged macro F1'), printed on a 0 to 100 scale)	AUPRC (area under the precision-recall curve, printed on a 0 to 100 scale)	R² (coefficient of determination)	Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split)	Accuracy (accuracy, printed on a 0 to 100 scale)
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Fluorescence (TAPE): MAE ↓, Fluorescence (TAPE)	19.9 (best in column)	Not reported	Not reported	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein CRISPR-Leenay repair outcome: MAE ↓, CRISPR-Leenay repair outcome	20.1	Not reported	Not reported	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein PPI affinity (PEER): MAE ↓, PPI affinity (PEER)	28.8	Not reported	Not reported	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein SAbDab-Chen antibody developability: MAE ↓, SAbDab-Chen antibody developability	32.3	Not reported	Not reported	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein TAP antibody developability: MAE ↓, TAP antibody developability	46	Not reported	Not reported	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein beta-lactamase (PEER): MAE ↓, beta-lactamase (PEER)	112	Not reported	Not reported	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Stability (TAPE): MAE ↓, Stability (TAPE)	46300	Not reported	Not reported	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein beta-lactamase (PEER): ρ ↑, beta-lactamase (PEER)	Not reported	Not reported	Not reported	Not reported	0.017 (best in column)	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Binary localization (PEER): Averaged F1 ↑, Binary localization (PEER)	Not reported	1.43%	Not reported	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Binary localization (PEER): PR-AUC ↑, Binary localization (PEER)	Not reported	Not reported	56.3% (best in column)	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein CRISPR-Leenay repair outcome: R2 ↑, CRISPR-Leenay repair outcome	Not reported	Not reported	Not reported	0.061	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Fluorescence (TAPE): ρ ↑, Fluorescence (TAPE)	Not reported	Not reported	Not reported	Not reported	−0.019	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Fold classification (TAPE): Acc ↑, Fold classification (TAPE)	Not reported	Not reported	Not reported	Not reported	Not reported	0.64%
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Fold classification (TAPE): Averaged F1 ↑, Fold classification (TAPE)	Not reported	0.04%	Not reported	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Human PPI (PEER): Averaged F1 ↑, Human PPI (PEER)	Not reported	15.5% (best in column)	Not reported	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Human PPI (PEER): PR-AUC ↑, Human PPI (PEER)	Not reported	Not reported	47.1%	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein PPI affinity (PEER): R2 ↑, PPI affinity (PEER)	Not reported	Not reported	Not reported	0.082	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein SAbDab-Chen antibody developability: R2 ↑, SAbDab-Chen antibody developability	Not reported	Not reported	Not reported	−0.006	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Solubility (PEER): Averaged F1 ↑, Solubility (PEER)	Not reported	1.64%	Not reported	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Solubility (PEER): PR-AUC ↑, Solubility (PEER)	Not reported	Not reported	50.6%	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Stability (TAPE): ρ ↑, Stability (TAPE)	Not reported	Not reported	Not reported	Not reported	−0.187	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Subcellular localization (PEER): Acc ↑, Subcellular localization (PEER)	Not reported	Not reported	Not reported	Not reported	Not reported	6.24% (best in column)
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Subcellular localization (PEER): Averaged F1 ↑, Subcellular localization (PEER)	Not reported	0.59%	Not reported	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein TAP antibody developability: R2 ↑, TAP antibody developability	Not reported	Not reported	Not reported	0.099 (best in column)	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Yeast PPI (PEER): Averaged F1 ↑, Yeast PPI (PEER)	Not reported	15.4%	Not reported	Not reported	Not reported	Not reported
ChemLLM-7B (DeepProtein benchmark)Evaluation	DeepProtein Yeast PPI (PEER): PR-AUC ↑, Yeast PPI (PEER)	Not reported	Not reported	53.6%	Not reported	Not reported	Not reported

All 26 result rows with coverage, uncertainty and sources

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Tested model or methodProtocolDatasetEvaluation setupMetricEvidence origin

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): MAE ↓ Dataset: beta-lactamase (PEER)	112 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 beta-lactamase (PEER) (MAE ↓) lit-protein-20261011-deepprotein-protocol-beta-lactamase-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'ChemLLM-7B', column group 'β-lactamase', column 'MAE ↓'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein beta-lactamase (PEER): ρ ↑ Dataset: beta-lactamase (PEER)	0.017 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) 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 beta-lactamase (PEER) (ρ ↑) lit-protein-20261011-deepprotein-protocol-beta-lactamase-rho Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'ChemLLM-7B', column group 'β-lactamase', column 'ρ ↑'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein Binary localization (PEER): Averaged F1 ↑ Dataset: Binary localization (PEER)	1.43% 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 Binary localization (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-binary-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 3. row 'ChemLLM-7B', column group 'Binary', column 'Averaged F1 ↑'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein Binary localization (PEER): PR-AUC ↑ Dataset: Binary localization (PEER)	56.3% 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 Binary localization (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-binary-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 3. row 'ChemLLM-7B', column group 'Binary', column 'PR-AUC ↑'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein CRISPR-Leenay repair outcome: MAE ↓ Dataset: CRISPR-Leenay repair outcome	20.1 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 CRISPR-Leenay repair outcome (MAE ↓) lit-protein-20261011-deepprotein-protocol-crispr-leenay-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'ChemLLM-7B', column group 'CRISPR-Leenay', column 'MAE ↓'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein CRISPR-Leenay repair outcome: R2 ↑ Dataset: CRISPR-Leenay repair outcome	0.061 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 CRISPR-Leenay repair outcome (R2 ↑) lit-protein-20261011-deepprotein-protocol-crispr-leenay-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'ChemLLM-7B', column group 'CRISPR-Leenay', column 'R2 ↑'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein Fluorescence (TAPE): MAE ↓ Dataset: Fluorescence (TAPE)	19.9 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 Fluorescence (TAPE) (MAE ↓) lit-protein-20261011-deepprotein-protocol-fluorescence-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'ChemLLM-7B', column group 'Fluorescence', column 'MAE ↓'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein Fluorescence (TAPE): ρ ↑ Dataset: Fluorescence (TAPE)	−0.019 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) 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 Fluorescence (TAPE) (ρ ↑) lit-protein-20261011-deepprotein-protocol-fluorescence-rho Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'ChemLLM-7B', column group 'Fluorescence', column 'ρ ↑'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein Fold classification (TAPE): Acc ↑ Dataset: Fold classification (TAPE)	0.64% Accuracy (accuracy, 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 Fold classification (TAPE) (Acc ↑) lit-protein-20261011-deepprotein-protocol-fold-acc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 7. row 'ChemLLM-7B', column group 'Fold', column 'Acc ↑'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein Fold classification (TAPE): Averaged F1 ↑ Dataset: Fold classification (TAPE)	0.04% 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 Fold classification (TAPE) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-fold-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 7. row 'ChemLLM-7B', column group 'Fold', column 'Averaged F1 ↑'
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: 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: 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: 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: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein SAbDab-Chen antibody developability: MAE ↓ Dataset: SAbDab-Chen antibody developability	32.3 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 ChemLLM-7B on DeepProtein SAbDab-Chen antibody developability (MAE ↓) lit-protein-20261011-deepprotein-protocol-sabdab-chen-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'ChemLLM-7B', column group 'SAbDab-Chen', column 'MAE ↓'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein SAbDab-Chen antibody developability: R2 ↑ Dataset: SAbDab-Chen antibody developability	−0.006 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 SAbDab-Chen antibody developability (R2 ↑) lit-protein-20261011-deepprotein-protocol-sabdab-chen-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'ChemLLM-7B', column group 'SAbDab-Chen', column 'R2 ↑'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein Solubility (PEER): Averaged F1 ↑ Dataset: Solubility (PEER)	1.64% 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 Solubility (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-solubility-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'ChemLLM-7B', column group 'Solubility', column 'Averaged F1 ↑'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein Solubility (PEER): PR-AUC ↑ Dataset: Solubility (PEER)	50.6% 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 Solubility (PEER) (PR-AUC ↑) lit-protein-20261011-deepprotein-protocol-solubility-pr-auc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'ChemLLM-7B', column group 'Solubility', column 'PR-AUC ↑'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein Stability (TAPE): MAE ↓ Dataset: Stability (TAPE)	46300 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 Stability (TAPE) (MAE ↓) lit-protein-20261011-deepprotein-protocol-stability-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'ChemLLM-7B', column group 'Stability', column 'MAE ↓'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE)	−0.187 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) 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 Stability (TAPE) (ρ ↑) lit-protein-20261011-deepprotein-protocol-stability-rho Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 2. row 'ChemLLM-7B', column group 'Stability', column 'ρ ↑'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein Subcellular localization (PEER): Acc ↑ Dataset: Subcellular localization (PEER)	6.24% Accuracy (accuracy, 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 Subcellular localization (PEER) (Acc ↑) lit-protein-20261011-deepprotein-protocol-subcellular-acc Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 3. row 'ChemLLM-7B', column group 'Subcellular', column 'Acc ↑'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein Subcellular localization (PEER): Averaged F1 ↑ Dataset: Subcellular localization (PEER)	0.59% 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 Subcellular localization (PEER) (Averaged F1 ↑) lit-protein-20261011-deepprotein-protocol-subcellular-avg-f1 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 3. row 'ChemLLM-7B', column group 'Subcellular', column 'Averaged F1 ↑'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein TAP antibody developability: MAE ↓ Dataset: TAP antibody developability	46 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 TAP antibody developability (MAE ↓) lit-protein-20261011-deepprotein-protocol-tap-mae Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'ChemLLM-7B', column group 'TAP', column 'MAE ↓'
Configuration: ChemLLM-7B (DeepProtein benchmark)	Protocol: DeepProtein TAP antibody developability: R2 ↑ Dataset: TAP antibody developability	0.099 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 TAP antibody developability (R2 ↑) lit-protein-20261011-deepprotein-protocol-tap-r2 Aggregation: Not reported DeepProtein: deep learning library and benchmark for protein sequence learning · Table 6. row 'ChemLLM-7B', column group 'TAP', column 'R2 ↑'
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 ↑'

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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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Stable ID: lit-protein-20261011-deepprotein-config-chemllm-7b

areas: protein-function
contexts: research
method types: foundation_model
reported name: ChemLLM-7B
reported configuration: chemistry large language model prompted for the task; default DeepProtein configuration (Table 9)
foundation model eligible: true
source locator: Tables 2 to 8, row 'ChemLLM-7B'; Table 9 for the default configuration
missing metadata: version: reason: unreported; note: The tables name the model without a release version
provenance note: ChemLLM-7B as trained and evaluated in the DeepProtein benchmark (chemistry large language model prompted for the task).

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