DeepProtein Stability (TAPE): ρ ↑
Protein stability regression, as distributed with TAPE. Scored by Spearman rank correlation on the task's test split.
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.
17 recorded evaluations, 17 metric rows. A comparison chart has not yet been validated for these results. The table retains the individual findings and their sources.
Results
Results are available, but no reviewed comparison panel is linked in this release.
All evaluations
17 evaluations · 17 results. Different protocols are not a single leaderboard.
Protocol: DeepProtein Stability (TAPE): ρ ↑ · Dataset: Stability (TAPE)
Sorted by Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) (higher 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.
All 17 result rows with coverage, uncertainty and sources
Filter evaluations
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: AttentiveFP (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.013±0.004 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.004 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceAttentiveFP 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 'AttentiveFP', column group 'Stability', column 'ρ ↑' |
| 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 checkedMethods, coverage and sourceChemLLM-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: CNN (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.715 ± 0.025 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.025 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN 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 'CNN', column group 'Stability', column 'ρ ↑' |
| Configuration: CNN-RNN (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.635±0.025 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.025 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCNN-RNN 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 'CNN-RNN', column group 'Stability', column 'ρ ↑' |
| Configuration: Deep Prot-T5 (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.725 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 checkedMethods, coverage and sourceDeep Prot-T5 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 'Deep Prot-T5', column group 'Stability', column 'ρ ↑' |
| Configuration: ESM-1b (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.682 ± 0.077 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.077 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-1b 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 'ESM-1b', column group 'Stability', column 'ρ ↑' |
| Configuration: ESM-2-650M (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.689 ± 0.020 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.020 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2-650M 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 'ESM-2-650M', column group 'Stability', column 'ρ ↑' |
| Configuration: GAT (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.101±0.001 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.001 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGAT 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 'GAT', column group 'Stability', column 'ρ ↑' |
| Configuration: GCN (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.443 ± 0.017 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.017 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceGCN 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 'GCN', column group 'Stability', column 'ρ ↑' |
| Configuration: Graphormer (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | OOM 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 checkedMethods, coverage and sourceGraphormer 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 'Graphormer', column group 'Stability', column 'ρ ↑' |
| Configuration: LlaSMol-Mistral-7B (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.094 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 checkedMethods, coverage and sourceLlaSMol-Mistral-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 'LlaSMol-Mistral-7B', column group 'Stability', column 'ρ ↑' |
| Configuration: MPNN (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.118±0.061 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.061 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceMPNN 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 'MPNN', column group 'Stability', column 'ρ ↑' |
| Configuration: NeuralFP (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.373±0.023 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.023 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceNeuralFP 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 'NeuralFP', column group 'Stability', column 'ρ ↑' |
| Configuration: PAGTN (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.088±0.194 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.194 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourcePAGTN 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 'PAGTN', column group 'Stability', column 'ρ ↑' |
| Configuration: Prot-T5-XL (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.767±0.008 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.008 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProt-T5-XL 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 'Prot-T5-XL', column group 'Stability', column 'ρ ↑' |
| Configuration: ProtBert (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.646 ± 0.064 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.064 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceProtBert 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 'ProtBert', column group 'Stability', column 'ρ ↑' |
| Configuration: Transformer (DeepProtein benchmark) | Protocol: DeepProtein Stability (TAPE): ρ ↑ Dataset: Stability (TAPE) | 0.375±0.052 Spearman (Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split) unitless · higher Uncertainty: SD 0.052 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceTransformer 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 'Transformer', column group 'Stability', column 'ρ ↑' |
Source checking is not independent reproduction. Release 2026-10-22-1b7cf027e4f6.
Methods and evaluation design
Procedure, tasks and evaluated configurations
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- AttentiveFP on DeepProtein Stability (TAPE) (ρ ↑)
- ChemLLM-7B on DeepProtein Stability (TAPE) (ρ ↑)
- CNN on DeepProtein Stability (TAPE) (ρ ↑)
- CNN-RNN on DeepProtein Stability (TAPE) (ρ ↑)
- Deep Prot-T5 on DeepProtein Stability (TAPE) (ρ ↑)
- ESM-1b on DeepProtein Stability (TAPE) (ρ ↑)
- ESM-2-650M on DeepProtein Stability (TAPE) (ρ ↑)
- GAT on DeepProtein Stability (TAPE) (ρ ↑)
- GCN on DeepProtein Stability (TAPE) (ρ ↑)
- Graphormer on DeepProtein Stability (TAPE) (ρ ↑)
- LlaSMol-Mistral-7B on DeepProtein Stability (TAPE) (ρ ↑)
- MPNN on DeepProtein Stability (TAPE) (ρ ↑)
Baseline coverage
Reference methods help show what a model adds beyond simple controls. We track a null control and a conventional method for each protocol.
0 of 2 active baseline roles have published Rewire measurements in this release. Measurements on a selected protocol do not establish coverage of an entire suite.
No execution recipe linked to this protocol. Recipe availability does not establish a completed evaluation.
- Author-reported evaluations
- 17
Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.
Null control
Proposed control: requires review
Training-set mean where supervised fitting is permitted
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Conventional reference
Proposed control: requires review
Simple features with train-only ridge regression
Protocol-specific applicability, permitted inputs, access, split, evaluator and execution requirements need review before implementation or execution.
This is a suggested selection rule, not a validated method or a measured score.
Protocol coverage CSV (gzip) · Model evaluation matrix (gzip) · Source table (gzip) · Release and checksums (gzip)
Coverage is derived from release 2026-10-22-1b7cf027e4f6. Source citations describe the original records; they do not validate an unreviewed baseline proposal. No results have been generated by this audit.
Run instructions
No runnable recipe has been reviewed for this protocol. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
Strengths, limitations and unresolved questions
Evidence
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Evidence table
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Sources and history
Release 2026-10-22-1b7cf027e4f6 · Record review: source checked
1 source record and release history
- DeepProtein: deep learning library and benchmark for protein sequence learning · Original source · Version of record, Bioinformatics 2025 (PMC12553333 JATS full text)
Technical metadata and extraction receipts
Stable ID: lit-protein-20261011-deepprotein-protocol-stability-rho
- areas
- protein-function
- contexts
- research
- protocol
- Train on the task's training split and score Stability (TAPE) on its test split; five random seeds per method, mean and standard deviation reported.
- metric
- spearman-correlation
- metric direction
- higher
- unit
- unitless
- metric qualifier
- Spearman rank correlation, as defined in the article's Evaluation metrics section; supervised split
- version
- As published 2025
- source locator
- Stability (TAPE): column 'ρ ↑' of its table in Tables 2 to 8
- replicates
- Five random seeds (table footnote a: 'we used five different random seeds to perform independent runs, reporting the average results along with their standard deviations')
- limitations
- Author-reported results: the DeepProtein authors ran every method.
- dataset
- Stability (TAPE); train/valid/test 53571/2512/12851
Related records
- part of: DeepProtein benchmark
- uses data: Stability (TAPE)
- assessment: AttentiveFP on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: ChemLLM-7B on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: CNN on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: CNN-RNN on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: Deep Prot-T5 on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: ESM-1b on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: ESM-2-650M on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: GAT on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: GCN on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: Graphormer on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: LlaSMol-Mistral-7B on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: MPNN on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: NeuralFP on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: PAGTN on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: Prot-T5-XL on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: ProtBert on DeepProtein Stability (TAPE) (ρ ↑)
- assessment: Transformer on DeepProtein Stability (TAPE) (ρ ↑)
- assessed by: Assess methods for protein stability experiments