rewirebio.iobenchmarks
Protocol

DeepProtein Stability (TAPE): ρ ↑

Protein stability regression, as distributed with TAPE. Scored by Spearman rank correlation on the task's test split.

17 evaluations · 17 results

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.

View coverage and remaining gaps across all benchmarks

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

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence 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 checked
Methods, coverage and source

AttentiveFP 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 checked
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: 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 checked
Methods, coverage and source

CNN 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 checked
Methods, coverage and source

CNN-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 checked
Methods, coverage and source

Deep 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 checked
Methods, coverage and source

ESM-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 checked
Methods, coverage and source

ESM-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 checked
Methods, coverage and source

GAT 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 checked
Methods, coverage and source

GCN 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 checked
Methods, coverage and source

Graphormer 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 checked
Methods, coverage and source

LlaSMol-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 checked
Methods, coverage and source

MPNN 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 checked
Methods, coverage and source

NeuralFP 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 checked
Methods, coverage and source

PAGTN 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 checked
Methods, coverage and source

Prot-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 checked
Methods, coverage and source

ProtBert 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 checked
Methods, coverage and source

Transformer 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.

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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.

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Evidence

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Evidence table

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Sources and history

Release 2026-10-22-1b7cf027e4f6 · Record review: source checked

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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
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