rewirebio.iobenchmarks
Protocol

DeepProtein Fluorescence (TAPE): MAE ↓

Green fluorescent protein brightness regression, as distributed with TAPE. Scored by mean absolute error.

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 Fluorescence (TAPE): MAE ↓ · Dataset: Fluorescence (TAPE)

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.

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 Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
1.285 ± 0.001 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.001

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

AttentiveFP 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 'AttentiveFP', column group 'Fluorescence', column 'MAE ↓'
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
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: CNN (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
0.194 ± 0.001 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.001

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN 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 'CNN', column group 'Fluorescence', column 'MAE ↓'
Configuration: CNN-RNN (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
0.268 ± 0.002 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.002

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

CNN-RNN 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 'CNN-RNN', column group 'Fluorescence', column 'MAE ↓'
Configuration: Deep Prot-T5 (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
0.642 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
Methods, coverage and source

Deep Prot-T5 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 'Deep Prot-T5', column group 'Fluorescence', column 'MAE ↓'
Configuration: ESM-1b (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
0.548 ± 0.004 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.004

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

ESM-1b 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 'ESM-1b', column group 'Fluorescence', column 'MAE ↓'
Configuration: ESM-2-650M (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
0.563 ± 0.002 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.002

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

ESM-2-650M 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 'ESM-2-650M', column group 'Fluorescence', column 'MAE ↓'
Configuration: GAT (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
1.201 ± 0.005 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.005

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

GAT 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 'GAT', column group 'Fluorescence', column 'MAE ↓'
Configuration: GCN (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
0.864 ± 0.018 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.018

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

GCN 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 'GCN', column group 'Fluorescence', column 'MAE ↓'
Configuration: Graphormer (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
1.201 ± 0.032 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.032

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

Graphormer 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 'Graphormer', column group 'Fluorescence', column 'MAE ↓'
Configuration: LlaSMol-Mistral-7B (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
2.08 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
Methods, coverage and source

LlaSMol-Mistral-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 'LlaSMol-Mistral-7B', column group 'Fluorescence', column 'MAE ↓'
Configuration: MPNN (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
1.275 ± 0.011 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.011

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

MPNN 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 'MPNN', column group 'Fluorescence', column 'MAE ↓'
Configuration: NeuralFP (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
1.016 ± 0.081 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.081

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

NeuralFP 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 'NeuralFP', column group 'Fluorescence', column 'MAE ↓'
Configuration: PAGTN (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
1.255 ± 0.040 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.040

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

PAGTN 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 'PAGTN', column group 'Fluorescence', column 'MAE ↓'
Configuration: Prot-T5-XL (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
0.535 ± 0.006 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.006

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

Prot-T5-XL 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 'Prot-T5-XL', column group 'Fluorescence', column 'MAE ↓'
Configuration: ProtBert (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
0.583 ± 0.007 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.007

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

ProtBert 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 'ProtBert', column group 'Fluorescence', column 'MAE ↓'
Configuration: Transformer (DeepProtein benchmark)Protocol: DeepProtein Fluorescence (TAPE): MAE ↓
Dataset: Fluorescence (TAPE)
0.371 ± 0.005 MAE (mean absolute error)
unit-unreported · lower

Uncertainty: SD 0.005

Coverage: Not reported scored / Not reported eligible

Author-reported evaluation · Source checked
Methods, coverage and source

Transformer 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 'Transformer', column group 'Fluorescence', column 'MAE ↓'

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

Methods and evaluation design

Procedure, tasks and evaluated configurations

Recorded evaluations

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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.

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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

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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

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Technical metadata and extraction receipts

Stable ID: lit-protein-20261011-deepprotein-protocol-fluorescence-mae

areas
protein-function
contexts
research
protocol
Train on the task's training split and score Fluorescence (TAPE) on its test split; five random seeds per method, mean and standard deviation reported.
metric
mean-absolute-error
metric direction
lower
unit
unit-unreported
metric qualifier
mean absolute error
version
As published 2025
source locator
Fluorescence (TAPE): column 'MAE ↓' 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.
unit detail
error in the task's own measurement units
dataset
Fluorescence (TAPE); train/valid/test 21446/5362/27217
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