rewire.itbenchmarks
Protocol

ProteinGym AMFR official zero-shot Spearman snapshot

Original official assay-level zero-shot comparison; mixed single/double substitutions, not the proposed singles-only experiment.

97 evaluations · 97 results

Overview

Original official assay-level zero-shot comparison; mixed single/double substitutions, not the proposed singles-only experiment.

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

97 recorded evaluations, 97 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

97 evaluations · 97 results. Different protocols are not a single leaderboard.

Filter evaluations

Applied filters: All linked evaluations

Exact evaluated configurations and original reported results
Tested configurationProtocol and datasetFindingEvidence and details
Configuration: AIDO Protein-RAG (16B) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.445 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

AIDO Protein-RAG (16B) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=AIDO Protein-RAG (16B)
Configuration: CARP (38M) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
-0.185 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

CARP (38M) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=CARP (38M)
Configuration: CARP (600K) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
-0.194 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

CARP (600K) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=CARP (600K)
Configuration: CARP (640M) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.165 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

CARP (640M) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=CARP (640M)
Configuration: CARP (76M) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.114 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

CARP (76M) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=CARP (76M)
Configuration: DeepSequence (ensemble) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.407 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

DeepSequence (ensemble) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=DeepSequence (ensemble)
Configuration: DeepSequence (single) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.419 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

DeepSequence (single) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=DeepSequence (single)
Configuration: ESCOTT [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.41 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

ESCOTT AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESCOTT
Configuration: ESM-1b [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.374 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

ESM-1b AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM-1b
Configuration: ESM-1v (ensemble) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.423 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

ESM-1v (ensemble) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM-1v (ensemble)
Configuration: ESM-1v (single) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.07 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

ESM-1v (single) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM-1v (single)
Configuration: ESM-C (300M) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.364 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

ESM-C (300M) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM-C (300M)
Configuration: ESM-C (600M) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.262 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

ESM-C (600M) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM-C (600M)
Configuration: ESM-IF1 [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.433 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

ESM-IF1 AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM-IF1
Configuration: ESM2 (150M) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.321 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

ESM2 (150M) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM2 (150M)
Configuration: ESM2 (15B) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.26 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

ESM2 (15B) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM2 (15B)
Configuration: ESM2 (35M) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.286 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

ESM2 (35M) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM2 (35M)
Configuration: ESM2 (3B) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.297 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

ESM2 (3B) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM2 (3B)
Configuration: ESM2 (650M) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.261 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

ESM2 (650M) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM2 (650M)
Configuration: ESM2 (8M) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
-0.209 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

ESM2 (8M) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM2 (8M)
Configuration: ESM3 open (1.4B) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.29 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

ESM3 open (1.4B) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=ESM3 open (1.4B)
Configuration: EVE (ensemble) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.398 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

EVE (ensemble) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=EVE (ensemble)
Configuration: EVE (single) [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.386 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

EVE (single) AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=EVE (single)
Configuration: EVmutation [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.418 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

EVmutation AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=EVmutation
Configuration: GEMME [ProteinGym 144fe22b snapshot]Protocol: ProteinGym AMFR official zero-shot Spearman snapshot
Dataset subset: ProteinGym AMFR 4G3O official snapshot cohort
0.396 spearman_rho
correlation · higher

Uncertainty: type: unreported

Coverage: Not reported scored / Not reported eligible

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

GEMME AMFR official snapshot

Not reported

Aggregation: Not reported

ProteinGym AMFR assay-level Spearman comparison · DMS_substitutions_Spearman_DMS_level.csv line 15, DMS ID=AMFR_HUMAN_Tsuboyama_2023_4G3O, column=GEMME

Source checking is not independent reproduction. Release 2026-09-30-e37e3ab1284d.

Methods and evaluation design

Procedure, tasks and evaluated configurations

Evaluation design

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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
97

Literature evidence is not a Rewire measurement. Executed but unpublished runs and private review status are not included.

Null control

Proposed control: requires review

Protocol-valid seeded random ranking; no fitting on assay labels

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

Established label-free reference with explicitly permitted sequence/MSA inputs

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 · Model evaluation matrix · Source table · Release and checksums

Coverage is derived from release 2026-09-30-e37e3ab1284d. 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
Applicable tests and references

Applicability is distinct from a completed evaluation.

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.

2 evidence rows matching the loaded filters

Claims, original sources and review scope · Release 2026-09-30-e37e3ab1284d
Property and statementOriginal source and locationReview and provenance
Relationship: part of
discovery-benchmark-proteingym
Individual claims
Protocol metadata evidence: proteingym-reference_files-DMS_substitutions.csv

Original source ↗

Official ProteinGym pinned benchmarks/DMS_zero_shot/substitutions/Spearman/DMS_substitutions_Spearman_DMS_level.csv; AMFR assay row

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c
Retrieved: 2026-09-23T18:39:35.604049+00:00

source checked

automated source review · 2026-09-30T21:44:09.612264+00:00

Audit details

Field: links:part_of:discovery-benchmark-proteingym

Claim: uc20260930-protocol-parent-fa51fe46268a4a99

Source artifact SHA-256: a8f498011532a74aa9fe556a50555a75e928c5837d19c06a87592ae04049b308

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Relationship: part of
discovery-benchmark-proteingym
Individual claims
ProteinGym AMFR assay-level Spearman comparison

Original source ↗

Official ProteinGym pinned benchmarks/DMS_zero_shot/substitutions/Spearman/DMS_substitutions_Spearman_DMS_level.csv; AMFR assay row

Shared locator for this statement’s cited sources; not a separate locator for each citation.

Version: 144fe22b07dfaeec2b366f2346203a9838a55b4c
Retrieved: 2026-09-30

source checked

automated source review · 2026-09-30T21:44:09.612264+00:00

Audit details

Field: links:part_of:discovery-benchmark-proteingym

Claim: uc20260930-protocol-parent-fa51fe46268a4a99

Source artifact SHA-256: f432423b87f79ac9778dfac86e3d95be041d246bc618dc0a406b35b0b7466437

Hash scope: Hash scope not separately documented; inspect source record

Inspected artifact

Sources and history

View linked audit checks and correction history

Release 2026-09-30-e37e3ab1284d · Record review: source checked

2 source records and release historyDownload this release
Technical metadata and extraction receipts

Stable ID: uc20260930-proteingym-amfr-protocol

areas
proteins-complexes
version
144fe22b07dfaeec2b366f2346203a9838a55b4c
source locator
DMS_substitutions_Spearman_DMS_level.csv row AMFR_HUMAN_Tsuboyama_2023_4G3O
review
method: automated_source_review; reviewer: Codex experimental-use-case curation; date: 2026-09-30; reviewed at: 2026-09-30T21:40:59.576893+00:00; scope: Primary-source transcription and catalogue applicability audit; not human scientific review or independent experimental reproduction.
limitations
Per-model scored counts, score transforms and checkpoint hashes unextracted; row Number of Mutants is assay count, not proof of complete predictions for each model.; Modalities differ across models; do not describe all as sequence-only.; Do not merge with local protocols.
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