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Dataset subset

ProteinGym indel DMS assays (ProteinGym split)

The split of ProteinGym indel DMS assays that ProteinGym evaluated on. The upstream dataset release is not catalogued here, so no claim is made that this matches its original splits.

Subset and evaluation context

This record describes a particular subset or cohort used in an evaluation. Its results do not describe the full dataset.

Evaluation results

Release 2026-09-17-134cd1815de8 · 36 evaluations · 36 metric rows. Different protocols are not a single leaderboard. Where several source tables report the same metric, the published comparisons above offer a pooled view that names what it does not hold constant.

Results grouped by the exact reported evaluation
Metric and findingCoverage and uncertaintyEvidence
HMM on ProteinGym ZS-INDEL-AUC: Zero-shot indels, all assays, AUC

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.744 auc

Unit: fraction · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(HMM), column(Zero-shot indels, all assays, AUC)

Source checking is not independent reproduction.

HMM on ProteinGym ZS-INDEL-SPEARMAN-ALL: Zero-shot indels, all assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.389 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(HMM), column(Zero-shot indels, all assays, Spearman)

Source checking is not independent reproduction.

HMM on ProteinGym ZS-INDEL-SPEARMAN-DESIGNED: Zero-shot indels, designed or natural assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.518 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(HMM), column(Zero-shot indels, designed or natural assays, Spearman)

Source checking is not independent reproduction.

HMM on ProteinGym ZS-INDEL-SPEARMAN-LIBRARY: Zero-shot indels, library assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.373 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(HMM), column(Zero-shot indels, library assays, Spearman)

Source checking is not independent reproduction.

ProGen2 M on ProteinGym ZS-INDEL-AUC: Zero-shot indels, all assays, AUC

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.776 auc

Unit: fraction · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(models ProGen2 M), column(Zero-shot indels, all assays, AUC)

Source checking is not independent reproduction.

ProGen2 M on ProteinGym ZS-INDEL-SPEARMAN-ALL: Zero-shot indels, all assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.465 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(models ProGen2 M), column(Zero-shot indels, all assays, Spearman)

Source checking is not independent reproduction.

ProGen2 M on ProteinGym ZS-INDEL-SPEARMAN-DESIGNED: Zero-shot indels, designed or natural assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.205 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(models ProGen2 M), column(Zero-shot indels, designed or natural assays, Spearman)

Source checking is not independent reproduction.

ProGen2 M on ProteinGym ZS-INDEL-SPEARMAN-LIBRARY: Zero-shot indels, library assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.472 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(models ProGen2 M), column(Zero-shot indels, library assays, Spearman)

Source checking is not independent reproduction.

ProtGPT2 on ProteinGym ZS-INDEL-AUC: Zero-shot indels, all assays, AUC

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.620 auc

Unit: fraction · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(language ProtGPT2), column(Zero-shot indels, all assays, AUC)

Source checking is not independent reproduction.

ProtGPT2 on ProteinGym ZS-INDEL-SPEARMAN-ALL: Zero-shot indels, all assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.191 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(language ProtGPT2), column(Zero-shot indels, all assays, Spearman)

Source checking is not independent reproduction.

ProtGPT2 on ProteinGym ZS-INDEL-SPEARMAN-DESIGNED: Zero-shot indels, designed or natural assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.128 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(language ProtGPT2), column(Zero-shot indels, designed or natural assays, Spearman)

Source checking is not independent reproduction.

ProtGPT2 on ProteinGym ZS-INDEL-SPEARMAN-LIBRARY: Zero-shot indels, library assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.185 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(language ProtGPT2), column(Zero-shot indels, library assays, Spearman)

Source checking is not independent reproduction.

PROVEAN on ProteinGym ZS-INDEL-AUC: Zero-shot indels, all assays, AUC

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.725 auc

Unit: fraction · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(PROVEAN), column(Zero-shot indels, all assays, AUC)

Source checking is not independent reproduction.

PROVEAN on ProteinGym ZS-INDEL-SPEARMAN-ALL: Zero-shot indels, all assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.347 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(PROVEAN), column(Zero-shot indels, all assays, Spearman)

Source checking is not independent reproduction.

PROVEAN on ProteinGym ZS-INDEL-SPEARMAN-DESIGNED: Zero-shot indels, designed or natural assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.585 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(PROVEAN), column(Zero-shot indels, designed or natural assays, Spearman)

Source checking is not independent reproduction.

PROVEAN on ProteinGym ZS-INDEL-SPEARMAN-LIBRARY: Zero-shot indels, library assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.306 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(PROVEAN), column(Zero-shot indels, library assays, Spearman)

Source checking is not independent reproduction.

RITA L on ProteinGym ZS-INDEL-AUC: Zero-shot indels, all assays, AUC

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.773 auc

Unit: fraction · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(Protein RITA L), column(Zero-shot indels, all assays, AUC)

Source checking is not independent reproduction.

RITA L on ProteinGym ZS-INDEL-SPEARMAN-ALL: Zero-shot indels, all assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.457 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(Protein RITA L), column(Zero-shot indels, all assays, Spearman)

Source checking is not independent reproduction.

RITA L on ProteinGym ZS-INDEL-SPEARMAN-DESIGNED: Zero-shot indels, designed or natural assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.519 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(Protein RITA L), column(Zero-shot indels, designed or natural assays, Spearman)

Source checking is not independent reproduction.

RITA L on ProteinGym ZS-INDEL-SPEARMAN-LIBRARY: Zero-shot indels, library assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.443 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(Protein RITA L), column(Zero-shot indels, library assays, Spearman)

Source checking is not independent reproduction.

TranceptEVE M on ProteinGym ZS-INDEL-AUC: Zero-shot indels, all assays, AUC

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.754 auc

Unit: fraction · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(TranceptEVE M), column(Zero-shot indels, all assays, AUC)

Source checking is not independent reproduction.

TranceptEVE M on ProteinGym ZS-INDEL-SPEARMAN-ALL: Zero-shot indels, all assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.424 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(TranceptEVE M), column(Zero-shot indels, all assays, Spearman)

Source checking is not independent reproduction.

TranceptEVE M on ProteinGym ZS-INDEL-SPEARMAN-DESIGNED: Zero-shot indels, designed or natural assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.587 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(TranceptEVE M), column(Zero-shot indels, designed or natural assays, Spearman)

Source checking is not independent reproduction.

TranceptEVE M on ProteinGym ZS-INDEL-SPEARMAN-LIBRARY: Zero-shot indels, library assays, Spearman

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.426 spearman

Unit: correlation · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(TranceptEVE M), column(Zero-shot indels, library assays, Spearman)

Source checking is not independent reproduction.

Tranception L on ProteinGym ZS-INDEL-AUC: Zero-shot indels, all assays, AUC

Zero-shot scoring of insertion and deletion assays, split by how the test sequences were generated.

Author-reported evaluation · Evaluation metadata: source checked

0.741 auc

Unit: fraction · Direction: higher

Uncertainty: Not reported

Scored: Not reported · Eligible: Not reported

source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(Tranception L), column(Zero-shot indels, all assays, AUC)

Source checking is not 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 2026-09-17-134cd1815de8
Property and statementOriginal source and locationReview and provenance
description

The split of ProteinGym indel DMS assays that ProteinGym evaluated on. The upstream dataset release is not catalogued here, so no claim is made that this matches its original splits.

Context-only references
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design

Original source ↗

No field-specific location recorded

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.522924+00:00

not individually reviewed

No individual claim review recorded

Audit details

Field: description

Source artifact SHA-256: a3b08cc4a6befd64620cf0f287d78d55a36dc2639955f52c5655f83833c50104

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

name

ProteinGym indel DMS assays (ProteinGym split)

Context-only references
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design

Original source ↗

No field-specific location recorded

Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Retrieved: 2026-09-17T08:06:28.522924+00:00

not individually reviewed

No individual claim review recorded

Audit details

Field: name

Source artifact SHA-256: a3b08cc4a6befd64620cf0f287d78d55a36dc2639955f52c5655f83833c50104

Hash scope: Exact retrieved primary paper artifact bytes.

Inspected artifact

Sources and history

Release 2026-09-17-134cd1815de8 · Record review: source checked

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

Stable ID: proteingym-dataset-proteingym-indel-dms-assays

areas
proteins-complexes
missing metadata
version: unreported; url: unextracted
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