ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
Supervised substitutions, contiguous split, Spearman. Scored with Spearman on ProteinGym substitution DMS assays. Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits.
Overview
Supervised substitutions, contiguous split, Spearman. Scored with Spearman on ProteinGym substitution DMS assays. Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits.
Consult the linked sources for architecture or protocol details. Missing evidence is not evidence of a missing capability.
Evaluation design
Benchmarks bring together tasks and protocols. A task describes the biological question; a protocol defines a particular test.
Benchmarks
These source-backed links do not make different protocols or scores interchangeable.
Recorded evaluations
Each evaluation records what was tested and under which conditions.
- Embed. ESM-1v on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- Embed. MSAT on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- Embed. Tranception on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- NPT ProteinNPT on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- OHE DeepSequence on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- OHE ESM-1v on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- OHE MSAT on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- OHE None on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- OHE TranceptEVE on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- OHE Tranception on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
Run instructions
No runnable recipe has been reviewed for this task. Dataset access, model requirements, licences and compute requirements must be checked against its sources before execution.
A task describes a biological question. Choose a linked protocol to obtain concrete split and scoring instructions.
Published comparisons
Explore the results reported under one evaluation protocol. Each figure keeps its source, dataset and metric together; it is not a ranking across studies. The pooled view gathers every source table that reports the same metric and names what it does not hold constant.
ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
spearman (correlation) · Higher values are better for this metric.
Every method ProteinGym reports on Supervised substitutions, contiguous split, Spearman, scored with Spearman on ProteinGym substitution DMS assays.
Evaluation protocol · ProteinGym substitution DMS assays (ProteinGym split)
- OHE None · Configuration · Author-reported evaluation0.064
- OHE DeepSequence · Configuration · Author-reported evaluation0.400
- OHE ESM-1v · Configuration · Author-reported evaluation0.367
- OHE MSAT · Configuration · Author-reported evaluation0.410
- OHE Tranception · Configuration · Author-reported evaluation0.419
- OHE TranceptEVE · Configuration · Author-reported evaluation0.441
- Embed. ESM-1v · Configuration · Author-reported evaluation0.481
- Embed. MSAT · Configuration · Author-reported evaluation0.525
- Embed. Tranception · Configuration · Author-reported evaluation0.490
- NPT ProteinNPT · Configuration · Author-reported evaluation0.547
Source order is preserved. Plotted marks show point estimates; uncertainty, where reported, is retained in the printed values and table. Differences do not establish statistical significance.
ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, column(Supervised substitutions, contiguous split, Spearman)Values, uncertainty and evidence
| Tested entity | Printed value | Uncertainty | Evidence |
|---|---|---|---|
| OHE None · Configuration | 0.064 correlation | Not reported | Author-reported evaluation · source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(OHE None), column(Supervised substitutions, contiguous split, Spearman) |
| OHE DeepSequence · Configuration | 0.400 correlation | Not reported | Author-reported evaluation · source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(DeepSequence), column(Supervised substitutions, contiguous split, Spearman) |
| OHE ESM-1v · Configuration | 0.367 correlation | Not reported | Author-reported evaluation · source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(ESM-1v), column(Supervised substitutions, contiguous split, Spearman) |
| OHE MSAT · Configuration | 0.410 correlation | Not reported | Author-reported evaluation · source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(MSAT), column(Supervised substitutions, contiguous split, Spearman) |
| OHE Tranception · Configuration | 0.419 correlation | Not reported | Author-reported evaluation · source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(Tranception), column(Supervised substitutions, contiguous split, Spearman) |
| OHE TranceptEVE · Configuration | 0.441 correlation | Not reported | Author-reported evaluation · source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(TranceptEVE), column(Supervised substitutions, contiguous split, Spearman) |
| Embed. ESM-1v · Configuration | 0.481 correlation | Not reported | Author-reported evaluation · source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(Embed. ESM-1v), column(Supervised substitutions, contiguous split, Spearman) |
| Embed. MSAT · Configuration | 0.525 correlation | Not reported | Author-reported evaluation · source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(MSAT), column(Supervised substitutions, contiguous split, Spearman) |
| Embed. Tranception · Configuration | 0.490 correlation | Not reported | Author-reported evaluation · source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(Tranception), column(Supervised substitutions, contiguous split, Spearman) |
| NPT ProteinNPT · Configuration | 0.547 correlation | Not reported | Author-reported evaluation · source checkedProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(NPT ProteinNPT), column(Supervised substitutions, contiguous split, Spearman) |
Scope and limitations
- Author-reported numbers, source checked but not independently reproduced.
- MSE is better when lower; every other metric here is better when higher.
- Zero-shot, supervised and indel benchmarks use different protocols and assay sets, so their figures are not comparable to each other.
Source transcription and grouping reviewed by automated source review on 2026-09-18. These experiments were not independently reproduced by rewire.
Tested entities and results
Release 2026-09-17-134cd1815de8 · 10 evaluations · 10 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.
| Metric and finding | Coverage and uncertainty | Evidence |
|---|---|---|
| Embed. ESM-1v on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman Configuration: Embed. ESM-1vTask: ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, SpearmanDataset subset: ProteinGym substitution DMS assays (ProteinGym split) Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.481 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 3, row(Embed. ESM-1v), column(Supervised substitutions, contiguous split, Spearman) Source checking is not independent reproduction. |
| Embed. MSAT on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman Configuration: Embed. MSATTask: ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, SpearmanDataset subset: ProteinGym substitution DMS assays (ProteinGym split) Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.525 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 3, row(MSAT), column(Supervised substitutions, contiguous split, Spearman) Source checking is not independent reproduction. |
| Embed. Tranception on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman Configuration: Embed. TranceptionTask: ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, SpearmanDataset subset: ProteinGym substitution DMS assays (ProteinGym split) Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.490 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 3, row(Tranception), column(Supervised substitutions, contiguous split, Spearman) Source checking is not independent reproduction. |
| NPT ProteinNPT on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman Configuration: NPT ProteinNPTTask: ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, SpearmanDataset subset: ProteinGym substitution DMS assays (ProteinGym split) Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.547 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 3, row(NPT ProteinNPT), column(Supervised substitutions, contiguous split, Spearman) Source checking is not independent reproduction. |
| OHE DeepSequence on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman Configuration: OHE DeepSequenceTask: ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, SpearmanDataset subset: ProteinGym substitution DMS assays (ProteinGym split) Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.400 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 3, row(DeepSequence), column(Supervised substitutions, contiguous split, Spearman) Source checking is not independent reproduction. |
| OHE ESM-1v on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman Configuration: OHE ESM-1vTask: ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, SpearmanDataset subset: ProteinGym substitution DMS assays (ProteinGym split) Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.367 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 3, row(ESM-1v), column(Supervised substitutions, contiguous split, Spearman) Source checking is not independent reproduction. |
| OHE MSAT on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman Configuration: OHE MSATTask: ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, SpearmanDataset subset: ProteinGym substitution DMS assays (ProteinGym split) Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.410 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 3, row(MSAT), column(Supervised substitutions, contiguous split, Spearman) Source checking is not independent reproduction. |
| OHE None on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman Configuration: OHE NoneTask: ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, SpearmanDataset subset: ProteinGym substitution DMS assays (ProteinGym split) Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.064 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 3, row(OHE None), column(Supervised substitutions, contiguous split, Spearman) Source checking is not independent reproduction. |
| OHE TranceptEVE on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman Configuration: OHE TranceptEVETask: ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, SpearmanDataset subset: ProteinGym substitution DMS assays (ProteinGym split) Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.441 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 3, row(TranceptEVE), column(Supervised substitutions, contiguous split, Spearman) Source checking is not independent reproduction. |
| OHE Tranception on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman Configuration: OHE TranceptionTask: ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, SpearmanDataset subset: ProteinGym substitution DMS assays (ProteinGym split) Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Author-reported evaluation · Evaluation metadata: source checked | ||
| 0.419 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 3, row(Tranception), column(Supervised substitutions, contiguous split, Spearman) 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.
1 evidence row matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| Relationship: part of discovery-benchmark-proteingym Individual claims | ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design Table 3, column(Supervised substitutions, contiguous split, Spearman) Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | source checked automated source review · 2026-09-18 Audit detailsPrimary-source transcription with no human sign-off and no independent reproduction. Field: Claim: proteingym-association-sup-sub-spearman-contig Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
Sources and history
Release 2026-09-17-134cd1815de8 · Record review: source checked
1 source records and release history
- ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256
Technical metadata and extraction receipts
Stable ID: proteingym-task-sup-sub-spearman-contig
- areas
- proteins-complexes
- tasks
- Supervised substitutions, contiguous split, Spearman
- metric
- Spearman
- metric direction
- higher
- dataset
- ProteinGym substitution DMS assays
- protocol
- Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits.
- source locator
- Table 3, column(Supervised substitutions, contiguous split, Spearman)
- comparison panels
- id: proteingym-panel-sup-sub-spearman-contig; title: ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman; protocol id: proteingym-task-sup-sub-spearman-contig; dataset id: proteingym-dataset-proteingym-substitution-dms-assays; metric: spearman; unit: correlation; direction: higher; result ids: proteingym-result-ohe-none-sup-sub-spearman-contig-spearman; proteingym-result-ohe-deepsequence-sup-sub-spearman-contig-spearman; proteingym-result-ohe-esm-1v-sup-sub-spearman-contig-spearman; proteingym-result-ohe-msat-sup-sub-spearman-contig-spearman; proteingym-result-ohe-tranception-sup-sub-spearman-contig-spearman; proteingym-result-ohe-trancepteve-sup-sub-spearman-contig-spearman; proteingym-result-embed-esm-1v-sup-sub-spearman-contig-spearman; proteingym-result-embed-msat-sup-sub-spearman-contig-spearman; proteingym-result-embed-tranception-sup-sub-spearman-contig-spearman; proteingym-result-npt-proteinnpt-sup-sub-spearman-contig-spearman; source ids: evidence-expansion-proteingym-a3b08cc4; source locator: Table 3, column(Supervised substitutions, contiguous split, Spearman); context: Every method ProteinGym reports on Supervised substitutions, contiguous split, Spearman, scored with Spearman on ProteinGym substitution DMS assays.; caveats: Author-reported numbers, source checked but not independently reproduced.; MSE is better when lower; every other metric here is better when higher.; Zero-shot, supervised and indel benchmarks use different protocols and assay sets, so their figures are not comparable to each other.; review: method: automated_source_review; date: 2026-09-18
Related records
- part of: ProteinGym
- subject: ProteinGym SUP-SUB-SPEARMAN-CONTIG: part of discovery-benchmark-proteingym
- benchmark: Embed. ESM-1v on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- benchmark: Embed. MSAT on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- benchmark: Embed. Tranception on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- benchmark: NPT ProteinNPT on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- benchmark: OHE DeepSequence on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- benchmark: OHE ESM-1v on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- benchmark: OHE MSAT on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- benchmark: OHE None on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- benchmark: OHE TranceptEVE on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman
- benchmark: OHE Tranception on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman