The split of ProteinGym substitution 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.
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61 evaluations · 185 results. Different protocols are not a single leaderboard.
Applied filters: All linked evaluations
| Tested configuration | Protocol and dataset | Finding | Evidence and details |
|---|---|---|---|
| Configuration: CARP (640M) | Task: ProteinGym ZS-SUB-AUC: Zero-shot substitutions, AUC Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.701 auc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCARP (640M) on ProteinGym ZS-SUB-AUC: Zero-shot substitutions, AUC Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(language CARP (640M)), column(Zero-shot substitutions, AUC) |
| Configuration: CARP (640M) | Task: ProteinGym ZS-SUB-MCC: Zero-shot substitutions, MCC Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.285 mcc correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCARP (640M) on ProteinGym ZS-SUB-MCC: Zero-shot substitutions, MCC Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(language CARP (640M)), column(Zero-shot substitutions, MCC) |
| Configuration: CARP (640M) | Task: ProteinGym ZS-SUB-NDCG: Zero-shot substitutions, NDCG@10% Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.748 ndcg fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCARP (640M) on ProteinGym ZS-SUB-NDCG: Zero-shot substitutions, NDCG@10% Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(language CARP (640M)), column(Zero-shot substitutions, NDCG@10%) |
| Configuration: CARP (640M) | Task: ProteinGym ZS-SUB-RECALL: Zero-shot substitutions, top 10% recall Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.208 recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCARP (640M) on ProteinGym ZS-SUB-RECALL: Zero-shot substitutions, top 10% recall Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(language CARP (640M)), column(Zero-shot substitutions, top 10% recall) |
| Configuration: CARP (640M) | Task: ProteinGym ZS-SUB-SPEARMAN: Zero-shot substitutions, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.368 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCARP (640M) on ProteinGym ZS-SUB-SPEARMAN: Zero-shot substitutions, Spearman Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(language CARP (640M)), column(Zero-shot substitutions, Spearman) |
| Configuration: DeepSequence (ensemble) | Task: ProteinGym ZS-SUB-AUC: Zero-shot substitutions, AUC Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.729 auc fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDeepSequence (ensemble) on ProteinGym ZS-SUB-AUC: Zero-shot substitutions, AUC Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(DeepSequence (ensemble)), column(Zero-shot substitutions, AUC) |
| Configuration: DeepSequence (ensemble) | Task: ProteinGym ZS-SUB-MCC: Zero-shot substitutions, MCC Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.328 mcc correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDeepSequence (ensemble) on ProteinGym ZS-SUB-MCC: Zero-shot substitutions, MCC Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(DeepSequence (ensemble)), column(Zero-shot substitutions, MCC) |
| Configuration: DeepSequence (ensemble) | Task: ProteinGym ZS-SUB-NDCG: Zero-shot substitutions, NDCG@10% Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.776 ndcg fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDeepSequence (ensemble) on ProteinGym ZS-SUB-NDCG: Zero-shot substitutions, NDCG@10% Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(DeepSequence (ensemble)), column(Zero-shot substitutions, NDCG@10%) |
| Configuration: DeepSequence (ensemble) | Task: ProteinGym ZS-SUB-RECALL: Zero-shot substitutions, top 10% recall Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.226 recall fraction · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDeepSequence (ensemble) on ProteinGym ZS-SUB-RECALL: Zero-shot substitutions, top 10% recall Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(DeepSequence (ensemble)), column(Zero-shot substitutions, top 10% recall) |
| Configuration: DeepSequence (ensemble) | Task: ProteinGym ZS-SUB-SPEARMAN: Zero-shot substitutions, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.419 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDeepSequence (ensemble) on ProteinGym ZS-SUB-SPEARMAN: Zero-shot substitutions, Spearman Zero-shot scoring of substitution assays, averaged over assays with the correction the paper describes. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 2, row(DeepSequence (ensemble)), column(Zero-shot substitutions, Spearman) |
| Configuration: Embed. ESM-1v | Task: ProteinGym SUP-SUB-MSE-AVG: Supervised substitutions, average over splits, MSE Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.787 mse error · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEmbed. ESM-1v on ProteinGym SUP-SUB-MSE-AVG: Supervised substitutions, average over splits, MSE Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(Embed. ESM-1v), column(Supervised substitutions, average over splits, MSE) |
| Configuration: Embed. ESM-1v | Task: ProteinGym SUP-SUB-MSE-CONTIG: Supervised substitutions, contiguous split, MSE Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.937 mse error · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEmbed. ESM-1v on ProteinGym SUP-SUB-MSE-CONTIG: Supervised substitutions, contiguous split, MSE Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(Embed. ESM-1v), column(Supervised substitutions, contiguous split, MSE) |
| Configuration: Embed. ESM-1v | Task: ProteinGym SUP-SUB-MSE-MOD: Supervised substitutions, modulo split, MSE Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.861 mse error · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEmbed. ESM-1v on ProteinGym SUP-SUB-MSE-MOD: Supervised substitutions, modulo split, MSE Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(Embed. ESM-1v), column(Supervised substitutions, modulo split, MSE) |
| Configuration: Embed. ESM-1v | Task: ProteinGym SUP-SUB-MSE-RAND: Supervised substitutions, random split, MSE Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.563 mse error · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEmbed. ESM-1v on ProteinGym SUP-SUB-MSE-RAND: Supervised substitutions, random split, MSE Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(Embed. ESM-1v), column(Supervised substitutions, random split, MSE) |
| Configuration: Embed. ESM-1v | Task: ProteinGym SUP-SUB-SPEARMAN-AVG: Supervised substitutions, average over splits, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.542 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(Embed. ESM-1v), column(Supervised substitutions, average over splits, Spearman) |
| Configuration: Embed. ESM-1v | Task: ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.481 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(Embed. ESM-1v), column(Supervised substitutions, contiguous split, Spearman) |
| Configuration: Embed. ESM-1v | Task: ProteinGym SUP-SUB-SPEARMAN-MOD: Supervised substitutions, modulo split, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.506 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEmbed. ESM-1v on ProteinGym SUP-SUB-SPEARMAN-MOD: Supervised substitutions, modulo split, Spearman Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(Embed. ESM-1v), column(Supervised substitutions, modulo split, Spearman) |
| Configuration: Embed. ESM-1v | Task: ProteinGym SUP-SUB-SPEARMAN-RAND: Supervised substitutions, random split, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.639 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEmbed. ESM-1v on ProteinGym SUP-SUB-SPEARMAN-RAND: Supervised substitutions, random split, Spearman Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(Embed. ESM-1v), column(Supervised substitutions, random split, Spearman) |
| Configuration: Embed. MSAT | Task: ProteinGym SUP-SUB-MSE-AVG: Supervised substitutions, average over splits, MSE Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.735 mse error · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEmbed. MSAT on ProteinGym SUP-SUB-MSE-AVG: Supervised substitutions, average over splits, MSE Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(MSAT), column(Supervised substitutions, average over splits, MSE) |
| Configuration: Embed. MSAT | Task: ProteinGym SUP-SUB-MSE-CONTIG: Supervised substitutions, contiguous split, MSE Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.836 mse error · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEmbed. MSAT on ProteinGym SUP-SUB-MSE-CONTIG: Supervised substitutions, contiguous split, MSE Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(MSAT), column(Supervised substitutions, contiguous split, MSE) |
| Configuration: Embed. MSAT | Task: ProteinGym SUP-SUB-MSE-MOD: Supervised substitutions, modulo split, MSE Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.795 mse error · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEmbed. MSAT on ProteinGym SUP-SUB-MSE-MOD: Supervised substitutions, modulo split, MSE Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(MSAT), column(Supervised substitutions, modulo split, MSE) |
| Configuration: Embed. MSAT | Task: ProteinGym SUP-SUB-MSE-RAND: Supervised substitutions, random split, MSE Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.573 mse error · lower Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEmbed. MSAT on ProteinGym SUP-SUB-MSE-RAND: Supervised substitutions, random split, MSE Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(MSAT), column(Supervised substitutions, random split, MSE) |
| Configuration: Embed. MSAT | Task: ProteinGym SUP-SUB-SPEARMAN-AVG: Supervised substitutions, average over splits, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.568 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(MSAT), column(Supervised substitutions, average over splits, Spearman) |
| Configuration: Embed. MSAT | Task: ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.525 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceSupervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(MSAT), column(Supervised substitutions, contiguous split, Spearman) |
| Configuration: Embed. MSAT | Task: ProteinGym SUP-SUB-SPEARMAN-MOD: Supervised substitutions, modulo split, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split) | 0.538 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceEmbed. MSAT on ProteinGym SUP-SUB-SPEARMAN-MOD: Supervised substitutions, modulo split, Spearman Supervised fitness prediction under three cross-validation schemes: contiguous, modulo and random splits. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 3, row(MSAT), column(Supervised substitutions, modulo split, Spearman) |
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2 evidence rows matching the loaded filters
| Property and statement | Original source and location | Review and provenance |
|---|---|---|
| description The split of ProteinGym substitution 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 No field-specific location recorded Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
| name ProteinGym substitution DMS assays (ProteinGym split) Context-only references | ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design No field-specific location recorded Version: Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256 | not individually reviewed No individual claim review recorded Audit detailsField: Source artifact SHA-256: Hash scope: Exact retrieved primary paper artifact bytes. |
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Release 2026-09-29-06401fd5b220 · Record review: source checked
Stable ID: proteingym-dataset-proteingym-substitution-dms-assays