NPT ProteinNPT | configuration

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Evaluations and results

4 evaluations · 8 results. Different protocols are not a single leaderboard.

Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)

Sorted by MSE (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.

Tested configuration	Protocol and dataset	MSE	Spearman
NPT ProteinNPTEvaluation	ProteinGym SUP-SUB-MSE-RAND: Supervised substitutions, random split, MSE	0.459 (best in column)	Not reported
NPT ProteinNPTEvaluation	ProteinGym SUP-SUB-MSE-AVG: Supervised substitutions, average over splits, MSE	0.683	Not reported
NPT ProteinNPTEvaluation	ProteinGym SUP-SUB-MSE-MOD: Supervised substitutions, modulo split, MSE	0.771	Not reported
NPT ProteinNPTEvaluation	ProteinGym SUP-SUB-MSE-CONTIG: Supervised substitutions, contiguous split, MSE	0.82	Not reported
NPT ProteinNPTEvaluation	ProteinGym SUP-SUB-SPEARMAN-AVG: Supervised substitutions, average over splits, Spearman	Not reported	0.613
NPT ProteinNPTEvaluation	ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman	Not reported	0.547
NPT ProteinNPTEvaluation	ProteinGym SUP-SUB-SPEARMAN-MOD: Supervised substitutions, modulo split, Spearman	Not reported	0.564
NPT ProteinNPTEvaluation	ProteinGym SUP-SUB-SPEARMAN-RAND: Supervised substitutions, random split, Spearman	Not reported	0.73 (best in column)

All 8 result rows with coverage, uncertainty and sources

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: NPT ProteinNPT	Task: ProteinGym SUP-SUB-MSE-AVG: Supervised substitutions, average over splits, MSE Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.683 MSE unit-unreported · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NPT ProteinNPT 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(NPT ProteinNPT), column(Supervised substitutions, average over splits, MSE)
Configuration: NPT ProteinNPT	Task: ProteinGym SUP-SUB-MSE-CONTIG: Supervised substitutions, contiguous split, MSE Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.82 MSE unit-unreported · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NPT ProteinNPT 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(NPT ProteinNPT), column(Supervised substitutions, contiguous split, MSE)
Configuration: NPT ProteinNPT	Task: ProteinGym SUP-SUB-MSE-MOD: Supervised substitutions, modulo split, MSE Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.771 MSE unit-unreported · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NPT ProteinNPT 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(NPT ProteinNPT), column(Supervised substitutions, modulo split, MSE)
Configuration: NPT ProteinNPT	Task: ProteinGym SUP-SUB-MSE-RAND: Supervised substitutions, random split, MSE Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.459 MSE unit-unreported · lower Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NPT ProteinNPT 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(NPT ProteinNPT), column(Supervised substitutions, random split, MSE)
Configuration: NPT ProteinNPT	Task: ProteinGym SUP-SUB-SPEARMAN-AVG: Supervised substitutions, average over splits, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.613 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NPT ProteinNPT on ProteinGym SUP-SUB-SPEARMAN-AVG: Supervised substitutions, average over splits, 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(NPT ProteinNPT), column(Supervised substitutions, average over splits, Spearman)
Configuration: NPT ProteinNPT	Task: ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous split, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.547 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NPT ProteinNPT on ProteinGym SUP-SUB-SPEARMAN-CONTIG: Supervised substitutions, contiguous 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(NPT ProteinNPT), column(Supervised substitutions, contiguous split, Spearman)
Configuration: NPT ProteinNPT	Task: ProteinGym SUP-SUB-SPEARMAN-MOD: Supervised substitutions, modulo split, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.564 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NPT ProteinNPT 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(NPT ProteinNPT), column(Supervised substitutions, modulo split, Spearman)
Configuration: NPT ProteinNPT	Task: ProteinGym SUP-SUB-SPEARMAN-RAND: Supervised substitutions, random split, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.73 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source NPT ProteinNPT 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(NPT ProteinNPT), column(Supervised substitutions, random split, Spearman)

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Release 2026-11-02-a7f03c9e55a5 · Record review: source checked

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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

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Technical metadata and extraction receipts

Stable ID: proteingym-method-npt-proteinnpt

areas: proteins-complexes
source locator: Table 3, row(NPT ProteinNPT)
missing metadata: checkpoint revision: reason: unreported; parameters: reason: unextracted
provenance note: Supervised fitness predictor evaluated by the ProteinGym authors. The leading term is the input representation the paper's model type column gives.

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