HMM | configuration

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Evaluations and results

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

Dataset subset: ProteinGym indel DMS assays (ProteinGym split)

Sorted by Spearman (higher 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	Spearman	AUROC
HMMEvaluation	ProteinGym ZS-INDEL-SPEARMAN-DESIGNED: Zero-shot indels, designed or natural assays, Spearman	0.518 (best in column)	Not reported
HMMEvaluation	ProteinGym ZS-INDEL-SPEARMAN-ALL: Zero-shot indels, all assays, Spearman	0.389	Not reported
HMMEvaluation	ProteinGym ZS-INDEL-SPEARMAN-LIBRARY: Zero-shot indels, library assays, Spearman	0.373	Not reported
HMMEvaluation	ProteinGym ZS-INDEL-AUC: Zero-shot indels, all assays, AUC	Not reported	0.744

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: HMM	Task: ProteinGym ZS-INDEL-AUC: Zero-shot indels, all assays, AUC Dataset subset: ProteinGym indel DMS assays (ProteinGym split)	0.744 AUROC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 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. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(HMM), column(Zero-shot indels, all assays, AUC)
Configuration: HMM	Task: ProteinGym ZS-INDEL-SPEARMAN-ALL: Zero-shot indels, all assays, Spearman Dataset subset: ProteinGym indel DMS assays (ProteinGym split)	0.389 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 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. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(HMM), column(Zero-shot indels, all assays, Spearman)
Configuration: HMM	Task: ProteinGym ZS-INDEL-SPEARMAN-DESIGNED: Zero-shot indels, designed or natural assays, Spearman Dataset subset: ProteinGym indel DMS assays (ProteinGym split)	0.518 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 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. Aggregation: Not reported ProteinGym: Large-Scale Benchmarks for Protein Fitness Prediction and Design · Table 4, row(HMM), column(Zero-shot indels, designed or natural assays, Spearman)
Configuration: HMM	Task: ProteinGym ZS-INDEL-SPEARMAN-LIBRARY: Zero-shot indels, library assays, Spearman Dataset subset: ProteinGym indel DMS assays (ProteinGym split)	0.373 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source 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. Aggregation: Not reported ProteinGym: 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. Release 2026-11-02-a7f03c9e55a5.

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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-hmm

areas: proteins-complexes
source locator: Table 4, row(HMM)
missing metadata: checkpoint revision: reason: unreported; parameters: reason: unextracted
provenance note: Fitness prediction model evaluated by the ProteinGym authors under their harness.

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