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ProGen2 XL

ProGen2 XL: Fitness prediction model.

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Evaluations and results

1 evaluation · 5 results. Different protocols are not a single leaderboard.

Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)

Sorted by AUROC (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	AUROC	MCC	NDCG at 10%	Spearman	Top 10% recall
ProGen2 XLEvaluation	ProteinGym ZS-SUB-AUC: Zero-shot substitutions, AUC	0.717	Not reported	Not reported	Not reported	Not reported
ProGen2 XLEvaluation	ProteinGym ZS-SUB-MCC: Zero-shot substitutions, MCC	Not reported	0.306	Not reported	Not reported	Not reported
ProGen2 XLEvaluation	ProteinGym ZS-SUB-NDCG: Zero-shot substitutions, NDCG@10%	Not reported	Not reported	0.767	Not reported	Not reported
ProGen2 XLEvaluation	ProteinGym ZS-SUB-RECALL: Zero-shot substitutions, top 10% recall	Not reported	Not reported	Not reported	Not reported	0.199
ProGen2 XLEvaluation	ProteinGym ZS-SUB-SPEARMAN: Zero-shot substitutions, Spearman	Not reported	Not reported	Not reported	0.391	Not reported

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Exact evaluated configurations and original reported results
Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ProGen2 XL	Task: ProteinGym ZS-SUB-AUC: Zero-shot substitutions, AUC Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.717 AUROC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ProGen2 XL 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(ProGen2 XL), column(Zero-shot substitutions, AUC)
Configuration: ProGen2 XL	Task: ProteinGym ZS-SUB-MCC: Zero-shot substitutions, MCC Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.306 MCC unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ProGen2 XL 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(ProGen2 XL), column(Zero-shot substitutions, MCC)
Configuration: ProGen2 XL	Task: ProteinGym ZS-SUB-NDCG: Zero-shot substitutions, NDCG@10% Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.767 NDCG at 10% unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ProGen2 XL 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(ProGen2 XL), column(Zero-shot substitutions, NDCG@10%)
Configuration: ProGen2 XL	Task: ProteinGym ZS-SUB-RECALL: Zero-shot substitutions, top 10% recall Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.199 Top 10% recall fraction · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ProGen2 XL 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(ProGen2 XL), column(Zero-shot substitutions, top 10% recall)
Configuration: ProGen2 XL	Task: ProteinGym ZS-SUB-SPEARMAN: Zero-shot substitutions, Spearman Dataset subset: ProteinGym substitution DMS assays (ProteinGym split)	0.391 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Independent external evaluation · Source checked Methods, coverage and source ProGen2 XL 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(ProGen2 XL), column(Zero-shot substitutions, 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-progen2-xl

areas: proteins-complexes
source locator: Table 2, row(ProGen2 XL)
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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