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Dayhoff likelihood

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16 evaluations · 32 results. Different protocols are not a single leaderboard.

Sorted by NDCG (cutoff not stated) (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	NDCG (cutoff not stated)	Spearman
Dayhoff likelihoodEvaluation	FLIP2 TrpB one-to-many; held-out test set · TrpB, TrpB	0.991 (best in column)	0.136
Dayhoff likelihoodEvaluation	FLIP2 TrpB two-to-many; held-out test set · TrpB, TrpB	0.991 (best in column)	0.139
Dayhoff likelihoodEvaluation	FLIP2 TrpB by-position; held-out test set · TrpB, TrpB	0.988	0.183
Dayhoff likelihoodEvaluation	FLIP2 hydro to-P0A9X9; held-out test set · hydro, hydro	0.973	0.151
Dayhoff likelihoodEvaluation	FLIP2 hydro three-to-many; held-out test set · hydro, hydro	0.97	0.387
Dayhoff likelihoodEvaluation	FLIP2 hydro to-P06241; held-out test set · hydro, hydro	0.967	0.426
Dayhoff likelihoodEvaluation	FLIP2 hydro to-P01053; held-out test set · hydro, hydro	0.964	0.229
Dayhoff likelihoodEvaluation	FLIP2 IRED two-to-many; held-out test set · IRED, IRED	0.955	0.142
Dayhoff likelihoodEvaluation	FLIP2 Amylase far-to-close; held-out test set · Amylase, Amylase	0.947	0.58 (best in column)
Dayhoff likelihoodEvaluation	FLIP2 Amylase close-to-far; held-out test set · Amylase, Amylase	0.943	0.538
Dayhoff likelihoodEvaluation	FLIP2 Amylase one-to-many; held-out test set · Amylase, Amylase	0.936	0.522
Dayhoff likelihoodEvaluation	FLIP2 hydro low-to-high; held-out test set · hydro, hydro	0.924	0.308
Dayhoff likelihoodEvaluation	FLIP2 NucB two-to-many; held-out test set · NucB, NucB	0.919	0.478
Dayhoff likelihoodEvaluation	FLIP2 Amylase by-mutation; held-out test set · Amylase, Amylase	0.917	0.499
Dayhoff likelihoodEvaluation	FLIP2 rhomax by-wild-type; held-out test set · rhomax, rhomax	0.902	0.019
Dayhoff likelihoodEvaluation	FLIP2 PDZ3 single-to-double; held-out test set · PDZ3, PDZ3	0.856	−0.007

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Release 2026-11-02-a7f03c9e55a5 · Record review: discovered

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FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Original source · Primary full-text snapshot retrieved 2026-09-17; exact bytes pinned by SHA-256

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Stable ID: acquired-configuration-e1bdc3803aaf3904490c

source locator: Table A1; row Dayhoff likelihood; column spearman
reported configuration: Dayhoff likelihood
missing metadata: checkpoint revision: reason: unreported; model family: reason: unextracted
provenance note: Exact source-reported configuration or submission label. Family membership, checkpoint identity and aliases have not been inferred.

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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: Dayhoff likelihood	Protocol: FLIP2 Amylase far-to-close; held-out test set · Amylase Dataset subset: Amylase	0.58 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 Amylase far-to-close; held-out test set · Amylase FLIP2 Amylase far-to-close; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A3; row Dayhoff likelihood; column spearman
Configuration: Dayhoff likelihood	Protocol: FLIP2 IRED two-to-many; held-out test set · IRED Dataset subset: IRED	0.955 NDCG (cutoff not stated) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 IRED two-to-many; held-out test set · IRED FLIP2 IRED two-to-many; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A5; row Dayhoff likelihood; column ndcg
Configuration: Dayhoff likelihood	Protocol: FLIP2 PDZ3 single-to-double; held-out test set · PDZ3 Dataset subset: PDZ3	0.856 NDCG (cutoff not stated) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 PDZ3 single-to-double; held-out test set · PDZ3 FLIP2 PDZ3 single-to-double; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A16; row Dayhoff likelihood; column ndcg
Configuration: Dayhoff likelihood	Protocol: FLIP2 TrpB by-position; held-out test set · TrpB Dataset subset: TrpB	0.183 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 TrpB by-position; held-out test set · TrpB FLIP2 TrpB by-position; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A9; row Dayhoff likelihood; column spearman
Configuration: Dayhoff likelihood	Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax	0.019 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 rhomax by-wild-type; held-out test set · rhomax FLIP2 rhomax by-wild-type; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A15; row Dayhoff likelihood; column spearman
Configuration: Dayhoff likelihood	Protocol: FLIP2 Amylase by-mutation; held-out test set · Amylase Dataset subset: Amylase	0.499 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 Amylase by-mutation; held-out test set · Amylase FLIP2 Amylase by-mutation; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A4; row Dayhoff likelihood; column spearman
Configuration: Dayhoff likelihood	Protocol: FLIP2 TrpB one-to-many; held-out test set · TrpB Dataset subset: TrpB	0.991 NDCG (cutoff not stated) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 TrpB one-to-many; held-out test set · TrpB FLIP2 TrpB one-to-many; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A7; row Dayhoff likelihood; column ndcg
Configuration: Dayhoff likelihood	Protocol: FLIP2 Amylase one-to-many; held-out test set · Amylase Dataset subset: Amylase	0.522 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 Amylase one-to-many; held-out test set · Amylase FLIP2 Amylase one-to-many; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A1; row Dayhoff likelihood; column spearman
Configuration: Dayhoff likelihood	Protocol: FLIP2 hydro to-P01053; held-out test set · hydro Dataset subset: hydro	0.964 NDCG (cutoff not stated) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 hydro to-P01053; held-out test set · hydro FLIP2 hydro to-P01053; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A14; row Dayhoff likelihood; column ndcg
Configuration: Dayhoff likelihood	Protocol: FLIP2 hydro to-P06241; held-out test set · hydro Dataset subset: hydro	0.967 NDCG (cutoff not stated) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 hydro to-P06241; held-out test set · hydro FLIP2 hydro to-P06241; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A12; row Dayhoff likelihood; column ndcg
Configuration: Dayhoff likelihood	Protocol: FLIP2 hydro to-P06241; held-out test set · hydro Dataset subset: hydro	0.426 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 hydro to-P06241; held-out test set · hydro FLIP2 hydro to-P06241; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A12; row Dayhoff likelihood; column spearman
Configuration: Dayhoff likelihood	Protocol: FLIP2 Amylase by-mutation; held-out test set · Amylase Dataset subset: Amylase	0.917 NDCG (cutoff not stated) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 Amylase by-mutation; held-out test set · Amylase FLIP2 Amylase by-mutation; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A4; row Dayhoff likelihood; column ndcg
Configuration: Dayhoff likelihood	Protocol: FLIP2 hydro to-P0A9X9; held-out test set · hydro Dataset subset: hydro	0.151 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 hydro to-P0A9X9; held-out test set · hydro FLIP2 hydro to-P0A9X9; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A13; row Dayhoff likelihood; column spearman
Configuration: Dayhoff likelihood	Protocol: FLIP2 TrpB two-to-many; held-out test set · TrpB Dataset subset: TrpB	0.991 NDCG (cutoff not stated) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 TrpB two-to-many; held-out test set · TrpB FLIP2 TrpB two-to-many; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A8; row Dayhoff likelihood; column ndcg
Configuration: Dayhoff likelihood	Protocol: FLIP2 TrpB by-position; held-out test set · TrpB Dataset subset: TrpB	0.988 NDCG (cutoff not stated) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 TrpB by-position; held-out test set · TrpB FLIP2 TrpB by-position; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A9; row Dayhoff likelihood; column ndcg
Configuration: Dayhoff likelihood	Protocol: FLIP2 Amylase close-to-far; held-out test set · Amylase Dataset subset: Amylase	0.943 NDCG (cutoff not stated) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 Amylase close-to-far; held-out test set · Amylase FLIP2 Amylase close-to-far; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A2; row Dayhoff likelihood; column ndcg
Configuration: Dayhoff likelihood	Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax	0.902 NDCG (cutoff not stated) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 rhomax by-wild-type; held-out test set · rhomax FLIP2 rhomax by-wild-type; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A15; row Dayhoff likelihood; column ndcg
Configuration: Dayhoff likelihood	Protocol: FLIP2 IRED two-to-many; held-out test set · IRED Dataset subset: IRED	0.142 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 IRED two-to-many; held-out test set · IRED FLIP2 IRED two-to-many; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A5; row Dayhoff likelihood; column spearman
Configuration: Dayhoff likelihood	Protocol: FLIP2 hydro low-to-high; held-out test set · hydro Dataset subset: hydro	0.308 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 hydro low-to-high; held-out test set · hydro FLIP2 hydro low-to-high; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A11; row Dayhoff likelihood; column spearman
Configuration: Dayhoff likelihood	Protocol: FLIP2 Amylase close-to-far; held-out test set · Amylase Dataset subset: Amylase	0.538 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 Amylase close-to-far; held-out test set · Amylase FLIP2 Amylase close-to-far; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A2; row Dayhoff likelihood; column spearman
Configuration: Dayhoff likelihood	Protocol: FLIP2 hydro three-to-many; held-out test set · hydro Dataset subset: hydro	0.387 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 hydro three-to-many; held-out test set · hydro FLIP2 hydro three-to-many; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A10; row Dayhoff likelihood; column spearman
Configuration: Dayhoff likelihood	Protocol: FLIP2 NucB two-to-many; held-out test set · NucB Dataset subset: NucB	0.919 NDCG (cutoff not stated) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 NucB two-to-many; held-out test set · NucB FLIP2 NucB two-to-many; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A6; row Dayhoff likelihood; column ndcg
Configuration: Dayhoff likelihood	Protocol: FLIP2 PDZ3 single-to-double; held-out test set · PDZ3 Dataset subset: PDZ3	−0.007 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 PDZ3 single-to-double; held-out test set · PDZ3 FLIP2 PDZ3 single-to-double; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A16; row Dayhoff likelihood; column spearman
Configuration: Dayhoff likelihood	Protocol: FLIP2 TrpB two-to-many; held-out test set · TrpB Dataset subset: TrpB	0.139 Spearman unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 TrpB two-to-many; held-out test set · TrpB FLIP2 TrpB two-to-many; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A8; row Dayhoff likelihood; column spearman
Configuration: Dayhoff likelihood	Protocol: FLIP2 hydro three-to-many; held-out test set · hydro Dataset subset: hydro	0.97 NDCG (cutoff not stated) unitless · higher Uncertainty: Not yet extracted Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source Dayhoff likelihood · FLIP2 hydro three-to-many; held-out test set · hydro FLIP2 hydro three-to-many; held-out test set Aggregation: reported point estimate FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A10; row Dayhoff likelihood; column ndcg