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ESMC-300M naive supervised

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16 evaluations · 31 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
ESMC-300M naive supervisedEvaluation	FLIP2 TrpB one-to-many; held-out test set · TrpB, TrpB	0.986 ± 0.002 (best in column)	0.369 ± 0.028
ESMC-300M naive supervisedEvaluation	FLIP2 TrpB two-to-many; held-out test set · TrpB, TrpB	0.986 ± 0.001 (best in column)	0.398 ± 0.020
ESMC-300M naive supervisedEvaluation	FLIP2 TrpB by-position; held-out test set · TrpB, TrpB	0.978 ± 0.004	0.154 ± 0.059
ESMC-300M naive supervisedEvaluation	FLIP2 hydro three-to-many; held-out test set · hydro, hydro	0.973 ± 0.002	0.367 ± 0.042
ESMC-300M naive supervisedEvaluation	FLIP2 hydro to-P0A9X9; held-out test set · hydro, hydro	0.958 ± 0.004	−0.050 ± 0.193
ESMC-300M naive supervisedEvaluation	FLIP2 NucB two-to-many; held-out test set · NucB, NucB	0.956 ± 0.003	0.635 ± 0.011 (best in column)
ESMC-300M naive supervisedEvaluation	FLIP2 IRED two-to-many; held-out test set · IRED, IRED	0.949 ± 0.001	0.106 ± 0.005
ESMC-300M naive supervisedEvaluation	FLIP2 rhomax by-wild-type; held-out test set · rhomax, rhomax	0.936 ± 0.022	0.036 ± 0.218
ESMC-300M naive supervisedEvaluation	FLIP2 hydro to-P06241; held-out test set · hydro, hydro	0.927 ± 0.001	0.098 ± 0.024
ESMC-300M naive supervisedEvaluation	FLIP2 hydro low-to-high; held-out test set · hydro, hydro	0.905 ± 0.008	0.270 ± 0.048
ESMC-300M naive supervisedEvaluation	FLIP2 hydro to-P01053; held-out test set · hydro, hydro	0.895 ± 0.006	−0.086 ± 0.135
ESMC-300M naive supervisedEvaluation	FLIP2 PDZ3 single-to-double; held-out test set · PDZ3, PDZ3	0.880 ± 0.006	Not reported
ESMC-300M naive supervisedEvaluation	FLIP2 Amylase close-to-far; held-out test set · Amylase, Amylase	0.864 ± 0.012	0.007 ± 0.032
ESMC-300M naive supervisedEvaluation	FLIP2 Amylase one-to-many; held-out test set · Amylase, Amylase	0.850 ± 0.007	0.044 ± 0.028
ESMC-300M naive supervisedEvaluation	FLIP2 Amylase by-mutation; held-out test set · Amylase, Amylase	0.819 ± 0.048	0.054 ± 0.115
ESMC-300M naive supervisedEvaluation	FLIP2 Amylase far-to-close; held-out test set · Amylase, Amylase	0.818 ± 0.002	0.015 ± 0.028

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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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source locator: Table A1; row ESMC-300M naive supervised; column spearman
reported configuration: ESMC-300M naive supervised
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Tested configuration	Protocol and dataset	Finding	Evidence and details
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 Amylase far-to-close; held-out test set · Amylase Dataset subset: Amylase	0.818 ± 0.002 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.002 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 Amylase far-to-close; held-out test set · Amylase FLIP2 Amylase far-to-close; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A3; row ESMC-300M naive supervised; column ndcg
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 hydro to-P06241; held-out test set · hydro Dataset subset: hydro	0.098 ± 0.024 Spearman unitless · higher Uncertainty: ± 0.024 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 hydro to-P06241; held-out test set · hydro FLIP2 hydro to-P06241; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A12; row ESMC-300M naive supervised; column spearman
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 IRED two-to-many; held-out test set · IRED Dataset subset: IRED	0.106 ± 0.005 Spearman unitless · higher Uncertainty: ± 0.005 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 IRED two-to-many; held-out test set · IRED FLIP2 IRED two-to-many; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A5; row ESMC-300M naive supervised; column spearman
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 PDZ3 single-to-double; held-out test set · PDZ3 Dataset subset: PDZ3	0.880 ± 0.006 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.006 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 PDZ3 single-to-double; held-out test set · PDZ3 FLIP2 PDZ3 single-to-double; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A16; row ESMC-300M naive supervised; column ndcg
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 Amylase one-to-many; held-out test set · Amylase Dataset subset: Amylase	0.850 ± 0.007 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.007 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 Amylase one-to-many; held-out test set · Amylase FLIP2 Amylase one-to-many; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A1; row ESMC-300M naive supervised; column ndcg
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 Amylase close-to-far; held-out test set · Amylase Dataset subset: Amylase	0.864 ± 0.012 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.012 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 Amylase close-to-far; held-out test set · Amylase FLIP2 Amylase close-to-far; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A2; row ESMC-300M naive supervised; column ndcg
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax	0.936 ± 0.022 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.022 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 rhomax by-wild-type; held-out test set · rhomax FLIP2 rhomax by-wild-type; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A15; row ESMC-300M naive supervised; column ndcg
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 TrpB one-to-many; held-out test set · TrpB Dataset subset: TrpB	0.986 ± 0.002 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.002 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 TrpB one-to-many; held-out test set · TrpB FLIP2 TrpB one-to-many; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A7; row ESMC-300M naive supervised; column ndcg
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 TrpB by-position; held-out test set · TrpB Dataset subset: TrpB	0.154 ± 0.059 Spearman unitless · higher Uncertainty: ± 0.059 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 TrpB by-position; held-out test set · TrpB FLIP2 TrpB by-position; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A9; row ESMC-300M naive supervised; column spearman
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 Amylase close-to-far; held-out test set · Amylase Dataset subset: Amylase	0.007 ± 0.032 Spearman unitless · higher Uncertainty: ± 0.032 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 Amylase close-to-far; held-out test set · Amylase FLIP2 Amylase close-to-far; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A2; row ESMC-300M naive supervised; column spearman
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 hydro three-to-many; held-out test set · hydro Dataset subset: hydro	0.367 ± 0.042 Spearman unitless · higher Uncertainty: ± 0.042 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 hydro three-to-many; held-out test set · hydro FLIP2 hydro three-to-many; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A10; row ESMC-300M naive supervised; column spearman
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax	0.036 ± 0.218 Spearman unitless · higher Uncertainty: ± 0.218 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 rhomax by-wild-type; held-out test set · rhomax FLIP2 rhomax by-wild-type; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A15; row ESMC-300M naive supervised; column spearman
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 hydro to-P06241; held-out test set · hydro Dataset subset: hydro	0.927 ± 0.001 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.001 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 hydro to-P06241; held-out test set · hydro FLIP2 hydro to-P06241; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A12; row ESMC-300M naive supervised; column ndcg
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 NucB two-to-many; held-out test set · NucB Dataset subset: NucB	0.956 ± 0.003 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.003 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 NucB two-to-many; held-out test set · NucB FLIP2 NucB two-to-many; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A6; row ESMC-300M naive supervised; column ndcg
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 TrpB two-to-many; held-out test set · TrpB Dataset subset: TrpB	0.398 ± 0.020 Spearman unitless · higher Uncertainty: ± 0.02 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 TrpB two-to-many; held-out test set · TrpB FLIP2 TrpB two-to-many; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A8; row ESMC-300M naive supervised; column spearman
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 hydro to-P01053; held-out test set · hydro Dataset subset: hydro	−0.086 ± 0.135 Spearman unitless · higher Uncertainty: ± 0.135 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 hydro to-P01053; held-out test set · hydro FLIP2 hydro to-P01053; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A14; row ESMC-300M naive supervised; column spearman
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 hydro low-to-high; held-out test set · hydro Dataset subset: hydro	0.905 ± 0.008 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.008 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 hydro low-to-high; held-out test set · hydro FLIP2 hydro low-to-high; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A11; row ESMC-300M naive supervised; column ndcg
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 IRED two-to-many; held-out test set · IRED Dataset subset: IRED	0.949 ± 0.001 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.001 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 IRED two-to-many; held-out test set · IRED FLIP2 IRED two-to-many; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A5; row ESMC-300M naive supervised; column ndcg
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 hydro to-P0A9X9; held-out test set · hydro Dataset subset: hydro	−0.050 ± 0.193 Spearman unitless · higher Uncertainty: ± 0.193 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 hydro to-P0A9X9; held-out test set · hydro FLIP2 hydro to-P0A9X9; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A13; row ESMC-300M naive supervised; column spearman
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 Amylase by-mutation; held-out test set · Amylase Dataset subset: Amylase	0.819 ± 0.048 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.048 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 Amylase by-mutation; held-out test set · Amylase FLIP2 Amylase by-mutation; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A4; row ESMC-300M naive supervised; column ndcg
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 TrpB by-position; held-out test set · TrpB Dataset subset: TrpB	0.978 ± 0.004 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.004 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 TrpB by-position; held-out test set · TrpB FLIP2 TrpB by-position; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A9; row ESMC-300M naive supervised; column ndcg
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 TrpB two-to-many; held-out test set · TrpB Dataset subset: TrpB	0.986 ± 0.001 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.001 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 TrpB two-to-many; held-out test set · TrpB FLIP2 TrpB two-to-many; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A8; row ESMC-300M naive supervised; column ndcg
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 hydro to-P01053; held-out test set · hydro Dataset subset: hydro	0.895 ± 0.006 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.006 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 hydro to-P01053; held-out test set · hydro FLIP2 hydro to-P01053; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A14; row ESMC-300M naive supervised; column ndcg
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 hydro low-to-high; held-out test set · hydro Dataset subset: hydro	0.270 ± 0.048 Spearman unitless · higher Uncertainty: ± 0.048 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 hydro low-to-high; held-out test set · hydro FLIP2 hydro low-to-high; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A11; row ESMC-300M naive supervised; column spearman
Configuration: ESMC-300M naive supervised	Protocol: FLIP2 hydro three-to-many; held-out test set · hydro Dataset subset: hydro	0.973 ± 0.002 NDCG (cutoff not stated) unitless · higher Uncertainty: ± 0.002 (type not stated) Coverage: Not reported scored / Not reported eligible	Author-reported evaluation · Source checked Methods, coverage and source ESMC-300M naive supervised · FLIP2 hydro three-to-many; held-out test set · hydro FLIP2 hydro three-to-many; held-out test set Aggregation: mean of five random-seed fits (Section 4.3) FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications · Table A10; row ESMC-300M naive supervised; column ndcg