| Configuration: ESMC-300M naive supervised | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.936 ± 0.022 ndcg unitless · higher Uncertainty: printed spread: 0.022; type: unreported; value: 0.022 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESMC-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 |
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| Configuration: Ridge (one-hot) | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.939 ndcg unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRidge (one-hot) · 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 Ridge (one-hot); column ndcg |
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| Configuration: Ridge (one-hot + likelihoods) | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.337 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRidge (one-hot + likelihoods) · 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 Ridge (one-hot + likelihoods); column spearman |
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| Configuration: Dayhoff likelihood | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.019 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDayhoff 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 |
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| Configuration: CARP-640M likelihood | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.937 ndcg unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCARP-640M 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 CARP-640M likelihood; column ndcg |
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| Configuration: ESMC-300M naive supervised | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.036 ± 0.218 spearman correlation · higher Uncertainty: printed spread: 0.218; type: unreported; value: 0.218 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESMC-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 |
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| Configuration: CARP-640M naive supervised | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.934 ± 0.009 ndcg unitless · higher Uncertainty: printed spread: 0.009; type: unreported; value: 0.009 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCARP-640M 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 CARP-640M naive supervised; column ndcg |
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| Configuration: CARP-640M naive supervised | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.056 ± 0.125 spearman correlation · higher Uncertainty: printed spread: 0.125; type: unreported; value: 0.125 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCARP-640M 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 CARP-640M naive supervised; column spearman |
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| Configuration: ESM2-650M likelihood | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | −0.177 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM2-650M 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 ESM2-650M likelihood; column spearman |
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| Configuration: Dayhoff likelihood | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.902 ndcg unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceDayhoff 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 |
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| Configuration: Ridge (one-hot) | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.327 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRidge (one-hot) · 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 Ridge (one-hot); column spearman |
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| Configuration: ESM2-650M likelihood | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.904 ndcg unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM2-650M 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 ESM2-650M likelihood; column ndcg |
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| Configuration: ESMC-300M supervised | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.942 ± 0.008 ndcg unitless · higher Uncertainty: printed spread: 0.008; type: unreported; value: 0.008 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESMC-300M 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 supervised; column ndcg |
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| Configuration: Ridge (one-hot + likelihoods) | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.936 ndcg unitless · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceRidge (one-hot + likelihoods) · 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 Ridge (one-hot + likelihoods); column ndcg |
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| Configuration: CARP-640M supervised | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.934 ± 0.029 ndcg unitless · higher Uncertainty: printed spread: 0.029; type: unreported; value: 0.029 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCARP-640M 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 CARP-640M supervised; column ndcg |
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| Configuration: CARP-640M likelihood | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | 0.379 spearman correlation · higher Uncertainty: Not reported Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceCARP-640M 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 CARP-640M likelihood; column spearman |
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| Configuration: ESMC-300M supervised | Protocol: FLIP2 rhomax by-wild-type; held-out test set · rhomax Dataset subset: rhomax | −0.016 ± 0.113 spearman correlation · higher Uncertainty: printed spread: 0.113; type: unreported; value: 0.113 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESMC-300M 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 supervised; column spearman |
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