| Configuration: ESM-2 150M, the CLS token embedding, fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.3354 ± 0.45 R² (RBD expression; Random split over RBD mutants; the CLS token embedding, fine-tuned) unitless · higher Uncertainty: SD 0.45 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 150M CLS finetuned: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 150M' / 'CLS' / '✓', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-2 150M, the CLS token embedding, not fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5409 ± 0.08 R² (RBD expression; Random split over RBD mutants; the CLS token embedding, frozen) unitless · higher Uncertainty: SD 0.08 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 150M CLS frozen: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 150M' / 'CLS' / '×', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-2 150M, the mean over residue embeddings, fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6693 ± 0.04 R² (RBD expression; Random split over RBD mutants; the mean over residue embeddings, fine-tuned) unitless · higher Uncertainty: SD 0.04 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 150M Mean finetuned: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 150M' / 'Mean' / '✓', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-2 150M, the mean over residue embeddings, not fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6131 ± 0.07 R² (RBD expression; Random split over RBD mutants; the mean over residue embeddings, frozen) unitless · higher Uncertainty: SD 0.07 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 150M Mean frozen: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 150M' / 'Mean' / '×', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-2 650M, the CLS token embedding, fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6758 ± 0.10 R² (RBD expression; Random split over RBD mutants; the CLS token embedding, fine-tuned) unitless · higher Uncertainty: SD 0.10 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 650M CLS finetuned: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 650M' / 'CLS' / '✓', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-2 650M, the CLS token embedding, not fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.7139 ± 0.13 R² (RBD expression; Random split over RBD mutants; the CLS token embedding, frozen) unitless · higher Uncertainty: SD 0.13 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 650M CLS frozen: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 650M' / 'CLS' / '×', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-2 650M, the mean over residue embeddings, fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.7354 ± 0.11 R² (RBD expression; Random split over RBD mutants; the mean over residue embeddings, fine-tuned) unitless · higher Uncertainty: SD 0.11 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 650M Mean finetuned: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 650M' / 'Mean' / '✓', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.7337 ± 0.15 R² (RBD expression; Random split over RBD mutants; the mean over residue embeddings, frozen) unitless · higher Uncertainty: SD 0.15 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 650M Mean frozen: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 650M' / 'Mean' / '×', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-2 8M, the CLS token embedding, fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5302 ± 0.03 R² (RBD expression; Random split over RBD mutants; the CLS token embedding, fine-tuned) unitless · higher Uncertainty: SD 0.03 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 8M CLS finetuned: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 8M' / 'CLS' / '✓', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-2 8M, the CLS token embedding, not fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5984 ± 0.07 R² (RBD expression; Random split over RBD mutants; the CLS token embedding, frozen) unitless · higher Uncertainty: SD 0.07 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 8M CLS frozen: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 8M' / 'CLS' / '×', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-2 8M, the mean over residue embeddings, fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5545 ± 0.07 R² (RBD expression; Random split over RBD mutants; the mean over residue embeddings, fine-tuned) unitless · higher Uncertainty: SD 0.07 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 8M Mean finetuned: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 8M' / 'Mean' / '✓', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-2 8M, the mean over residue embeddings, not fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6576 ± 0.04 R² (RBD expression; Random split over RBD mutants; the mean over residue embeddings, frozen) unitless · higher Uncertainty: SD 0.04 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 8M Mean frozen: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-2 8M' / 'Mean' / '×', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-C 300M, the CLS token embedding, fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6678 ± 0.07 R² (RBD expression; Random split over RBD mutants; the CLS token embedding, fine-tuned) unitless · higher Uncertainty: SD 0.07 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 300M CLS finetuned: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-C 300M' / 'CLS' / '✓', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-C 300M, the CLS token embedding, not fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6026 ± 0.08 R² (RBD expression; Random split over RBD mutants; the CLS token embedding, frozen) unitless · higher Uncertainty: SD 0.08 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 300M CLS frozen: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-C 300M' / 'CLS' / '×', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-C 300M, the mean over residue embeddings, fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.7165 ± 0.06 R² (RBD expression; Random split over RBD mutants; the mean over residue embeddings, fine-tuned) unitless · higher Uncertainty: SD 0.06 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 300M Mean finetuned: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-C 300M' / 'Mean' / '✓', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-C 300M, the mean over residue embeddings, not fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6546 ± 0.04 R² (RBD expression; Random split over RBD mutants; the mean over residue embeddings, frozen) unitless · higher Uncertainty: SD 0.04 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 300M Mean frozen: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-C 300M' / 'Mean' / '×', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-C 600M, the CLS token embedding, fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5388 ± 0.21 R² (RBD expression; Random split over RBD mutants; the CLS token embedding, fine-tuned) unitless · higher Uncertainty: SD 0.21 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 600M CLS finetuned: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-C 600M' / 'CLS' / '✓', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-C 600M, the CLS token embedding, not fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6030 ± 0.09 R² (RBD expression; Random split over RBD mutants; the CLS token embedding, frozen) unitless · higher Uncertainty: SD 0.09 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 600M CLS frozen: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-C 600M' / 'CLS' / '×', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-C 600M, the mean over residue embeddings, fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.7342 ± 0.06 R² (RBD expression; Random split over RBD mutants; the mean over residue embeddings, fine-tuned) unitless · higher Uncertainty: SD 0.06 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 600M Mean finetuned: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-C 600M' / 'Mean' / '✓', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: ESM-C 600M, the mean over residue embeddings, not fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6610 ± 0.08 R² (RBD expression; Random split over RBD mutants; the mean over residue embeddings, frozen) unitless · higher Uncertainty: SD 0.08 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 600M Mean frozen: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'ESM-C 600M' / 'Mean' / '×', columns 'Random Split' / 'Expression' / 'R²' |
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| Configuration: One-hot mean representation (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.0617 ± 0.02 R² (RBD expression; Random split over RBD mutants; one-hot mean representation) unitless · higher Uncertainty: SD 0.02 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceOne-Hot Mean: RBD expression R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-r2 Aggregation: Not reported PRIME: An evaluation framework for protein representation inference and generalization in viral mutation space · Table 1, row 'One-Hot Mean', columns 'Random Split' / 'Expression' / 'R²' |
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