| Configuration: ESM-2 150M, the CLS token embedding, fine-tuned (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.7664 ± 0.26 RMSE (RBD expression; Random split over RBD mutants; the CLS token embedding, fine-tuned) unit-unreported · lower Uncertainty: SD 0.26 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 150M CLS finetuned: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6709 ± 0.06 RMSE (RBD expression; Random split over RBD mutants; the CLS token embedding, frozen) unit-unreported · lower Uncertainty: SD 0.06 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 150M CLS frozen: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5704 ± 0.03 RMSE (RBD expression; Random split over RBD mutants; the mean over residue embeddings, fine-tuned) unit-unreported · lower Uncertainty: SD 0.03 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 150M Mean finetuned: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6150 ± 0.06 RMSE (RBD expression; Random split over RBD mutants; the mean over residue embeddings, frozen) unit-unreported · lower Uncertainty: SD 0.06 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 150M Mean frozen: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5582 ± 0.09 RMSE (RBD expression; Random split over RBD mutants; the CLS token embedding, fine-tuned) unit-unreported · lower Uncertainty: SD 0.09 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 650M CLS finetuned: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5171 ± 0.12 RMSE (RBD expression; Random split over RBD mutants; the CLS token embedding, frozen) unit-unreported · lower Uncertainty: SD 0.12 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 650M CLS frozen: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.4999 ± 0.10 RMSE (RBD expression; Random split over RBD mutants; the mean over residue embeddings, fine-tuned) unit-unreported · lower Uncertainty: SD 0.10 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 650M Mean finetuned: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.4942 ± 0.14 RMSE (RBD expression; Random split over RBD mutants; the mean over residue embeddings, frozen) unit-unreported · lower Uncertainty: SD 0.14 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 650M Mean frozen: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6808 ± 0.02 RMSE (RBD expression; Random split over RBD mutants; the CLS token embedding, fine-tuned) unit-unreported · lower Uncertainty: SD 0.02 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 8M CLS finetuned: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6272 ± 0.05 RMSE (RBD expression; Random split over RBD mutants; the CLS token embedding, frozen) unit-unreported · lower Uncertainty: SD 0.05 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 8M CLS frozen: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6613 ± 0.05 RMSE (RBD expression; Random split over RBD mutants; the mean over residue embeddings, fine-tuned) unit-unreported · lower Uncertainty: SD 0.05 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 8M Mean finetuned: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5807 ± 0.03 RMSE (RBD expression; Random split over RBD mutants; the mean over residue embeddings, frozen) unit-unreported · lower Uncertainty: SD 0.03 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 8M Mean frozen: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5691 ± 0.06 RMSE (RBD expression; Random split over RBD mutants; the CLS token embedding, fine-tuned) unit-unreported · lower Uncertainty: SD 0.06 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 300M CLS finetuned: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6230 ± 0.06 RMSE (RBD expression; Random split over RBD mutants; the CLS token embedding, frozen) unit-unreported · lower Uncertainty: SD 0.06 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 300M CLS frozen: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5261 ± 0.05 RMSE (RBD expression; Random split over RBD mutants; the mean over residue embeddings, fine-tuned) unit-unreported · lower Uncertainty: SD 0.05 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 300M Mean finetuned: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5830 ± 0.03 RMSE (RBD expression; Random split over RBD mutants; the mean over residue embeddings, frozen) unit-unreported · lower Uncertainty: SD 0.03 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 300M Mean frozen: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6577 ± 0.15 RMSE (RBD expression; Random split over RBD mutants; the CLS token embedding, fine-tuned) unit-unreported · lower Uncertainty: SD 0.15 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 600M CLS finetuned: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6219 ± 0.07 RMSE (RBD expression; Random split over RBD mutants; the CLS token embedding, frozen) unit-unreported · lower Uncertainty: SD 0.07 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 600M CLS frozen: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5087 ± 0.06 RMSE (RBD expression; Random split over RBD mutants; the mean over residue embeddings, fine-tuned) unit-unreported · lower 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 RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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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, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5738 ± 0.07 RMSE (RBD expression; Random split over RBD mutants; the mean over residue embeddings, frozen) unit-unreported · lower Uncertainty: SD 0.07 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 600M Mean frozen: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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| Configuration: One-hot mean representation (PRIME) | Protocol: PRIME RBD expression regression, Random split over RBD mutants, RMSE Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.9625 ± 0.01 RMSE (RBD expression; Random split over RBD mutants; one-hot mean representation) unit-unreported · lower Uncertainty: SD 0.01 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceOne-Hot Mean: RBD expression RMSE, Random split over RBD mutants lit-protein-20261011-prime-protocol-random-expression-rmse 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' / 'RMSE' |
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