| Configuration: ESM-2 150M, the CLS token embedding, fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5836 ± 0.28 R² (ACE2 binding; Random split over RBD mutants; the CLS token embedding, fine-tuned) unitless · higher Uncertainty: SD 0.28 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 150M CLS finetuned: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-2 150M, the CLS token embedding, not fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5788 ± 0.14 R² (ACE2 binding; Random split over RBD mutants; the CLS token embedding, frozen) unitless · higher Uncertainty: SD 0.14 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 150M CLS frozen: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-2 150M, the mean over residue embeddings, fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.7461 ± 0.08 R² (ACE2 binding; Random split over RBD mutants; the mean over residue embeddings, fine-tuned) unitless · higher Uncertainty: SD 0.08 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 150M Mean finetuned: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-2 150M, the mean over residue embeddings, not fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6713 ± 0.13 R² (ACE2 binding; Random split over RBD mutants; the mean over residue embeddings, frozen) unitless · higher Uncertainty: SD 0.13 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 150M Mean frozen: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-2 650M, the CLS token embedding, fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.7584 ± 0.11 R² (ACE2 binding; Random split over RBD mutants; the CLS token embedding, 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 CLS finetuned: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-2 650M, the CLS token embedding, not fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.7694 ± 0.13 R² (ACE2 binding; 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: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-2 650M, the mean over residue embeddings, fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.8189 ± 0.10 R² (ACE2 binding; Random split over RBD mutants; the mean over residue embeddings, 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 Mean finetuned: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-2 650M, the mean over residue embeddings, not fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.7981 ± 0.13 R² (ACE2 binding; Random split over RBD mutants; the mean over residue embeddings, frozen) unitless · higher Uncertainty: SD 0.13 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 650M Mean frozen: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-2 8M, the CLS token embedding, fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5897 ± 0.03 R² (ACE2 binding; 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: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-2 8M, the CLS token embedding, not fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5876 ± 0.07 R² (ACE2 binding; 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: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-2 8M, the mean over residue embeddings, fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6225 ± 0.07 R² (ACE2 binding; 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: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-2 8M, the mean over residue embeddings, not fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6794 ± 0.02 R² (ACE2 binding; Random split over RBD mutants; the mean over residue embeddings, frozen) unitless · higher Uncertainty: SD 0.02 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-2 8M Mean frozen: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-C 300M, the CLS token embedding, fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.7647 ± 0.08 R² (ACE2 binding; Random split over RBD mutants; the CLS token embedding, fine-tuned) unitless · higher Uncertainty: SD 0.08 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 300M CLS finetuned: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-C 300M, the CLS token embedding, not fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.5869 ± 0.15 R² (ACE2 binding; Random split over RBD mutants; the CLS token embedding, frozen) unitless · higher Uncertainty: SD 0.15 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 300M CLS frozen: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-C 300M, the mean over residue embeddings, fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.8057 ± 0.06 R² (ACE2 binding; 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: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-C 300M, the mean over residue embeddings, not fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.7155 ± 0.07 R² (ACE2 binding; 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-C 300M Mean frozen: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-C 600M, the CLS token embedding, fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.7552 ± 0.07 R² (ACE2 binding; 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 600M CLS finetuned: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-C 600M, the CLS token embedding, not fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.6616 ± 0.12 R² (ACE2 binding; Random split over RBD mutants; the CLS token embedding, frozen) unitless · higher Uncertainty: SD 0.12 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 600M CLS frozen: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-C 600M, the mean over residue embeddings, fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.8346 ± 0.07 R² (ACE2 binding; 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-C 600M Mean finetuned: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: ESM-C 600M, the mean over residue embeddings, not fine-tuned (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.7355 ± 0.12 R² (ACE2 binding; Random split over RBD mutants; the mean over residue embeddings, frozen) unitless · higher Uncertainty: SD 0.12 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceESM-C 600M Mean frozen: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|
| Configuration: One-hot mean representation (PRIME) | Protocol: PRIME ACE2 binding regression, Random split over RBD mutants, R² Dataset: SARS-CoV-2 RBD mutant binding and expression measurements | 0.1136 ± 0.03 R² (ACE2 binding; Random split over RBD mutants; one-hot mean representation) unitless · higher Uncertainty: SD 0.03 Coverage: Not reported scored / Not reported eligible | Author-reported evaluation · Source checkedMethods, coverage and sourceOne-Hot Mean: ACE2 binding R², Random split over RBD mutants lit-protein-20261011-prime-protocol-random-binding-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' / 'Binding' / 'R²' |
|---|