| Model,AA Recall %,Pep Acc %,Metric,Notes |
| LSTM Baseline,31.51,2.68,positional,teacher-forced eval |
| GRU Ablation,44.30,6.70,positional,teacher-forced eval |
| Diffusion V1 seed 0,43.56,11.23,positional,mass loss + iterative + cosine LR |
| Diffusion V1 seed 1,39.43,7.63,positional,mass loss + iterative + cosine LR |
| Diffusion V1 seed 2,43.41,9.11,positional,mass loss + iterative + cosine LR |
| Diffusion V1 mean,42.13,9.32,positional,42.13 +/- 2.34% AA | 9.32 +/- 1.81% pep |
| Absorbing mean (argmax),41.88,5.44,positional,absorbing diffusion 50ep seed mean |
| Absorbing mean (CFID),43.05,6.36,positional,absorbing diffusion + mask-predict 43.05 +/- 0.95% AA |
| PeakEncoder+BYBias seed 0 (argmax),74.76,33.47,positional,PeakEncoder+BYBias+absorbing 150ep |
| PeakEncoder+BYBias seed 1 (argmax),74.75,41.31,positional,PeakEncoder+BYBias+absorbing 150ep |
| PeakEncoder+BYBias seed 2 (argmax),74.84,34.75,positional,PeakEncoder+BYBias+absorbing 150ep |
| PeakEncoder+BYBias mean (argmax),74.78,36.51,positional,74.78 +/- 0.04% AA | 36.51 +/- 3.44% pep |
| PeakEncoder+BYBias seed 0 (CFID),75.12,45.13,positional,PeakEncoder+BYBias+absorbing+mask-predict 150ep |
| PeakEncoder+BYBias seed 1 (CFID),75.37,47.03,positional,PeakEncoder+BYBias+absorbing+mask-predict 150ep |
| PeakEncoder+BYBias seed 2 (CFID),75.08,42.80,positional,PeakEncoder+BYBias+absorbing+mask-predict 150ep |
| PeakEncoder+BYBias mean (CFID),75.19,44.99,positional,75.19 +/- 0.13% AA | 44.99 +/- 1.73% pep |
| V2+SelfCond seed 0 (argmax),76.36,58.47,positional,+self-cond+cosine+AdamW+200ep |
| V2+SelfCond seed 1 (argmax),76.31,51.48,positional,+self-cond+cosine+AdamW+200ep |
| V2+SelfCond seed 2 (argmax),76.24,62.50,positional,+self-cond+cosine+AdamW+200ep |
| V2+SelfCond mean (argmax),76.30,57.49,positional,76.30 +/- 0.05% AA | 57.49 +/- 4.55% pep |
| V2+SelfCond seed 0 (CFID),76.08,60.59,positional,+self-cond+cosine+AdamW+200ep+CFID-n8 |
| V2+SelfCond seed 1 (CFID),76.04,55.08,positional,+self-cond+cosine+AdamW+200ep+CFID-n8 |
| V2+SelfCond seed 2 (CFID),75.95,63.14,positional,+self-cond+cosine+AdamW+200ep+CFID-n8 |
| V2+SelfCond mean (CFID),76.02,59.60,positional,76.02 +/- 0.05% AA | 59.60 +/- 3.36% pep |
| InstaNovo (ref),72.9,33.1,positional,beam search |
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