GyroNovo
algorithm · Transformer (AR)
GyroNovo: algorithm · Transformer (AR). Attacks missing b- and y-ion fragments on two fronts. Rather than treating imputation as a fixed reconstruction task, it uses the decoder errors seen during training to…
Attacks missing b- and y-ion fragments on two fronts. Rather than treating imputation as a fixed reconstruction task, it uses the decoder errors seen during training to steer the imputation objective toward the fragments that actually cause mistakes, and to build easy and hard augmented views of each spectrum so the decoder learns under varying spectral corruption. It also gives self-attention a mass-aware inductive bias, using rotary embeddings to encode pairwise mass differences between peaks. Inference needs no extra inputs or search. Reports about 9 points of peptide-level and 7 points of amino-acid-level precision over the previous best on NovoBench.
| Kind | algorithm |
| Family | Transformer (AR) |
| Deep learning | yes |
| Acquisition | DDA |