CPC spectrum encoder pretraining
adjacent · Transformer (encoder-only)
CPC spectrum encoder pretraining: adjacent · Transformer (encoder-only). Unsupervised pretraining of a transformer spectrum encoder by Contrastive Predictive Coding, aimed at the two things that limit supervised de novo sequencing: scarce…
Unsupervised pretraining of a transformer spectrum encoder by Contrastive Predictive Coding, aimed at the two things that limit supervised de novo sequencing: scarce training data for post-translational modifications, and noisy or incomplete spectra. Exploits the large volume of unlabelled tandem mass spectra that supervised training cannot use. Evaluated on spectral library search rather than sequencing, where on 9-species-V2 it beats OpenMS by 3.73% average amino-acid precision and 4.15% recall, gains 3.8% peptide-level recall, and scales better on inference speed across dataset sizes.
| Kind | adjacent |
| Family | Transformer (encoder-only) |
| Deep learning | yes |
| Acquisition | DDA |