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 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 |
| Deep learning | yes |
| Acquisition | DDA |
| Family | Transformer (encoder-only) |
Data
What the papers describing this method trained it on and reported its results on, as each paper states it. A version is named only where the paper names one.
Also used, purpose not recorded
- Nine-species benchmark (version not stated)
- Seven-species benchmark (NovoBench split)