# Improved proteasomal cleavage prediction with positive-unlabeled learning

arXiv: https://arxiv.org/abs/2209.07527 · HTML: https://mlsanity.com/paper/2209.07527/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 5 of its 30 references that are in the map.
- First posted on arXiv 14 Sep 2022.

## Builds on (most cited first, 5 of 5)

- [Hyperband: A Novel Bandit-Based Approach to Hyperparameter Optimization](https://mlsanity.com/paper/1603.06560/) (2016)
- [Positive-Unlabeled Learning with Non-Negative Risk Estimator](https://mlsanity.com/paper/1703.00593/) (2017)
- [Learning from positive and unlabeled data: a survey](https://mlsanity.com/paper/1811.04820/) (2018)
- [Recovering True Classifier Performance in Positive-Unlabeled Learning](https://mlsanity.com/paper/1702.00518/) (2017)
- [Uncertainty-aware Pseudo-label Selection for Positive-Unlabeled Learning](https://mlsanity.com/paper/2201.13192/) (2022)

## Abstract (arXiv)

Accurate in silico modeling of the antigen processing pathway is crucial to enable personalized epitope vaccine design for cancer. An important step of such pathway is the degradation of the vaccine into smaller peptides by the proteasome, some of which are going to be presented to T cells by the MHC complex. While predicting MHC-peptide presentation has received a lot of attention recently, proteasomal cleavage prediction remains a relatively unexplored area in light of recent advancesin high-throughput mass spectrometry-based MHC ligandomics. Moreover, as such experimental techniques do not allow to identify regions that cannot be cleaved, the latest predictors generate decoy negative samples and treat them as true negatives when training, even though some of them could actually be positives. In this work, we thus present a new predictor trained with an expanded dataset and the solid theoretical underpinning of positive-unlabeled learning, achieving a new state-of-the-art in proteasomal cleavage prediction. The improved predictive capabilities will in turn enable more precise vaccine development improving the efficacy of epitope-based vaccines. Pretrained models are available on GitHub