Abstract
Tandem mass spectrometry (MS/MS) is a high-throughput technology used to identify the proteins in a complex biological sample, such as a drop of blood. A collection of spectra is generated at the output of the process, each spectrum of which is representative of a peptide (protein subsequence) present in the original complex sample. In this work, we leverage the log-likelihood gradients of generative models to improve the identification of such spectra. In particular, we show that the gradient of a recently proposed dynamic Bayesian network (DBN) [7] may be naturally employed by a kernel-based discriminative classifier. The resulting Fisher kernel substantially improves upon recent attempts to combine generative and discriminative models for post-processing analysis, outperforming all other methods on the evaluated datasets. We extend the improved accuracy offered by the Fisher kernel framework to other search algorithms by introducing Theseus, a DBN representing a large number of widely used MS/MS scoring functions. Furthermore, with gradient ascent and max-product inference at hand, we use Theseus to learn model parameters without any supervision.
Original language | English (US) |
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Pages (from-to) | 5725-5734 |
Number of pages | 10 |
Journal | Advances in Neural Information Processing Systems |
Volume | 2017-December |
State | Published - Jan 1 2017 |
Event | 31st Annual Conference on Neural Information Processing Systems, NIPS 2017 - Long Beach, United States Duration: Dec 4 2017 → Dec 9 2017 |
ASJC Scopus subject areas
- Computer Networks and Communications
- Information Systems
- Signal Processing