Gradients of generative models for improved discriminative analysis of tandem mass spectra

John T. Halloran, David M Rocke

Research output: Contribution to journalConference articlepeer-review

5 Scopus citations


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 languageEnglish (US)
Pages (from-to)5725-5734
Number of pages10
JournalAdvances in Neural Information Processing Systems
StatePublished - Jan 1 2017
Event31st Annual Conference on Neural Information Processing Systems, NIPS 2017 - Long Beach, United States
Duration: Dec 4 2017Dec 9 2017

ASJC Scopus subject areas

  • Computer Networks and Communications
  • Information Systems
  • Signal Processing


Dive into the research topics of 'Gradients of generative models for improved discriminative analysis of tandem mass spectra'. Together they form a unique fingerprint.

Cite this