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DOI: 10.4230/OASIcs.GCB.2012.39
URN: urn:nbn:de:0030-drops-37163
URL: http://drops.dagstuhl.de/opus/volltexte/2012/3716/
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Chernyavsky, Ilya ; Alexandrov, Theodore ; Maass, Peter ; Nikolenko, Sergey I.

A Two-Step Soft Segmentation Procedure for MALDI Imaging Mass Spectrometry Data

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Abstract

We propose a new method for soft spatial segmentation of matrix assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS) data which is based on probabilistic clustering with subsequent smoothing. Clustering of spectra is done with the Latent Dirichlet Allocation (LDA) model. Then, clustering results are smoothed with a Markov random field (MRF) resulting in a soft probabilistic segmentation map. We show several extensions of the basic MRF model specifically tuned for MALDI-IMS data segmentation. We describe a highly parallel implementation of the smoothing algorithm based on GraphLab framework and show experimental results.

BibTeX - Entry

@InProceedings{chernyavsky_et_al:OASIcs:2012:3716,
  author =	{Ilya Chernyavsky and Theodore Alexandrov and Peter Maass and Sergey I. Nikolenko},
  title =	{{A Two-Step Soft Segmentation Procedure for MALDI Imaging Mass Spectrometry Data}},
  booktitle =	{German Conference on Bioinformatics 2012},
  pages =	{39--48},
  series =	{OpenAccess Series in Informatics (OASIcs)},
  ISBN =	{978-3-939897-44-6},
  ISSN =	{2190-6807},
  year =	{2012},
  volume =	{26},
  editor =	{Sebastian B{\"o}cker and Franziska Hufsky and Kerstin Scheubert and Jana Schleicher and Stefan Schuster},
  publisher =	{Schloss Dagstuhl--Leibniz-Zentrum fuer Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{http://drops.dagstuhl.de/opus/volltexte/2012/3716},
  URN =		{urn:nbn:de:0030-drops-37163},
  doi =		{http://dx.doi.org/10.4230/OASIcs.GCB.2012.39},
  annote =	{Keywords: MALDI imaging mass spectrometry, hyperspectral image segmentation, probabilistic graphical models, latent Dirichlet allocation, Markov random field}
}

Keywords: MALDI imaging mass spectrometry, hyperspectral image segmentation, probabilistic graphical models, latent Dirichlet allocation, Markov random field
Seminar: German Conference on Bioinformatics 2012
Issue Date: 2012
Date of publication: 13.09.2012


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