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DOI: 10.4230/OASIcs.GCB.2012.39
A Two-Step Soft Segmentation Procedure for MALDI Imaging Mass Spectrometry Data

Authors: Ilya Chernyavsky, Theodore Alexandrov, Peter Maass, and Sergey I. Nikolenko

Published in: OASIcs, Volume 26, German Conference on Bioinformatics 2012

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.
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Ilya Chernyavsky, Theodore Alexandrov, Peter Maass, and Sergey I. Nikolenko. A Two-Step Soft Segmentation Procedure for MALDI Imaging Mass Spectrometry Data. In German Conference on Bioinformatics 2012. Open Access Series in Informatics (OASIcs), Volume 26, pp. 39-48, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2012)

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