2 Search Results for "Ciach, Michal Aleksander"

Document
DOI: 10.4230/LIPIcs.WABI.2018.25
The Wasserstein Distance as a Dissimilarity Measure for Mass Spectra with Application to Spectral Deconvolution

Authors: Szymon Majewski, Michal Aleksander Ciach, Michal Startek, Wanda Niemyska, Blazej Miasojedow, and Anna Gambin

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
We propose a new approach for the comparison of mass spectra using a metric known in the computer science under the name of Earth Mover's Distance and in mathematics as the Wasserstein distance. We argue that this approach allows for natural and robust solutions to various problems in the analysis of mass spectra. In particular, we show an application to the problem of deconvolution, in which we infer proportions of several overlapping isotopic envelopes of similar compounds. Combined with the previously proposed generator of isotopic envelopes, IsoSpec, our approach works for a wide range of masses and charges in the presence of several types of measurement inaccuracies. To reduce the computational complexity of the solution, we derive an effective implementation of the Interior Point Method as the optimization procedure. The software for mass spectral comparison and deconvolution based on Wasserstein distance is available at https://github.com/mciach/wassersteinms.
Cite as

Szymon Majewski, Michal Aleksander Ciach, Michal Startek, Wanda Niemyska, Blazej Miasojedow, and Anna Gambin. The Wasserstein Distance as a Dissimilarity Measure for Mass Spectra with Application to Spectral Deconvolution. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 25:1-25:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{majewski_et_al:LIPIcs.WABI.2018.25,
  author =	{Majewski, Szymon and Ciach, Michal Aleksander and Startek, Michal and Niemyska, Wanda and Miasojedow, Blazej and Gambin, Anna},
  title =	{{The Wasserstein Distance as a Dissimilarity Measure for Mass Spectra with Application to Spectral Deconvolution}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{25:1--25:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.25},
  URN =		{urn:nbn:de:0030-drops-93270},
  doi =		{10.4230/LIPIcs.WABI.2018.25},
  annote =	{Keywords: Mass spectrometry, Tandem mass spectrometry, Wasserstein distance, Earth mover's distance, Similarity measure, Jaccard score, Tanimoto similarity}
}
Document
DOI: 10.4230/LIPIcs.WABI.2017.5
Detecting Locus Acquisition Events in Gene Trees

Authors: Michal Aleksander Ciach, Anna Muszewska, and Pawel Górecki

Published in: LIPIcs, Volume 88, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017)

Abstract
Horizontal Gene Transfer (HGT), a process of acquisition and fixation of foreign genetic material, is an important biological phenomenon. Several approaches to HGT inference have been proposed. However, most of them either rely on approximate, non-phylogenetic methods or on the tree reconciliation, which is computationally intensive and sensitive to parameter values. In this work, we investigate the Locus Tree Inference problem as a possible alternative that combines the advantages of both approaches. We show several algorithms to solve the problem in the parsimony framework. We introduce a novel tree mapping, which allows us to obtain a heuristic solution to the problems of locus tree inference and duplication classification. Our approach allows not only for faster comparisons of gene and species trees but also to improve known algorithms for duplication inference in the presence of polytomies in the species trees.
Cite as

Michal Aleksander Ciach, Anna Muszewska, and Pawel Górecki. Detecting Locus Acquisition Events in Gene Trees. In 17th International Workshop on Algorithms in Bioinformatics (WABI 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 88, pp. 5:1-5:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

Copy BibTex To Clipboard

@InProceedings{ciach_et_al:LIPIcs.WABI.2017.5,
  author =	{Ciach, Michal Aleksander and Muszewska, Anna and G\'{o}recki, Pawel},
  title =	{{Detecting Locus Acquisition Events in Gene Trees}},
  booktitle =	{17th International Workshop on Algorithms in Bioinformatics (WABI 2017)},
  pages =	{5:1--5:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-050-7},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{88},
  editor =	{Schwartz, Russell and Reinert, Knut},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops-dev.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2017.5},
  URN =		{urn:nbn:de:0030-drops-76545},
  doi =		{10.4230/LIPIcs.WABI.2017.5},
  annote =	{Keywords: rank, taxon, ranked species tree, speciation, gene duplication, gene loss, horizontal gene transfer}
}
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