1 Search Results for "Malikic, Salem"


Document
A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression

Authors: Nikolai Karpov, Salem Malikic, Md. Khaledur Rahman, and S. Cenk Sahinalp

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


Abstract
We introduce a new edit distance measure between a pair of "clonal trees", each representing the progression and mutational heterogeneity of a tumor sample, constructed by the use of single cell or bulk high throughput sequencing data. In a clonal tree, each vertex represents a specific tumor clone, and is labeled with one or more mutations in a way that each mutation is assigned to the oldest clone that harbors it. Given two clonal trees, our multi-labeled tree edit distance (MLTED) measure is defined as the minimum number of mutation/label deletions, (empty) leaf deletions, and vertex (clonal) expansions, applied in any order, to convert each of the two trees to the maximal common tree. We show that the MLTED measure can be computed efficiently in polynomial time and it captures the similarity between trees of different clonal granularity well. We have implemented our algorithm to compute MLTED exactly and applied it to a variety of data sets successfully. The source code of our method can be found in: https://github.com/khaled-rahman/leafDelTED.

Cite as

Nikolai Karpov, Salem Malikic, Md. Khaledur Rahman, and S. Cenk Sahinalp. A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 22:1-22:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)


Copy BibTex To Clipboard

@InProceedings{karpov_et_al:LIPIcs.WABI.2018.22,
  author =	{Karpov, Nikolai and Malikic, Salem and Rahman, Md. Khaledur and Sahinalp, S. Cenk},
  title =	{{A Multi-labeled Tree Edit Distance for Comparing "Clonal Trees" of Tumor Progression}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{22:1--22:19},
  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.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.22},
  URN =		{urn:nbn:de:0030-drops-93242},
  doi =		{10.4230/LIPIcs.WABI.2018.22},
  annote =	{Keywords: Intra-tumor heterogeneity, tumor evolution, multi-labeled tree, tree edit distance, dynamic programming}
}
  • Refine by Author
  • 1 Karpov, Nikolai
  • 1 Malikic, Salem
  • 1 Rahman, Md. Khaledur
  • 1 Sahinalp, S. Cenk

  • Refine by Classification
  • 1 Applied computing → Computational genomics
  • 1 Computing methodologies → Combinatorial algorithms

  • Refine by Keyword
  • 1 Intra-tumor heterogeneity
  • 1 dynamic programming
  • 1 multi-labeled tree
  • 1 tree edit distance
  • 1 tumor evolution

  • Refine by Type
  • 1 document

  • Refine by Publication Year
  • 1 2018