3 Search Results for "Sharan, Roded"

Document
DOI: 10.4230/LIPIcs.WABI.2025.11
Mutational Signature Refitting on Sparse Pan-Cancer Data

Authors: Gal Gilad, Teresa M. Przytycka, and Roded Sharan

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
Mutational processes shape cancer genomes, leaving characteristic marks that are termed signatures. The level of activity of each such process, or its signature exposure, provides important information on the disease, improving patient stratification and the prediction of drug response. Thus, there is growing interest in developing refitting methods that decipher those exposures. Previous work in this domain was unsupervised in nature, employing algebraic decomposition and probabilistic inference methods. Here we provide a supervised approach to the problem of signature refitting and show its superiority over current methods. Our method, SuRe, leverages a neural network model to capture correlations between signature exposures in real data. We show that SuRe outperforms previous methods on sparse mutation data from tumor type specific data sets, as well as pan-cancer data sets, with an increasing advantage as the data become sparser. We further demonstrate its utility in clinical settings.
Cite as

Gal Gilad, Teresa M. Przytycka, and Roded Sharan. Mutational Signature Refitting on Sparse Pan-Cancer Data. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 11:1-11:23, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{gilad_et_al:LIPIcs.WABI.2025.11,
  author =	{Gilad, Gal and Przytycka, Teresa M. and Sharan, Roded},
  title =	{{Mutational Signature Refitting on Sparse Pan-Cancer Data}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{11:1--11:23},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.11},
  URN =		{urn:nbn:de:0030-drops-239374},
  doi =		{10.4230/LIPIcs.WABI.2025.11},
  annote =	{Keywords: mutational signatures, signature refitting, cancer genomics, genomic data analysis, somatic mutations}
}
Document
DOI: 10.4230/LIPIcs.STACS.2025.64
Cluster Editing on Cographs and Related Classes

Authors: Manuel Lafond, Alitzel López Sánchez, and Weidong Luo

Published in: LIPIcs, Volume 327, 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)

Abstract
In the Cluster Editing problem, sometimes known as (unweighted) Correlation Clustering, we must insert and delete a minimum number of edges to achieve a graph in which every connected component is a clique. Owing to its applications in computational biology, social network analysis, machine learning, and others, this problem has been widely studied for decades and is still undergoing active research. There exist several parameterized algorithms for general graphs, but little is known about the complexity of the problem on specific classes of graphs. Among the few important results in this direction, if only deletions are allowed, the problem can be solved in polynomial time on cographs, which are the P₄-free graphs. However, the complexity of the broader editing problem on cographs is still open. We show that even on a very restricted subclass of cographs, the problem is NP-hard, W[1]-hard when parameterized by the number p of desired clusters, and that time n^o(p/log p) is forbidden under the ETH. This shows that the editing variant is substantially harder than the deletion-only case, and that hardness holds for the many superclasses of cographs (including graphs of clique-width at most 2, perfect graphs, circle graphs, permutation graphs). On the other hand, we provide an almost tight upper bound of time n^O(p), which is a consequence of a more general n^O(cw⋅p) time algorithm, where cw is the clique-width. Given that forbidding P₄s maintains NP-hardness, we look at {P₄, C₄}-free graphs, also known as trivially perfect graphs, and provide a cubic-time algorithm for this class.
Cite as

Manuel Lafond, Alitzel López Sánchez, and Weidong Luo. Cluster Editing on Cographs and Related Classes. In 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 327, pp. 64:1-64:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

Copy BibTex To Clipboard

@InProceedings{lafond_et_al:LIPIcs.STACS.2025.64,
  author =	{Lafond, Manuel and L\'{o}pez S\'{a}nchez, Alitzel and Luo, Weidong},
  title =	{{Cluster Editing on Cographs and Related Classes}},
  booktitle =	{42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)},
  pages =	{64:1--64:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-365-2},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{327},
  editor =	{Beyersdorff, Olaf and Pilipczuk, Micha{\l} and Pimentel, Elaine and Thắng, Nguy\~{ê}n Kim},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2025.64},
  URN =		{urn:nbn:de:0030-drops-228895},
  doi =		{10.4230/LIPIcs.STACS.2025.64},
  annote =	{Keywords: Cluster editing, cographs, parameterized algorithms, clique-width, trivially perfect graphs}
}
Document
DOI: 10.4230/LIPIcs.WABI.2018.7
A Dynamic Algorithm for Network Propagation

Authors: Barak Sternberg and Roded Sharan

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

Abstract
Network propagation is a powerful transformation that amplifies signal-to-noise ratio in biological and other data. To date, most of its applications in the biological domain employed standard techniques for its computation that require O(m) time for a network with n vertices and m edges. When applied in a dynamic setting where the network is constantly modified, the cost of these computations becomes prohibitive. Here we study, for the first time in the biological context, the complexity of dynamic algorithms for network propagation. We develop a vertex decremental algorithm that is motivated by various biological applications and can maintain propagation scores over general weights at an amortized cost of O(m/(n^{1/4})) per update. In application to real networks, the dynamic algorithm achieves significant, 50- to 100-fold, speedups over conventional static methods for network propagation, demonstrating its great potential in practice.
Cite as

Barak Sternberg and Roded Sharan. A Dynamic Algorithm for Network Propagation. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 7:1-7:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

Copy BibTex To Clipboard

@InProceedings{sternberg_et_al:LIPIcs.WABI.2018.7,
  author =	{Sternberg, Barak and Sharan, Roded},
  title =	{{A Dynamic Algorithm for Network Propagation}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{7:1--7:13},
  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.2018.7},
  URN =		{urn:nbn:de:0030-drops-93095},
  doi =		{10.4230/LIPIcs.WABI.2018.7},
  annote =	{Keywords: Network propagation, Dynamic graph algorithm, protein-protein interaction network}
}
  • Refine by Type
  • 3 Document/PDF
  • 2 Document/HTML

  • Refine by Publication Year
  • 2 2025
  • 1 2018

  • Refine by Author
  • 2 Sharan, Roded
  • 1 Gilad, Gal
  • 1 Lafond, Manuel
  • 1 Luo, Weidong
  • 1 López Sánchez, Alitzel
  • Show More...

  • Refine by Series/Journal
  • 3 LIPIcs

  • Refine by Classification
  • 1 Applied computing → Bioinformatics
  • 1 Theory of computation → Design and analysis of algorithms
  • 1 Theory of computation → Dynamic graph algorithms

  • Refine by Keyword
  • 1 Cluster editing
  • 1 Dynamic graph algorithm
  • 1 Network propagation
  • 1 cancer genomics
  • 1 clique-width
  • Show More...

Any Issues?
X

Feedback on the Current Page

CAPTCHA

Thanks for your feedback!

Feedback submitted to Dagstuhl Publishing

Could not send message

Please try again later or send an E-mail
© 2023-2025 Schloss Dagstuhl – LZI GmbH About DROPS Imprint Privacy Contact