2 Search Results for "Benz, Dominik"

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)

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@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/DagSemProc.08391.6
08391 Working Group Summary – Analyzing Tag Semantics Across Tagging Systems

Authors: Dominik Benz, Marko Grobelnik, Andreas Hotho, Robert Jäschke, Dunja Mladenic, Vito D. P. Servedio, Sergej Sizov, and Martin Szomszor

Published in: Dagstuhl Seminar Proceedings, Volume 8391, Social Web Communities (2008)

Abstract
The objective of our group was to exploit state-of-the-art Information Retrieval methods for finding associations and dependencies between tags, capturing and representing differences in tagging behavior and vocabulary of various folksonomies, with the overall aim to better understand the semantics of tags and the tagging process. Therefore we analyze the semantic content of tags in the Flickr and Delicious folksonomies. We find that: tag context similarity leads to meaningful results in Flickr, despite its narrow folksonomy character; the comparison of tags across Flickr and Delicious shows little semantic overlap, being tags in Flickr associated more to visual aspects rather than technological as it seems to be in Delicious; there are regions in the tag-tag space, provided with the cosine similarity metric, that are characterized by high density; the order of tags inside a post has a semantic relevance.
Cite as

Dominik Benz, Marko Grobelnik, Andreas Hotho, Robert Jäschke, Dunja Mladenic, Vito D. P. Servedio, Sergej Sizov, and Martin Szomszor. 08391 Working Group Summary – Analyzing Tag Semantics Across Tagging Systems. In Social Web Communities. Dagstuhl Seminar Proceedings, Volume 8391, pp. 1-15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2008)

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@InProceedings{benz_et_al:DagSemProc.08391.6,
  author =	{Benz, Dominik and Grobelnik, Marko and Hotho, Andreas and J\"{a}schke, Robert and Mladenic, Dunja and Servedio, Vito D. P. and Sizov, Sergej and Szomszor, Martin},
  title =	{{08391 Working Group Summary – Analyzing Tag Semantics Across Tagging Systems}},
  booktitle =	{Social Web Communities},
  pages =	{1--15},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2008},
  volume =	{8391},
  editor =	{Harith Alani and Steffen Staab and Gerd Stumme},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08391.6},
  URN =		{urn:nbn:de:0030-drops-17854},
  doi =		{10.4230/DagSemProc.08391.6},
  annote =	{Keywords: Social Web Communities, Folksonomy, Tag, Semantics}
}
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