4 Search Results for "Anderson, Todd A."

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/LIPIcs.STACS.2025.41
Residue Domination in Bounded-Treewidth Graphs

Authors: Jakob Greilhuber, Philipp Schepper, and Philip Wellnitz

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

Abstract
For the vertex selection problem (σ,ρ)-DomSet one is given two fixed sets σ and ρ of integers and the task is to decide whether we can select vertices of the input graph such that, for every selected vertex, the number of selected neighbors is in σ and, for every unselected vertex, the number of selected neighbors is in ρ [Telle, Nord. J. Comp. 1994]. This framework covers many fundamental graph problems such as Independent Set and Dominating Set. We significantly extend the recent result by Focke et al. [SODA 2023] to investigate the case when σ and ρ are two (potentially different) residue classes modulo m ≥ 2. We study the problem parameterized by treewidth and present an algorithm that solves in time m^tw ⋅ n^O(1) the decision, minimization and maximization version of the problem. This significantly improves upon the known algorithms where for the case m ≥ 3 not even an explicit running time is known. We complement our algorithm by providing matching lower bounds which state that there is no (m-ε)^pw ⋅ n^O(1)-time algorithm parameterized by pathwidth pw, unless SETH fails. For m = 2, we extend these bounds to the minimization version as the decision version is efficiently solvable.
Cite as

Jakob Greilhuber, Philipp Schepper, and Philip Wellnitz. Residue Domination in Bounded-Treewidth Graphs. In 42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 327, pp. 41:1-41:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{greilhuber_et_al:LIPIcs.STACS.2025.41,
  author =	{Greilhuber, Jakob and Schepper, Philipp and Wellnitz, Philip},
  title =	{{Residue Domination in Bounded-Treewidth Graphs}},
  booktitle =	{42nd International Symposium on Theoretical Aspects of Computer Science (STACS 2025)},
  pages =	{41:1--41:20},
  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.2025.41},
  URN =		{urn:nbn:de:0030-drops-228675},
  doi =		{10.4230/LIPIcs.STACS.2025.41},
  annote =	{Keywords: Parameterized Complexity, Treewidth, Generalized Dominating Set, Strong Exponential Time Hypothesis}
}
Document
DOI: 10.4230/DARTS.3.2.7
Parallelizing Julia with a Non-Invasive DSL (Artifact)

Authors: Todd A. Anderson, Hai Liu, Lindsey Kuper, Ehsan Totoni, Jan Vitek, and Tatiana Shpeisman

Published in: DARTS, Volume 3, Issue 2, Special Issue of the 31st European Conference on Object-Oriented Programming (ECOOP 2017)

Abstract
This artifact is based on ParallelAccelerator, an embedded domain-specific language (DSL) and compiler for speeding up compute-intensive Julia programs. In particular, Julia code that makes heavy use of aggregate array operations is a good candidate for speeding up with ParallelAccelerator. ParallelAccelerator is a non-invasive DSL that makes as few changes to the host programming model as possible.
Cite as

Todd A. Anderson, Hai Liu, Lindsey Kuper, Ehsan Totoni, Jan Vitek, and Tatiana Shpeisman. Parallelizing Julia with a Non-Invasive DSL (Artifact). In Special Issue of the 31st European Conference on Object-Oriented Programming (ECOOP 2017). Dagstuhl Artifacts Series (DARTS), Volume 3, Issue 2, pp. 7:1-7:2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@Article{anderson_et_al:DARTS.3.2.7,
  author =	{Anderson, Todd A. and Liu, Hai and Kuper, Lindsey and Totoni, Ehsan and Vitek, Jan and Shpeisman, Tatiana},
  title =	{{Parallelizing Julia with a Non-Invasive DSL (Artifact)}},
  pages =	{7:1--7:2},
  journal =	{Dagstuhl Artifacts Series},
  ISSN =	{2509-8195},
  year =	{2017},
  volume =	{3},
  number =	{2},
  editor =	{Anderson, Todd A. and Liu, Hai and Kuper, Lindsey and Totoni, Ehsan and Vitek, Jan and Shpeisman, Tatiana},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DARTS.3.2.7},
  URN =		{urn:nbn:de:0030-drops-72888},
  doi =		{10.4230/DARTS.3.2.7},
  annote =	{Keywords: parallelism, scientific computing, domain-specific languages, Julia}
}
Document
DOI: 10.4230/LIPIcs.ECOOP.2017.4
Parallelizing Julia with a Non-Invasive DSL

Authors: Todd A. Anderson, Hai Liu, Lindsey Kuper, Ehsan Totoni, Jan Vitek, and Tatiana Shpeisman

Published in: LIPIcs, Volume 74, 31st European Conference on Object-Oriented Programming (ECOOP 2017)

Abstract
Computational scientists often prototype software using productivity languages that offer high-level programming abstractions. When higher performance is needed, they are obliged to rewrite their code in a lower-level efficiency language. Different solutions have been proposed to address this trade-off between productivity and efficiency. One promising approach is to create embedded domain-specific languages that sacrifice generality for productivity and performance, but practical experience with DSLs points to some road blocks preventing widespread adoption. This paper proposes a non-invasive domain-specific language that makes as few visible changes to the host programming model as possible. We present ParallelAccelerator, a library and compiler for high-level, high-performance scientific computing in Julia. ParallelAccelerator's programming model is aligned with existing Julia programming idioms. Our compiler exposes the implicit parallelism in high-level array-style programs and compiles them to fast, parallel native code. Programs can also run in "library-only" mode, letting users benefit from the full Julia environment and libraries. Our results show encouraging performance improvements with very few changes to source code required. In particular, few to no additional type annotations are necessary.
Cite as

Todd A. Anderson, Hai Liu, Lindsey Kuper, Ehsan Totoni, Jan Vitek, and Tatiana Shpeisman. Parallelizing Julia with a Non-Invasive DSL. In 31st European Conference on Object-Oriented Programming (ECOOP 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 74, pp. 4:1-4:29, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{anderson_et_al:LIPIcs.ECOOP.2017.4,
  author =	{Anderson, Todd A. and Liu, Hai and Kuper, Lindsey and Totoni, Ehsan and Vitek, Jan and Shpeisman, Tatiana},
  title =	{{Parallelizing Julia with a Non-Invasive DSL}},
  booktitle =	{31st European Conference on Object-Oriented Programming (ECOOP 2017)},
  pages =	{4:1--4:29},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-035-4},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{74},
  editor =	{M\"{u}ller, Peter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECOOP.2017.4},
  URN =		{urn:nbn:de:0030-drops-72693},
  doi =		{10.4230/LIPIcs.ECOOP.2017.4},
  annote =	{Keywords: parallelism, scientific computing, domain-specific languages, Julia}
}
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