6 Search Results for "Marek, Ivo"

Document
Invited Talk
DOI: 10.4230/LIPIcs.IPEC.2025.1
A Brief History of Parameterized Algorithms for Block-Structured Integer Programs (Invited Talk)

Authors: Martin Koutecký

Published in: LIPIcs, Volume 358, 20th International Symposium on Parameterized and Exact Computation (IPEC 2025)

Abstract
Integer Programming (IP) is a fundamental but computationally hard problem. Still, certain efficiently solvable subclasses have been identified over time, most notably totally unimodular IPs in the 1950s, and fixed-dimension IPs in the 1980s. Starting around the year 2000, a stream of research has identified block-structured IPs as yet another tractable subclass. In this paper, we give a brief and incomplete review of this history, with a focus on several of the author’s contributions.
Cite as

Martin Koutecký. A Brief History of Parameterized Algorithms for Block-Structured Integer Programs (Invited Talk). In 20th International Symposium on Parameterized and Exact Computation (IPEC 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 358, pp. 1:1-1:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{koutecky:LIPIcs.IPEC.2025.1,
  author =	{Kouteck\'{y}, Martin},
  title =	{{A Brief History of Parameterized Algorithms for Block-Structured Integer Programs}},
  booktitle =	{20th International Symposium on Parameterized and Exact Computation (IPEC 2025)},
  pages =	{1:1--1:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-407-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{358},
  editor =	{Agrawal, Akanksha and van Leeuwen, Erik Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2025.1},
  URN =		{urn:nbn:de:0030-drops-251338},
  doi =		{10.4230/LIPIcs.IPEC.2025.1},
  annote =	{Keywords: Integer Programming, Parameterized Algorithm, Graver Basis, Treedepth, n-fold, tree-fold, 2-stage stochastic, multistage stochastic, Mixed-Integer Programming}
}
Document
DOI: 10.4230/LIPIcs.ESA.2025.13
Tight Bounds for Some Classical Problems Parameterized by Cutwidth

Authors: Narek Bojikian, Vera Chekan, and Stefan Kratsch

Published in: LIPIcs, Volume 351, 33rd Annual European Symposium on Algorithms (ESA 2025)

Abstract
Cutwidth is a widely studied parameter and it quantifies how well a graph can be decomposed along small edge-cuts. It complements pathwidth, which captures decomposition by small vertex separators, and it is well-known that cutwidth upper-bounds pathwidth. The SETH-tight parameterized complexity of problems on graphs of bounded pathwidth (and treewidth) has been actively studied over the past decade while for cutwidth the complexity of many classical problems remained open. For Hamiltonian Cycle, it is known that a (2+√2)^{pw} n^𝒪(1) algorithm is optimal for pathwidth under SETH [Cygan et al. JACM 2018]. Van Geffen et al. [J. Graph Algorithms Appl. 2020] and Bojikian et al. [STACS 2023] asked which running time is optimal for this problem parameterized by cutwidth. We answer this question with (1+√2)^{ctw} n^𝒪(1) by providing matching upper and lower bounds. Second, as our main technical contribution, we close the gap left by van Heck [2018] for Partition Into Triangles (and Triangle Packing) by improving both upper and lower bound and getting a tight bound of ∛{3}^{ctw} n^𝒪(1), which to our knowledge exhibits the only known tight non-integral basis apart from Hamiltonian Cycle [Cygan et al. JACM 2018] and C₄-Hitting Set [SODA 2025]. We show that the cuts inducing a disjoint union of paths of length three (unions of so-called Z-cuts) lie at the core of the complexity of the problem - usually lower-bound constructions use simpler cuts inducing either a matching or a disjoint union of bicliques. Finally, we determine the optimal running times for Max Cut (2^{ctw} n^𝒪(1)) and Induced Matching (3^{ctw} n^𝒪(1)) by providing matching lower bounds for the existing algorithms - the latter result also answers an open question for treewidth by Chaudhary and Zehavi [WG 2023].
Cite as

Narek Bojikian, Vera Chekan, and Stefan Kratsch. Tight Bounds for Some Classical Problems Parameterized by Cutwidth. In 33rd Annual European Symposium on Algorithms (ESA 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 351, pp. 13:1-13:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{bojikian_et_al:LIPIcs.ESA.2025.13,
  author =	{Bojikian, Narek and Chekan, Vera and Kratsch, Stefan},
  title =	{{Tight Bounds for Some Classical Problems Parameterized by Cutwidth}},
  booktitle =	{33rd Annual European Symposium on Algorithms (ESA 2025)},
  pages =	{13:1--13:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-395-9},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{351},
  editor =	{Benoit, Anne and Kaplan, Haim and Wild, Sebastian and Herman, Grzegorz},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2025.13},
  URN =		{urn:nbn:de:0030-drops-244815},
  doi =		{10.4230/LIPIcs.ESA.2025.13},
  annote =	{Keywords: Parameterized complexity, cutwidth, Hamiltonian cycle, triangle packing, max cut, induced matching}
}
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
Resource Paper
DOI: 10.4230/TGDK.2.2.7
Whelk: An OWL EL+RL Reasoner Enabling New Use Cases

Authors: James P. Balhoff and Christopher J. Mungall

Published in: TGDK, Volume 2, Issue 2 (2024): Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 2, Issue 2

Abstract
Many tasks in the biosciences rely on reasoning with large OWL terminologies (Tboxes), often combined with even larger databases. In particular, a common task is retrieval queries that utilize relational expressions; for example, “find all genes expressed in the brain or any part of the brain”. Automated reasoning on these ontologies typically relies on scalable reasoners targeting the EL subset of OWL, such as ELK. While the introduction of ELK has been transformative in the incorporation of reasoning into bio-ontology quality control and production pipelines, we have encountered limitations when applying it to use cases involving high throughput query answering or reasoning about datasets describing instances (Aboxes). Whelk is a fast OWL reasoner for combined EL+RL reasoning. As such, it is particularly useful for many biological ontology tasks, particularly those characterized by large Tboxes using the EL subset of OWL, combined with Aboxes targeting the RL subset of OWL. Whelk is implemented in Scala and utilizes immutable functional data structures, which provides advantages when performing incremental or dynamic reasoning tasks. Whelk supports querying complex class expressions at a substantially greater rate than ELK, and can answer queries or perform incremental reasoning tasks in parallel, enabling novel applications of OWL reasoning.
Cite as

James P. Balhoff and Christopher J. Mungall. Whelk: An OWL EL+RL Reasoner Enabling New Use Cases. In Special Issue on Resources for Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 2, pp. 7:1-7:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@Article{balhoff_et_al:TGDK.2.2.7,
  author =	{Balhoff, James P. and Mungall, Christopher J.},
  title =	{{Whelk: An OWL EL+RL Reasoner Enabling New Use Cases}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{7:1--7:17},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{2},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.2.7},
  URN =		{urn:nbn:de:0030-drops-225918},
  doi =		{10.4230/TGDK.2.2.7},
  annote =	{Keywords: Web Ontology Language, OWL, Semantic Web, ontology, reasoner}
}
Document
Position
DOI: 10.4230/TGDK.1.1.5
Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities

Authors: Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma

Published in: TGDK, Volume 1, Issue 1 (2023): Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge, Volume 1, Issue 1

Abstract
The term life sciences refers to the disciplines that study living organisms and life processes, and include chemistry, biology, medicine, and a range of other related disciplines. Research efforts in life sciences are heavily data-driven, as they produce and consume vast amounts of scientific data, much of which is intrinsically relational and graph-structured. The volume of data and the complexity of scientific concepts and relations referred to therein promote the application of advanced knowledge-driven technologies for managing and interpreting data, with the ultimate aim to advance scientific discovery. In this survey and position paper, we discuss recent developments and advances in the use of graph-based technologies in life sciences and set out a vision for how these technologies will impact these fields into the future. We focus on three broad topics: the construction and management of Knowledge Graphs (KGs), the use of KGs and associated technologies in the discovery of new knowledge, and the use of KGs in artificial intelligence applications to support explanations (explainable AI). We select a few exemplary use cases for each topic, discuss the challenges and open research questions within these topics, and conclude with a perspective and outlook that summarizes the overarching challenges and their potential solutions as a guide for future research.
Cite as

Jiaoyan Chen, Hang Dong, Janna Hastings, Ernesto Jiménez-Ruiz, Vanessa López, Pierre Monnin, Catia Pesquita, Petr Škoda, and Valentina Tamma. Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities. In Special Issue on Trends in Graph Data and Knowledge. Transactions on Graph Data and Knowledge (TGDK), Volume 1, Issue 1, pp. 5:1-5:33, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@Article{chen_et_al:TGDK.1.1.5,
  author =	{Chen, Jiaoyan and Dong, Hang and Hastings, Janna and Jim\'{e}nez-Ruiz, Ernesto and L\'{o}pez, Vanessa and Monnin, Pierre and Pesquita, Catia and \v{S}koda, Petr and Tamma, Valentina},
  title =	{{Knowledge Graphs for the Life Sciences: Recent Developments, Challenges and Opportunities}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{5:1--5:33},
  year =	{2023},
  volume =	{1},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.1.1.5},
  URN =		{urn:nbn:de:0030-drops-194791},
  doi =		{10.4230/TGDK.1.1.5},
  annote =	{Keywords: Knowledge graphs, Life science, Knowledge discovery, Explainable AI}
}
Document
DOI: 10.4230/DagSemProc.07071.7
Convergence of iterative aggregation/disaggregation methods based on splittings with cyclic iteration matrices

Authors: Ivo Marek, Ivana Pultarová, and Petr Mayer

Published in: Dagstuhl Seminar Proceedings, Volume 7071, Web Information Retrieval and Linear Algebra Algorithms (2007)

Abstract
Iterative aggregation/disaggregation methods (IAD) belong to competitive tools for computation the characteristics of Markov chains as shown in some publications devoted to testing and comparing various methods designed to this purpose. According to Dayar T., Stewart W.J., ``Comparison of partitioning techniques for two-level iterative solvers on large, sparse Markov chains,'' SIAM J. Sci. Comput., Vol.21, No. 5, 1691-1705 (2000), the IAD methods are effective in particular when applied to large ill posed problems. One of the purposes of this paper is to contribute to a possible explanation of this fact. The novelty may consist of the fact that the IAD algorithms do converge independently of whether the iteration matrix of the corresponding process is primitive or not. Some numerical tests are presented and possible applications mentioned; e.g. computing the PageRank.
Cite as

Ivo Marek, Ivana Pultarová, and Petr Mayer. Convergence of iterative aggregation/disaggregation methods based on splittings with cyclic iteration matrices. In Web Information Retrieval and Linear Algebra Algorithms. Dagstuhl Seminar Proceedings, Volume 7071, pp. 1-27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2007)

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@InProceedings{marek_et_al:DagSemProc.07071.7,
  author =	{Marek, Ivo and Pultarov\'{a}, Ivana and Mayer, Petr},
  title =	{{Convergence of iterative aggregation/disaggregation methods based on splittings with cyclic iteration matrices}},
  booktitle =	{Web Information Retrieval and Linear Algebra Algorithms},
  pages =	{1--27},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2007},
  volume =	{7071},
  editor =	{Andreas Frommer and Michael W. Mahoney and Daniel B. Szyld},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.07071.7},
  URN =		{urn:nbn:de:0030-drops-10679},
  doi =		{10.4230/DagSemProc.07071.7},
  annote =	{Keywords: Iterative aggregation methods, stochastic matrix, stationary probability vector, Markov chains, cyclic iteration matrix, Google matrix, PageRank.}
}
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