12 Search Results for "Popa, Alexandru"

Document
DOI: 10.4230/LIPIcs.SEA.2024.14
Accelerating ILP Solvers for Minimum Flow Decompositions Through Search Space and Dimensionality Reductions

Authors: Andreas Grigorjew, Fernando H. C. Dias, Andrea Cracco, Romeo Rizzi, and Alexandru I. Tomescu

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)

Abstract
Given a flow network, the Minimum Flow Decomposition (MFD) problem is finding the smallest possible set of weighted paths whose superposition equals the flow. It is a classical, strongly NP-hard problem that is proven to be useful in RNA transcript assembly and applications outside of Bioinformatics. We improve an existing ILP (Integer Linear Programming) model by Dias et al. [RECOMB 2022] for DAGs by decreasing the solver’s search space using solution safety and several other optimizations. This results in a significant speedup compared to the original ILP, of up to 34× on average on the hardest instances. Moreover, we show that our optimizations apply also to MFD problem variants, resulting in speedups that go up to 219× on the hardest instances. We also developed an ILP model of reduced dimensionality for an MFD variant in which the solution path weights are restricted to a given set. This model can find an optimal MFD solution for most instances, and overall, its accuracy significantly outperforms that of previous greedy algorithms while being up to an order of magnitude faster than our optimized ILP.
Cite as

Andreas Grigorjew, Fernando H. C. Dias, Andrea Cracco, Romeo Rizzi, and Alexandru I. Tomescu. Accelerating ILP Solvers for Minimum Flow Decompositions Through Search Space and Dimensionality Reductions. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 14:1-14:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

Copy BibTex To Clipboard

@InProceedings{grigorjew_et_al:LIPIcs.SEA.2024.14,
  author =	{Grigorjew, Andreas and Dias, Fernando H. C. and Cracco, Andrea and Rizzi, Romeo and Tomescu, Alexandru I.},
  title =	{{Accelerating ILP Solvers for Minimum Flow Decompositions Through Search Space and Dimensionality Reductions}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{14:1--14:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.14},
  URN =		{urn:nbn:de:0030-drops-203792},
  doi =		{10.4230/LIPIcs.SEA.2024.14},
  annote =	{Keywords: Flow decomposition, Integer Linear Programming, Safety, RNA-seq, RNA transcript assembly, isoform}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.17
Barcode Selection and Layout Optimization in Spatial Transcriptomics

Authors: Frederik L. Jatzkowski, Antonia Schmidt, Robert Mank, Steffen Schüler, and Matthias Müller-Hannemann

Published in: LIPIcs, Volume 301, 22nd International Symposium on Experimental Algorithms (SEA 2024)

Abstract
An important special case of the quadratic assignment problem arises in the synthesis of DNA microarrays for high-resolution spatial transcriptomics. The task is to select a suitable subset from a set of barcodes, i. e. short DNA strings that serve as unique identifiers, and to assign the selected barcodes to positions on a two-dimensional array in such a way that a position-dependent cost function is minimized. A typical microarray with dimensions of 768×1024 requires 786,432 many barcodes to be placed, leading to very challenging large-scale combinatorial optimization problems. The general quadratic assignment problem is well-known for its hardness, both in theory and in practice. It turns out that this also holds for the special case of the barcode layout problem. We show that the problem is even hard to approximate: It is MaxSNP-hard. An ILP formulation theoretically allows the computation of optimal results, but it is only applicable for tiny instances. Therefore, we have developed layout constructing and improving heuristics with the aim of computing near-optimal solutions for instances of realistic size. These include a sorting-based algorithm, a greedy algorithm, 2-OPT-based local search and a genetic algorithm. To assess the quality of the results, we compare the generated solutions with the expected cost of a random layout and with lower bounds. A combination of the greedy algorithm and 2-OPT local search produces the most promising results in terms of both quality and runtime. Solutions to large-scale instances with arrays of dimension 768×1024 show a 37% reduction in cost over a random solution and can be computed in about 3 minutes. Since the universe of suitable barcodes is much larger than the number of barcodes needed, this can be exploited. Experiments with different surpluses of barcodes show that a significant improvement in layout quality can be achieved at the cost of a reasonable increase in runtime. Another interesting finding is that the restriction of the barcode design space by biochemical constraints is actually beneficial for the overall layout cost.
Cite as

Frederik L. Jatzkowski, Antonia Schmidt, Robert Mank, Steffen Schüler, and Matthias Müller-Hannemann. Barcode Selection and Layout Optimization in Spatial Transcriptomics. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 17:1-17:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

Copy BibTex To Clipboard

@InProceedings{jatzkowski_et_al:LIPIcs.SEA.2024.17,
  author =	{Jatzkowski, Frederik L. and Schmidt, Antonia and Mank, Robert and Sch\"{u}ler, Steffen and M\"{u}ller-Hannemann, Matthias},
  title =	{{Barcode Selection and Layout Optimization in Spatial Transcriptomics}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{17:1--17:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-325-6},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{301},
  editor =	{Liberti, Leo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2024.17},
  URN =		{urn:nbn:de:0030-drops-203821},
  doi =		{10.4230/LIPIcs.SEA.2024.17},
  annote =	{Keywords: Spatial Transcriptomics, Array Layout, Optimization, Computational Complexity, GPU Computing, Integer Linear Programming, Metaheuristics}
}
Document
DOI: 10.4230/LIPIcs.ECRTS.2024.1
JuMP2start: Time-Aware Stop-Start Technology for a Software-Defined Vehicle System

Authors: Anam Farrukh and Richard West

Published in: LIPIcs, Volume 298, 36th Euromicro Conference on Real-Time Systems (ECRTS 2024)

Abstract
Software-defined vehicle (SDV) systems replace traditional ECU architectures with software tasks running on centralized multicore processors in automotive-grade PCs. However, PC boot delays to cold-start an integrated vehicle management system (VMS) are problematic for time-critical functions, which must process sensor and actuator data within specific time bounds. To tackle this challenge, we present JuMP2start: a time-aware multicore stop-start approach for SDVs. JuMP2start leverages PC-class suspend-to-RAM techniques to capture a system snapshot when the vehicle is stopped. Upon restart, critical services are resumed-from-RAM within order of milliseconds compared to normal cold-start times. This work showcases how JuMP2start manages global suspension and resumption mechanisms for a state-of-the-art dual-domain vehicle management system comprising real-time OS (RTOS) and Linux SMP guests. JuMP2start models automotive tasks as continuable or restartable to ensure timing- and safety-critical function pipelines are reactively resumed with low latency, while discarding stale task state. Experiments with the VMS show that critical CAN traffic processing resumes within 500 milliseconds of waking the RTOS guest, and reaches steady-state throughput in under 7ms.
Cite as

Anam Farrukh and Richard West. JuMP2start: Time-Aware Stop-Start Technology for a Software-Defined Vehicle System. In 36th Euromicro Conference on Real-Time Systems (ECRTS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 298, pp. 1:1-1:27, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

Copy BibTex To Clipboard

@InProceedings{farrukh_et_al:LIPIcs.ECRTS.2024.1,
  author =	{Farrukh, Anam and West, Richard},
  title =	{{JuMP2start: Time-Aware Stop-Start Technology for a Software-Defined Vehicle System}},
  booktitle =	{36th Euromicro Conference on Real-Time Systems (ECRTS 2024)},
  pages =	{1:1--1:27},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-324-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{298},
  editor =	{Pellizzoni, Rodolfo},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ECRTS.2024.1},
  URN =		{urn:nbn:de:0030-drops-203046},
  doi =		{10.4230/LIPIcs.ECRTS.2024.1},
  annote =	{Keywords: Time-aware stop-start, Real-time power management, Suspend-to-RAM, Partitioning hypervisor, Vehicle management system, Vehicle-OS, Software-defined vehicles (SDV)}
}
Document
Position
DOI: 10.4230/TGDK.2.1.2
Grounding Stream Reasoning Research

Authors: Pieter Bonte, Jean-Paul Calbimonte, Daniel de Leng, Daniele Dell'Aglio, Emanuele Della Valle, Thomas Eiter, Federico Giannini, Fredrik Heintz, Konstantin Schekotihin, Danh Le-Phuoc, Alessandra Mileo, Patrik Schneider, Riccardo Tommasini, Jacopo Urbani, and Giacomo Ziffer

Published in: TGDK, Volume 2, Issue 1 (2024): Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge, Volume 2, Issue 1

Abstract
In the last decade, there has been a growing interest in applying AI technologies to implement complex data analytics over data streams. To this end, researchers in various fields have been organising a yearly event called the "Stream Reasoning Workshop" to share perspectives, challenges, and experiences around this topic. In this paper, the previous organisers of the workshops and other community members provide a summary of the main research results that have been discussed during the first six editions of the event. These results can be categorised into four main research areas: The first is concerned with the technological challenges related to handling large data streams. The second area aims at adapting and extending existing semantic technologies to data streams. The third and fourth areas focus on how to implement reasoning techniques, either considering deductive or inductive techniques, to extract new and valuable knowledge from the data in the stream. This summary is written not only to provide a crystallisation of the field, but also to point out distinctive traits of the stream reasoning community. Moreover, it also provides a foundation for future research by enumerating a list of use cases and open challenges, to stimulate others to join this exciting research area.
Cite as

Pieter Bonte, Jean-Paul Calbimonte, Daniel de Leng, Daniele Dell'Aglio, Emanuele Della Valle, Thomas Eiter, Federico Giannini, Fredrik Heintz, Konstantin Schekotihin, Danh Le-Phuoc, Alessandra Mileo, Patrik Schneider, Riccardo Tommasini, Jacopo Urbani, and Giacomo Ziffer. Grounding Stream Reasoning Research. In Special Issue on Trends in Graph Data and Knowledge - Part 2. Transactions on Graph Data and Knowledge (TGDK), Volume 2, Issue 1, pp. 2:1-2:47, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

Copy BibTex To Clipboard

@Article{bonte_et_al:TGDK.2.1.2,
  author =	{Bonte, Pieter and Calbimonte, Jean-Paul and de Leng, Daniel and Dell'Aglio, Daniele and Della Valle, Emanuele and Eiter, Thomas and Giannini, Federico and Heintz, Fredrik and Schekotihin, Konstantin and Le-Phuoc, Danh and Mileo, Alessandra and Schneider, Patrik and Tommasini, Riccardo and Urbani, Jacopo and Ziffer, Giacomo},
  title =	{{Grounding Stream Reasoning Research}},
  journal =	{Transactions on Graph Data and Knowledge},
  pages =	{2:1--2:47},
  ISSN =	{2942-7517},
  year =	{2024},
  volume =	{2},
  number =	{1},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/TGDK.2.1.2},
  URN =		{urn:nbn:de:0030-drops-198597},
  doi =		{10.4230/TGDK.2.1.2},
  annote =	{Keywords: Stream Reasoning, Stream Processing, RDF streams, Streaming Linked Data, Continuous query processing, Temporal Logics, High-performance computing, Databases}
}
Document
DOI: 10.4230/LIPIcs.CPM.2023.5
Faster Algorithms for Computing the Hairpin Completion Distance and Minimum Ancestor

Authors: Itai Boneh, Dvir Fried, Adrian Miclăuş, and Alexandru Popa

Published in: LIPIcs, Volume 259, 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)

Abstract
Hairpin completion is an operation on formal languages that has been inspired by hairpin formation in DNA biochemistry and has many applications especially in DNA computing. Consider s to be a string over the alphabet {A, C, G, T} such that a prefix/suffix of it matches the reversed complement of a substring of s. Then, in a hairpin completion operation the reversed complement of this prefix/suffix is added to the start/end of s forming a new string. In this paper we study two problems related to the hairpin completion. The first problem asks the minimum number of hairpin operations necessary to transform one string into another, number that is called the hairpin completion distance. For this problem we show an algorithm of running time O(n²), where n is the maximum length of the two strings. Our algorithm improves on the algorithm of Manea (TCS 2010), that has running time O(n² log n). In the minimum distance common hairpin completion ancestor problem we want to find, for two input strings x and y, a string w that minimizes the sum of the hairpin completion distances to x and y. Similarly, we present an algorithm with running time O(n²) that improves by a O(log n) factor the algorithm of Manea (TCS 2010).
Cite as

Itai Boneh, Dvir Fried, Adrian Miclăuş, and Alexandru Popa. Faster Algorithms for Computing the Hairpin Completion Distance and Minimum Ancestor. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 5:1-5:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

Copy BibTex To Clipboard

@InProceedings{boneh_et_al:LIPIcs.CPM.2023.5,
  author =	{Boneh, Itai and Fried, Dvir and Micl\u{a}u\c{s}, Adrian and Popa, Alexandru},
  title =	{{Faster Algorithms for Computing the Hairpin Completion Distance and Minimum Ancestor}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{5:1--5:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-276-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{259},
  editor =	{Bulteau, Laurent and Lipt\'{a}k, Zsuzsanna},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2023.5},
  URN =		{urn:nbn:de:0030-drops-179592},
  doi =		{10.4230/LIPIcs.CPM.2023.5},
  annote =	{Keywords: dynamic programming, incremental trees, exact algorithm}
}
Document
DOI: 10.4230/LIPIcs.CPM.2023.19
String Factorization via Prefix Free Families

Authors: Matan Kraus, Moshe Lewenstein, Alexandru Popa, Ely Porat, and Yonathan Sadia

Published in: LIPIcs, Volume 259, 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)

Abstract
A factorization of a string S is a partition of w into substrings u_1,… ,u_k such that S = u_1 u_2 ⋯ u_k. Such a partition is called equality-free if no two factors are equal: u_i ≠ u_j, ∀ i,j with i ≠ j. The maximum equality-free factorization problem is to find for a given string S, the largest integer k for which S admits an equality-free factorization with k factors. Equality-free factorizations have lately received attention because of their applications in DNA self-assembly. The best approximation algorithm known for the problem is the natural greedy algorithm, that chooses iteratively from left to right the shortest factor that does not appear before. This algorithm has a √n approximation ratio (SOFSEM 2020) and it is an open problem whether there is a better solution. Our main result is to show that the natural greedy algorithm is a Θ(n^{1/4}) approximation algorithm for the maximum equality-free factorization problem. Thus, we disprove one of the conjectures of Mincu and Popa (SOFSEM 2020) according to which the greedy algorithm is a Θ(√n) approximation. The most challenging part of the proof is to show that the greedy algorithm is an O(n^{1/4}) approximation. We obtain this algorithm via prefix free factor families, i.e. a set of non-overlapping factors of the string which are pairwise non-prefixes of each other. In the paper we show the relation between prefix free factor families and the maximum equality-free factorization. Moreover, as a byproduct we present another approximation algorithm that achieves an approximation ratio of O(n^{1/4}) that we believe is of independent interest and may lead to improved algorithms. We then show that the natural greedy algorithm has an approximation ratio that is Ω(n^{1/4}) via a clever analysis which shows that the greedy algorithm is Θ(n^{1/4}) for the maximum equality-free factorization problem.
Cite as

Matan Kraus, Moshe Lewenstein, Alexandru Popa, Ely Porat, and Yonathan Sadia. String Factorization via Prefix Free Families. In 34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 259, pp. 19:1-19:10, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

Copy BibTex To Clipboard

@InProceedings{kraus_et_al:LIPIcs.CPM.2023.19,
  author =	{Kraus, Matan and Lewenstein, Moshe and Popa, Alexandru and Porat, Ely and Sadia, Yonathan},
  title =	{{String Factorization via Prefix Free Families}},
  booktitle =	{34th Annual Symposium on Combinatorial Pattern Matching (CPM 2023)},
  pages =	{19:1--19:10},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-276-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{259},
  editor =	{Bulteau, Laurent and Lipt\'{a}k, Zsuzsanna},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2023.19},
  URN =		{urn:nbn:de:0030-drops-179738},
  doi =		{10.4230/LIPIcs.CPM.2023.19},
  annote =	{Keywords: string factorization, NP-hard problem, approximation algorithm}
}
Document
DOI: 10.4230/LIPIcs.CPM.2022.15
Polynomial-Time Equivalences and Refined Algorithms for Longest Common Subsequence Variants

Authors: Yuichi Asahiro, Jesper Jansson, Guohui Lin, Eiji Miyano, Hirotaka Ono, and Tadatoshi Utashima

Published in: LIPIcs, Volume 223, 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)

Abstract
The problem of computing the longest common subsequence of two sequences (LCS for short) is a classical and fundamental problem in computer science. In this paper, we study four variants of LCS: the Repetition-Bounded Longest Common Subsequence problem (RBLCS) [Yuichi Asahiro et al., 2020], the Multiset-Restricted Common Subsequence problem (MRCS) [Radu Stefan Mincu and Alexandru Popa, 2018], the Two-Side-Filled Longest Common Subsequence problem (2FLCS), and the One-Side-Filled Longest Common Subsequence problem (1FLCS) [Mauro Castelli et al., 2017; Mauro Castelli et al., 2019]. Although the original LCS can be solved in polynomial time, all these four variants are known to be NP-hard. Recently, an exact, O(1.44225ⁿ)-time, dynamic programming (DP)-based algorithm for RBLCS was proposed [Yuichi Asahiro et al., 2020], where the two input sequences have lengths n and poly(n). We first establish that each of MRCS, 1FLCS, and 2FLCS is polynomially equivalent to RBLCS. Then, we design a refined DP-based algorithm for RBLCS that runs in O(1.41422ⁿ) time, which implies that MRCS, 1FLCS, and 2FLCS can also be solved in O(1.41422ⁿ) time. Finally, we give a polynomial-time 2-approximation algorithm for 2FLCS.
Cite as

Yuichi Asahiro, Jesper Jansson, Guohui Lin, Eiji Miyano, Hirotaka Ono, and Tadatoshi Utashima. Polynomial-Time Equivalences and Refined Algorithms for Longest Common Subsequence Variants. In 33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 223, pp. 15:1-15:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

Copy BibTex To Clipboard

@InProceedings{asahiro_et_al:LIPIcs.CPM.2022.15,
  author =	{Asahiro, Yuichi and Jansson, Jesper and Lin, Guohui and Miyano, Eiji and Ono, Hirotaka and Utashima, Tadatoshi},
  title =	{{Polynomial-Time Equivalences and Refined Algorithms for Longest Common Subsequence Variants}},
  booktitle =	{33rd Annual Symposium on Combinatorial Pattern Matching (CPM 2022)},
  pages =	{15:1--15:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-234-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{223},
  editor =	{Bannai, Hideo and Holub, Jan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2022.15},
  URN =		{urn:nbn:de:0030-drops-161424},
  doi =		{10.4230/LIPIcs.CPM.2022.15},
  annote =	{Keywords: Repetition-bounded longest common subsequence problem, multiset restricted longest common subsequence problem, one-side-filled longest common subsequence problem, two-side-filled longest common subsequence problem, exact algorithms, and approximation algorithms}
}
Document
DOI: 10.4230/LIPIcs.CPM.2021.23
Efficient Algorithms for Counting Gapped Palindromes

Authors: Andrei Popa and Alexandru Popa

Published in: LIPIcs, Volume 191, 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)

Abstract
A gapped palindrome is a string uvu^{R}, where u^{R} represents the reverse of string u. In this paper we show three efficient algorithms for counting the occurrences of gapped palindromes in a given string S of length N. First, we present a solution in O(N) time for counting all gapped palindromes without additional constraints. Then, in the case where the length of v is constrained to be in an interval [g, G], we show an algorithm with running time O(N log N). Finally, we show an algorithm in O(N log² N) time for a more general case where we count gapped palindromes uvu^{R}, where u^{R} starts at position i with g(i) ≤ v ≤ G(i), for all positions i.
Cite as

Andrei Popa and Alexandru Popa. Efficient Algorithms for Counting Gapped Palindromes. In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, pp. 23:1-23:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

Copy BibTex To Clipboard

@InProceedings{popa_et_al:LIPIcs.CPM.2021.23,
  author =	{Popa, Andrei and Popa, Alexandru},
  title =	{{Efficient Algorithms for Counting Gapped Palindromes}},
  booktitle =	{32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)},
  pages =	{23:1--23:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-186-3},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{191},
  editor =	{Gawrychowski, Pawe{\l} and Starikovskaya, Tatiana},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2021.23},
  URN =		{urn:nbn:de:0030-drops-139746},
  doi =		{10.4230/LIPIcs.CPM.2021.23},
  annote =	{Keywords: pattern matching, gapped palindromes, suffix tree}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2020.6
Complexity of Computing the Anti-Ramsey Numbers for Paths

Authors: Saeed Akhoondian Amiri, Alexandru Popa, Mohammad Roghani, Golnoosh Shahkarami, Reza Soltani, and Hossein Vahidi

Published in: LIPIcs, Volume 170, 45th International Symposium on Mathematical Foundations of Computer Science (MFCS 2020)

Abstract
The anti-Ramsey numbers are a fundamental notion in graph theory, introduced in 1978, by Erdös, Simonovits and Sós. For given graphs G and H the anti-Ramsey number ar(G,H) is defined to be the maximum number k such that there exists an assignment of k colors to the edges of G in which every copy of H in G has at least two edges with the same color. Usually, combinatorists study extremal values of anti-Ramsey numbers for various classes of graphs. There are works on the computational complexity of the problem when H is a star. Along this line of research, we study the complexity of computing the anti-Ramsey number ar(G,P_k), where P_k is a path of length k. First, we observe that when k is close to n, the problem is hard; hence, the challenging part is the computational complexity of the problem when k is a fixed constant. We provide a characterization of the problem for paths of constant length. Our first main contribution is to prove that computing ar(G,P_k) for every integer k > 2 is NP-hard. We obtain this by providing several structural properties of such coloring in graphs. We investigate further and show that approximating ar(G,P₃) to a factor of n^{-1/2 - ε} is hard already in 3-partite graphs, unless P = NP. We also study the exact complexity of the precolored version and show that there is no subexponential algorithm for the problem unless ETH fails for any fixed constant k. Given the hardness of approximation and parametrization of the problem, it is natural to study the problem on restricted graph families. Along this line, we first introduce the notion of color connected coloring, and, employing this structural property, we obtain a linear time algorithm to compute ar(G,P_k), for every integer k, when the host graph, G, is a tree.
Cite as

Saeed Akhoondian Amiri, Alexandru Popa, Mohammad Roghani, Golnoosh Shahkarami, Reza Soltani, and Hossein Vahidi. Complexity of Computing the Anti-Ramsey Numbers for Paths. In 45th International Symposium on Mathematical Foundations of Computer Science (MFCS 2020). Leibniz International Proceedings in Informatics (LIPIcs), Volume 170, pp. 6:1-6:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2020)

Copy BibTex To Clipboard

@InProceedings{akhoondianamiri_et_al:LIPIcs.MFCS.2020.6,
  author =	{Akhoondian Amiri, Saeed and Popa, Alexandru and Roghani, Mohammad and Shahkarami, Golnoosh and Soltani, Reza and Vahidi, Hossein},
  title =	{{Complexity of Computing the Anti-Ramsey Numbers for Paths}},
  booktitle =	{45th International Symposium on Mathematical Foundations of Computer Science (MFCS 2020)},
  pages =	{6:1--6:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-159-7},
  ISSN =	{1868-8969},
  year =	{2020},
  volume =	{170},
  editor =	{Esparza, Javier and Kr\'{a}l', Daniel},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2020.6},
  URN =		{urn:nbn:de:0030-drops-126781},
  doi =		{10.4230/LIPIcs.MFCS.2020.6},
  annote =	{Keywords: Coloring, Anti-Ramsey, Approximation, NP-hard, Algorithm, ETH}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2018.6
The Use of a Pruned Modular Decomposition for Maximum Matching Algorithms on Some Graph Classes

Authors: Guillaume Ducoffe and Alexandru Popa

Published in: LIPIcs, Volume 123, 29th International Symposium on Algorithms and Computation (ISAAC 2018)

Abstract
We address the following general question: given a graph class C on which we can solve Maximum Matching in (quasi) linear time, does the same hold true for the class of graphs that can be modularly decomposed into C? As a way to answer this question for distance-hereditary graphs and some other superclasses of cographs, we study the combined effect of modular decomposition with a pruning process over the quotient subgraphs. We remove sequentially from all such subgraphs their so-called one-vertex extensions (i.e., pendant, anti-pendant, twin, universal and isolated vertices). Doing so, we obtain a "pruned modular decomposition", that can be computed in quasi linear time. Our main result is that if all the pruned quotient subgraphs have bounded order then a maximum matching can be computed in linear time. The latter result strictly extends a recent framework in (Coudert et al., SODA'18). Our work is the first to explain why the existence of some nice ordering over the modules of a graph, instead of just over its vertices, can help to speed up the computation of maximum matchings on some graph classes.
Cite as

Guillaume Ducoffe and Alexandru Popa. The Use of a Pruned Modular Decomposition for Maximum Matching Algorithms on Some Graph Classes. In 29th International Symposium on Algorithms and Computation (ISAAC 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 123, pp. 6:1-6:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

Copy BibTex To Clipboard

@InProceedings{ducoffe_et_al:LIPIcs.ISAAC.2018.6,
  author =	{Ducoffe, Guillaume and Popa, Alexandru},
  title =	{{The Use of a Pruned Modular Decomposition for Maximum Matching Algorithms on Some Graph Classes}},
  booktitle =	{29th International Symposium on Algorithms and Computation (ISAAC 2018)},
  pages =	{6:1--6:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-094-1},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{123},
  editor =	{Hsu, Wen-Lian and Lee, Der-Tsai and Liao, Chung-Shou},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2018.6},
  URN =		{urn:nbn:de:0030-drops-99549},
  doi =		{10.4230/LIPIcs.ISAAC.2018.6},
  annote =	{Keywords: maximum matching, FPT in P, modular decomposition, pruned graphs, one-vertex extensions, P\underline4-structure}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2018.30
The b-Matching Problem in Distance-Hereditary Graphs and Beyond

Authors: Guillaume Ducoffe and Alexandru Popa

Published in: LIPIcs, Volume 123, 29th International Symposium on Algorithms and Computation (ISAAC 2018)

Abstract
We make progress on the fine-grained complexity of Maximum-Cardinality Matching on graphs of bounded clique-width. Quasi linear-time algorithms for this problem have been recently proposed for the important subclasses of bounded-treewidth graphs (Fomin et al., SODA'17) and graphs of bounded modular-width (Coudert et al., SODA'18). We present such algorithm for bounded split-width graphs - a broad generalization of graphs of bounded modular-width, of which an interesting subclass are the distance-hereditary graphs. Specifically, we solve Maximum-Cardinality Matching in O((k log^2{k})*(m+n) * log{n})-time on graphs with split-width at most k. We stress that the existence of such algorithm was not even known for distance-hereditary graphs until our work. Doing so, we improve the state of the art (Dragan, WG'97) and we answer an open question of (Coudert et al., SODA'18). Our work brings more insights on the relationships between matchings and splits, a.k.a., join operations between two vertex-subsets in different connected components. Furthermore, our analysis can be extended to the more general (unit cost) b-Matching problem. On the way, we introduce new tools for b-Matching and dynamic programming over split decompositions, that can be of independent interest.
Cite as

Guillaume Ducoffe and Alexandru Popa. The b-Matching Problem in Distance-Hereditary Graphs and Beyond. In 29th International Symposium on Algorithms and Computation (ISAAC 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 123, pp. 30:1-30:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

Copy BibTex To Clipboard

@InProceedings{ducoffe_et_al:LIPIcs.ISAAC.2018.30,
  author =	{Ducoffe, Guillaume and Popa, Alexandru},
  title =	{{The b-Matching Problem in Distance-Hereditary Graphs and Beyond}},
  booktitle =	{29th International Symposium on Algorithms and Computation (ISAAC 2018)},
  pages =	{30:1--30:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-094-1},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{123},
  editor =	{Hsu, Wen-Lian and Lee, Der-Tsai and Liao, Chung-Shou},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2018.30},
  URN =		{urn:nbn:de:0030-drops-99783},
  doi =		{10.4230/LIPIcs.ISAAC.2018.30},
  annote =	{Keywords: maximum-cardinality matching, b-matching, FPT in P, split decomposition, distance-hereditary graphs}
}
Document
DOI: 10.4230/LIPIcs.OPODIS.2015.19
Making "Fast" Atomic Operations Computationally Tractable

Authors: Antonio Fernández Anta, Nicolas Nicolaou, and Alexandru Popa

Published in: LIPIcs, Volume 46, 19th International Conference on Principles of Distributed Systems (OPODIS 2015)

Abstract
Communication overhead is the most commonly used performance metric for the operation complexity of distributed algorithms in message-passing environments. However, aside with communication, many distributed operations utilize complex computations to reach their desired outcomes. Therefore, a most accurate operation latency measure should account of both computation and communication metrics. In this paper we focus on the efficiency of read and write operations in an atomic read/write shared memory emulation in the message-passing environment. We examine the operation complexity of the best known atomic register algorithm, that allows all read and write operations to complete in a single communication round-trip. Such operations are called fast. At its heart, the algorithm utilizes a predicate to allow processes to compute their outcome. We show that the predicate used is computationally hard, by devising a computationally equivalent problem and reducing that to Maximum Biclique, a known NP-hard problem. To improve the computational complexity of the algorithm we derive a new predicate that leads to a new algorithm, we call ccFast, and has the following properties: (i) can be computed in polynomial time, rendering each read operation in ccFast tractable compared to the read operations in the original algorithm, (ii) the messages used in ccFast are reduced in size, compared to the original algorithm, by almost a linear factor, (iii) allows all operations in ccFast to be fast, and (iv) allows ccFast to preserve atomicity. A linear time}algorithm for the computation of the new predicate is presented along with an analysis of the message complexity of the new algorithm. We believe that the new algorithm redefines the term fast capturing both the communication and the computation metrics of each operation.
Cite as

Antonio Fernández Anta, Nicolas Nicolaou, and Alexandru Popa. Making "Fast" Atomic Operations Computationally Tractable. In 19th International Conference on Principles of Distributed Systems (OPODIS 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 46, pp. 19:1-19:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

Copy BibTex To Clipboard

@InProceedings{fernandezanta_et_al:LIPIcs.OPODIS.2015.19,
  author =	{Fern\'{a}ndez Anta, Antonio and Nicolaou, Nicolas and Popa, Alexandru},
  title =	{{Making "Fast" Atomic Operations Computationally Tractable}},
  booktitle =	{19th International Conference on Principles of Distributed Systems (OPODIS 2015)},
  pages =	{19:1--19:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-98-9},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{46},
  editor =	{Anceaume, Emmanuelle and Cachin, Christian and Potop-Butucaru, Maria},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2015.19},
  URN =		{urn:nbn:de:0030-drops-66108},
  doi =		{10.4230/LIPIcs.OPODIS.2015.19},
  annote =	{Keywords: atomicity, read/write objects, shared memory, computational complexity}
}
  • Refine by Author
  • 7 Popa, Alexandru
  • 2 Ducoffe, Guillaume
  • 1 Akhoondian Amiri, Saeed
  • 1 Asahiro, Yuichi
  • 1 Boneh, Itai
  • Show More...

  • Refine by Classification
  • 3 Mathematics of computing → Graph theory
  • 3 Theory of computation → Design and analysis of algorithms
  • 2 Theory of computation → Pattern matching
  • 1 Applied computing → Bioinformatics
  • 1 Applied computing → Operations research
  • Show More...

  • Refine by Keyword
  • 2 FPT in P
  • 2 Integer Linear Programming
  • 1 Algorithm
  • 1 Anti-Ramsey
  • 1 Approximation
  • Show More...

  • Refine by Type
  • 12 document

  • Refine by Publication Year
  • 4 2024
  • 2 2018
  • 2 2023
  • 1 2016
  • 1 2020
  • Show More...

© 2023-2024 Schloss Dagstuhl – LZI GmbH Imprint Privacy Contact