41 Search Results for "Italiano, Giuseppe F."

Volume

OASIcs, Volume 48

15th Workshop on Algorithmic Approaches for Transportation Modelling, Optimization, and Systems (ATMOS 2015)

ATMOS 2015, September 17, 2015, Patras, Greece

Editors: Giuseppe F. Italiano and Marie Schmidt

Document
DOI: 10.4230/LIPIcs.WABI.2024.5
Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests

Authors: Lukas Hübner and Alexandros Stamatakis

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
The field of population genetics attempts to advance our understanding of evolutionary processes. It has applications, for example, in medical research, wildlife conservation, and - in conjunction with recent advances in ancient DNA sequencing technology - studying human migration patterns over the past few thousand years. The basic toolbox of population genetics includes genealogical trees, which describe the shared evolutionary history among individuals of the same species. They are calculated on the basis of genetic variations. However, in recombining organisms, a single tree is insufficient to describe the evolutionary history of the whole genome. Instead, a collection of correlated trees can be used, where each describes the evolutionary history of a consecutive region of the genome. The current corresponding state of-the-art data structure, tree sequences, compresses these genealogical trees via edit operations when moving from one tree to the next along the genome instead of storing the full, often redundant, description for each tree. We propose a new data structure, genealogical forests, which compresses the set of genealogical trees into a DAG. In this DAG identical subtrees that are shared across the input trees are encoded only once, thereby allowing for straight-forward memoization of intermediate results. Additionally, we provide a C++ implementation of our proposed data structure, called gfkit, which is 2.1 to 11.2 (median 4.0) times faster than the state-of-the-art tool on empirical and simulated datasets at computing important population genetics statistics such as the Allele Frequency Spectrum, Patterson’s f, the Fixation Index, Tajima’s D, pairwise Lowest Common Ancestors, and others. On Lowest Common Ancestor queries with more than two samples as input, gfkit scales asymptotically better than the state-of-the-art, and is thus up to 990 times faster. In conclusion, our proposed data structure compresses genealogical trees by storing shared subtrees only once, thereby enabling straight-forward memoization of intermediate results, yielding a substantial runtime reduction and a potentially more intuitive data representation over the state-of-the-art. Our improvements will boost the development of novel analyses and models in the field of population genetics and increases scalability to ever-growing genomic datasets.
Cite as

Lukas Hübner and Alexandros Stamatakis. Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 5:1-5:22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{hubner_et_al:LIPIcs.WABI.2024.5,
  author =	{H\"{u}bner, Lukas and Stamatakis, Alexandros},
  title =	{{Memoization on Shared Subtrees Accelerates Computations on Genealogical Forests}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{5:1--5:22},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.5},
  URN =		{urn:nbn:de:0030-drops-206499},
  doi =		{10.4230/LIPIcs.WABI.2024.5},
  annote =	{Keywords: bioinformatics, population genetics, algorithms}
}
Document
DOI: 10.4230/LIPIcs.WABI.2024.8
Applying the Safe-And-Complete Framework to Practical Genome Assembly

Authors: Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, and Alexandru I. Tomescu

Published in: LIPIcs, Volume 312, 24th International Workshop on Algorithms in Bioinformatics (WABI 2024)

Abstract
Despite the long history of genome assembly research, there remains a large gap between the theoretical and practical work. There is practical software with little theoretical underpinning of accuracy on one hand and theoretical algorithms which have not been adopted in practice on the other. In this paper we attempt to bridge the gap between theory and practice by showing how the theoretical safe-and-complete framework can be integrated into existing assemblers in order to improve contiguity. The optimal algorithm in this framework, called the omnitig algorithm, has not been used in practice due to its complexity and its lack of robustness to real data. Instead, we pursue a simplified notion of omnitigs (simple omnitigs), giving an efficient algorithm to compute them and demonstrating their safety under certain conditions. We modify two assemblers (wtdbg2 and Flye) by replacing their unitig algorithm with the simple omnitig algorithm. We test our modifications using real HiFi data from the D. melanogaster and the C. elegans genomes. Our modified algorithms lead to a substantial improvement in alignment-based contiguity, with negligible additional computational costs and either no or a small increase in the number of misassemblies.
Cite as

Sebastian Schmidt, Santeri Toivonen, Paul Medvedev, and Alexandru I. Tomescu. Applying the Safe-And-Complete Framework to Practical Genome Assembly. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 8:1-8:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{schmidt_et_al:LIPIcs.WABI.2024.8,
  author =	{Schmidt, Sebastian and Toivonen, Santeri and Medvedev, Paul and Tomescu, Alexandru I.},
  title =	{{Applying the Safe-And-Complete Framework to Practical Genome Assembly}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{8:1--8:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-340-9},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{312},
  editor =	{Pissis, Solon P. and Sung, Wing-Kin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2024.8},
  URN =		{urn:nbn:de:0030-drops-206520},
  doi =		{10.4230/LIPIcs.WABI.2024.8},
  annote =	{Keywords: Genome assembly, Omnitigs, Safe-and-complete framework, graph algorithm, HiFi sequencing data, Assembly evaluation}
}
Document
DOI: 10.4230/LIPIcs.SAND.2024.6
Black Hole Search in Dynamic Tori

Authors: Adri Bhattacharya, Giuseppe F. Italiano, and Partha Sarathi Mandal

Published in: LIPIcs, Volume 292, 3rd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2024)

Abstract
We investigate the black hole search problem using a set of mobile agents in a dynamic torus. A black hole is defined as a dangerous stationary node that has the capability to destroy any number of incoming agents without leaving any trace of its existence. A torus of size n× m (3 ≤ n ≤ m) is a collection of n row rings and m column rings, and the dynamicity is such that each ring is considered to be 1-interval connected, i.e., in other words at most one edge can be missing from each ring at any round. The parameters which define the efficiency of any black hole search algorithm are: the number of agents and the number of rounds (or time) for termination. We consider two initial configurations of mobile agents: first, the agents are co-located, second, the agents are scattered. In each case, we establish lower and upper bounds on the number of agents and on the amount of time required to solve the black hole search problem.
Cite as

Adri Bhattacharya, Giuseppe F. Italiano, and Partha Sarathi Mandal. Black Hole Search in Dynamic Tori. In 3rd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 292, pp. 6:1-6:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{bhattacharya_et_al:LIPIcs.SAND.2024.6,
  author =	{Bhattacharya, Adri and Italiano, Giuseppe F. and Mandal, Partha Sarathi},
  title =	{{Black Hole Search in Dynamic Tori}},
  booktitle =	{3rd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2024)},
  pages =	{6:1--6:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-315-7},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{292},
  editor =	{Casteigts, Arnaud and Kuhn, Fabian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2024.6},
  URN =		{urn:nbn:de:0030-drops-198840},
  doi =		{10.4230/LIPIcs.SAND.2024.6},
  annote =	{Keywords: Black Hole Search, Time Varying Graphs, Dynamic Torus, Distributed Algorithms, Mobile Agents}
}
Document
DOI: 10.4230/LIPIcs.MFCS.2023.39
Dynamic Planar Embedding Is in DynFO

Authors: Samir Datta, Asif Khan, and Anish Mukherjee

Published in: LIPIcs, Volume 272, 48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023)

Abstract
Planar Embedding is a drawing of a graph on the plane such that the edges do not intersect each other except at the vertices. We know that testing the planarity of a graph and computing its embedding (if it exists), can efficiently be computed, both sequentially [John E. Hopcroft and Robert Endre Tarjan, 1974] and in parallel [Vijaya Ramachandran and John H. Reif, 1994], when the entire graph is presented as input. In the dynamic setting, the input graph changes one edge at a time through insertion and deletions and planarity testing/embedding has to be updated after every change. By storing auxilliary information we can improve the complexity of dynamic planarity testing/embedding over the obvious recomputation from scratch. In the sequential dynamic setting, there has been a series of works [David Eppstein et al., 1996; Giuseppe F. Italiano et al., 1993; Jacob Holm et al., 2018; Jacob Holm and Eva Rotenberg, 2020], culminating in the breakthrough result of polylog(n) sequential time (amortized) planarity testing algorithm of Holm and Rotenberg [Jacob Holm and Eva Rotenberg, 2020]. In this paper we study planar embedding through the lens of DynFO, a parallel dynamic complexity class introduced by Patnaik et al [Sushant Patnaik and Neil Immerman, 1997] (also [Guozhu Dong et al., 1995]). We show that it is possible to dynamically maintain whether an edge can be inserted to a planar graph without causing non-planarity in DynFO. We extend this to show how to maintain an embedding of a planar graph under both edge insertions and deletions, while rejecting edge insertions that violate planarity. Our main idea is to maintain embeddings of only the triconnected components and a special two-colouring of separating pairs that enables us to side-step cascading flips when embedding of a biconnected planar graph changes, a major issue for sequential dynamic algorithms [Jacob Holm and Eva Rotenberg, 2020; Jacob Holm and Eva Rotenberg, 2020].
Cite as

Samir Datta, Asif Khan, and Anish Mukherjee. Dynamic Planar Embedding Is in DynFO. In 48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 272, pp. 39:1-39:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{datta_et_al:LIPIcs.MFCS.2023.39,
  author =	{Datta, Samir and Khan, Asif and Mukherjee, Anish},
  title =	{{Dynamic Planar Embedding Is in DynFO}},
  booktitle =	{48th International Symposium on Mathematical Foundations of Computer Science (MFCS 2023)},
  pages =	{39:1--39:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-292-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{272},
  editor =	{Leroux, J\'{e}r\^{o}me and Lombardy, Sylvain and Peleg, David},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2023.39},
  URN =		{urn:nbn:de:0030-drops-185736},
  doi =		{10.4230/LIPIcs.MFCS.2023.39},
  annote =	{Keywords: Dynamic Complexity, Planar graphs, Planar embedding}
}
Document
DOI: 10.4230/LIPIcs.ESA.2022.60
Computing the 4-Edge-Connected Components of a Graph: An Experimental Study

Authors: Loukas Georgiadis, Giuseppe F. Italiano, and Evangelos Kosinas

Published in: LIPIcs, Volume 244, 30th Annual European Symposium on Algorithms (ESA 2022)

Abstract
The notions of edge-cuts and k-edge-connected components are fundamental in graph theory with numerous practical applications. Very recently, the first linear-time algorithms for computing all the 3-edge cuts and the 4-edge-connected components of a graph have been introduced. In this paper we present carefully engineered implementations of these algorithms and evaluate their efficiency in practice, by performing a thorough empirical study using both real-world graphs taken from a variety of application areas, as well as artificial graphs. To the best of our knowledge, this is the first experimental study for these problems, which highlights the merits and weaknesses of each technique. Furthermore, we present an improved algorithm for computing the 4-edge-connected components of an undirected graph in linear time. The new algorithm uses only elementary data structures, and is implementable in the pointer machine model of computation.
Cite as

Loukas Georgiadis, Giuseppe F. Italiano, and Evangelos Kosinas. Computing the 4-Edge-Connected Components of a Graph: An Experimental Study. In 30th Annual European Symposium on Algorithms (ESA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 244, pp. 60:1-60:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{georgiadis_et_al:LIPIcs.ESA.2022.60,
  author =	{Georgiadis, Loukas and Italiano, Giuseppe F. and Kosinas, Evangelos},
  title =	{{Computing the 4-Edge-Connected Components of a Graph: An Experimental Study}},
  booktitle =	{30th Annual European Symposium on Algorithms (ESA 2022)},
  pages =	{60:1--60:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-247-1},
  ISSN =	{1868-8969},
  year =	{2022},
  volume =	{244},
  editor =	{Chechik, Shiri and Navarro, Gonzalo and Rotenberg, Eva 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.2022.60},
  URN =		{urn:nbn:de:0030-drops-169988},
  doi =		{10.4230/LIPIcs.ESA.2022.60},
  annote =	{Keywords: Connectivity Cuts, Edge Connectivity, Graph Algorithms}
}
Document
DOI: 10.4230/LIPIcs.ESA.2021.47
Computing the 4-Edge-Connected Components of a Graph in Linear Time

Authors: Loukas Georgiadis, Giuseppe F. Italiano, and Evangelos Kosinas

Published in: LIPIcs, Volume 204, 29th Annual European Symposium on Algorithms (ESA 2021)

Abstract
We present the first linear-time algorithm that computes the 4-edge-connected components of an undirected graph. Hence, we also obtain the first linear-time algorithm for testing 4-edge connectivity. Our results are based on a linear-time algorithm that computes the 3-edge cuts of a 3-edge-connected graph G, and a linear-time procedure that, given the collection of all 3-edge cuts, partitions the vertices of G into the 4-edge-connected components.
Cite as

Loukas Georgiadis, Giuseppe F. Italiano, and Evangelos Kosinas. Computing the 4-Edge-Connected Components of a Graph in Linear Time. In 29th Annual European Symposium on Algorithms (ESA 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 204, pp. 47:1-47:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{georgiadis_et_al:LIPIcs.ESA.2021.47,
  author =	{Georgiadis, Loukas and Italiano, Giuseppe F. and Kosinas, Evangelos},
  title =	{{Computing the 4-Edge-Connected Components of a Graph in Linear Time}},
  booktitle =	{29th Annual European Symposium on Algorithms (ESA 2021)},
  pages =	{47:1--47:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-204-4},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{204},
  editor =	{Mutzel, Petra and Pagh, Rasmus 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.2021.47},
  URN =		{urn:nbn:de:0030-drops-146286},
  doi =		{10.4230/LIPIcs.ESA.2021.47},
  annote =	{Keywords: Cuts, Edge Connectivity, Graph Algorithms}
}
Document
DOI: 10.4230/LIPIcs.WABI.2021.13
Compressing and Indexing Aligned Readsets

Authors: Travis Gagie, Garance Gourdel, and Giovanni Manzini

Published in: LIPIcs, Volume 201, 21st International Workshop on Algorithms in Bioinformatics (WABI 2021)

Abstract
Compressed full-text indexes are one of the main success stories of bioinformatics data structures but even they struggle to handle some DNA readsets. This may seem surprising since, at least when dealing with short reads from the same individual, the readset will be highly repetitive and, thus, highly compressible. If we are not careful, however, this advantage can be more than offset by two disadvantages: first, since most base pairs are included in at least tens reads each, the uncompressed readset is likely to be at least an order of magnitude larger than the individual’s uncompressed genome; second, these indexes usually pay some space overhead for each string they store, and the total overhead can be substantial when dealing with millions of reads. The most successful compressed full-text indexes for readsets so far are based on the Extended Burrows-Wheeler Transform (EBWT) and use a sorting heuristic to try to reduce the space overhead per read, but they still treat the reads as separate strings and thus may not take full advantage of the readset’s structure. For example, if we have already assembled an individual’s genome from the readset, then we can usually use it to compress the readset well: e.g., we store the gap-coded list of reads' starting positions; we store the list of their lengths, which is often highly compressible; and we store information about the sequencing errors, which are rare with short reads. There is nowhere, however, where we can plug an assembled genome into the EBWT. In this paper we show how to use one or more assembled or partially assembled genome as the basis for a compressed full-text index of its readset. Specifically, we build a labelled tree by taking the assembled genome as a trunk and grafting onto it the reads that align to it, at the starting positions of their alignments. Next, we compute the eXtended Burrows-Wheeler Transform (XBWT) of the resulting labelled tree and build a compressed full-text index on that. Although this index can occasionally return false positives, it is usually much more compact than the alternatives. Following the established practice for datasets with many repetitions, we compare different full-text indices by looking at the number of runs in the transformed strings. For a human Chr19 readset our preliminary experiments show that eliminating separators characters from the EBWT reduces the number of runs by 19%, from 220 million to 178 million, and using the XBWT reduces it by a further 15%, to 150 million.
Cite as

Travis Gagie, Garance Gourdel, and Giovanni Manzini. Compressing and Indexing Aligned Readsets. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 13:1-13:21, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{gagie_et_al:LIPIcs.WABI.2021.13,
  author =	{Gagie, Travis and Gourdel, Garance and Manzini, Giovanni},
  title =	{{Compressing and Indexing Aligned Readsets}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{13:1--13:21},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-200-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{201},
  editor =	{Carbone, Alessandra and El-Kebir, Mohammed},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2021.13},
  URN =		{urn:nbn:de:0030-drops-143660},
  doi =		{10.4230/LIPIcs.WABI.2021.13},
  annote =	{Keywords: data compression, compact data structures, FM-index, Burrows-Wheeler Transform, EBWT, XBWT, DNA reads}
}
Document
DOI: 10.4230/LIPIcs.CPM.2021.16
Compressed Weighted de Bruijn Graphs

Authors: Giuseppe F. Italiano, Nicola Prezza, Blerina Sinaimeri, and Rossano Venturini

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

Abstract
We propose a new compressed representation for weighted de Bruijn graphs, which is based on the idea of delta-encoding the variations of k-mer abundances on a spanning branching of the graph. Our new data structure is likely to be of practical value: to give an idea, when combined with the compressed BOSS de Bruijn graph representation, it encodes the weighted de Bruijn graph of a 16x-covered DNA read-set (60M distinct k-mers, k = 28) within 4.15 bits per distinct k-mer and can answer abundance queries in about 60 microseconds on a standard machine. In contrast, state of the art tools declare a space usage of at least 30 bits per distinct k-mer for the same task, which is confirmed by our experiments. As a by-product of our new data structure, we exhibit efficient compressed data structures for answering partial sums on edge-weighted trees, which might be of independent interest.
Cite as

Giuseppe F. Italiano, Nicola Prezza, Blerina Sinaimeri, and Rossano Venturini. Compressed Weighted de Bruijn Graphs. In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, pp. 16:1-16:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{italiano_et_al:LIPIcs.CPM.2021.16,
  author =	{Italiano, Giuseppe F. and Prezza, Nicola and Sinaimeri, Blerina and Venturini, Rossano},
  title =	{{Compressed Weighted de Bruijn Graphs}},
  booktitle =	{32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)},
  pages =	{16:1--16:16},
  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.2021.16},
  URN =		{urn:nbn:de:0030-drops-139675},
  doi =		{10.4230/LIPIcs.CPM.2021.16},
  annote =	{Keywords: weighted de Bruijn graphs, k-mer annotation, compressed data structures, partial sums}
}
Document
DOI: 10.4230/LIPIcs.SEA.2021.20
Computing Vertex-Edge Cut-Pairs and 2-Edge Cuts in Practice

Authors: Loukas Georgiadis, Konstantinos Giannis, Giuseppe F. Italiano, and Evangelos Kosinas

Published in: LIPIcs, Volume 190, 19th International Symposium on Experimental Algorithms (SEA 2021)

Abstract
We consider two problems regarding the computation of connectivity cuts in undirected graphs, namely identifying vertex-edge cut-pairs and identifying 2-edge cuts, and present an experimental study of efficient algorithms for their computation. In the first problem, we are given a biconnected graph G and our goal is to find all vertices v such that G⧵v is not 2-edge-connected, while in the second problem, we are given a 2-edge-connected graph G and our goal is to find all edges e such that G⧵e is not 2-edge-connected. These problems are motivated by the notion of twinless strong connectivity in directed graphs but are also of independent interest. Moreover, the computation of 2-edge cuts is a main step in algorithms that compute the 3-edge-connected components of a graph. In this paper, we present streamlined versions of two recent linear-time algorithms of Georgiadis and Kosinas that compute all vertex-edge cut-pairs and all 2-edge cuts, respectively. We compare the empirical performance of our vertex-edge cut-pairs algorithm with an alternative linear-time method that exploits the structure of the triconnected components of G. Also, we compare the empirical performance of our 2-edge cuts algorithm with the algorithm of Tsin, which was reported to be the fastest one among the previously existing for this problem. To that end, we conduct a thorough experimental study to highlight the merits and weaknesses of each technique.
Cite as

Loukas Georgiadis, Konstantinos Giannis, Giuseppe F. Italiano, and Evangelos Kosinas. Computing Vertex-Edge Cut-Pairs and 2-Edge Cuts in Practice. In 19th International Symposium on Experimental Algorithms (SEA 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 190, pp. 20:1-20:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{georgiadis_et_al:LIPIcs.SEA.2021.20,
  author =	{Georgiadis, Loukas and Giannis, Konstantinos and Italiano, Giuseppe F. and Kosinas, Evangelos},
  title =	{{Computing Vertex-Edge Cut-Pairs and 2-Edge Cuts in Practice}},
  booktitle =	{19th International Symposium on Experimental Algorithms (SEA 2021)},
  pages =	{20:1--20:19},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-185-6},
  ISSN =	{1868-8969},
  year =	{2021},
  volume =	{190},
  editor =	{Coudert, David and Natale, Emanuele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SEA.2021.20},
  URN =		{urn:nbn:de:0030-drops-137920},
  doi =		{10.4230/LIPIcs.SEA.2021.20},
  annote =	{Keywords: 2-Connectivity, Graph Algorithms, Split Components}
}
Document
DOI: 10.4230/LIPIcs.ESA.2019.50
Dynamic Dominators and Low-High Orders in DAGs

Authors: Loukas Georgiadis, Konstantinos Giannis, Giuseppe F. Italiano, Aikaterini Karanasiou, and Luigi Laura

Published in: LIPIcs, Volume 144, 27th Annual European Symposium on Algorithms (ESA 2019)

Abstract
We consider practical algorithms for maintaining the dominator tree and a low-high order in directed acyclic graphs (DAGs) subject to dynamic operations. Let G be a directed graph with a distinguished start vertex s. The dominator tree D of G is a tree rooted at s, such that a vertex v is an ancestor of a vertex w if and only if all paths from s to w in G include v. The dominator tree is a central tool in program optimization and code generation, and has many applications in other diverse areas including constraint programming, circuit testing, biology, and in algorithms for graph connectivity problems. A low-high order of G is a preorder of D that certifies the correctness of D, and has further applications in connectivity and path-determination problems. We first provide a practical and carefully engineered version of a recent algorithm [ICALP 2017] for maintaining the dominator tree of a DAG through a sequence of edge deletions. The algorithm runs in O(mn) total time and O(m) space, where n is the number of vertices and m is the number of edges before any deletion. In addition, we present a new algorithm that maintains a low-high order of a DAG under edge deletions within the same bounds. Both results extend to the case of reducible graphs (a class that includes DAGs). Furthermore, we present a fully dynamic algorithm for maintaining the dominator tree of a DAG under an intermixed sequence of edge insertions and deletions. Although it does not maintain the O(mn) worst-case bound of the decremental algorithm, our experiments highlight that the fully dynamic algorithm performs very well in practice. Finally, we study the practical efficiency of all our algorithms by conducting an extensive experimental study on real-world and synthetic graphs.
Cite as

Loukas Georgiadis, Konstantinos Giannis, Giuseppe F. Italiano, Aikaterini Karanasiou, and Luigi Laura. Dynamic Dominators and Low-High Orders in DAGs. In 27th Annual European Symposium on Algorithms (ESA 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 144, pp. 50:1-50:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{georgiadis_et_al:LIPIcs.ESA.2019.50,
  author =	{Georgiadis, Loukas and Giannis, Konstantinos and Italiano, Giuseppe F. and Karanasiou, Aikaterini and Laura, Luigi},
  title =	{{Dynamic Dominators and Low-High Orders in DAGs}},
  booktitle =	{27th Annual European Symposium on Algorithms (ESA 2019)},
  pages =	{50:1--50:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-124-5},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{144},
  editor =	{Bender, Michael A. and Svensson, Ola 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.2019.50},
  URN =		{urn:nbn:de:0030-drops-111715},
  doi =		{10.4230/LIPIcs.ESA.2019.50},
  annote =	{Keywords: Connectivity, dominators, low-high orders}
}
Document
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2019.7
Faster Algorithms for All-Pairs Bounded Min-Cuts

Authors: Amir Abboud, Loukas Georgiadis, Giuseppe F. Italiano, Robert Krauthgamer, Nikos Parotsidis, Ohad Trabelsi, Przemysław Uznański, and Daniel Wolleb-Graf

Published in: LIPIcs, Volume 132, 46th International Colloquium on Automata, Languages, and Programming (ICALP 2019)

Abstract
The All-Pairs Min-Cut problem (aka All-Pairs Max-Flow) asks to compute a minimum s-t cut (or just its value) for all pairs of vertices s,t. We study this problem in directed graphs with unit edge/vertex capacities (corresponding to edge/vertex connectivity). Our focus is on the k-bounded case, where the algorithm has to find all pairs with min-cut value less than k, and report only those. The most basic case k=1 is the Transitive Closure (TC) problem, which can be solved in graphs with n vertices and m edges in time O(mn) combinatorially, and in time O(n^{omega}) where omega<2.38 is the matrix-multiplication exponent. These time bounds are conjectured to be optimal. We present new algorithms and conditional lower bounds that advance the frontier for larger k, as follows: - A randomized algorithm for vertex capacities that runs in time {O}((nk)^{omega}). This is only a factor k^omega away from the TC bound, and nearly matches it for all k=n^{o(1)}. - Two deterministic algorithms for edge capacities (which is more general) that work in DAGs and further reports a minimum cut for each pair. The first algorithm is combinatorial (does not involve matrix multiplication) and runs in time {O}(2^{{O}(k^2)}* mn). The second algorithm can be faster on dense DAGs and runs in time {O}((k log n)^{4^{k+o(k)}}* n^{omega}). Previously, Georgiadis et al. [ICALP 2017], could match the TC bound (up to n^{o(1)} factors) only when k=2, and now our two algorithms match it for all k=o(sqrt{log n}) and k=o(log log n). - The first super-cubic lower bound of n^{omega-1-o(1)} k^2 time under the 4-Clique conjecture, which holds even in the simplest case of DAGs with unit vertex capacities. It improves on the previous (SETH-based) lower bounds even in the unbounded setting k=n. For combinatorial algorithms, our reduction implies an n^{2-o(1)} k^2 conditional lower bound. Thus, we identify new settings where the complexity of the problem is (conditionally) higher than that of TC. Our three sets of results are obtained via different techniques. The first one adapts the network coding method of Cheung, Lau, and Leung [SICOMP 2013] to vertex-capacitated digraphs. The second set exploits new insights on the structure of latest cuts together with suitable algebraic tools. The lower bounds arise from a novel reduction of a different structure than the SETH-based constructions.
Cite as

Amir Abboud, Loukas Georgiadis, Giuseppe F. Italiano, Robert Krauthgamer, Nikos Parotsidis, Ohad Trabelsi, Przemysław Uznański, and Daniel Wolleb-Graf. Faster Algorithms for All-Pairs Bounded Min-Cuts. In 46th International Colloquium on Automata, Languages, and Programming (ICALP 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 132, pp. 7:1-7:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{abboud_et_al:LIPIcs.ICALP.2019.7,
  author =	{Abboud, Amir and Georgiadis, Loukas and Italiano, Giuseppe F. and Krauthgamer, Robert and Parotsidis, Nikos and Trabelsi, Ohad and Uzna\'{n}ski, Przemys{\l}aw and Wolleb-Graf, Daniel},
  title =	{{Faster Algorithms for All-Pairs Bounded Min-Cuts}},
  booktitle =	{46th International Colloquium on Automata, Languages, and Programming (ICALP 2019)},
  pages =	{7:1--7:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-109-2},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{132},
  editor =	{Baier, Christel and Chatzigiannakis, Ioannis and Flocchini, Paola and Leonardi, Stefano},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2019.7},
  URN =		{urn:nbn:de:0030-drops-105833},
  doi =		{10.4230/LIPIcs.ICALP.2019.7},
  annote =	{Keywords: All-pairs min-cut, k-reachability, network coding, Directed graphs, fine-grained complexity}
}
Document
DOI: 10.4230/LIPIcs.STACS.2019.35
Dominating Sets and Connected Dominating Sets in Dynamic Graphs

Authors: Niklas Hjuler, Giuseppe F. Italiano, Nikos Parotsidis, and David Saulpic

Published in: LIPIcs, Volume 126, 36th International Symposium on Theoretical Aspects of Computer Science (STACS 2019)

Abstract
In this paper we study the dynamic versions of two basic graph problems: Minimum Dominating Set and its variant Minimum Connected Dominating Set. For those two problems, we present algorithms that maintain a solution under edge insertions and edge deletions in time O(Delta * polylog n) per update, where Delta is the maximum vertex degree in the graph. In both cases, we achieve an approximation ratio of O(log n), which is optimal up to a constant factor (under the assumption that P != NP). Although those two problems have been widely studied in the static and in the distributed settings, to the best of our knowledge we are the first to present efficient algorithms in the dynamic setting. As a further application of our approach, we also present an algorithm that maintains a Minimal Dominating Set in O(min(Delta, sqrt{m})) per update.
Cite as

Niklas Hjuler, Giuseppe F. Italiano, Nikos Parotsidis, and David Saulpic. Dominating Sets and Connected Dominating Sets in Dynamic Graphs. In 36th International Symposium on Theoretical Aspects of Computer Science (STACS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 126, pp. 35:1-35:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)

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@InProceedings{hjuler_et_al:LIPIcs.STACS.2019.35,
  author =	{Hjuler, Niklas and Italiano, Giuseppe F. and Parotsidis, Nikos and Saulpic, David},
  title =	{{Dominating Sets and Connected Dominating Sets in Dynamic Graphs}},
  booktitle =	{36th International Symposium on Theoretical Aspects of Computer Science (STACS 2019)},
  pages =	{35:1--35:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-100-9},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{126},
  editor =	{Niedermeier, Rolf and Paul, Christophe},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.STACS.2019.35},
  URN =		{urn:nbn:de:0030-drops-102741},
  doi =		{10.4230/LIPIcs.STACS.2019.35},
  annote =	{Keywords: Dominating Set, Connected Dominating Set, Dynamic Graph Algorithms}
}
Document
DOI: 10.4230/LIPIcs.ESA.2018.46
Decremental SPQR-trees for Planar Graphs

Authors: Jacob Holm, Giuseppe F. Italiano, Adam Karczmarz, Jakub Lacki, and Eva Rotenberg

Published in: LIPIcs, Volume 112, 26th Annual European Symposium on Algorithms (ESA 2018)

Abstract
We present a decremental data structure for maintaining the SPQR-tree of a planar graph subject to edge contractions and deletions. The update time, amortized over Omega(n) operations, is O(log^2 n). Via SPQR-trees, we give a decremental data structure for maintaining 3-vertex connectivity in planar graphs. It answers queries in O(1) time and processes edge deletions and contractions in O(log^2 n) amortized time. The previous best supported deletions and insertions in O(sqrt{n}) time.
Cite as

Jacob Holm, Giuseppe F. Italiano, Adam Karczmarz, Jakub Lacki, and Eva Rotenberg. Decremental SPQR-trees for Planar Graphs. In 26th Annual European Symposium on Algorithms (ESA 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 112, pp. 46:1-46:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{holm_et_al:LIPIcs.ESA.2018.46,
  author =	{Holm, Jacob and Italiano, Giuseppe F. and Karczmarz, Adam and Lacki, Jakub and Rotenberg, Eva},
  title =	{{Decremental SPQR-trees for Planar Graphs}},
  booktitle =	{26th Annual European Symposium on Algorithms (ESA 2018)},
  pages =	{46:1--46:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-081-1},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{112},
  editor =	{Azar, Yossi and Bast, Hannah 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.2018.46},
  URN =		{urn:nbn:de:0030-drops-95091},
  doi =		{10.4230/LIPIcs.ESA.2018.46},
  annote =	{Keywords: Graph embeddings, data structures, graph algorithms, planar graphs, SPQR-trees, triconnectivity}
}
Document
DOI: 10.4230/LIPIcs.ESA.2017.50
Contracting a Planar Graph Efficiently

Authors: Jacob Holm, Giuseppe F. Italiano, Adam Karczmarz, Jakub Lacki, Eva Rotenberg, and Piotr Sankowski

Published in: LIPIcs, Volume 87, 25th Annual European Symposium on Algorithms (ESA 2017)

Abstract
We present a data structure that can maintain a simple planar graph under edge contractions in linear total time. The data structure supports adjacency queries and provides access to neighbor lists in O(1) time. Moreover, it can report all the arising self-loops and parallel edges. By applying the data structure, we can achieve optimal running times for decremental bridge detection, 2-edge connectivity, maximal 3-edge connected components, and the problem of finding a unique perfect matching for a static planar graph. Furthermore, we improve the running times of algorithms for several planar graph problems, including decremental 2-vertex and 3-edge connectivity, and we show that using our data structure in a black-box manner, one obtains conceptually simple optimal algorithms for computing MST and 5-coloring in planar graphs.
Cite as

Jacob Holm, Giuseppe F. Italiano, Adam Karczmarz, Jakub Lacki, Eva Rotenberg, and Piotr Sankowski. Contracting a Planar Graph Efficiently. In 25th Annual European Symposium on Algorithms (ESA 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 87, pp. 50:1-50:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

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@InProceedings{holm_et_al:LIPIcs.ESA.2017.50,
  author =	{Holm, Jacob and Italiano, Giuseppe F. and Karczmarz, Adam and Lacki, Jakub and Rotenberg, Eva and Sankowski, Piotr},
  title =	{{Contracting a Planar Graph Efficiently}},
  booktitle =	{25th Annual European Symposium on Algorithms (ESA 2017)},
  pages =	{50:1--50:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-049-1},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{87},
  editor =	{Pruhs, Kirk and Sohler, Christian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ESA.2017.50},
  URN =		{urn:nbn:de:0030-drops-78755},
  doi =		{10.4230/LIPIcs.ESA.2017.50},
  annote =	{Keywords: planar graphs, algorithms, data structures, connectivity, coloring}
}
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