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Documents authored by Dondi, Riccardo

Document
DOI: 10.4230/LIPIcs.TIME.2025.8
Heuristics for Covering the Timeline in Temporal Graphs

Authors: Riccardo Dondi, Rares-Ioan Mateiu, and Alexandru Popa

Published in: LIPIcs, Volume 355, 32nd International Symposium on Temporal Representation and Reasoning (TIME 2025)

Abstract
We consider a variant of the Vertex Cover problem on temporal graphs, called Minimum Timeline Cover (k-MinTimelineCover). Temporal graphs are used to model complex systems, describing how edges (relations) change in a discrete time domain. The k-MinTimelineCover problem has been introduced in complex data summarization and synthesis jobs. Given a temporal graph G, k-MinTimelineCover asks to define k activity intervals for each vertex, such that each temporal edge is covered by at least one active interval. The objective function is the minimization of the sum of interval lengths. k-MinTimelineCover is NP-hard and even hard to approximate within any factor for k > 1. While the literature has mainly focused on the cases k = 1, in this contribution we consider the case k > 1. We first present an ILP formulation that is able to solve the problem on moderate size instances. Then we develop an efficient heuristic, based on local search which is built on top of the solution of an existing literature method. Finally, we present an experimental evaluation of our algorithms on synthetic data sets, that shows in particular that our heuristic has a consistent improvement on the state-of-the art method.
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Riccardo Dondi, Rares-Ioan Mateiu, and Alexandru Popa. Heuristics for Covering the Timeline in Temporal Graphs. In 32nd International Symposium on Temporal Representation and Reasoning (TIME 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 355, pp. 8:1-8:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{dondi_et_al:LIPIcs.TIME.2025.8,
  author =	{Dondi, Riccardo and Mateiu, Rares-Ioan and Popa, Alexandru},
  title =	{{Heuristics for Covering the Timeline in Temporal Graphs}},
  booktitle =	{32nd International Symposium on Temporal Representation and Reasoning (TIME 2025)},
  pages =	{8:1--8:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-401-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{355},
  editor =	{Vidal, Thierry and Wa{\l}\k{e}ga, Przemys{\l}aw Andrzej},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TIME.2025.8},
  URN =		{urn:nbn:de:0030-drops-244542},
  doi =		{10.4230/LIPIcs.TIME.2025.8},
  annote =	{Keywords: Temporal Networks, Activity Timeline, Vertex Cover, Heuristic, Dynamic Programming}
}
Document
DOI: 10.4230/LIPIcs.WADS.2025.23
Novel Complexity Results for Temporal Separators with Deadlines

Authors: Riccardo Dondi and Manuel Lafond

Published in: LIPIcs, Volume 349, 19th International Symposium on Algorithms and Data Structures (WADS 2025)

Abstract
We consider two variants, (s,z,𝓁)-Temporal Separator and (s,z,𝓁)-Temporal Cut, respectively, of the vertex separator and the edge cut problem in temporal graphs. The goal is to remove the minimum number of vertices (temporal edges, respectively) in order to delete all the temporal paths that have time travel at most 𝓁 between a source vertex s and target vertex z. First, we solve an open problem in the literature showing that (s,z,𝓁)-Temporal Separator is NP-hard even when the underlying graph has pathwidth bounded by four. We complement this result showing that (s,z,𝓁)-Temporal Separator can be solved in polynomial time for graphs of pathwidth bounded by three. Then we consider the approximability of (s,z,𝓁)-Temporal Separator and we show that it cannot be approximated within factor 2^Ω(log^{1-ε}|V|) for any constant ε > 0, unless NP ⊆ ZPP (V is the vertex set of the input temporal graph) and that the strict version is approximable within factor 𝓁-1 (we show also that it is unliklely that this factor can be improved). Then we consider the (s,z,𝓁)-Temporal Cut problem, we show that it is APX-hard and we present a 2 log₂(2𝓁) approximation algorithm.
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Riccardo Dondi and Manuel Lafond. Novel Complexity Results for Temporal Separators with Deadlines. In 19th International Symposium on Algorithms and Data Structures (WADS 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 349, pp. 23:1-23:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{dondi_et_al:LIPIcs.WADS.2025.23,
  author =	{Dondi, Riccardo and Lafond, Manuel},
  title =	{{Novel Complexity Results for Temporal Separators with Deadlines}},
  booktitle =	{19th International Symposium on Algorithms and Data Structures (WADS 2025)},
  pages =	{23:1--23:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-398-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{349},
  editor =	{Morin, Pat and Oh, Eunjin},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WADS.2025.23},
  URN =		{urn:nbn:de:0030-drops-242545},
  doi =		{10.4230/LIPIcs.WADS.2025.23},
  annote =	{Keywords: Temporal Graphs, Graph Algorithms, Graph Separators, Parameterized Complexity, Approximation Complexity}
}
Document
DOI: 10.4230/LIPIcs.CPM.2025.1
Representing Paths in Digraphs

Authors: Riccardo Dondi and Alexandru Popa

Published in: LIPIcs, Volume 331, 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)

Abstract
In this contribution we consider two combinatorial problems related to graph string matching, motivated by recent approaches in computational genomics. Given a DAG where each node is labeled by a symbol, the problems aim to find a path in the DAG whose nodes contain all (or the maximum number of) symbols of the alphabet. We introduce a decision problem, Σ-Representing Path, that asks whether there exists a path that contains all the symbols of the alphabet, and an optimization problem, called Maximum Representing Path, that asks for a path that contains the maximum number of symbols. We analyze the complexity of the problems, showing the NP-completeness of {Σ-Representing Path} when each symbol labels at most three nodes in the DAG, and showing the APX-hardness of Maximum Representing Path when each symbol labels at most two nodes in the DAG. We complement the first result by giving a polynomial-time algorithm for Σ-Representing Path when each symbol labels at most two nodes in the DAG. Then we investigate the parameterized complexity of the two problems when the DAG has a limited distance from a set of disjoint paths and we show that both problems are W[1]-hard for this parameter. We consider the approximation of Maximum Representing Path, giving an approximation algorithm of factor √OPT, where OPT is the value of an optimal solution of the problem. We also show that Maximum Representing Path cannot be approximated within factor e/(e-1) - α, for any constant α > 0, unless NP ⊆ DTIME(|V|^{O(log log |V|)}) (V is the set of nodes of the DAG).
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Riccardo Dondi and Alexandru Popa. Representing Paths in Digraphs. In 36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 331, pp. 1:1-1:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{dondi_et_al:LIPIcs.CPM.2025.1,
  author =	{Dondi, Riccardo and Popa, Alexandru},
  title =	{{Representing Paths in Digraphs}},
  booktitle =	{36th Annual Symposium on Combinatorial Pattern Matching (CPM 2025)},
  pages =	{1:1--1:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-369-0},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{331},
  editor =	{Bonizzoni, Paola and M\"{a}kinen, Veli},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2025.1},
  URN =		{urn:nbn:de:0030-drops-230954},
  doi =		{10.4230/LIPIcs.CPM.2025.1},
  annote =	{Keywords: Graph String Matching, Computational Complexity, Parameterized Complexity, Algorithms}
}
Document
DOI: 10.4230/LIPIcs.SAND.2025.8
Matching and Edge Cover in Temporal Graphs

Authors: Lapo Cioni, Riccardo Dondi, Andrea Marino, Jason Schoeters, and Ana Silva

Published in: LIPIcs, Volume 330, 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)

Abstract
Temporal graphs are a special class of graphs for which a temporal component is added to edges, that is, each edge possesses a set of times at which it is available and can be traversed. Many classical problems on graphs can be translated to temporal graphs, and the results may differ. In this paper, we define the {Temporal Edge Cover} and {Temporal Matching} problems and show that they are NP-complete even when fixing the lifetime or when the underlying graph is a tree. We then describe two FPT algorithms, with parameters lifetime and treewidth, that solve the two problems. We also find lower bounds for the approximation of the two problems and give two approximation algorithms which match these bounds. Finally, we discuss the differences between the problems in the temporal and the static framework.
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Lapo Cioni, Riccardo Dondi, Andrea Marino, Jason Schoeters, and Ana Silva. Matching and Edge Cover in Temporal Graphs. In 4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 330, pp. 8:1-8:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{cioni_et_al:LIPIcs.SAND.2025.8,
  author =	{Cioni, Lapo and Dondi, Riccardo and Marino, Andrea and Schoeters, Jason and Silva, Ana},
  title =	{{Matching and Edge Cover in Temporal Graphs}},
  booktitle =	{4th Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2025)},
  pages =	{8:1--8:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-368-3},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{330},
  editor =	{Meeks, Kitty and Scheideler, Christian},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.SAND.2025.8},
  URN =		{urn:nbn:de:0030-drops-230614},
  doi =		{10.4230/LIPIcs.SAND.2025.8},
  annote =	{Keywords: graphs, temporal graphs, edge cover, matching, parameterized algorithm, approximation algorithm}
}
Document
DOI: 10.4230/LIPIcs.TIME.2024.20
FastMinTC+: A Fast and Effective Heuristic for Minimum Timeline Cover on Temporal Networks

Authors: Giorgio Lazzarinetti, Sara Manzoni, Italo Zoppis, and Riccardo Dondi

Published in: LIPIcs, Volume 318, 31st International Symposium on Temporal Representation and Reasoning (TIME 2024)

Abstract
The analysis and summarization of temporal networks are crucial for understanding complex interactions over time, yet pose significant computational challenges. This paper introduces FastMinTC+, an innovative heuristic approach designed to efficiently solve the Minimum Timeline Cover (MinTCover) problem in temporal networks. Our approach focuses on the optimization of activity timelines within temporal networks, aiming to provide both effective and computationally feasible solutions. By employing a low-complexity approach, FastMinTC+ adeptly handles massive temporal graphs, improving upon existing methods. Indeed, comparative evaluations on both synthetic and real-world datasets demonstrate that our algorithm outperforms established benchmarks with remarkable efficiency and accuracy. The results highlight the potential of heuristic approaches in the domain of temporal network analysis and open up new avenues for further research incorporating other computational techniques, for example deep learning, to enhance the adaptability and precision of such heuristics.
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Giorgio Lazzarinetti, Sara Manzoni, Italo Zoppis, and Riccardo Dondi. FastMinTC+: A Fast and Effective Heuristic for Minimum Timeline Cover on Temporal Networks. In 31st International Symposium on Temporal Representation and Reasoning (TIME 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 318, pp. 20:1-20:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{lazzarinetti_et_al:LIPIcs.TIME.2024.20,
  author =	{Lazzarinetti, Giorgio and Manzoni, Sara and Zoppis, Italo and Dondi, Riccardo},
  title =	{{FastMinTC+: A Fast and Effective Heuristic for Minimum Timeline Cover on Temporal Networks}},
  booktitle =	{31st International Symposium on Temporal Representation and Reasoning (TIME 2024)},
  pages =	{20:1--20:18},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-349-2},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{318},
  editor =	{Sala, Pietro and Sioutis, Michael and Wang, Fusheng},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.TIME.2024.20},
  URN =		{urn:nbn:de:0030-drops-212275},
  doi =		{10.4230/LIPIcs.TIME.2024.20},
  annote =	{Keywords: Temporal Networks, Activity Timeline, Timeline Cover, Vertex Cover, Optimization, Heuristic}
}
Document
DOI: 10.4230/LIPIcs.SAND.2024.10
On the Complexity of Temporal Arborescence Reconfiguration

Authors: Riccardo Dondi and Manuel Lafond

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

Abstract
We analyze the complexity of Arborescence Reconfiguration on temporal digraphs (Temporal Arborescence Reconfiguration). The problem, given two temporal arborescences in a temporal digraph, asks for the minimum number of arc flips, i.e. arc exchanges, that result in a sequence of temporal arborescences that transforms one into the other. We analyze the complexity of the problem, taking into account also its approximation and parameterized complexity, even in restricted cases. First, we solve an open problem showing that Temporal Arborescence Reconfiguration is NP-hard for two timestamps. Then we show that even if the two temporal arborescences differ only by two arcs, then the problem is not approximable within factor bln|V(D)|, for any constant 0 < b < 1, where V(D) is the set of vertices of the temporal arborescences. Finally, we prove that Temporal Arborescence Reconfiguration is W[1]-hard when parameterized by the number of arc flips needed to transform one temporal arborescence into the other.
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Riccardo Dondi and Manuel Lafond. On the Complexity of Temporal Arborescence Reconfiguration. In 3rd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 292, pp. 10:1-10:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{dondi_et_al:LIPIcs.SAND.2024.10,
  author =	{Dondi, Riccardo and Lafond, Manuel},
  title =	{{On the Complexity of Temporal Arborescence Reconfiguration}},
  booktitle =	{3rd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2024)},
  pages =	{10:1--10:15},
  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.2024.10},
  URN =		{urn:nbn:de:0030-drops-198888},
  doi =		{10.4230/LIPIcs.SAND.2024.10},
  annote =	{Keywords: Arborescence, Temporal Graphs, Graph Algorithms, Parameterized Complexity, Approximation Complexity}
}
Document
DOI: 10.4230/LIPIcs.SAND.2024.11
Partial Temporal Vertex Cover with Bounded Activity Intervals

Authors: Riccardo Dondi, Fabrizio Montecchiani, Giacomo Ortali, Tommaso Piselli, and Alessandra Tappini

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

Abstract
Different variants of Vertex Cover have recently garnered attention in the context of temporal graphs. One of these variants is motivated by the need to summarize timeline activities in social networks. Here, the activities of individual vertices, representing users, are characterized by time intervals. In this paper, we explore a scenario where the temporal span of each vertex’s activity interval is bounded by an integer 𝓁, and the objective is to maximize the number of (temporal) edges that are covered. We establish the APX-hardness of this problem and the NP-hardness of the corresponding decision problem, even under the restricted condition where the temporal domain comprises only two timestamps and each edge appears at most once. Subsequently, we delve into the parameterized complexity of the problem, offering two fixed-parameter algorithms parameterized by: (i) the number k of temporal edges covered by the solution, and (ii) the number h of temporal edges not covered by the solution. Finally, we present a polynomial-time approximation algorithm achieving a factor of 3/4.
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Riccardo Dondi, Fabrizio Montecchiani, Giacomo Ortali, Tommaso Piselli, and Alessandra Tappini. Partial Temporal Vertex Cover with Bounded Activity Intervals. In 3rd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 292, pp. 11:1-11:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{dondi_et_al:LIPIcs.SAND.2024.11,
  author =	{Dondi, Riccardo and Montecchiani, Fabrizio and Ortali, Giacomo and Piselli, Tommaso and Tappini, Alessandra},
  title =	{{Partial Temporal Vertex Cover with Bounded Activity Intervals}},
  booktitle =	{3rd Symposium on Algorithmic Foundations of Dynamic Networks (SAND 2024)},
  pages =	{11:1--11:14},
  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.2024.11},
  URN =		{urn:nbn:de:0030-drops-198892},
  doi =		{10.4230/LIPIcs.SAND.2024.11},
  annote =	{Keywords: Temporal Graphs, Temporal Vertex Cover, Parameterized Complexity, Approximation Algorithms}
}
Document
DOI: 10.4230/LIPIcs.IPEC.2023.12
An FPT Algorithm for Temporal Graph Untangling

Authors: Riccardo Dondi and Manuel Lafond

Published in: LIPIcs, Volume 285, 18th International Symposium on Parameterized and Exact Computation (IPEC 2023)

Abstract
Several classical combinatorial problems have been considered and analysed on temporal graphs. Recently, a variant of Vertex Cover on temporal graphs, called MinTimelineCover, has been introduced to summarize timeline activities in social networks. The problem asks to cover every temporal edge while minimizing the total span of the vertices (where the span of a vertex is the length of the timestamp interval it must remain active in). While the problem has been shown to be NP-hard even in very restricted cases, its parameterized complexity has not been fully understood. The problem is known to be in FPT under the span parameter only for graphs with two timestamps, but the parameterized complexity for the general case is open. We settle this open problem by giving an FPT algorithm that is based on a combination of iterative compression and a reduction to the Digraph Pair Cut problem, a powerful problem that has received significant attention recently.
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Riccardo Dondi and Manuel Lafond. An FPT Algorithm for Temporal Graph Untangling. In 18th International Symposium on Parameterized and Exact Computation (IPEC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 285, pp. 12:1-12:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{dondi_et_al:LIPIcs.IPEC.2023.12,
  author =	{Dondi, Riccardo and Lafond, Manuel},
  title =	{{An FPT Algorithm for Temporal Graph Untangling}},
  booktitle =	{18th International Symposium on Parameterized and Exact Computation (IPEC 2023)},
  pages =	{12:1--12:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-305-8},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{285},
  editor =	{Misra, Neeldhara and Wahlstr\"{o}m, Magnus},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.IPEC.2023.12},
  URN =		{urn:nbn:de:0030-drops-194311},
  doi =		{10.4230/LIPIcs.IPEC.2023.12},
  annote =	{Keywords: Temporal Graphs, Vertex Cover, Graph Algorithms, Parameterized Complexity}
}
Document
DOI: 10.4230/LIPIcs.CPM.2021.14
The Longest Run Subsequence Problem: Further Complexity Results

Authors: Riccardo Dondi and Florian Sikora

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

Abstract
Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one run for each symbol (a run is a maximum substring of consecutive identical symbols). The problem has been shown to be NP-hard and to be fixed-parameter tractable when the parameter is the size of the alphabet on which the input string is defined. In this paper we further investigate the complexity of the problem and we show that it is fixed-parameter tractable when it is parameterized by the number of runs in a solution, a smaller parameter. Moreover, we investigate the kernelization complexity of Longest Run Subsequence and we prove that it does not admit a polynomial kernel when parameterized by the size of the alphabet or by the number of runs. Finally, we consider the restriction of Longest Run Subsequence when each symbol has at most two occurrences in the input string and we show that it is APX-hard.
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Riccardo Dondi and Florian Sikora. The Longest Run Subsequence Problem: Further Complexity Results. In 32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 191, pp. 14:1-14:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{dondi_et_al:LIPIcs.CPM.2021.14,
  author =	{Dondi, Riccardo and Sikora, Florian},
  title =	{{The Longest Run Subsequence Problem: Further Complexity Results}},
  booktitle =	{32nd Annual Symposium on Combinatorial Pattern Matching (CPM 2021)},
  pages =	{14:1--14:15},
  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.2021.14},
  URN =		{urn:nbn:de:0030-drops-139652},
  doi =		{10.4230/LIPIcs.CPM.2021.14},
  annote =	{Keywords: Parameterized complexity, Kernelization, Approximation Hardness, Longest Subsequence}
}
Document
DOI: 10.4230/LIPIcs.WABI.2018.5
Reconciling Multiple Genes Trees via Segmental Duplications and Losses

Authors: Riccardo Dondi, Manuel Lafond, and Celine Scornavacca

Published in: LIPIcs, Volume 113, 18th International Workshop on Algorithms in Bioinformatics (WABI 2018)

Abstract
Reconciling gene trees with a species tree is a fundamental problem to understand the evolution of gene families. Many existing approaches reconcile each gene tree independently. However, it is well-known that the evolution of gene families is interconnected. In this paper, we extend a previous approach to reconcile a set of gene trees with a species tree based on segmental macro-evolutionary events, where segmental duplication events and losses are associated with cost delta and lambda, respectively. We show that the problem is polynomial-time solvable when delta <= lambda (via LCA-mapping), while if delta > lambda the problem is NP-hard, even when lambda = 0 and a single gene tree is given, solving a long standing open problem on the complexity of the reconciliation problem. On the positive side, we give a fixed-parameter algorithm for the problem, where the parameters are delta/lambda and the number d of segmental duplications, of time complexity O(ceil[delta/lambda]^d * n * delta/lambda). Finally, we demonstrate the usefulness of this algorithm on two previously studied real datasets: we first show that our method can be used to confirm or refute hypothetical segmental duplications on a set of 16 eukaryotes, then show how we can detect whole genome duplications in yeast genomes.
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Riccardo Dondi, Manuel Lafond, and Celine Scornavacca. Reconciling Multiple Genes Trees via Segmental Duplications and Losses. In 18th International Workshop on Algorithms in Bioinformatics (WABI 2018). Leibniz International Proceedings in Informatics (LIPIcs), Volume 113, pp. 5:1-5:16, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2018)

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@InProceedings{dondi_et_al:LIPIcs.WABI.2018.5,
  author =	{Dondi, Riccardo and Lafond, Manuel and Scornavacca, Celine},
  title =	{{Reconciling Multiple Genes Trees via Segmental Duplications and Losses}},
  booktitle =	{18th International Workshop on Algorithms in Bioinformatics (WABI 2018)},
  pages =	{5:1--5:16},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-082-8},
  ISSN =	{1868-8969},
  year =	{2018},
  volume =	{113},
  editor =	{Parida, Laxmi and Ukkonen, Esko},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2018.5},
  URN =		{urn:nbn:de:0030-drops-93079},
  doi =		{10.4230/LIPIcs.WABI.2018.5},
  annote =	{Keywords: Gene trees/species tree reconciliation, phylogenetics, computational complexity, fixed-parameter algorithms}
}
Document
DOI: 10.4230/LIPIcs.CPM.2017.14
The Longest Filled Common Subsequence Problem

Authors: Mauro Castelli, Riccardo Dondi, Giancarlo Mauri, and Italo Zoppis

Published in: LIPIcs, Volume 78, 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017)

Abstract
Inspired by a recent approach for genome reconstruction from incomplete data, we consider a variant of the longest common subsequence problem for the comparison of two sequences, one of which is incomplete, i.e. it has some missing elements. The new combinatorial problem, called Longest Filled Common Subsequence, given two sequences A and B, and a multiset M of symbols missing in B, asks for a sequence B* obtained by inserting the symbols of M into B so that B* induces a common subsequence with A of maximum length. First, we investigate the computational and approximation complexity of the problem and we show that it is NP-hard and APX-hard when A contains at most two occurrences of each symbol. Then, we give a 3/5 approximation algorithm for the problem. Finally, we present a fixed-parameter algorithm, when the problem is parameterized by the number of symbols inserted in B that "match" symbols of A.
Cite as

Mauro Castelli, Riccardo Dondi, Giancarlo Mauri, and Italo Zoppis. The Longest Filled Common Subsequence Problem. In 28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017). Leibniz International Proceedings in Informatics (LIPIcs), Volume 78, pp. 14:1-14:13, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2017)

Copy BibTex To Clipboard

@InProceedings{castelli_et_al:LIPIcs.CPM.2017.14,
  author =	{Castelli, Mauro and Dondi, Riccardo and Mauri, Giancarlo and Zoppis, Italo},
  title =	{{The Longest Filled Common Subsequence Problem}},
  booktitle =	{28th Annual Symposium on Combinatorial Pattern Matching (CPM 2017)},
  pages =	{14:1--14:13},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-039-2},
  ISSN =	{1868-8969},
  year =	{2017},
  volume =	{78},
  editor =	{K\"{a}rkk\"{a}inen, Juha and Radoszewski, Jakub and Rytter, Wojciech},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CPM.2017.14},
  URN =		{urn:nbn:de:0030-drops-73293},
  doi =		{10.4230/LIPIcs.CPM.2017.14},
  annote =	{Keywords: longest common subsequence, approximation algorithms, computational complexity, fixed-parameter algorithms}
}
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