6 Search Results for "Mumey, Brendan"

Document
DOI: 10.4230/LIPIcs.MFCS.2024.38
Algorithms and Complexity for Path Covers of Temporal DAGs

Authors: Dibyayan Chakraborty, Antoine Dailly, Florent Foucaud, and Ralf Klasing

Published in: LIPIcs, Volume 306, 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)

Abstract
A path cover of a digraph is a collection of paths collectively containing its vertex set. A path cover with minimum cardinality for a directed acyclic graph can be found in polynomial time [Fulkerson, AMS'56; Cáceres et al., SODA'22]. Moreover, Dilworth’s celebrated theorem on chain coverings of partially ordered sets equivalently states that the minimum size of a path cover of a DAG is equal to the maximum size of a set of mutually unreachable vertices. In this paper, we examine how far these classic results can be extended to a dynamic setting. A temporal digraph has an arc set that changes over discrete time-steps; if the underlying digraph is acyclic, then it is a temporal DAG. A temporal path is a directed path in the underlying digraph, such that the time-steps of arcs are strictly increasing along the path. Two temporal paths are temporally disjoint if they do not occupy any vertex at the same time. A temporal path cover is a collection 𝒞 of temporal paths that covers all vertices, and 𝒞 is temporally disjoint if all its temporal paths are pairwise temporally disjoint. We study the computational complexities of the problems of finding a minimum-size temporal (disjoint) path cover (denoted as Temporal Path Cover and Temporally Disjoint Path Cover). On the negative side, we show that both Temporal Path Cover and Temporally Disjoint Path Cover are NP-hard even when the underlying DAG is planar, bipartite, subcubic, and there are only two arc-disjoint time-steps. Moreover, Temporally Disjoint Path Cover remains NP-hard even on temporal oriented trees. We also observe that natural temporal analogues of Dilworth’s theorem on these classes of temporal DAGs do not hold. In contrast, we show that Temporal Path Cover is polynomial-time solvable on temporal oriented trees by a reduction to Clique Cover for (static undirected) weakly chordal graphs (a subclass of perfect graphs for which Clique Cover admits an efficient algorithm). This highlights an interesting algorithmic difference between the two problems. Although it is NP-hard on temporal oriented trees, Temporally Disjoint Path Cover becomes polynomial-time solvable on temporal oriented lines and temporal rooted directed trees. Motivated by the hardness result on trees, we show that, in contrast, Temporal Path Cover admits an XP time algorithm with respect to parameter t_max + tw, where t_max is the maximum time-step and tw is the treewidth of the underlying static undirected graph; moreover, Temporally Disjoint Path Cover admits an FPT algorithm with respect to the same parameterization.
Cite as

Dibyayan Chakraborty, Antoine Dailly, Florent Foucaud, and Ralf Klasing. Algorithms and Complexity for Path Covers of Temporal DAGs. In 49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 306, pp. 38:1-38:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{chakraborty_et_al:LIPIcs.MFCS.2024.38,
  author =	{Chakraborty, Dibyayan and Dailly, Antoine and Foucaud, Florent and Klasing, Ralf},
  title =	{{Algorithms and Complexity for Path Covers of Temporal DAGs}},
  booktitle =	{49th International Symposium on Mathematical Foundations of Computer Science (MFCS 2024)},
  pages =	{38:1--38:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-335-5},
  ISSN =	{1868-8969},
  year =	{2024},
  volume =	{306},
  editor =	{Kr\'{a}lovi\v{c}, Rastislav and Ku\v{c}era, Anton{\'\i}n},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2024.38},
  URN =		{urn:nbn:de:0030-drops-205940},
  doi =		{10.4230/LIPIcs.MFCS.2024.38},
  annote =	{Keywords: Temporal Graphs, Dilworth’s Theorem, DAGs, Path Cover, Temporally Disjoint Paths, Algorithms, Oriented Trees, Treewidth}
}
Document
DOI: 10.4230/LIPIcs.SEA.2024.3
Practical Minimum Path Cover

Authors: Manuel Cáceres, Brendan Mumey, Santeri Toivonen, and Alexandru I. Tomescu

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

Abstract
Computing a minimum path cover (MPC) of a directed acyclic graph (DAG) is a fundamental problem with a myriad of applications, including reachability. Although it is known how to solve the problem by a simple reduction to minimum flow, recent theoretical advances exploit this idea to obtain algorithms parameterized by the number of paths of an MPC, known as the width. These results obtain fast [Mäkinen et al., TALG 2019] and even linear time [Cáceres et al., SODA 2022] algorithms in the small-width regime. In this paper, we present the first publicly available high-performance implementation of state-of-the-art MPC algorithms, including the parameterized approaches. Our experiments on random DAGs show that parameterized algorithms are orders-of-magnitude faster on dense graphs. Additionally, we present new fast pre-processing heuristics based on transitive edge sparsification. We show that our heuristics improve MPC-solvers by orders of magnitude.
Cite as

Manuel Cáceres, Brendan Mumey, Santeri Toivonen, and Alexandru I. Tomescu. Practical Minimum Path Cover. In 22nd International Symposium on Experimental Algorithms (SEA 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 301, pp. 3:1-3:19, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{caceres_et_al:LIPIcs.SEA.2024.3,
  author =	{C\'{a}ceres, Manuel and Mumey, Brendan and Toivonen, Santeri and Tomescu, Alexandru I.},
  title =	{{Practical Minimum Path Cover}},
  booktitle =	{22nd International Symposium on Experimental Algorithms (SEA 2024)},
  pages =	{3:1--3:19},
  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.2024.3},
  URN =		{urn:nbn:de:0030-drops-203687},
  doi =		{10.4230/LIPIcs.SEA.2024.3},
  annote =	{Keywords: minimum path cover, directed acyclic graph, maximum flow, parameterized algorithms, edge sparsification, algorithm engineering}
}
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)

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@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
Track A: Algorithms, Complexity and Games
DOI: 10.4230/LIPIcs.ICALP.2023.31
Minimum Chain Cover in Almost Linear Time

Authors: Manuel Cáceres

Published in: LIPIcs, Volume 261, 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)

Abstract
A minimum chain cover (MCC) of a k-width directed acyclic graph (DAG) G = (V, E) is a set of k chains (paths in the transitive closure) of G such that every vertex appears in at least one chain in the cover. The state-of-the-art solutions for MCC run in time Õ(k(|V|+|E|)) [Mäkinen et at., TALG], O(T_{MF}(|E|) + k|V|), O(k²|V| + |E|) [Cáceres et al., SODA 2022], Õ(|V|^{3/2} + |E|) [Kogan and Parter, ICALP 2022] and Õ(T_{MCF}(|E|) + √k|V|) [Kogan and Parter, SODA 2023], where T_{MF}(|E|) and T_{MCF}(|E|) are the running times for solving maximum flow (MF) and minimum-cost flow (MCF), respectively. In this work we present an algorithm running in time O(T_{MF}(|E|) + (|V|+|E|)log k). By considering the recent result for solving MF [Chen et al., FOCS 2022] our algorithm is the first running in almost linear time. Moreover, our techniques are deterministic and derive a deterministic near-linear time algorithm for MCC if the same is provided for MF. At the core of our solution we use a modified version of the mergeable dictionaries [Farach and Thorup, Algorithmica], [Iacono and Özkan, ICALP 2010] data structure boosted with the SIZE-SPLIT operation and answering queries in amortized logarithmic time, which can be of independent interest.
Cite as

Manuel Cáceres. Minimum Chain Cover in Almost Linear Time. In 50th International Colloquium on Automata, Languages, and Programming (ICALP 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 261, pp. 31:1-31:12, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{caceres:LIPIcs.ICALP.2023.31,
  author =	{C\'{a}ceres, Manuel},
  title =	{{Minimum Chain Cover in Almost Linear Time}},
  booktitle =	{50th International Colloquium on Automata, Languages, and Programming (ICALP 2023)},
  pages =	{31:1--31:12},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-278-5},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{261},
  editor =	{Etessami, Kousha and Feige, Uriel and Puppis, Gabriele},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ICALP.2023.31},
  URN =		{urn:nbn:de:0030-drops-180834},
  doi =		{10.4230/LIPIcs.ICALP.2023.31},
  annote =	{Keywords: Minimum chain cover, directed acyclic graph, minimum flow, flow decomposition, mergeable dictionaries, amortized running time}
}
Document
DOI: 10.4230/LIPIcs.ESA.2022.31
Width Helps and Hinders Splitting Flows

Authors: Manuel Cáceres, Massimo Cairo, Andreas Grigorjew, Shahbaz Khan, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu, and Lucia Williams

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

Abstract
Minimum flow decomposition (MFD) is the NP-hard problem of finding a smallest decomposition of a network flow X on directed graph G into weighted source-to-sink paths whose superposition equals X. We focus on a common formulation of the problem where the path weights must be non-negative integers and also on a new variant where these weights can be negative. We show that, for acyclic graphs, considering the width of the graph (the minimum number of s-t paths needed to cover all of its edges) yields advances in our understanding of its approximability. For the non-negative version, we show that a popular heuristic is a O(log |X|)-approximation (|X| being the total flow of X) on graphs satisfying two properties related to the width (satisfied by e.g., series-parallel graphs), and strengthen its worst-case approximation ratio from Ω(√m) to Ω(m / log m) for sparse graphs, where m is the number of edges in the graph. For the negative version, we give a (⌈log ║X║⌉+1)-approximation (║X║ being the maximum absolute value of X on any edge) using a power-of-two approach, combined with parity fixing arguments and a decomposition of unitary flows (║X║ ≤ 1) into at most width paths. We also disprove a conjecture about the linear independence of minimum (non-negative) flow decompositions posed by Kloster et al. [ALENEX 2018], but show that its useful implication (polynomial-time assignments of weights to a given set of paths to decompose a flow) holds for the negative version.
Cite as

Manuel Cáceres, Massimo Cairo, Andreas Grigorjew, Shahbaz Khan, Brendan Mumey, Romeo Rizzi, Alexandru I. Tomescu, and Lucia Williams. Width Helps and Hinders Splitting Flows. In 30th Annual European Symposium on Algorithms (ESA 2022). Leibniz International Proceedings in Informatics (LIPIcs), Volume 244, pp. 31:1-31:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2022)

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@InProceedings{caceres_et_al:LIPIcs.ESA.2022.31,
  author =	{C\'{a}ceres, Manuel and Cairo, Massimo and Grigorjew, Andreas and Khan, Shahbaz and Mumey, Brendan and Rizzi, Romeo and Tomescu, Alexandru I. and Williams, Lucia},
  title =	{{Width Helps and Hinders Splitting Flows}},
  booktitle =	{30th Annual European Symposium on Algorithms (ESA 2022)},
  pages =	{31:1--31:14},
  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.2022.31},
  URN =		{urn:nbn:de:0030-drops-169695},
  doi =		{10.4230/LIPIcs.ESA.2022.31},
  annote =	{Keywords: Flow decomposition, approximation algorithms, graph width}
}
Document
DOI: 10.4230/LIPIcs.WABI.2021.16
Flow Decomposition with Subpath Constraints

Authors: Lucia Williams, Alexandru I. Tomescu, and Brendan Mumey

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

Abstract
Flow network decomposition is a natural model for problems where we are given a flow network arising from superimposing a set of weighted paths and would like to recover the underlying data, i.e., decompose the flow into the original paths and their weights. Thus, variations on flow decomposition are often used as subroutines in multiassembly problems such as RNA transcript assembly. In practice, we frequently have access to information beyond flow values in the form of subpaths, and many tools incorporate these heuristically. But despite acknowledging their utility in practice, previous work has not formally addressed the effect of subpath constraints on the accuracy of flow network decomposition approaches. We formalize the flow decomposition with subpath constraints problem, give the first algorithms for it, and study its usefulness for recovering ground truth decompositions. For finding a minimum decomposition, we propose both a heuristic and an FPT algorithm. Experiments on RNA transcript datasets show that for instances with larger solution path sets, the addition of subpath constraints finds 13% more ground truth solutions when minimal decompositions are found exactly, and 30% more ground truth solutions when minimal decompositions are found heuristically.
Cite as

Lucia Williams, Alexandru I. Tomescu, and Brendan Mumey. Flow Decomposition with Subpath Constraints. In 21st International Workshop on Algorithms in Bioinformatics (WABI 2021). Leibniz International Proceedings in Informatics (LIPIcs), Volume 201, pp. 16:1-16:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2021)

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@InProceedings{williams_et_al:LIPIcs.WABI.2021.16,
  author =	{Williams, Lucia and Tomescu, Alexandru I. and Mumey, Brendan},
  title =	{{Flow Decomposition with Subpath Constraints}},
  booktitle =	{21st International Workshop on Algorithms in Bioinformatics (WABI 2021)},
  pages =	{16:1--16:15},
  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.2021.16},
  URN =		{urn:nbn:de:0030-drops-143695},
  doi =		{10.4230/LIPIcs.WABI.2021.16},
  annote =	{Keywords: Flow decomposition, subpath constraints, RNA-Seq}
}
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