4 Search Results for "Edmonds, Jack R."

Document
DOI: 10.4230/LIPIcs.WABI.2024.23
AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction

Authors: Adam Cicherski, Anna Lisiecka, and Norbert Dojer

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

Abstract
The success of pangenome-based approaches to genomics analysis depends largely on the existence of efficient methods for constructing pangenome graphs that are applicable to large genome collections. In the current paper we present AlfaPang, a new pangenome graph building algorithm. AlfaPang is based on a novel alignment-free approach that allows to construct pangenome graphs using significantly less computational resources than state-of-the-art tools. The code of AlfaPang is freely available at https://github.com/AdamCicherski/AlfaPang.
Cite as

Adam Cicherski, Anna Lisiecka, and Norbert Dojer. AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction. In 24th International Workshop on Algorithms in Bioinformatics (WABI 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 312, pp. 23:1-23:18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2024)

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@InProceedings{cicherski_et_al:LIPIcs.WABI.2024.23,
  author =	{Cicherski, Adam and Lisiecka, Anna and Dojer, Norbert},
  title =	{{AlfaPang: Alignment Free Algorithm for Pangenome Graph Construction}},
  booktitle =	{24th International Workshop on Algorithms in Bioinformatics (WABI 2024)},
  pages =	{23:1--23:18},
  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.2024.23},
  URN =		{urn:nbn:de:0030-drops-206673},
  doi =		{10.4230/LIPIcs.WABI.2024.23},
  annote =	{Keywords: pangenome, variation graph, genome alignment, population genomics}
}
Document
DOI: 10.4230/LIPIcs.ISAAC.2023.57
A Strongly Polynomial-Time Algorithm for Weighted General Factors with Three Feasible Degrees

Authors: Shuai Shao and Stanislav Živný

Published in: LIPIcs, Volume 283, 34th International Symposium on Algorithms and Computation (ISAAC 2023)

Abstract
General factors are a generalization of matchings. Given a graph G with a set π(v) of feasible degrees, called a degree constraint, for each vertex v of G, the general factor problem is to find a (spanning) subgraph F of G such that deg_F(v) ∈ π(v) for every v of G. When all degree constraints are symmetric Δ-matroids, the problem is solvable in polynomial time. The weighted general factor problem is to find a general factor of the maximum total weight in an edge-weighted graph. Strongly polynomial-time algorithms are only known for weighted general factor problems that are reducible to the weighted matching problem by gadget constructions. In this paper, we present a strongly polynomial-time algorithm for a type of weighted general factor problems with real-valued edge weights that is provably not reducible to the weighted matching problem by gadget constructions. As an application, we obtain a strongly polynomial-time algorithm for the terminal backup problem by reducing it to the weighted general factor problem.
Cite as

Shuai Shao and Stanislav Živný. A Strongly Polynomial-Time Algorithm for Weighted General Factors with Three Feasible Degrees. In 34th International Symposium on Algorithms and Computation (ISAAC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 283, pp. 57:1-57:17, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{shao_et_al:LIPIcs.ISAAC.2023.57,
  author =	{Shao, Shuai and \v{Z}ivn\'{y}, Stanislav},
  title =	{{A Strongly Polynomial-Time Algorithm for Weighted General Factors with Three Feasible Degrees}},
  booktitle =	{34th International Symposium on Algorithms and Computation (ISAAC 2023)},
  pages =	{57:1--57:17},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-289-1},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{283},
  editor =	{Iwata, Satoru and Kakimura, Naonori},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.ISAAC.2023.57},
  URN =		{urn:nbn:de:0030-drops-193597},
  doi =		{10.4230/LIPIcs.ISAAC.2023.57},
  annote =	{Keywords: matchings, factors, edge constraint satisfaction problems, terminal backup problem, delta matroids}
}
Document
DOI: 10.4230/LIPIcs.CCC.2023.2
Border Complexity of Symbolic Determinant Under Rank One Restriction

Authors: Abhranil Chatterjee, Sumanta Ghosh, Rohit Gurjar, and Roshan Raj

Published in: LIPIcs, Volume 264, 38th Computational Complexity Conference (CCC 2023)

Abstract
VBP is the class of polynomial families that can be computed by the determinant of a symbolic matrix of the form A_0 + ∑_{i=1}^n A_i x_i where the size of each A_i is polynomial in the number of variables (equivalently, computable by polynomial-sized algebraic branching programs (ABP)). A major open problem in geometric complexity theory (GCT) is to determine whether VBP is closed under approximation i.e. whether VBP = VBP^ ̅. The power of approximation is well understood for some restricted models of computation, e.g. the class of depth-two circuits, read-once oblivious ABPs (ROABP), monotone ABPs, depth-three circuits of bounded top fan-in, and width-two ABPs. The former three classes are known to be closed under approximation [Markus Bläser et al., 2020], whereas the approximative closure of the last one captures the entire class of polynomial families computable by polynomial-sized formulas [Bringmann et al., 2017]. In this work, we consider the subclass of VBP computed by the determinant of a symbolic matrix of the form A_0 + ∑_{i=1}^n A_i x_i where for each 1 ≤ i ≤ n, A_i is of rank one. This class has been studied extensively [Edmonds, 1968; Jack Edmonds, 1979; Murota, 1993] and efficient identity testing algorithms are known for it [Lovász, 1989; Rohit Gurjar and Thomas Thierauf, 2020]. We show that this class is closed under approximation. In the language of algebraic geometry, we show that the set obtained by taking coordinatewise products of pairs of points from (the Plücker embedding of) a Grassmannian variety is closed.
Cite as

Abhranil Chatterjee, Sumanta Ghosh, Rohit Gurjar, and Roshan Raj. Border Complexity of Symbolic Determinant Under Rank One Restriction. In 38th Computational Complexity Conference (CCC 2023). Leibniz International Proceedings in Informatics (LIPIcs), Volume 264, pp. 2:1-2:15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2023)

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@InProceedings{chatterjee_et_al:LIPIcs.CCC.2023.2,
  author =	{Chatterjee, Abhranil and Ghosh, Sumanta and Gurjar, Rohit and Raj, Roshan},
  title =	{{Border Complexity of Symbolic Determinant Under Rank One Restriction}},
  booktitle =	{38th Computational Complexity Conference (CCC 2023)},
  pages =	{2:1--2:15},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-282-2},
  ISSN =	{1868-8969},
  year =	{2023},
  volume =	{264},
  editor =	{Ta-Shma, Amnon},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2023.2},
  URN =		{urn:nbn:de:0030-drops-182721},
  doi =		{10.4230/LIPIcs.CCC.2023.2},
  annote =	{Keywords: Border Complexity, Symbolic Determinant, Valuated Matroid}
}
Document
DOI: 10.4230/LIPIcs.CCC.2016.23
Understanding PPA-Completeness

Authors: Xiaotie Deng, Jack R. Edmonds, Zhe Feng, Zhengyang Liu, Qi Qi, and Zeying Xu

Published in: LIPIcs, Volume 50, 31st Conference on Computational Complexity (CCC 2016)

Abstract
We consider the problem of finding a fully colored base triangle on the 2-dimensional Möbius band under the standard boundary condition, proving it to be PPA-complete. The proof is based on a construction for the DPZP problem, that of finding a zero point under a discrete version of continuity condition. It further derives PPA-completeness for versions on the Möbius band of other related discrete fixed point type problems, and a special version of the Tucker problem, finding an edge such that if the value of one end vertex is x, the other is -x, given a special anti-symmetry boundary condition. More generally, this applies to other non-orientable spaces, including the projective plane and the Klein bottle. However, since those models have a closed boundary, we rely on a version of the PPA that states it as to find another fixed point giving a fixed point. This model also makes it presentationally simple for an extension to a high dimensional discrete fixed point problem on a non-orientable (nearly) hyper-grid with a constant side length.
Cite as

Xiaotie Deng, Jack R. Edmonds, Zhe Feng, Zhengyang Liu, Qi Qi, and Zeying Xu. Understanding PPA-Completeness. In 31st Conference on Computational Complexity (CCC 2016). Leibniz International Proceedings in Informatics (LIPIcs), Volume 50, pp. 23:1-23:25, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2016)

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@InProceedings{deng_et_al:LIPIcs.CCC.2016.23,
  author =	{Deng, Xiaotie and Edmonds, Jack R. and Feng, Zhe and Liu, Zhengyang and Qi, Qi and Xu, Zeying},
  title =	{{Understanding PPA-Completeness}},
  booktitle =	{31st Conference on Computational Complexity (CCC 2016)},
  pages =	{23:1--23:25},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-008-8},
  ISSN =	{1868-8969},
  year =	{2016},
  volume =	{50},
  editor =	{Raz, Ran},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.CCC.2016.23},
  URN =		{urn:nbn:de:0030-drops-58310},
  doi =		{10.4230/LIPIcs.CCC.2016.23},
  annote =	{Keywords: Fixed Point Computation, PPA-Completeness}
}
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