6 Search Results for "Edmonds, Jack R."


Document
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
Synteny Paths for Assembly Graphs Comparison

Authors: Evgeny Polevikov and Mikhail Kolmogorov

Published in: LIPIcs, Volume 143, 19th International Workshop on Algorithms in Bioinformatics (WABI 2019)


Abstract
Despite the recent developments of long-read sequencing technologies, it is still difficult to produce complete assemblies of eukaryotic genomes in an automated fashion. Genome assembly software typically output assembled fragments (contigs) along with assembly graphs, that encode all possible layouts of these contigs. Graph representation of the assembled genome can be useful for gene discovery, haplotyping, structural variations analysis and other applications. To facilitate the development of new graph-based approaches, it is important to develop algorithms for comparison and evaluation of assembly graphs produced by different software. In this work, we introduce synteny paths: maximal paths of homologous sequence between the compared assembly graphs. We describe Asgan - an algorithm for efficient synteny paths decomposition, and use it to evaluate assembly graphs of various bacterial assemblies produced by different approaches. We then apply Asgan to discover structural variations between the assemblies of 15 Drosophila genomes, and show that synteny paths are robust to contig fragmentation. The Asgan tool is freely available at: https://github.com/epolevikov/Asgan.

Cite as

Evgeny Polevikov and Mikhail Kolmogorov. Synteny Paths for Assembly Graphs Comparison. In 19th International Workshop on Algorithms in Bioinformatics (WABI 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 143, pp. 24:1-24:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{polevikov_et_al:LIPIcs.WABI.2019.24,
  author =	{Polevikov, Evgeny and Kolmogorov, Mikhail},
  title =	{{Synteny Paths for Assembly Graphs Comparison}},
  booktitle =	{19th International Workshop on Algorithms in Bioinformatics (WABI 2019)},
  pages =	{24:1--24:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-123-8},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{143},
  editor =	{Huber, Katharina T. and Gusfield, Dan},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2019.24},
  URN =		{urn:nbn:de:0030-drops-110545},
  doi =		{10.4230/LIPIcs.WABI.2019.24},
  annote =	{Keywords: Assembly graphs, Genome assembly, Synteny blocks, Comparative Genomics}
}
Document
Counting Induced Subgraphs: An Algebraic Approach to #W[1]-hardness

Authors: Julian Dörfler, Marc Roth, Johannes Schmitt, and Philip Wellnitz

Published in: LIPIcs, Volume 138, 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)


Abstract
We study the problem #IndSub(Phi) of counting all induced subgraphs of size k in a graph G that satisfy the property Phi. This problem was introduced by Jerrum and Meeks and shown to be #W[1]-hard when parameterized by k for some families of properties Phi including, among others, connectivity [JCSS 15] and even- or oddness of the number of edges [Combinatorica 17]. Very recently [IPEC 18], two of the authors introduced a novel technique for the complexity analysis of #IndSub(Phi), inspired by the "topological approach to evasiveness" of Kahn, Saks and Sturtevant [FOCS 83] and the framework of graph motif parameters due to Curticapean, Dell and Marx [STOC 17], allowing them to prove hardness of a wide range of properties Phi. In this work, we refine this technique for graph properties that are non-trivial on edge-transitive graphs with a prime power number of edges. In particular, we fully classify the case of monotone bipartite graph properties: It is shown that, given any graph property Phi that is closed under the removal of vertices and edges, and that is non-trivial for bipartite graphs, the problem #IndSub(Phi) is #W[1]-hard and cannot be solved in time f(k)* n^{o(k)} for any computable function f, unless the Exponential Time Hypothesis fails. This holds true even if the input graph is restricted to be bipartite and counting is done modulo a fixed prime. A similar result is shown for properties that are closed under the removal of edges only.

Cite as

Julian Dörfler, Marc Roth, Johannes Schmitt, and Philip Wellnitz. Counting Induced Subgraphs: An Algebraic Approach to #W[1]-hardness. In 44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019). Leibniz International Proceedings in Informatics (LIPIcs), Volume 138, pp. 26:1-26:14, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2019)


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@InProceedings{dorfler_et_al:LIPIcs.MFCS.2019.26,
  author =	{D\"{o}rfler, Julian and Roth, Marc and Schmitt, Johannes and Wellnitz, Philip},
  title =	{{Counting Induced Subgraphs: An Algebraic Approach to #W\lbrack1\rbrack-hardness}},
  booktitle =	{44th International Symposium on Mathematical Foundations of Computer Science (MFCS 2019)},
  pages =	{26:1--26:14},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-117-7},
  ISSN =	{1868-8969},
  year =	{2019},
  volume =	{138},
  editor =	{Rossmanith, Peter and Heggernes, Pinar and Katoen, Joost-Pieter},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.MFCS.2019.26},
  URN =		{urn:nbn:de:0030-drops-109703},
  doi =		{10.4230/LIPIcs.MFCS.2019.26},
  annote =	{Keywords: counting complexity, edge-transitive graphs, graph homomorphisms, induced subgraphs, parameterized complexity}
}
Document
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}
}
Document
Finding Even Subgraphs Even Faster

Authors: Prachi Goyal, Pranabendu Misra, Fahad Panolan, Geevarghese Philip, and Saket Saurabh

Published in: LIPIcs, Volume 45, 35th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2015)


Abstract
Problems of the following kind have been the focus of much recent research in the realm of parameterized complexity: Given an input graph (digraph) on n vertices and a positive integer parameter k, find if there exist k edges(arcs) whose deletion results in a graph that satisfies some specified parity constraints. In particular, when the objective is to obtain a connected graph in which all the vertices have even degrees--where the resulting graph is Eulerian,the problem is called Undirected Eulerian Edge Deletion. The corresponding problem in digraphs where the resulting graph should be strongly connected and every vertex should have the same in-degree as its out-degree is called Directed Eulerian Edge Deletion. Cygan et al.[Algorithmica, 2014] showed that these problems are fixed parameter tractable (FPT), and gave algorithms with the running time 2^O(k log k)n^O(1). They also asked, as an open problem, whether there exist FPT algorithms which solve these problems in time 2^O(k)n^O(1). It was also posed as an open problem at the School on Parameterized Algorithms and Complexity 2014, Bedlewo, Poland. In this paper we answer their question in the affirmative: using the technique of computing representative families of co-graphic matroids we design algorithms which solve these problems in time 2^O(k)n^O(1). The crucial insight we bring to these problems is to view the solution as an independent set of a co-graphic matroid. We believe that this view-point/approach will be useful in other problems where one of the constraints that need to be satisfied is that of connectivity.

Cite as

Prachi Goyal, Pranabendu Misra, Fahad Panolan, Geevarghese Philip, and Saket Saurabh. Finding Even Subgraphs Even Faster. In 35th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2015). Leibniz International Proceedings in Informatics (LIPIcs), Volume 45, pp. 434-447, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2015)


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@InProceedings{goyal_et_al:LIPIcs.FSTTCS.2015.434,
  author =	{Goyal, Prachi and Misra, Pranabendu and Panolan, Fahad and Philip, Geevarghese and Saurabh, Saket},
  title =	{{Finding Even Subgraphs Even Faster}},
  booktitle =	{35th IARCS Annual Conference on Foundations of Software Technology and Theoretical Computer Science (FSTTCS 2015)},
  pages =	{434--447},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-97-2},
  ISSN =	{1868-8969},
  year =	{2015},
  volume =	{45},
  editor =	{Harsha, Prahladh and Ramalingam, G.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2015.434},
  URN =		{urn:nbn:de:0030-drops-56336},
  doi =		{10.4230/LIPIcs.FSTTCS.2015.434},
  annote =	{Keywords: Eulerian Edge Deletion, FPT, Representative Family.}
}
Document
Editing to Eulerian Graphs

Authors: Konrad K. Dabrowski, Petr A. Golovach, Pim van 't Hof, and Daniel Paulusma

Published in: LIPIcs, Volume 29, 34th International Conference on Foundation of Software Technology and Theoretical Computer Science (FSTTCS 2014)


Abstract
We investigate the problem of modifying a graph into a connected graph in which the degree of each vertex satisfies a prescribed parity constraint. Let ea, ed and vd denote the operations edge addition, edge deletion and vertex deletion respectively. For any S subseteq {ea,ed,vd}, we define Connected Degree Parity Editing (S) (CDPE(S)) to be the problem that takes as input a graph G, an integer k and a function delta: V(G) -> {0,1}, and asks whether G can be modified into a connected graph H with d_H(v) = delta(v)(mod 2) for each v in V(H), using at most k operations from S. We prove that (*) if S={ea} or S={ea,ed}, then CDPE(S) can be solved in polynomial time; (*) if {vd} subseteq S subseteq {ea,ed,vd}, then CDPE(S) is NP-complete and W-hard when parameterized by k, even if delta = 0. Together with known results by Cai and Yang and by Cygan, Marx, Pilipczuk, Pilipczuk and Schlotter, our results completely classify the classical and parameterized complexity of the CDPE(S) problem for all S subseteq {ea,ed,vd}. We obtain the same classification for a natural variant of the cdpe(S) problem on directed graphs, where the target is a weakly connected digraph in which the difference between the in- and out-degree of every vertex equals a prescribed value. As an important implication of our results, we obtain polynomial-time algorithms for Eulerian Editing problem and its directed variant. To the best of our knowledge, the only other natural non-trivial graph class H for which the H-Editing problem is known to be polynomial-time solvable is the class of split graphs.

Cite as

Konrad K. Dabrowski, Petr A. Golovach, Pim van 't Hof, and Daniel Paulusma. Editing to Eulerian Graphs. In 34th International Conference on Foundation of Software Technology and Theoretical Computer Science (FSTTCS 2014). Leibniz International Proceedings in Informatics (LIPIcs), Volume 29, pp. 97-108, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2014)


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@InProceedings{dabrowski_et_al:LIPIcs.FSTTCS.2014.97,
  author =	{Dabrowski, Konrad K. and Golovach, Petr A. and van 't Hof, Pim and Paulusma, Daniel},
  title =	{{Editing to Eulerian Graphs}},
  booktitle =	{34th International Conference on Foundation of Software Technology and Theoretical Computer Science (FSTTCS 2014)},
  pages =	{97--108},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-939897-77-4},
  ISSN =	{1868-8969},
  year =	{2014},
  volume =	{29},
  editor =	{Raman, Venkatesh and Suresh, S. P.},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.FSTTCS.2014.97},
  URN =		{urn:nbn:de:0030-drops-48356},
  doi =		{10.4230/LIPIcs.FSTTCS.2014.97},
  annote =	{Keywords: Eulerian graphs, graph editing, polynomial algorithm}
}
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