scholarly journals A polynomial time equivalence between DNA sequencing and the exact perfect matching problem

2007 ◽  
Vol 4 (2) ◽  
pp. 154-162 ◽  
Author(s):  
Jacek Błażewicz ◽  
Piotr Formanowicz ◽  
Marta Kasprzak ◽  
Petra Schuurman ◽  
Gerhard J. Woeginger
2010 ◽  
Vol 21 (06) ◽  
pp. 905-924 ◽  
Author(s):  
MAREK KARPIŃSKI ◽  
ANDRZEJ RUCIŃSKI ◽  
EDYTA SZYMAŃSKA

In this paper we consider the computational complexity of deciding the existence of a perfect matching in certain classes of dense k-uniform hypergraphs. It has been known that the perfect matching problem for the classes of hypergraphs H with minimum ((k - 1)–wise) vertex degreeδ(H) at least c|V(H)| is NP-complete for [Formula: see text] and trivial for c ≥ ½, leaving the status of the problem with c in the interval [Formula: see text] widely open. In this paper we show, somehow surprisingly, that ½ is not the threshold for tractability of the perfect matching problem, and prove the existence of an ε > 0 such that the perfect matching problem for the class of hypergraphs H with δ(H) ≥ (½ - ε)|V(H)| is solvable in polynomial time. This seems to be the first polynomial time algorithm for the perfect matching problem on hypergraphs for which the existence problem is nontrivial. In addition, we consider parallel complexity of the problem, which could be also of independent interest.


Author(s):  
Jacek Błażewicz ◽  
Piotr Formanowicz ◽  
Marta Kasprzak ◽  
Petra Schuurman ◽  
Gerhard J. Woeginger

2021 ◽  
Vol 2 (2) ◽  
Author(s):  
Daniel Vert ◽  
Renaud Sirdey ◽  
Stéphane Louise

AbstractThis paper experimentally investigates the behavior of analog quantum computers as commercialized by D-Wave when confronted to instances of the maximum cardinality matching problem which is specifically designed to be hard to solve by means of simulated annealing. We benchmark a D-Wave “Washington” (2X) with 1098 operational qubits on various sizes of such instances and observe that for all but the most trivially small of these it fails to obtain an optimal solution. Thus, our results suggest that quantum annealing, at least as implemented in a D-Wave device, falls in the same pitfalls as simulated annealing and hence provides additional evidences suggesting that there exist polynomial-time problems that such a machine cannot solve efficiently to optimality. Additionally, we investigate the extent to which the qubits interconnection topologies explains these latter experimental results. In particular, we provide evidences that the sparsity of these topologies which, as such, lead to QUBO problems of artificially inflated sizes can partly explain the aforementioned disappointing observations. Therefore, this paper hints that denser interconnection topologies are necessary to unleash the potential of the quantum annealing approach.


10.37236/3540 ◽  
2014 ◽  
Vol 21 (4) ◽  
Author(s):  
Dong Ye ◽  
Heping Zhang

A graph $G$ with a perfect matching is Pfaffian if it admits an orientation $D$ such that every central cycle $C$ (i.e. $C$ is of even size and $G-V(C)$ has a perfect matching) has an odd number of edges oriented in either direction of the cycle. It is known that the number of perfect matchings of a Pfaffian graph can be computed in polynomial time. In this paper, we show that every embedding of a Pfaffian brace (i.e. 2-extendable bipartite graph)  on a surface with a positive genus has face-width at most 3.  Further, we study Pfaffian cubic braces and obtain a characterization of Pfaffian polyhex graphs: a polyhex graph is Pfaffian if and only if it is either non-bipartite or isomorphic to the cube, or the Heawood graph, or the Cartesian product $C_k\times K_2$ for even integers $k\ge 6$.


2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Jakub Tarnawski

Abstract This article gives a short overview of my dissertation, where new algorithms are given for two fundamental graph problems. We develop novel ways of using linear programming formulations, even exponential-sized ones, to extract structure from problem instances and to guide algorithms in making progress. The first part of the dissertation addresses a benchmark problem in combinatorial optimization: the asymmetric traveling salesman problem (ATSP). It consists in finding the shortest tour that visits all vertices of a given edge-weighted directed graph. A ρ-approximation algorithm for ATSP is one that runs in polynomial time and always produces a tour at most ρ times longer than the shortest tour. Finding such an algorithm with constant ρ had been a long-standing open problem. Here we give such an algorithm. The second part of the dissertation addresses the perfect matching problem. We have known since the 1980s that it has efficient parallel algorithms if the use of randomness is allowed. However, we do not know if randomness is necessary – that is, whether the matching problem is in the class NC. We show that it is in the class quasi-NC. That is, we give a deterministic parallel algorithm that runs in poly-logarithmic time on quasi-polynomially many processors.


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