A 2-approximation algorithm for the contig-based genomic scaffold filling problem

2018 ◽  
Vol 16 (06) ◽  
pp. 1850022 ◽  
Author(s):  
Haitao Jiang ◽  
Letu Qingge ◽  
Daming Zhu ◽  
Binhai Zhu
Keyword(s):  
Approximation Algorithm ◽  
Reference Genome ◽  
Constant Factor ◽  
Important Case ◽  
Completeness Proof ◽  
Np Completeness ◽  
Genomic Scaffold ◽  
Np Complete ◽  
Filling Problem ◽  
Input Formula

The genomic scaffold filling problem has attracted a lot of attention recently. The problem is on filling an incomplete sequence (scaffold) [Formula: see text] into [Formula: see text], with respect to a complete reference genome [Formula: see text], such that the number of common/shared adjacencies between [Formula: see text] and [Formula: see text] is maximized. The problem is NP-complete, and admits a constant-factor approximation. However, the sequence input [Formula: see text] is not quite practical and does not fit most of the real datasets (where a scaffold is more often given as a list of contigs). In this paper, we revisit the genomic scaffold filling problem by considering this important case when a scaffold [Formula: see text] is given, the missing genes can only be inserted in between the contigs, and the objective is to maximize the number of common adjacencies between [Formula: see text] and the filled genome [Formula: see text]. For this problem, we present a simple NP-completeness proof, we then present a factor-2 approximation algorithm.

scholarly journals Constant factor approximation algorithm for TSP satisfying a biased triangle inequality

2017 ◽  
Vol 657 ◽  
pp. 111-126 ◽  
Author(s):  
Usha Mohan ◽  
Sivaramakrishnan Ramani ◽  
Sounaka Mishra
Keyword(s):  
Approximation Algorithm ◽  
Triangle Inequality ◽  
Constant Factor

scholarly journals A note on compact and compact circular edge-colorings of graphs

2008 ◽  
Vol Vol. 10 no. 3 (Graph and Algorithms) ◽  
Author(s):  
Dariusz Dereniowski ◽  
Adam Nadolski
Keyword(s):  
Approximation Algorithm ◽  
Decision Problem ◽  
Edge Coloring ◽  
Exact Algorithm ◽  
Weighted Graphs ◽  
Edge Colorings ◽  
Odd Cycle ◽  
International Audience ◽  
Np Complete ◽  
Odd Cycles

Graphs and Algorithms International audience We study two variants of edge-coloring of edge-weighted graphs, namely compact edge-coloring and circular compact edge-coloring. First, we discuss relations between these two coloring models. We prove that every outerplanar bipartite graph admits a compact edge-coloring and that the decision problem of the existence of compact circular edge-coloring is NP-complete in general. Then we provide a polynomial time 1:5-approximation algorithm and pseudo-polynomial exact algorithm for compact circular coloring of odd cycles and prove that it is NP-hard to optimally color these graphs. Finally, we prove that if a path P2 is joined by an edge to an odd cycle then the problem of the existence of a compact circular coloring becomes NP-complete.

scholarly journals Randomized heuristic for the maximum clique problem

2020 ◽  
Author(s):  
Shalin Shah
Keyword(s):  
Approximation Algorithm ◽  
Randomized Algorithm ◽  
Maximum Clique ◽  
Constant Factor ◽  
Maximum Clique Problem ◽  
Hard Problem ◽  
Np Hard ◽  
Np Hard Problem ◽  
Java Code ◽  
Clique Problem

<p>A clique in a graph is a set of vertices that are all directly connected</p><p>to each other i.e. a complete sub-graph. A clique of the largest size is</p><p>called a maximum clique. Finding the maximum clique in a graph is an</p><p>NP-hard problem and it cannot be solved by an approximation algorithm</p><p>that returns a solution within a constant factor of the optimum. In this</p><p>work, we present a simple and very fast randomized algorithm for the</p><p>maximum clique problem. We also provide Java code of the algorithm</p><p>in our git repository. Results show that the algorithm is able to find</p><p>reasonably good solutions to some randomly chosen DIMACS benchmark</p><p>graphs. Rather than aiming for optimality, we aim to find good solutions</p><p>very fast.</p>

scholarly journals Randomized heuristic for the maximum clique problem

2020 ◽  
Author(s):  
Shalin Shah
Keyword(s):  
Approximation Algorithm ◽  
Randomized Algorithm ◽  
Maximum Clique ◽  
Constant Factor ◽  
Maximum Clique Problem ◽  
Hard Problem ◽  
Np Hard ◽  
Np Hard Problem ◽  
Java Code ◽  
Clique Problem

<p>A clique in a graph is a set of vertices that are all directly connected</p><p>to each other i.e. a complete sub-graph. A clique of the largest size is</p><p>called a maximum clique. Finding the maximum clique in a graph is an</p><p>NP-hard problem and it cannot be solved by an approximation algorithm</p><p>that returns a solution within a constant factor of the optimum. In this</p><p>work, we present a simple and very fast randomized algorithm for the</p><p>maximum clique problem. We also provide Java code of the algorithm</p><p>in our git repository. Results show that the algorithm is able to find</p><p>reasonably good solutions to some randomly chosen DIMACS benchmark</p><p>graphs. Rather than aiming for optimality, we aim to find good solutions</p><p>very fast.</p>

scholarly journals FOLDING EQUILATERAL PLANE GRAPHS

2013 ◽  
Vol 23 (02) ◽  
pp. 75-92 ◽  
Author(s):  
ZACHARY ABEL ◽  
ERIK D. DEMAINE ◽  
MARTIN L. DEMAINE ◽  
SARAH EISENSTAT ◽  
JAYSON LYNCH ◽  
...  
Keyword(s):  
Plane Graph ◽  
Analogous Problem ◽  
Central Vertex ◽  
Polyhedral Complex ◽  
Plane Graphs ◽  
Single Vertex ◽  
Np Completeness ◽  
Np Complete ◽  
Polyhedral Manifold

We consider two types of folding applied to equilateral plane graph linkages. First, under continuous folding motions, we show how to reconfigure any linear equilateral tree (lying on a line) into a canonical configuration. By contrast, it is known that such reconfiguration is not always possible for linear (nonequilateral) trees and for (nonlinear) equilateral trees. Second, under instantaneous folding motions, we show that an equilateral plane graph has a noncrossing linear folded state if and only if it is bipartite. Furthermore, we show that the equilateral constraint is necessary for this result, by proving that it is strongly NP-complete to decide whether a (nonequilateral) plane graph has a linear folded state. Equivalently, we show strong NP-completeness of deciding whether an abstract metric polyhedral complex with one central vertex has a noncrossing flat folded state. By contrast, the analogous problem for a polyhedral manifold with one central vertex (single-vertex origami) is only weakly NP-complete.

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