scholarly journals Using graph models to find transcription factor modules: the hitting set problem and an exact algorithm

2013 ◽  
Vol 8 (1) ◽  
Author(s):  
Songjian Lu ◽  
Xinghua Lu
Keyword(s):  
Transcription Factor ◽  
Exact Algorithm ◽  
Graph Models ◽  
Hitting Set ◽  
Hitting Set Problem

scholarly journals A Hybrid CPU-GPU-MIC Algorithm for the Hitting Set Problem

2017 ◽  
Author(s):  
Danilo Carastan-Santos ◽  
David C. Martins-Jr ◽  
Luiz C. S. Rozante ◽  
Siang W. Song ◽  
Raphael Y. de Camargo
Keyword(s):  
Load Balancing ◽  
High Performance Computing ◽  
High Performance ◽  
Exact Algorithm ◽  
Communication Cost ◽  
Heterogeneous Clusters ◽  
Hitting Set ◽  
Reasonable Time ◽  
Performance Computing ◽  
Hitting Set Problem

We present a hybrid exact algorithm for the Hitting Set Problem (HSP) for highly heterogeneous CPU-GPU-MIC platforms. With several techniques that permit an efficient exploitation of each architecture, low communication cost and effective load balancing, we were able to solve large HSP instances in reasonable time, achieving good performance and scalability. We obtained speedups of up to 25.32 in comparison with using two six-core CPUs and exact HSP solutions for instances with tens of thousands of variables in less than 5 hours. These results reinforce the statement that heterogeneous clusters of CPUs, GPUs and MICs can be used efficiently for high-performance computing.

scholarly journals AN IMPLICIT COVER PROBLEM IN WILD POPULATION STUDY

2010 ◽  
Vol 02 (01) ◽  
pp. 21-31 ◽  
Author(s):  
MARY V. ASHLEY ◽  
TANYA Y. BERGER-WOLF ◽  
WANPRACHA CHAOVALITWONGSE ◽  
BHASKAR DASGUPTA ◽  
ASHFAQ KHOKHAR ◽  
...  
Keyword(s):  
Optimization Problem ◽  
Wild Population ◽  
Combinatorial Optimization Problem ◽  
Set Cover ◽  
Not Given ◽  
Wild Populations ◽  
Feedback Arc Set ◽  
Hitting Set ◽  
Cover Problem ◽  
Hitting Set Problem

In an implicit combinatorial optimization problem, the constraints are not enumerated explicitly but rather stated implicitly through equations, other constraints or auxiliary algorithms. An important subclass of such problems is the implicit set cover (or, equivalently, hitting set) problem in which the sets are not given explicitly but rather defined implicitly. For example, the well-known minimum feedback arc set problem is such a problem. In this paper, we consider such a cover problem that arises in the study of wild populations in biology in which the sets are defined implicitly via the Mendelian constraints and prove approximability results for this problem.

scholarly journals A randomised approximation algorithm for the hitting set problem

2014 ◽  
Vol 555 ◽  
pp. 23-34 ◽  
Author(s):  
Mourad El Ouali ◽  
Helena Fohlin ◽  
Anand Srivastav
Keyword(s):  
Approximation Algorithm ◽  
Hitting Set ◽  
Hitting Set Problem
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