A Molecular Computing Model for Maximum Independent Set Based on Origami and Greedy Algorithm

2014 ◽  
Vol 11 (8) ◽  
pp. 1773-1778 ◽  
Author(s):  
Wang Xixu ◽  
Li Jing ◽  
Song Zhichao ◽  
Jing Yang ◽  
Cheng Zhang ◽  
...  
2013 ◽  
Vol 690-693 ◽  
pp. 445-449
Author(s):  
Jing Yang ◽  
Cheng Zhang ◽  
Hao Wang

With the progress of DNA computing and nanotechnology, DNA/AuNP conjugation becomes an emerging interdisciplinary field. In this paper, a novel DNA computing model based on DNA/AuNP conjugation is developed to solve a maximum independent set problem (MIS). Making use of the hybridization between long DNA strands and short strands conjugated with gold nanoparticles, a series of searching process is implemented. After that, based on the number of DNA/AuNP conjugation on one DNA strand, the answer of the MIS is obtained. To verify the proposed algorithm, a simple paradigm is calculated by using the DNA computing model. In this model, there are some significant advantages such as easy detecting, and controllable automation. This work may demonstrate that DNA computing has the great potentiality in huge parallelism computation.


2011 ◽  
Vol 328-330 ◽  
pp. 1729-1733
Author(s):  
Yan Yang ◽  
Zhi Xiang Yin

About thirty years ago, the concept of the complexity of the problem was proposed. The most important complex class is P and NP class. Fruitful results of this concept are the existence of the so-called complex class complete problem. If the other issues of this class once solved in polynomial time, then the problem must exist polynomial time algorithms. Therefore, the complete problem is most difficult to solve, but because of their presence, we can choose any of them improved algorithm for a problem, so this kind of problem to get a good solution. DNA computing is a novel method that solving a class of intractable computational problems, in which the computing speeds up exponentially with the problem size. Up to now, many accomplishments have been made to improve its performance and increase its reliability. Maximum Independent Set problem (MIS) is a well-known NP-complete problem. Maximum Clique and Minimum Vertex Covering problem is equivalent to Maximum Independent Set problem. In this paper, we explore solving Maximum Independent Set problem by transforming it into equivalent 0-1 programming problem, and utilizing the surface computing model of that. The proposed method demonstrates universal nature of NP-complete problem.


2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yaoxin Li ◽  
Jing Liu ◽  
Guozheng Lin ◽  
Yueyuan Hou ◽  
Muyun Mou ◽  
...  

AbstractIn computer science, there exist a large number of optimization problems defined on graphs, that is to find a best node state configuration or a network structure, such that the designed objective function is optimized under some constraints. However, these problems are notorious for their hardness to solve, because most of them are NP-hard or NP-complete. Although traditional general methods such as simulated annealing (SA), genetic algorithms (GA), and so forth have been devised to these hard problems, their accuracy and time consumption are not satisfying in practice. In this work, we proposed a simple, fast, and general algorithm framework based on advanced automatic differentiation technique empowered by deep learning frameworks. By introducing Gumbel-softmax technique, we can optimize the objective function directly by gradient descent algorithm regardless of the discrete nature of variables. We also introduce evolution strategy to parallel version of our algorithm. We test our algorithm on four representative optimization problems on graph including modularity optimization from network science, Sherrington–Kirkpatrick (SK) model from statistical physics, maximum independent set (MIS) and minimum vertex cover (MVC) problem from combinatorial optimization on graph, and Influence Maximization problem from computational social science. High-quality solutions can be obtained with much less time-consuming compared to the traditional approaches.


1977 ◽  
Vol 6 (3) ◽  
pp. 537-546 ◽  
Author(s):  
Robert Endre Tarjan ◽  
Anthony E. Trojanowski

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