scholarly journals Minimal controllability of conjunctive Boolean networks is NP-complete

Automatica ◽  
2018 ◽  
Vol 92 ◽  
pp. 56-62 ◽  
Author(s):  
Eyal Weiss ◽  
Michael Margaliot ◽  
Guy Even
Keyword(s):  
Boolean Networks ◽  
Np Complete

scholarly journals A Novel Algorithm for the Maximal Fit Problem in Boolean Networks

2016 ◽  
Author(s):  
Guy Karlebach
Keyword(s):  
Time Series ◽  
Regulatory Networks ◽  
Time Series Data ◽  
Boolean Networks ◽  
Large Datasets ◽  
Series Data ◽  
Np Complete ◽  
Regulation Functions ◽  
Regulatory Controls ◽  
Novel Algorithm

AbstractGene regulatory networks (GRNs) are increasingly used for explaining biological processes with complex transcriptional regulation. A GRN links the expression levels of a set of genes via regulatory controls that gene products exert on one another. Boolean networks are a common modeling choice since they balance between detail and ease of analysis. However, even for Boolean networks the problem of fitting a given network model to an expression dataset is NP-Complete. Previous methods have addressed this issue heuristically or by focusing on acyclic networks and specific classes of regulation functions. In this paper we introduce a novel algorithm for this problem that makes use of sampling in order to handle large datasets. Our algorithm can handle time series data for any network type and steady state data for acyclic networks. Using in-silico time series data we demonstrate good performance on large datasets with a significant level of noise.

Algorithmic and Stochastic Representations of Gene Regulatory Networks and Protein-Protein Interactions

2019 ◽  
Vol 19 (6) ◽  
pp. 413-425 ◽  
Author(s):  
Athanasios Alexiou ◽  
Stylianos Chatzichronis ◽  
Asma Perveen ◽  
Abdul Hafeez ◽  
Ghulam Md. Ashraf
Keyword(s):  
Protein Interactions ◽  
Biological Networks ◽  
Regulatory Networks ◽  
Review Paper ◽  
Boolean Networks ◽  
Diagnostic Tools ◽  
Complex Nature ◽  
Cellular Interactions ◽  
Protein Protein Interactions ◽  
Deterministic Models

Background:Latest studies reveal the importance of Protein-Protein interactions on physiologic functions and biological structures. Several stochastic and algorithmic methods have been published until now, for the modeling of the complex nature of the biological systems.Objective:Biological Networks computational modeling is still a challenging task. The formulation of the complex cellular interactions is a research field of great interest. In this review paper, several computational methods for the modeling of GRN and PPI are presented analytically.Methods:Several well-known GRN and PPI models are presented and discussed in this review study such as: Graphs representation, Boolean Networks, Generalized Logical Networks, Bayesian Networks, Relevance Networks, Graphical Gaussian models, Weight Matrices, Reverse Engineering Approach, Evolutionary Algorithms, Forward Modeling Approach, Deterministic models, Static models, Hybrid models, Stochastic models, Petri Nets, BioAmbients calculus and Differential Equations.Results:GRN and PPI methods have been already applied in various clinical processes with potential positive results, establishing promising diagnostic tools.Conclusion:In literature many stochastic algorithms are focused in the simulation, analysis and visualization of the various biological networks and their dynamics interactions, which are referred and described in depth in this review paper.

scholarly journals Discovering the maximum k-clique on social networks using bat optimization algorithm

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Akram Khodadadi ◽  
Shahram Saeidi
Keyword(s):  
Genetic Algorithm ◽  
Social Networks ◽  
Social Network ◽  
Coding Theory ◽  
Evaluation Criteria ◽  
Convergence Speed ◽  
Optimization Approach ◽  
Computational Results ◽  
Complete Subgraph ◽  
Np Complete

AbstractThe k-clique problem is identifying the largest complete subgraph of size k on a network, and it has many applications in Social Network Analysis (SNA), coding theory, geometry, etc. Due to the NP-Complete nature of the problem, the meta-heuristic approaches have raised the interest of the researchers and some algorithms are developed. In this paper, a new algorithm based on the Bat optimization approach is developed for finding the maximum k-clique on a social network to increase the convergence speed and evaluation criteria such as Precision, Recall, and F1-score. The proposed algorithm is simulated in Matlab® software over Dolphin social network and DIMACS dataset for k = 3, 4, 5. The computational results show that the convergence speed on the former dataset is increased in comparison with the Genetic Algorithm (GA) and Ant Colony Optimization (ACO) approaches. Besides, the evaluation criteria are also modified on the latter dataset and the F1-score is obtained as 100% for k = 5.

scholarly journals Popular Matching in Roommates Setting Is NP-hard

2021 ◽  
Vol 13 (2) ◽  
pp. 1-20
Author(s):  
Sushmita Gupta ◽  
Pranabendu Misra ◽  
Saket Saurabh ◽  
Meirav Zehavi
Keyword(s):  
Computational Complexity ◽  
Np Hard ◽  
Np Complete ◽  
Open Question ◽  
Popular Matching

An input to the P OPULAR M ATCHING problem, in the roommates setting (as opposed to the marriage setting), consists of a graph G (not necessarily bipartite) where each vertex ranks its neighbors in strict order, known as its preference. In the P OPULAR M ATCHING problem the objective is to test whether there exists a matching M * such that there is no matching M where more vertices prefer their matched status in M (in terms of their preferences) over their matched status in M *. In this article, we settle the computational complexity of the P OPULAR M ATCHING problem in the roommates setting by showing that the problem is NP-complete. Thus, we resolve an open question that has been repeatedly and explicitly asked over the last decade.

scholarly journals Shellability is NP-complete

2019 ◽  
Vol 66 (3) ◽  
pp. 1-18
Author(s):  
Xavier Goaoc ◽  
Pavel Paták ◽  
Zuzana Patáková ◽  
Martin Tancer ◽  
Uli Wagner
Keyword(s):  
Np Complete

scholarly journals Total Roman {3}-Domination: The Complexity and Linear-Time Algorithm for Trees

Mathematics ◽  
2021 ◽  
Vol 9 (3) ◽  
pp. 293
Author(s):  
Xinyue Liu ◽  
Huiqin Jiang ◽  
Pu Wu ◽  
Zehui Shao
Keyword(s):  
Linear Time ◽  
Minimum Weight ◽  
Domination Number ◽  
Time Algorithm ◽  
Simple Graph ◽  
Linear Time Algorithm ◽  
Domination Problem ◽  
Np Complete ◽  
Chordal Bipartite Graphs ◽  
Dominating Function

For a simple graph G=(V,E) with no isolated vertices, a total Roman {3}-dominating function(TR3DF) on G is a function f:V(G)→{0,1,2,3} having the property that (i) ∑w∈N(v)f(w)≥3 if f(v)=0; (ii) ∑w∈N(v)f(w)≥2 if f(v)=1; and (iii) every vertex v with f(v)≠0 has a neighbor u with f(u)≠0 for every vertex v∈V(G). The weight of a TR3DF f is the sum f(V)=∑v∈V(G)f(v) and the minimum weight of a total Roman {3}-dominating function on G is called the total Roman {3}-domination number denoted by γt{R3}(G). In this paper, we show that the total Roman {3}-domination problem is NP-complete for planar graphs and chordal bipartite graphs. Finally, we present a linear-time algorithm to compute the value of γt{R3} for trees.

Optimal output tracking of switched Boolean networks

2021 ◽  
Author(s):  
Yuzhi Chen ◽  
Pengfei Sun ◽  
Tao Sun ◽  
Madini O. Alassafi ◽  
Adil M. Ahmad
Keyword(s):  
Boolean Networks ◽  
Output Tracking ◽  
Optimal Output
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