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Register a new userOn Analysis and Generation of some Biologically Important Boolean Functions
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Camellia Ray
Publication date
2014
fields
Informatics Engineering
and research's language is
English
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Boolean networks are used to model biological networks such as gene regulatory networks. Often Boolean networks show very chaotic behaviour which is sensitive to any small perturbations. In order to reduce the chaotic behaviour and to attain stability in the gene regulatory network, nested Canalizing Functions (NCFs) are best suited. NCFs and its variants have a wide range of applications in systems biology. Previously, many works were done on the application of canalizing functions, but there were fewer methods to check if any arbitrary Boolean function is canalizing or not. In this paper, by using Karnaugh Map this problem is solved and also it has been shown that when the canalizing functions of variable is given, all the canalizing functions of variable could be generated by the method of concatenation. In this paper we have uniquely identified the number of NCFs having a particular Hamming Distance (H.D) generated by each variable as starting canalizing input. Partially NCFs of 4 variables has also been studied in this paper.
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Boolean networks are used to model biological networks such as gene regulatory networks. Often Boolean networks show very chaotic behavior which is sensitive to any small perturbations.In order to reduce the chaotic behavior and to attain stability in the gene regulatory network,nested canalizing functions(NCF)are best suited NCF and its variants have a wide range of applications in system biology. Previously many work were done on the application of canalizing functions but there were fewer methods to check if any arbitrary Boolean function is canalizing or not. In this paper, by using Karnaugh Map this problem gas been solved and also it has been shown that when the canalizing functions of n variable is given, all the canalizing functions of n+1 variable could be generated by the method of concatenation. In this paper we have uniquely identified the number of NCFs having a particular hamming distance (H.D) generated by each variable x as starting canalizing input. Partially nested canalizing functions of 4 variables have also been studied in this paper. Keywords: Karnaugh Map, Canalizing function, Nested canalizing function, Partially nested canalizing function,concatenation
Interaction graphs provide an important qualitative modeling approach for System Biology. This paper presents a novel approach for construction of interaction graph with the help of Boolean function decomposition. Each decomposition part (Consisting of 2-bits) of the Boolean functions has some important significance. In the dynamics of a biological system, each variable or node is nothing but gene or protein. Their regulation has been explored in terms of interaction graphs which are generated by Boolean functions. In this paper, different classes of Boolean functions with regards to Interaction Graph with biologically significant properties have been adumbrated.
The subject of this textbook is the analysis of Boolean functions. Roughly speaking, this refers to studying Boolean functions $f : {0,1}^n to {0,1}$ via their Fourier expansion and other analytic means. Boolean functions are perhaps the most basic object of study in theoretical computer science, and Fourier analysis has become an indispensable tool in the field. The topic has also played a key role in several other areas of mathematics, from combinatorics, random graph theory, and statistical physics, to Gaussian geometry, metric/Banach spaces, and social choice theory. The intent of this book is both to develop the foundations of the field and to give a wide (though far from exhaustive) overview of its applications. Each chapter ends with a highlight showing the power of analysis of Boolean functions in different subject areas: property testing, social choice, cryptography, circuit complexity, learning theory, pseudorandomness, hardness of approximation, concrete complexity, and random graph theory. The book can be used as a reference for working researchers or as the basis of a one-semester graduate-level course. The author has twice taught such a course at Carnegie Mellon University, attended mainly by graduate students in computer science and mathematics but also by advanced undergraduates, postdocs, and researchers in adjacent fields. In both years most of Chapters 1-5 and 7 were covered, along with parts of Chapters 6, 8, 9, and 11, and some additional material on additive combinatorics. Nearly 500 exercises are provided at the ends of the books chapters.
Observabililty is an important topic of Boolean control networks (BCNs). In this paper, we propose a new type of observability named online observability to present the sufficient and necessary condition of determining the initial states of BCNs, when their initial states cannot be reset. And we design an algorithm to decide whether a BCN has the online observability. Moreover, we prove that a BCN is identifiable iff it satisfies controllability and the online observability, which reveals the essence of identification problem of BCNs.
We initiate the study of Boolean function analysis on high-dimensional expanders. We give a random-walk based definition of high dimensional expansion, which coincides with the earlier definition in terms of two-sided link expanders. Using this definition, we describe an analogue of the Fourier expansion and the Fourier levels of the Boolean hypercube for simplicial complexes. Our analogue is a decomposition into approximate eigenspaces of random walks associated with the simplicial complexes. We then use this decomposition to extend the Friedgut-Kalai-Naor theorem to high-dimensional expanders. Our results demonstrate that a high-dimensional expander can sometimes serve as a sparse model for the Boolean slice or hypercube, and quite possibly additional results from Boolean function analysis can be carried over to this sparse model. Therefore, this model can be viewed as a derandomization of the Boolean slice, containing only $|X(k-1)|=O(n)$ points in contrast to $binom{n}{k}$ points in the $(k)$-slice (which consists of all $n$-bit strings with exactly $k$ ones). Our random-walk definition and the decomposition has the additional advantage that they extend to the more general setting of posets, which include both high-dimensional expanders and the Grassmann poset, which appears in recent works on the unique games conjecture.
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