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Computing preimages of Boolean Networks [article]

Johannes Georg Klotz, Martin Bossert, Steffen Schober
2013 arXiv   pre-print
Finally, we evaluate our algorithm for random Boolean networks and the regulatory network of Escherichia coli.  ...  In this paper we present an algorithm to address the predecessor problem of feed-forward Boolean networks.  ...  INTRODUCTION In systems and computational biology Boolean networks (BN) are widely used to model regulative dependencies of organisms [1, 2] .  ... 
arXiv:1302.3723v1 fatcat:zmeuirmoufdq7alvm4hpo3kdua

Computing preimages of Boolean networks

Johannes Klotz, Martin Bossert, Steffen Schober
2013 BMC Bioinformatics  
In this paper we present an algorithm based on the sum-product algorithm that finds elements in the preimage of a feed-forward Boolean networks given an output of the network.  ...  We evaluate our algorithm for randomly constructed Boolean networks and a regulatory network of Escherichia coli and found that it gives a valid solution in most cases.  ...  Acknowledgements The authors would like to thank Shrief Rizkalla for implementing parts of the simulation. Declarations  ... 
doi:10.1186/1471-2105-14-s10-s4 pmid:24267277 pmcid:PMC3750533 fatcat:k3y3qgjmwfhypicpplfvverhue

Algorithms for computing preimages of cellular automata configurations

Iztok Jeras, Andrej Dobnikar
2007 Physica D : Non-linear phenomena  
The first algorithm traces paths in the preimage network and focuses on local knowledge of the network. The second performs a complete analysis of the network before proceeding with listing.  ...  The counting of preimages is performed as multiplication of topological matrices of de Bruijn diagrams. Listing of preimages is described using two algorithms.  ...  The preimage network is constructed from preimage diagrams of a string of cells. By definition of the preimage diagram, all links in the preimage network are locally valid.  ... 
doi:10.1016/j.physd.2007.06.003 fatcat:7343k5q3pzbt3nd7ynmkdn7fra

Algorithms for the Sequential Reprogramming of Boolean Networks

Hugues Mandon, Cui Su, Jun Pang, Soumya Paul, Stefan Haar, Loic Pauleve
2019 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
Most of the existing computational methods for controlling which attractor (steady state) the cell will reach focus on finding mutations to apply to the initial state.  ...  To identify such sequential perturbations, we consider a qualitative model of regulatory networks, and rely on Binary Decision Diagrams to model their dynamics and the putative perturbations.  ...  the program "Investissement d'Avenir" Idex Paris-Saclay (ANR-11-IDEX-0003-02); CNRS PEPS INS2I 2017 "FoRCe"; and by the project "SEC-PBN" funded by University of Luxembourg.  ... 
doi:10.1109/tcbb.2019.2914383 pmid:31056515 fatcat:gpxkcfonqbeqvoyfiqbaw5t3a4

Theory and practice of natural computing: seventh edition

Carlos Martín-Vide, Miguel A. Vega-Rodríguez
2021 Soft Computing - A Fusion of Foundations, Methodologies and Applications  
In the paper Characterization and Computation of Ancestors in Reaction Systems, Roberto Barbuti, Anna Bernasconi, Roberta Gori, and Paolo Milazzo tackle the computational complexity of preimages and nth  ...  Despite the intractability of many of the problems, the authors find a Boolean formula computable in polynomial time that, once duly simplified, allows solving ancestor problems for classes of reaction  ...  In the paper Characterization and Computation of Ancestors in Reaction Systems, Roberto Barbuti, Anna Bernasconi, Roberta Gori, and Paolo Milazzo tackle the computational complexity of preimages and nth  ... 
doi:10.1007/s00500-020-05526-y fatcat:kuonjlf5fjc3pghkql7dqefwle

Characterization and computation of ancestors in reaction systems

Roberto Barbuti, Anna Bernasconi, Roberta Gori, Paolo Milazzo
2020 Soft Computing - A Fusion of Foundations, Methodologies and Applications  
In this paper, we characterize all nth ancestors using a Boolean formula that can be computed in polynomial time.  ...  Many computational problems on preimages and ancestors, such as finding all minimum-cardinality nth ancestors, computing their size or counting them, are intractable.  ...  This study was funded by the University of Pisa (grant PRA 2017_44, project "Metodologie informatiche avanzate per l'analisi di dati biomedici").  ... 
doi:10.1007/s00500-020-05300-0 fatcat:nn5vumi3q5gmbm254qy7v3fvcy

An Efficient Algorithm for the Detection of Eden

David J. Warne, Ross F. Hayward, Neil A. Kelson, Dann G. Mallet
2013 Complex Systems  
The algorithm is based on our neighborhood elimination operation, which removes local neighborhood configurations that cannot be used in a preimage of the given configuration.  ...  In the case of time complexity, it is shown that the averagecase time complexity of the algorithm is QIn 2 M, and the best and worst cases are WHnL and OIn 3 M, respectively.  ...  This random wiring makes random Boolean networks useful for theoretical biological models of genetic regulatory networks [9,!10] .  ... 
doi:10.25088/complexsystems.22.4.377 fatcat:xwbkqaroevdbhhcqvq3yifbvxm

Page 2877 of Mathematical Reviews Vol. , Issue 2003d [page]

2003 Mathematical Reviews  
Processing huge data streams is important in fields like monitoring of network traffic, marketing, and others.  ...  Summary: “We define a variant of the H-coloring problem by fixing the number of preimages of a subset C of the vertices of H, thus allowing parameterization.  ... 

A New Decomposition Method for Attractor Detection in Large Synchronous Boolean Networks [chapter]

Andrzej Mizera, Jun Pang, Hongyang Qu, Qixia Yuan
2017 Lecture Notes in Computer Science  
Boolean networks is a well-established formalism for modelling biological systems. An important challenge for analysing a Boolean network is to identify all its attractors.  ...  This becomes challenging for large Boolean networks due to the well-known state-space explosion problem.  ...  Definition 1 (Boolean network).  ... 
doi:10.1007/978-3-319-69483-2_14 fatcat:ekt7tcq6kfdjxkk5lyu5ro2sfe

IoT Light Weight (LWT) Crypto Functions

Nubila Nabeel, Mohamed Hadi Habaebi, Nurul Arfah Che Mustapha, Md Rafiqul Islam
2019 International Journal of Interactive Mobile Technologies  
We are in the era of IoT and 5G technologies. IoT has wide range of applications in Smart Home, Smart cities, Agriculture, Health etc.  ...  In this paper, we compare different types of LW hash families in terms of their design and introduce the possibility of variable length hash function using Mersenne number based transform.  ...  The main difficulty with PH LW hash family is the dependence of the memory registers required for the computation.  ... 
doi:10.3991/ijim.v13i04.10524 fatcat:fdorjuoonbekjbnmsyiyvwerbe

Taming Asynchrony for Attractor Detection in Large Boolean Networks (Technical Report) [article]

Andrzej Mizera and Jun Pang and Hongyang Qu and Qixia Yuan
2017 arXiv   pre-print
We prove the correctness of our proposed method and demonstrate its efficiency with two real-life biological networks.  ...  Boolean networks is a well-established formalism for modelling biological systems. A vital challenge for analysing a Boolean network is to identify all the attractors.  ...  Definition 1 (Boolean network).  ... 
arXiv:1704.06530v3 fatcat:7xktngvm6zgvflsmtfuwphdezy

Generating Property-Directed Potential Invariants By Backward Analysis

Adrien Champion, Rémi Delmas, Michael Dierkes
2012 Electronic Proceedings in Theoretical Computer Science  
A backward analysis, powered by quantifier elimination, is used to output preimages of the negation of the proof objective, viewed as unauthorized states, or gray states.  ...  These heuristics can be used on the first preimage of the backward exploration, and each time a new one is output, refining the information on the gray states.  ...  We use Quantifier Elimination (QE [19, 22, 3] ) to compute successive preimages of the negation of the PO, in the spirit of [21, 10] .  ... 
doi:10.4204/eptcs.105.3 fatcat:cza4wymxcfbr3pl4boc752577i


Jarkko Kari
2017 Natural Computing  
The fifth paper, Activity in Boolean Networks, is by Abhijin Adiga, Hilton Galyean, Chris J. Kuhlman, Michael Levet, Henning S. Mortveit and Sichao Wu.  ...  The first paper, Computing the Periods of Preimages in Surjective Cellular Automata by Luca Mariot, Alberto Leporati, Alberto Dennunzio and Enrico Formenti, investigates the pre-images of spatially periodic  ... 
doi:10.1007/s11047-017-9615-4 fatcat:32c2ksyhtjcn7pcnsc25aptpaa

Translation of Algorithmic Descriptions of Discrete Functions to SAT with Applications to Cryptanalysis Problems

Alexander Semenov, Ilya Otpuschennikov, Irina Gribanova, Oleg Zaikin, Stepan Kochemazov
2018 Logical Methods in Computer Science  
We demonstrate the results of applications of Transalg to construction of a number of attacks on various cryptographic functions. Some of the corresponding attacks are state of the art.  ...  In~the theoretical part of the paper we justify the main principles of general reduction to SAT for discrete functions from a class containing the majority of functions employed in cryptography.  ...  We are grateful to anonymous reviewers for their valuable comments that made it possible to significantly improve the quality of the present paper.  ... 
doi:10.23638/lmcs-16(1:29)2020 fatcat:fuji3nvk75ggzb5535kccwdmbu

Software Model Checking via IC3 [chapter]

Alessandro Cimatti, Alberto Griggio
2012 Lecture Notes in Computer Science  
The algorithm relies on aggressive use of Boolean satisfiability (SAT) techniques, and has demonstrated impressive effectiveness.  ...  In this paper, we present the first investigation of IC3 in the setting of software verification.  ...  We would like to thank Ken McMillan and the anonymous referees for their very helpful comments on early versions of the paper.  ... 
doi:10.1007/978-3-642-31424-7_23 fatcat:a2bgpg6v5zbgdpnn3lrbq4kgli
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