A Multi-Agent System for Environmental Monitoring Using Boolean Networks and Reinforcement Learning
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Markov Model Checking of Probabilistic Boolean Networks Representations of Genes
Markov Model Checking of Probabilistic Boolean Networks Representations of Genes Marie Lluberes1, Jaime Seguel2 and Jaime Ramírez-Vick3 1, 2 Electrical and Computer Engineering Department, University of Puerto Rico, Mayagüez, Puerto Rico 3 General Engineering Department, University of Puerto Rico, Mayagüez, Puerto Rico or, on contrary, to prevent or to stop an undesirable Abstract - Our goal is to develop an algorithm for the behavior. This “guiding” of the network dynamics is automated study of the dynamics of Probabilistic Boolean referred to as intervention. The power to intervene with the Network (PBN) representation of genes. Model checking is network dynamics has a significant impact in diagnostics an automated method for the verification of properties on and drug design. systems. Continuous Stochastic Logic (CSL), an extension of Biological phenomena manifest in the continuous-time Computation Tree Logic (CTL), is a model-checking tool domain. But, in describing such phenomena we usually that can be used to specify measures for Continuous-time employ a binary language, for instance, expressed or not Markov Chains (CTMC). Thus, as PBNs can be analyzed in expressed; on or off; up or down regulated. Studies the context of Markov theory, the use of CSL as a method for conducted restricting genes expression to only two levels (0 model checking PBNs could be a powerful tool for the or 1) suggested that information retained by these when simulation of gene network dynamics. Particularly, we are binarized is meaningful to the extent that it is remains in a interested in the subject of intervention. This refers to the continuous domain [2]. -
Shared Sensor Networks Fundamentals, Challenges, Opportunities, Virtualization Techniques, Comparative Analysis, Novel Architecture and Taxonomy
Journal of Sensor and Actuator Networks Review Shared Sensor Networks Fundamentals, Challenges, Opportunities, Virtualization Techniques, Comparative Analysis, Novel Architecture and Taxonomy Nahla S. Abdel Azeem 1, Ibrahim Tarrad 2, Anar Abdel Hady 3,4, M. I. Youssef 2 and Sherine M. Abd El-kader 3,* 1 Information Technology Center, Electronics Research Institute (ERI), El Tahrir st, El Dokki, Giza 12622, Egypt; [email protected] 2 Electrical Engineering Department, Al-Azhar University, Naser City, Cairo 11651, Egypt; [email protected] (I.T.); [email protected] (M.I.Y.) 3 Computers & Systems Department, Electronics Research Institute (ERI), El Tahrir st, El Dokki, Giza 12622, Egypt; [email protected] 4 Department of Computer Science & Engineering, School of Engineering and Applied Science, Washington University in St. Louis, St. Louis, MO 63130, 1045, USA; [email protected] * Correspondence: [email protected] Received: 19 March 2019; Accepted: 7 May 2019; Published: 15 May 2019 Abstract: The rabid growth of today’s technological world has led us to connecting every electronic device worldwide together, which guides us towards the Internet of Things (IoT). Gathering the produced information based on a very tiny sensing devices under the umbrella of Wireless Sensor Networks (WSNs). The nature of these networks suffers from missing sharing among them in both hardware and software, which causes redundancy and more budget to be used. Thus, the appearance of Shared Sensor Networks (SSNs) provides a real modern revolution in it. Where it targets making a real change in its nature from domain specific networks to concurrent running domain networks. That happens by merging it with the technology of virtualization that enables the sharing feature over different levels of its hardware and software to provide the optimal utilization of the deployed infrastructure with a reduced cost. -
Contemporary Developments in Wireless Sensor Networks
I.J.Modern Education and Computer Science, 2012, 3, 1-13 Published Online April 2012 in MECS (http://www.mecs-press.org/) DOI: 10.5815/ijmecs.2012.03.01 Contemporary Developments in Wireless Sensor Networks Sangeeta Mittal Department of Computer Science & Information Technology, Jaypee Institute of Information Technology, Noida, India Email: [email protected] Alok Aggarwal Department of Computer Science & Information Technology, Jaypee Institute of Information Technology, Noida, India Email: [email protected] S.L. Maskara G2W - Soura Niloy. 1 - Kailash Ghosh Road.Kolkata - 700 008. ( WB ). India Email: [email protected] Abstract—Wireless Sensor Networks (WSN) since their made a tremendous progress. An analysis of inception, a decade ago, have grown well in research and contemporary developments in these sub areas of WSN is implementation. In this work the developments in WSNs are the subject matter of this paper and we elaborate on these reported in three sub areas of wireless sensor networks that aspects. The applications of WSN encompass many areas is, wireless sensor node (hardware and software), like healthcare, environmental monitoring, smart Communication & Networking issues in WSNs and application areas. WSNs are characterized by huge data dwellings and civil & battle field security. Still challenges hence research work in aggregation & mining is also such as design of new sensor devices to sense & calibrate discussed. Contemporary issues of integration of WSNs with phenomenon of new interests, integration of WSNs with other prevalent networks, sensor enabled smartness and co existing networks and meaningful interpretation of role of artificial intelligence methods is elaborated. Insight sensor data has to be addressed [4][5]. -
Online Spectral Clustering on Network Streams Yi
Online Spectral Clustering on Network Streams By Yi Jia Submitted to the graduate degree program in Electrical Engineering and Computer Science and the Graduate Faculty of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy Jun Huan, Chairperson Swapan Chakrabarti Committee members Jerzy Grzymala-Busse Bo Luo Alfred Tat-Kei Ho Date defended: The Dissertation Committee for Yi Jia certifies that this is the approved version of the following dissertation : Online Spectral Clustering on Network Streams Jun Huan, Chairperson Date approved: ii Abstract Graph is an extremely useful representation of a wide variety of practical systems in data analysis. Recently, with the fast accumulation of stream data from various type of networks, significant research interests have arisen on spectral clustering for network streams (or evolving networks). Compared with the general spectral clustering problem, the data analysis of this new type of problems may have additional requirements, such as short processing time, scalability in distributed computing environments, and temporal variation tracking. However, to design a spectral clustering method to satisfy these requirement cer- tainly presents non-trivial efforts. There are three major challenges for the new algorithm design. The first challenge is online clustering computation. Most of the existing spectral methods on evolving networks are off-line methods, using standard eigensystem solvers such as the Lanczos method. It needs to recompute solutions from scratch at each time point. The second challenge is the paralleliza- tion of algorithms. To parallelize such algorithms is non-trivial since standard eigen solvers are iterative algorithms and the number of iterations can not be pre- determined. -
Inference of a Probabilistic Boolean Network from a Single Observed Temporal Sequence
Hindawi Publishing Corporation EURASIP Journal on Bioinformatics and Systems Biology Volume 2007, Article ID 32454, 15 pages doi:10.1155/2007/32454 Research Article Inference of a Probabilistic Boolean Network from a Single Observed Temporal Sequence Stephen Marshall,1 Le Yu,1 Yufei Xiao,2 and Edward R. Dougherty2, 3, 4 1 Department of Electronic and Electrical Engineering, Faculty of Engineering, University of Strathclyde, Glasgow, G1 1XW, UK 2 Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX 77843-3128, USA 3 Computational Biology Division, Translational Genomics Research Institute, Phoenix, AZ 85004, USA 4 Department of Pathology, University of Texas M. D. Anderson Cancer Center, Houston, TX 77030, USA Received 10 July 2006; Revised 29 January 2007; Accepted 26 February 2007 Recommended by Tatsuya Akutsu The inference of gene regulatory networks is a key issue for genomic signal processing. This paper addresses the inference of proba- bilistic Boolean networks (PBNs) from observed temporal sequences of network states. Since a PBN is composed of a finite number of Boolean networks, a basic observation is that the characteristics of a single Boolean network without perturbation may be de- termined by its pairwise transitions. Because the network function is fixed and there are no perturbations, a given state will always be followed by a unique state at the succeeding time point. Thus, a transition counting matrix compiled over a data sequence will be sparse and contain only one entry per line. If the network also has perturbations, with small perturbation probability, then the transition counting matrix would have some insignificant nonzero entries replacing some (or all) of the zeros. -
Boolean Network Control with Ideals
Portland State University PDXScholar Mathematics and Statistics Faculty Fariborz Maseeh Department of Mathematics Publications and Presentations and Statistics 1-2021 Boolean Network Control with Ideals Ian H. Dinwoodie Portland State University, [email protected] Follow this and additional works at: https://pdxscholar.library.pdx.edu/mth_fac Part of the Physical Sciences and Mathematics Commons Let us know how access to this document benefits ou.y Citation Details Dinwoodie, Ian H., "Boolean Network Control with Ideals" (2021). Mathematics and Statistics Faculty Publications and Presentations. 302. https://pdxscholar.library.pdx.edu/mth_fac/302 This Working Paper is brought to you for free and open access. It has been accepted for inclusion in Mathematics and Statistics Faculty Publications and Presentations by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Boolean Network Control with Ideals I H Dinwoodie Portland State University January 2021 Abstract A method is given for finding controls to transition an initial state x0 to a target set in deterministic or stochastic Boolean network control models. The algorithms use multivariate polynomial algebra. Examples illustrate the application. 1 Introduction A Boolean network is a dynamical system on d nodes (or coordinates) with binary node values, and with transition map F : {0, 1}d → {0, 1}d. The c coordinate maps F = (f1,...,fd) may use binary parameters u ∈ {0, 1} that can be adjusted or controlled at each step, so the image can be writ- ten F (x, u) and F takes {0, 1}d+c → {0, 1}d, usually written in logical nota- tion. -
Random Boolean Networks As a Toy Model for the Brain
UNIVERSITY OF GENEVA SCIENCE FACULTY VRIJE UNIVERSITEIT OF AMSTERDAM PHYSICS SECTION Random Boolean Networks as a toy model for the brain MASTER THESIS presented at the science faculty of the University of Geneva for obtaining the Master in Theoretical Physics by Chlo´eB´eguin Supervisor (VU): Pr. Greg J Stephens Co-Supervisor (UNIGE): Pr. J´er^ome Kasparian July 2017 Contents Introduction1 1 Biology, physics and the brain4 1.1 Biological description of the brain................4 1.2 Criticality in the brain......................8 1.2.1 Physics reminder..................... 10 1.2.2 Experimental evidences.................. 15 2 Models of neural networks 20 2.1 Classes of models......................... 21 2.1.1 Spiking models...................... 21 2.1.2 Rate-based models.................... 23 2.1.3 Attractor networks.................... 24 2.1.4 Links between the classes of models........... 25 2.2 Random Boolean Networks.................... 28 2.2.1 General definition..................... 28 2.2.2 Kauffman network.................... 30 2.2.3 Hopfield network..................... 31 2.2.4 Towards a RBN for the brain.............. 32 2.2.5 The model......................... 33 3 Characterisation of RBNs 34 3.1 Attractors............................. 34 3.2 Damage spreading........................ 36 3.3 Canonical specific heat...................... 37 4 Results 40 4.1 One population with Gaussian weights............. 40 4.2 Dale's principle and balance of inhibition - excitation..... 46 4.3 Lognormal distribution of the weights.............. 51 4.4 Discussion............................. 55 i 5 Conclusion 58 Bibliography 60 Acknowledgements 66 A Python Code 67 A.1 Dynamics............................. 67 A.2 Attractor search.......................... 69 A.3 Hamming Distance........................ 73 A.4 Canonical specific heat..................... -
A Random Boolean Network Model and Deterministic Chaos
A Random Boolean Network Model and Deterministic Chaos Mihaela T. Matache* Jack Heidel Department of Mathematics University of Nebraska at Omaha Omaha, NE 68182-0243, USA *[email protected] Abstract This paper considers a simple Boolean network with N nodes, each node’s state at time t being determined by a certain number of parent nodes, which may vary from one node to another. This is an extension of a model studied by Andrecut and Ali ( [5]) who consider the same number of parents for all nodes. We make use of the same Boolean rule as the authors of [5], provide a generalization of the formula for the probability of finding a node in state 1 at a time t and use simulation methods to generate consecutive states of the network for both the real system and the model. The results match well. We study the dynamics of the model through sensitivity of the orbits to initial values, bifurcation diagrams, and fixed point analysis. We show that the route to chaos is due to a cascade of period- doubling bifurcations which turn into reversed (period - halving) bifurcations for certain combinations of parameter values. 1. Introduction In recent years various studies ( [5], [16], [19], [20], [21], [22], [30], [31]) have shown that a large class of biological networks and cellular automata can be modelled as Boolean networks. These models, besides being easy to understand, are relatively easy to handle. The interest for Boolean networks and their appli- cations in biology and automata networks has actually started much earlier ( [8], [13], [14], [15], [25], [29], [32]), with publications such as the one of Kauffman ( [25]) whose work on the self-organization and adap- tation in complex systems has inspired many other research endeavors. -
Reward-Driven Training of Random Boolean Network Reservoirs for Model-Free Environments
Portland State University PDXScholar Dissertations and Theses Dissertations and Theses Winter 3-27-2013 Reward-driven Training of Random Boolean Network Reservoirs for Model-Free Environments Padmashri Gargesa Portland State University Follow this and additional works at: https://pdxscholar.library.pdx.edu/open_access_etds Part of the Dynamics and Dynamical Systems Commons, and the Electrical and Computer Engineering Commons Let us know how access to this document benefits ou.y Recommended Citation Gargesa, Padmashri, "Reward-driven Training of Random Boolean Network Reservoirs for Model-Free Environments" (2013). Dissertations and Theses. Paper 669. https://doi.org/10.15760/etd.669 This Thesis is brought to you for free and open access. It has been accepted for inclusion in Dissertations and Theses by an authorized administrator of PDXScholar. Please contact us if we can make this document more accessible: [email protected]. Reward-driven Training of Random Boolean Network Reservoirs for Model-Free Environments by Padmashri Gargesa A thesis submitted in partial fulfillment of the requirements for the degree of Master of Science in Electrical and Computer Engineering Thesis Committee: Christof Teuscher, Chair Richard P. Tymerski Marek A. Perkowski Portland State University 2013 Abstract Reservoir Computing (RC) is an emerging machine learning paradigm where a fixed kernel, built from a randomly connected "reservoir" with sufficiently rich dynamics, is capable of expanding the problem space in a non-linear fashion to a higher dimensional feature space. These features can then be interpreted by a linear readout layer that is trained by a gradient descent method. In comparison to traditional neural networks, only the output layer needs to be trained, which leads to a significant computational advantage. -
A Smart Sensor Grid to Enhance Irrigation Techniques in Jordan Using a Novel Event-Based Routing Protocol
Multimodal Technologies and Interaction Conference Report A Smart Sensor Grid to Enhance Irrigation Techniques in Jordan Using a Novel Event-Based Routing Protocol Maher Ali Al Rantisi 1,*, Glenford Mapp 2,3 and Orhan Gemikonakli 3 1 Department of Communications, School of Science and Technology, Middlesex University London, London NW4 4BT, UK 2 Department of Computer Science, School of Science and Technology, Middlesex University London, London NW4 4BT, UK 3 Department of Design Engineering & Maths, School of Science and Technology, Middlesex University, London NW4 4BT, UK; [email protected] (G.M.); [email protected] (O.G.) * Correspondence: [email protected] Academic Editor: Cristina Portalés Ricart Received: 7 February 2017; Accepted: 11 May 2017; Published: 16 May 2017 Abstract: Due to rapid changes in climatic conditions worldwide, environmental monitoring has become one of the greatest concerns in the last few years. With the advancement in wireless sensing technology, it is now possible to monitor and track fine-grained changes in harsh outdoor environments. Wireless sensor networks (WSN) provide very high quality and accurate analysis for monitoring of both spatial and temporal data, thus providing the opportunity to monitor harsh outdoor environments. However, to deploy and maintain a WSN in such harsh environments is a great challenge for researchers and scientists. Several routing protocols exist for data dissemination and power management but they suffer from various disadvantages. In our case study, there are very limited water resources in the Middle East, hence soil moisture measurements must be taken into account to manage irrigation and agricultural projects. -
Solving Satisfiability Problem by Quantum Annealing
UNIVERSITY OF CALIFORNIA Los Angeles Towards Quantum Computing: Solving Satisfiability Problem by Quantum Annealing A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Electrical Engineering by Juexiao Su 2018 c Copyright by Juexiao Su 2018 ABSTRACT OF THE DISSERTATION Towards Quantum Computing: Solving Satisfiability Problem by Quantum Annealing by Juexiao Su Doctor of Philosophy in Electrical Engineering University of California, Los Angeles, 2018 Professor Lei He, Chair To date, conventional computers have never been able to efficiently handle certain tasks, where the number of computation steps is likely to blow up as the problem size increases. As an emerging technology and new computing paradigm, quantum computing has a great potential to tackle those hard tasks efficiently. Among all the existing quantum computation models, quantum annealing has drawn significant attention in recent years due to the real- ization of the commercialized quantum annealer, sparking research interests in developing applications to solve problems that are intractable for classical computers. However, designing and implementing algorithms that manage to harness the enormous computation power from quantum annealer remains a challenging task. Generally, it requires mapping of the given optimization problem into quadratic unconstrained binary optimiza- tion(QUBO) problem and embedding the subsequent QUBO onto the physical architecture of quantum annealer. Additionally, practical quantum annealers are susceptible to errors leading to low probability of the correct solution. In this study, we focus on solving Boolean satisfiability (SAT) problem using quantum annealer while addressing practical limitations. We have proposed a mapping technique that maps SAT problem to QUBO, and we have further devised a tool flow that embeds the QUBO onto the architecture of a quantum annealing device. -
Survey of Energy Harvesting Systems for Wireless Sensor Networks in Environmental Monitoring
Metrol. Meas. Syst. , Vol. 23 (2016), No. 4, pp. 495–512. METROLOGY AND MEASUREMENT SYSTEMS Index 330930, ISSN 0860-8229 www.metrology.pg.gda.pl SURVEY OF ENERGY HARVESTING SYSTEMS FOR WIRELESS SENSOR NETWORKS IN ENVIRONMENTAL MONITORING 1) 1) 1,2) Bogdan Dziadak , Łukasz Makowski , Andrzej Michalski 1) Warsaw University of Technology, Faculty of Electrical Engineering, Koszykowa 75, 00-661 Warsaw, Poland ([email protected], [email protected], * [email protected], +48 22 234 7427 ) 2) Military University of Technology, Institute of Electronic Systems Gen. S. Kaliskiego 2, 00-908 Warsaw, Poland Abstract Wireless Sensor Networks (WSNs) have existed for many years and had assimilated many interesting innovations. Advances in electronics, radio transceivers, processes of IC manufacturing and development of algorithms for operation of such networks now enable creating energy-efficient devices that provide practical levels of performance and a sufficient number of features. Environmental monitoring is one of the areas in which WSNs can be successfully used. At the same time this is a field where devices must either bring their own power reservoir , such as a battery, or scavenge energy locally from some natural phenomena. Improving the efficiency of energy harvesting methods reduces complexity of WSN structures . This survey is based on practical examples from the real world and provides an overview of state-of-the-art methods and techniques that are used to create energy- efficient WSNs with energy harvesting. Keywords: environmental monitoring, wireless sensor networks, energy harvesting. © 2016 Polish Academy of Sciences. All rights reserved 1. Introduction Wireless Sensor Networks (WSNs) are swarms of small measurement devices that employ a microcontroller and are able to communicate with each other to cooperatively constitute a superior, networked form that is not a simple sum of these single objects but a virtual organism of nodes that unite for the network’s common goal.