Evolutionary synthesis of stochastic gene network models using feature-based search spaces

A feature-based fitness function is applied in a genetic programming system to synthesize stochastic gene regulatory network models whose behaviour is defined by a time course of protein expression levels. Typically, when targeting time series data, the fitness function is based on a sum-of-errors involving the values of the fluctuating signal. While this approach is successful in many instances, its performance can deteriorate in the presence of noise. This thesis explores a fitness measure determined from a set of statistical features characterizing the time series' sequence of values, rather than the actual values themselves. Through a series of experiments involving symbolic regression with added noise and gene regulatory network models based on the stochastic 'if-calculus, it is shown to successfully target oscillating and non-oscillating signals. This practical and versatile fitness function offers an alternate approach, worthy of consideration for use in algorithms that evaluate noisy or stochastic behaviour.

Solution Methods for Service Network Design with Resource Management Consideration

La gestion des ressources, équipements, équipes de travail, et autres, devrait être prise en compte lors de la conception de tout plan réalisable pour le problème de conception de réseaux de services. Cependant, les travaux de recherche portant sur la gestion des ressources et la conception de réseaux de services restent limités. La présente thèse a pour objectif de combler cette lacune en faisant l’examen de problèmes de conception de réseaux de services prenant en compte la gestion des ressources. Pour ce faire, cette thèse se décline en trois études portant sur la conception de réseaux. La première étude considère le problème de capacitated multi-commodity fixed cost network design with design-balance constraints(DBCMND). La structure multi-produits avec capacité sur les arcs du DBCMND, de même que ses contraintes design-balance, font qu’il apparaît comme sous-problème dans de nombreux problèmes reliés à la conception de réseaux de services, d’où l’intérêt d’étudier le DBCMND dans le contexte de cette thèse. Nous proposons une nouvelle approche pour résoudre ce problème combinant la recherche tabou, la recomposition de chemin, et une procédure d’intensification de la recherche dans une région particulière de l’espace de solutions. Dans un premier temps la recherche tabou identifie de bonnes solutions réalisables. Ensuite la recomposition de chemin est utilisée pour augmenter le nombre de solutions réalisables. Les solutions trouvées par ces deux méta-heuristiques permettent d’identifier un sous-ensemble d’arcs qui ont de bonnes chances d’avoir un statut ouvert ou fermé dans une solution optimale. Le statut de ces arcs est alors fixé selon la valeur qui prédomine dans les solutions trouvées préalablement. Enfin, nous utilisons la puissance d’un solveur de programmation mixte en nombres entiers pour intensifier la recherche sur le problème restreint par le statut fixé ouvert/fermé de certains arcs. Les tests montrent que cette approche est capable de trouver de bonnes solutions aux problèmes de grandes tailles dans des temps raisonnables. Cette recherche est publiée dans la revue scientifique Journal of heuristics. La deuxième étude introduit la gestion des ressources au niveau de la conception de réseaux de services en prenant en compte explicitement le nombre fini de véhicules utilisés à chaque terminal pour le transport de produits. Une approche de solution faisant appel au slope-scaling, la génération de colonnes et des heuristiques basées sur une formulation en cycles est ainsi proposée. La génération de colonnes résout une relaxation linéaire du problème de conception de réseaux, générant des colonnes qui sont ensuite utilisées par le slope-scaling. Le slope-scaling résout une approximation linéaire du problème de conception de réseaux, d’où l’utilisation d’une heuristique pour convertir les solutions obtenues par le slope-scaling en solutions réalisables pour le problème original. L’algorithme se termine avec une procédure de perturbation qui améliore les solutions réalisables. Les tests montrent que l’algorithme proposé est capable de trouver de bonnes solutions au problème de conception de réseaux de services avec un nombre fixe des ressources à chaque terminal. Les résultats de cette recherche seront publiés dans la revue scientifique Transportation Science. La troisième étude élargie nos considérations sur la gestion des ressources en prenant en compte l’achat ou la location de nouvelles ressources de même que le repositionnement de ressources existantes. Nous faisons les hypothèses suivantes: une unité de ressource est nécessaire pour faire fonctionner un service, chaque ressource doit retourner à son terminal d’origine, il existe un nombre fixe de ressources à chaque terminal, et la longueur du circuit des ressources est limitée. Nous considérons les alternatives suivantes dans la gestion des ressources: 1) repositionnement de ressources entre les terminaux pour tenir compte des changements de la demande, 2) achat et/ou location de nouvelles ressources et leur distribution à différents terminaux, 3) externalisation de certains services. Nous présentons une formulation intégrée combinant les décisions reliées à la gestion des ressources avec les décisions reliées à la conception des réseaux de services. Nous présentons également une méthode de résolution matheuristique combinant le slope-scaling et la génération de colonnes. Nous discutons des performances de cette méthode de résolution, et nous faisons une analyse de l’impact de différentes décisions de gestion des ressources dans le contexte de la conception de réseaux de services. Cette étude sera présentée au XII International Symposium On Locational Decision, en conjonction avec XXI Meeting of EURO Working Group on Locational Analysis, Naples/Capri (Italy), 2014. En résumé, trois études différentes sont considérées dans la présente thèse. La première porte sur une nouvelle méthode de solution pour le "capacitated multi-commodity fixed cost network design with design-balance constraints". Nous y proposons une matheuristique comprenant la recherche tabou, la recomposition de chemin, et l’optimisation exacte. Dans la deuxième étude, nous présentons un nouveau modèle de conception de réseaux de services prenant en compte un nombre fini de ressources à chaque terminal. Nous y proposons une matheuristique avancée basée sur la formulation en cycles comprenant le slope-scaling, la génération de colonnes, des heuristiques et l’optimisation exacte. Enfin, nous étudions l’allocation des ressources dans la conception de réseaux de services en introduisant des formulations qui modèlent le repositionnement, l’acquisition et la location de ressources, et l’externalisation de certains services. À cet égard, un cadre de solution slope-scaling développé à partir d’une formulation en cycles est proposé. Ce dernier comporte la génération de colonnes et une heuristique. Les méthodes proposées dans ces trois études ont montré leur capacité à trouver de bonnes solutions.

Tunnel-Based Artificial Neural Network Technique to Calculate the Resonant Frequency of a Thick-Substrate Microstrip Antenna

The mathematical formulation of empirically developed formulas Jirr the calculation of the resonant frequency of a thick-substrate (h s 0.08151 A,,) microstrip antenna has been analyzed. With the use qt' tunnel-based artificial neural networks (ANNs), the resonant frequency of antennas with h satisfying the thick-substrate condition are calculated and compared with the existing experimental results and also with the simulation results obtained with the use of an IE3D software package. The artificial neural network results are in very good agreement with the experimental results

Propagation of Microwaves in the Troposphere with Potential Application to GPS based Navigation and Meteorology with emphasis on Indian region

Global Positioning System (GPS), with its high integrity, continuous availability and reliability, revolutionized the navigation system based on radio ranging. With four or more GPS satellites in view, a GPS receiver can find its location anywhere over the globe with accuracy of few meters. High accuracy - within centimeters, or even millimeters is achievable by correcting the GPS signal with external augmentation system. The use of satellite for critical application like navigation has become a reality through the development of these augmentation systems (like W AAS, SDCM, and EGNOS, etc.) with a primary objective of providing essential integrity information needed for navigation service in their respective regions. Apart from these, many countries have initiated developing space-based regional augmentation systems like GAGAN and IRNSS of India, MSAS and QZSS of Japan, COMPASS of China, etc. In future, these regional systems will operate simultaneously and emerge as a Global Navigation Satellite System or GNSS to support a broad range of activities in the global navigation sector.Among different types of error sources in the GPS precise positioning, the propagation delay due to the atmospheric refraction is a limiting factor on the achievable accuracy using this system. The WADGPS, aimed for accurate positioning over a large area though broadcasts different errors involved in GPS ranging including ionosphere and troposphere errors, due to the large temporal and spatial variations in different atmospheric parameters especially in lower atmosphere (troposphere), the use of these broadcasted tropospheric corrections are not sufficiently accurate. This necessitated the estimation of tropospheric error based on realistic values of tropospheric refractivity. Presently available methodologies for the estimation of tropospheric delay are mostly based on the atmospheric data and GPS measurements from the mid-latitude regions, where the atmospheric conditions are significantly different from that over the tropics. No such attempts were made over the tropics. In a practical approach when the measured atmospheric parameters are not available analytical models evolved using data from mid-latitudes for this purpose alone can be used. The major drawback of these existing models is that it neglects the seasonal variation of the atmospheric parameters at stations near the equator. At tropics the model underestimates the delay in quite a few occasions. In this context, the present study is afirst and major step towards the development of models for tropospheric delay over the Indian region which is a prime requisite for future space based navigation program (GAGAN and IRNSS). Apart from the models based on the measured surface parameters, a region specific model which does not require any measured atmospheric parameter as input, but depends on latitude and day of the year was developed for the tropical region with emphasis on Indian sector.Large variability of atmospheric water vapor content in short spatial and/or temporal scales makes its measurement rather involved and expensive. A local network of GPS receivers is an effective tool for water vapor remote sensing over the land. This recently developed technique proves to be an effective tool for measuring PW. The potential of using GPS to estimate water vapor in the atmosphere at all-weather condition and with high temporal resolution is attempted. This will be useful for retrieving columnar water vapor from ground based GPS data. A good network of GPS could be a major source of water vapor information for Numerical Weather Prediction models and could act as surrogate to the data gap in microwave remote sensing for water vapor over land.

Optically transparent magnetic nanocomposites based on encapsulated Fe3O4 nanoparticles in a sol–gel silica network

Composite Fe3O4–SiO2 materials were prepared by the sol–gel method with tetraethoxysilane and aqueous-based Fe3O4 ferrofluids as precursors. The monoliths obtained were crack free and showed both optical and magnetic properties. The structural properties were determined by infrared spectroscopy, x-ray diffractometry and transmission electron microscopy. Fe3O4 particles of 20 nm size lie within the pores of the matrix without any strong Si–O–Fe bonding. The well established silica network provides effective confinement to these nanoparticles. The composites were transparent in the 600–800 nm regime and the field dependent magnetization curves suggest that the composite exhibits superparamagnetic characteristics

Plane-to-plane positioning from image-based visual servoing and structured light

In this paper we face the problem of positioning a camera attached to the end-effector of a robotic manipulator so that it gets parallel to a planar object. Such problem has been treated for a long time in visual servoing. Our approach is based on linking to the camera several laser pointers so that its configuration is aimed to produce a suitable set of visual features. The aim of using structured light is not only for easing the image processing and to allow low-textured objects to be treated, but also for producing a control scheme with nice properties like decoupling, stability, well conditioning and good camera trajectory

Availability analysis of GMPLS connections based on physical network topology

This paper presents a study of connection availability in GMPLS over optical transport networks (OTN) taking into account different network topologies. Two basic path protection schemes are considered and compared with the no protection case. The selected topologies are heterogeneous in geographic coverage, network diameter, link lengths, and average node degree. Connection availability is also computed considering the reliability data of physical components and a well-known network availability model. Results show several correspondences between suitable path protection algorithms and several network topology characteristics

Dynamic bandwidth management as part of an integrated network management system based on distributed agents

We present a system for dynamic network resource configuration in environments with bandwidth reservation and path restoration mechanisms. Our focus is on the dynamic bandwidth management results, although the main goal of the system is the integration of the different mechanisms that manage the reserved paths (bandwidth, restoration, and spare capacity planning). The objective is to avoid conflicts between these mechanisms. The system is able to dynamically manage a logical network such as a virtual path network in ATM or a label switch path network in MPLS. This system has been designed to be modular in the sense that in can be activated or deactivated, and it can be applied only in a sub-network. The system design and implementation is based on a multi-agent system (MAS). We also included details of its architecture and implementation

SB.TV's successful yet unconventional establishment of a Brand based solely on Social Network Success may present a problem in long-term survival

Research Proposal in SB.TV case study. New dimension to brand model for Web 2.0 success

Epidemiological risk assessment using linked network and grid based modelling: Phytophthora ramorum and Phytophthora kernoviae in the UK

We developed a stochastic simulation model incorporating most processes likely to be important in the spread of Phytophthora ramorum and similar diseases across the British landscape (covering Rhododendron ponticum in woodland and nurseries, and Vaccinium myrtillus in heathland). The simulation allows for movements of diseased plants within a realistically modelled trade network and long-distance natural dispersal. A series of simulation experiments were run with the model, representing an experiment varying the epidemic pressure and linkage between natural vegetation and horticultural trade, with or without disease spread in commercial trade, and with or without inspections-with-eradication, to give a 2 x 2 x 2 x 2 factorial started at 10 arbitrary locations spread across England. Fifty replicate simulations were made at each set of parameter values. Individual epidemics varied dramatically in size due to stochastic effects throughout the model. Across a range of epidemic pressures, the size of the epidemic was 5-13 times larger when commercial movement of plants was included. A key unknown factor in the system is the area of susceptible habitat outside the nursery system. Inspections, with a probability of detection and efficiency of infected-plant removal of 80% and made at 90-day intervals, reduced the size of epidemics by about 60% across the three sectors with a density of 1% susceptible plants in broadleaf woodland and heathland. Reducing this density to 0.1% largely isolated the trade network, so that inspections reduced the final epidemic size by over 90%, and most epidemics ended without escape into nature. Even in this case, however, major wild epidemics developed in a few percent of cases. Provided the number of new introductions remains low, the current inspection policy will control most epidemics. However, as the rate of introduction increases, it can overwhelm any reasonable inspection regime, largely due to spread prior to detection. (C) 2009 Elsevier B.V. All rights reserved.

A fast identification algorithm for Box-Cox transformation based radial basis function neural network

In this letter, a Box-Cox transformation-based radial basis function (RBF) neural network is introduced using the RBF neural network to represent the transformed system output. Initially a fixed and moderate sized RBF model base is derived based on a rank revealing orthogonal matrix triangularization (QR decomposition). Then a new fast identification algorithm is introduced using Gauss-Newton algorithm to derive the required Box-Cox transformation, based on a maximum likelihood estimator. The main contribution of this letter is to explore the special structure of the proposed RBF neural network for computational efficiency by utilizing the inverse of matrix block decomposition lemma. Finally, the Box-Cox transformation-based RBF neural network, with good generalization and sparsity, is identified based on the derived optimal Box-Cox transformation and a D-optimality-based orthogonal forward regression algorithm. The proposed algorithm and its efficacy are demonstrated with an illustrative example in comparison with support vector machine regression.

Givens rotation based fast backward elimination algorithm for RBF neural network pruning

A fast backward elimination algorithm is introduced based on a QR decomposition and Givens transformations to prune radial-basis-function networks. Nodes are sequentially removed using an increment of error variance criterion. The procedure is terminated by using a prediction risk criterion so as to obtain a model structure with good generalisation properties. The algorithm can be used to postprocess radial basis centres selected using a k-means routine and, in this mode, it provides a hybrid supervised centre selection approach.

Cloud based global positioning system as a safety monitor for dementia patients

The aim of using GPS for Alzheimer's Patients is to give carers and families of those affected by Alzheimer's Disease, as well as all the other dementia related conditions, a service that can, via SMS text message, notify them should their loved one leave their home. Through a custom website, it enables the carer to remotely manage a contour boundary that is specifically assigned to the patient as well as the telephone numbers of the carers. The technique makes liberal use of such as Google Maps.