Modeling associations between genetic markers using Bayesian networks

Motivation: Understanding the patterns of association between polymorphisms at different loci in a population ( linkage disequilibrium, LD) is of fundamental importance in various genetic studies. Many coefficients were proposed for measuring the degree of LD, but they provide only a static view of the current LD structure. Generative models (GMs) were proposed to go beyond these measures, giving not only a description of the actual LD structure but also a tool to help understanding the process that generated such structure. GMs based in coalescent theory have been the most appealing because they link LD to evolutionary factors. Nevertheless, the inference and parameter estimation of such models is still computationally challenging. Results: We present a more practical method to build GM that describe LD. The method is based on learning weighted Bayesian network structures from haplotype data, extracting equivalence structure classes and using them to model LD. The results obtained in public data from the HapMap database showed that the method is a promising tool for modeling LD. The associations represented by the learned models are correlated with the traditional measure of LD D`. The method was able to represent LD blocks found by standard tools. The granularity of the association blocks and the readability of the models can be controlled in the method. The results suggest that the causality information gained by our method can be useful to tell about the conservability of the genetic markers and to guide the selection of subset of representative markers.

Using Bayesian networks with rule extraction to infer the risk of weed infestation in a corn-crop

This paper describes the modeling of a weed infestation risk inference system that implements a collaborative inference scheme based on rules extracted from two Bayesian network classifiers. The first Bayesian classifier infers a categorical variable value for the weed-crop competitiveness using as input categorical variables for the total density of weeds and corresponding proportions of narrow and broad-leaved weeds. The inferred categorical variable values for the weed-crop competitiveness along with three other categorical variables extracted from estimated maps for the weed seed production and weed coverage are then used as input for a second Bayesian network classifier to infer categorical variables values for the risk of infestation. Weed biomass and yield loss data samples are used to learn the probability relationship among the nodes of the first and second Bayesian classifiers in a supervised fashion, respectively. For comparison purposes, two types of Bayesian network structures are considered, namely an expert-based Bayesian classifier and a naive Bayes classifier. The inference system focused on the knowledge interpretation by translating a Bayesian classifier into a set of classification rules. The results obtained for the risk inference in a corn-crop field are presented and discussed. (C) 2009 Elsevier Ltd. All rights reserved.

Neural network model for designing automotive devices using SMD LED

The advantages offered by the electronic component LED (Light Emitting Diode) have resulted in a quick and extensive application of this device in the replacement of incandescent lights. In this combined application, however, the relationship between the design variables and the desired effect or result is very complex and renders it difficult to model using conventional techniques. This paper consists of the development of a technique using artificial neural networks that makes it possible to obtain the luminous intensity values of brake lights using SMD (Surface Mounted Device) LEDs from design data. This technique can be utilized to design any automotive device that uses groups of SMD LEDs. The results of industrial applications using SMD LED are presented to validate the proposed technique.

Data Mining Applied to Harmonic Current Sources Identification in Residential Consumers

This work proposes a method based on both preprocessing and data mining with the objective of identify harmonic current sources in residential consumers. In addition, this methodology can also be applied to identify linear and nonlinear loads. It should be emphasized that the entire database was obtained through laboratory essays, i.e., real data were acquired from residential loads. Thus, the residential system created in laboratory was fed by a configurable power source and in its output were placed the loads and the power quality analyzers (all measurements were stored in a microcomputer). So, the data were submitted to pre-processing, which was based on attribute selection techniques in order to minimize the complexity in identifying the loads. A newer database was generated maintaining only the attributes selected, thus, Artificial Neural Networks were trained to realized the identification of loads. In order to validate the methodology proposed, the loads were fed both under ideal conditions (without harmonics), but also by harmonic voltages within limits pre-established. These limits are in accordance with IEEE Std. 519-1992 and PRODIST (procedures to delivery energy employed by Brazilian`s utilities). The results obtained seek to validate the methodology proposed and furnish a method that can serve as alternative to conventional methods.

Neural network-based H(infinity) control for fully actuated and underactuated cooperative manipulators

This paper develops H(infinity) control designs based on neural networks for fully actuated and underactuated cooperative manipulators. The neural networks proposed in this paper only adapt the uncertain dynamics of the robot manipulators. They work as a complement of the nominal model. The H(infinity) performance index includes the position errors as well the squeeze force errors between the manipulator end-effectors and the object, which represents a complete disturbance rejection scenario. For the underactuated case, the squeeze force control problem is more difficult to solve due to the loss of some degrees of manipulator actuation. Results obtained from an actual cooperative manipulator, which is able to work as a fully actuated and an underactuated manipulator, are presented. (C) 2008 Elsevier Ltd. All rights reserved.

Hybrid Algorithms for Routing and Assignment Wavelengths in Optical Networks

This paper presents a strategy for the solution of the WDM optical networks planning. Specifically, the problem of Routing and Wavelength Allocation (RWA) in order to minimize the amount of wavelengths used. In this case, the problem is known as the Min-RWA. Two meta-heuristics (Tabu Search and Simulated Annealing) are applied to take solutions of good quality and high performance. The key point is the degradation of the maximum load on the virtual links in favor of minimization of number of wavelengths used; the objective is to find a good compromise between the metrics of virtual topology (load in Gb/s) and of the physical topology (quantity of wavelengths). The simulations suggest good results when compared to some existing in the literature.

A survey on key management mechanisms for distributed Wireless Sensor Networks

Wireless Sensor Networks (WSNs) have a vast field of applications, including deployment in hostile environments. Thus, the adoption of security mechanisms is fundamental. However, the extremely constrained nature of sensors and the potentially dynamic behavior of WSNs hinder the use of key management mechanisms commonly applied in modern networks. For this reason, many lightweight key management solutions have been proposed to overcome these constraints. In this paper, we review the state of the art of these solutions and evaluate them based on metrics adequate for WSNs. We focus on pre-distribution schemes well-adapted for homogeneous networks (since this is a more general network organization), thus identifying generic features that can improve some of these metrics. We also discuss some challenges in the area and future research directions. (C) 2010 Elsevier B.V. All rights reserved.

A Taxonomy for Locality Algorithms on Peer-to-Peer Networks

The continuous growth of peer-to-peer networks has made them responsible for a considerable portion of the current Internet traffic. For this reason, improvements in P2P network resources usage are of central importance. One effective approach for addressing this issue is the deployment of locality algorithms, which allow the system to optimize the peers` selection policy for different network situations and, thus, maximize performance. To date, several locality algorithms have been proposed for use in P2P networks. However, they usually adopt heterogeneous criteria for measuring the proximity between peers, which hinders a coherent comparison between the different solutions. In this paper, we develop a thoroughly review of popular locality algorithms, based on three main characteristics: the adopted network architecture, distance metric, and resulting peer selection algorithm. As result of this study, we propose a novel and generic taxonomy for locality algorithms in peer-to-peer networks, aiming to enable a better and more coherent evaluation of any individual locality algorithm.

A New Approach for Video Adaptation through Overlay Services Networks

Video adaptation is an extensively explored content providing technique aimed at appropriately suiting several usage scenarios featured by different network requirements and constraints, user`s terminal and preferences. However, its usage in high-demand video distribution systems, such as CNDs, has been badly approached, ignoring several aspects of optimization of network use. To address such deficiencies, this paper presents an approach for implementing the adaptation service by exploring the concept of overlay services networks. As a result of demonstrate the benefits of this proposal, it is made a comparison of this proposed adaptation service with other strategies of video adaptation.

Adaptive Approach for a Maximum Entropy Algorithm in Ecological Niche Modeling

This paper presents an Adaptive Maximum Entropy (AME) approach for modeling biological species. The Maximum Entropy algorithm (MaxEnt) is one of the most used methods in modeling biological species geographical distribution. The approach presented here is an alternative to the classical algorithm. Instead of using the same set features in the training, the AME approach tries to insert or to remove a single feature at each iteration. The aim is to reach the convergence faster without affect the performance of the generated models. The preliminary experiments were well performed. They showed an increasing on performance both in accuracy and in execution time. Comparisons with other algorithms are beyond the scope of this paper. Some important researches are proposed as future works.

Evaluation of Adaptive Genetic Algorithm to Environmental Modeling of Peponapis and Cucurbita

This paper presents a free software tool that supports the next-generation Mobile Communications, through the automatic generation of models of components and electronic devices based on neural networks. This tool enables the creation, training, validation and simulation of the model directly from measurements made on devices of interest, using an interface totally oriented to non-experts in neural models. The resulting model can be exported automatically to a traditional circuit simulator to test different scenarios.

Falling sheet envelope method for non-destructive testing time-dependent signals

In this work, an algorithm to compute the envelope of non-destructive testing (NDT) signals is proposed. This method allows increasing the speed and reducing the memory in extensive data processing. Also, this procedure presents advantage of preserving the data information for physical modeling applications of time-dependent measurements. The algorithm is conceived to be applied for analyze data from non-destructive testing. The comparison between different envelope methods and the proposed method, applied to Magnetic Bark Signal (MBN), is studied. (C) 2010 Elsevier Ltd. All rights reserved.

Approximate algorithms for credal networks with binary variables

This paper presents a family of algorithms for approximate inference in credal networks (that is, models based on directed acyclic graphs and set-valued probabilities) that contain only binary variables. Such networks can represent incomplete or vague beliefs, lack of data, and disagreements among experts; they can also encode models based on belief functions and possibilistic measures. All algorithms for approximate inference in this paper rely on exact inferences in credal networks based on polytrees with binary variables, as these inferences have polynomial complexity. We are inspired by approximate algorithms for Bayesian networks; thus the Loopy 2U algorithm resembles Loopy Belief Propagation, while the Iterated Partial Evaluation and Structured Variational 2U algorithms are, respectively, based on Localized Partial Evaluation and variational techniques. (C) 2007 Elsevier Inc. All rights reserved.

Treatment of Aqueous Effluents Containing Phenol by the O(3), O(3)-UV, and O(3)-H(2)O(2) Processes: Experimental Study and Neural Network Modeling

In this work, the oxidation of the model pollutant phenol has been studied by means of the O(3), O(3)-UV, and O(3)-H(2)O(2) processes. Experiments were carried out in a fed-batch system to investigate the effects of initial dissolved organic carbon concentration, initial, ozone concentration in the gas phase, the presence or absence of UVC radiation, and initial hydrogen peroxide concentration. Experimental results were used in the modeling of the degradation processes by neural networks in order to simulate DOC-time profiles and evaluate the relative importance of process variables.

The choice of the best among the shortest routes in transparent optical networks

This work introduces the problem of the best choice among M combinations of the shortest paths for dynamic provisioning of lightpaths in all-optical networks. To solve this problem in an optimized way (shortest path and load balance), a new fixed routing algorithm, named Best among the Shortest Routes (BSR), is proposed. The BSR`s performance is compared in terms of blocking probability and network utilization with Dijkstra`s shortest path algorithm and others algorithms proposed in the literature. The evaluated scenarios include several representative topologies for all-optical networking and different wavelength conversion architectures. For all studied scenarios, BSR achieved superior performance. (C) 2010 Elsevier B.V. All rights reserved.