Detection of recombination in DNA multiple alignments with hidden markov models

CConventional phylogenetic tree estimation methods assume that all sites in a DNA multiple alignment have the same evolutionary history. This assumption is violated in data sets from certain bacteria and viruses due to recombination, a process that leads to the creation of mosaic sequences from different strains and, if undetected, causes systematic errors in phylogenetic tree estimation. In the current work, a hidden Markov model (HMM) is employed to detect recombination events in multiple alignments of DNA sequences. The emission probabilities in a given state are determined by the branching order (topology) and the branch lengths of the respective phylogenetic tree, while the transition probabilities depend on the global recombination probability. The present study improves on an earlier heuristic parameter optimization scheme and shows how the branch lengths and the recombination probability can be optimized in a maximum likelihood sense by applying the expectation maximization (EM) algorithm. The novel algorithm is tested on a synthetic benchmark problem and is found to clearly outperform the earlier heuristic approach. The paper concludes with an application of this scheme to a DNA sequence alignment of the argF gene from four Neisseria strains, where a likely recombination event is clearly detected

Designing a Belief Function-Based Accessibility Indicator to Improve Web Browsing for Disabled People

The purpose of this study is to provide an accessibility measure of web-pages, in order to draw disabled users to the pages that have been designed to be ac-cessible to them. Our approach is based on the theory of belief functions, using data which are supplied by reports produced by automatic web content assessors that test the validity of criteria defined by the WCAG 2.0 guidelines proposed by the World Wide Web Consortium (W3C) organization. These tools detect errors with gradual degrees of certainty and their results do not always converge. For these reasons, to fuse information coming from the reports, we choose to use an information fusion framework which can take into account the uncertainty and imprecision of infor-mation as well as divergences between sources. Our accessibility indicator covers four categories of deficiencies. To validate the theoretical approach in this context, we propose an evaluation completed on a corpus of 100 most visited French news websites, and 2 evaluation tools. The results obtained illustrate the interest of our accessibility indicator

Electrostatic Field Classifier for Deficient Data

This paper investigates the suitability of recently developed models based on the physical field phenomena for classification problems with incomplete datasets. An original approach to exploiting incomplete training data with missing features and labels, involving extensive use of electrostatic charge analogy, has been proposed. Classification of incomplete patterns has been investigated using a local dimensionality reduction technique, which aims at exploiting all available information rather than trying to estimate the missing values. The performance of all proposed methods has been tested on a number of benchmark datasets for a wide range of missing data scenarios and compared to the performance of some standard techniques. Several modifications of the original electrostatic field classifier aiming at improving speed and robustness in higher dimensional spaces are also discussed

Evidential-EM Algorithm Applied to Progressively Censored Observations

Evidential-EM (E2M) algorithm is an effective approach for computing maximum likelihood estimations under finite mixture models, especially when there is uncertain information about data. In this paper we present an extension of the E2M method in a particular case of incom-plete data, where the loss of information is due to both mixture models and censored observations. The prior uncertain information is expressed by belief functions, while the pseudo-likelihood function is derived based on imprecise observations and prior knowledge. Then E2M method is evoked to maximize the generalized likelihood function to obtain the optimal estimation of parameters. Numerical examples show that the proposed method could effectively integrate the uncertain prior infor-mation with the current imprecise knowledge conveyed by the observed data

Diagonal and Low-Rank Matrix Decompositions, Correlation Matrices, and Ellipsoid Fitting

In this paper we establish links between, and new results for, three problems that are not usually considered together. The first is a matrix decomposition problem that arises in areas such as statistical modeling and signal processing: given a matrix $X$ formed as the sum of an unknown diagonal matrix and an unknown low rank positive semidefinite matrix, decompose $X$ into these constituents. The second problem we consider is to determine the facial structure of the set of correlation matrices, a convex set also known as the elliptope. This convex body, and particularly its facial structure, plays a role in applications from combinatorial optimization to mathematical finance. The third problem is a basic geometric question: given points $v_1,v_2,...,v_n\in \R^k$ (where $n > k$) determine whether there is a centered ellipsoid passing \emph{exactly} through all of the points. We show that in a precise sense these three problems are equivalent. Furthermore we establish a simple sufficient condition on a subspace $U$ that ensures any positive semidefinite matrix $L$ with column space $U$ can be recovered from $D+L$ for any diagonal matrix $D$ using a convex optimization-based heuristic known as minimum trace factor analysis. This result leads to a new understanding of the structure of rank-deficient correlation matrices and a simple condition on a set of points that ensures there is a centered ellipsoid passing through them.Comment: 20 page

SACOC: A spectral-based ACO clustering algorithm

The application of ACO-based algorithms in data mining is growing over the last few years and several supervised and unsupervised learning algorithms have been developed using this bio-inspired approach. Most recent works concerning unsupervised learning have been focused on clustering, where ACO-based techniques have showed a great potential. At the same time, new clustering techniques that seek the continuity of data, specially focused on spectral-based approaches in opposition to classical centroid-based approaches, have attracted an increasing research interest–an area still under study by ACO clustering techniques. This work presents a hybrid spectral-based ACO clustering algorithm inspired by the ACO Clustering (ACOC) algorithm. The proposed approach combines ACOC with the spectral Laplacian to generate a new search space for the algorithm in order to obtain more promising solutions. The new algorithm, called SACOC, has been compared against well-known algorithms (K-means and Spectral Clustering) and with ACOC. The experiments measure the accuracy of the algorithm for both synthetic datasets and real-world datasets extracted from the UCI Machine Learning Repository

Classification of Message Spreading in a Heterogeneous Social Network

Nowadays, social networks such as Twitter, Facebook and LinkedIn become increasingly popular. In fact, they introduced new habits, new ways of communication and they collect every day several information that have different sources. Most existing research works fo-cus on the analysis of homogeneous social networks, i.e. we have a single type of node and link in the network. However, in the real world, social networks offer several types of nodes and links. Hence, with a view to preserve as much information as possible, it is important to consider so-cial networks as heterogeneous and uncertain. The goal of our paper is to classify the social message based on its spreading in the network and the theory of belief functions. The proposed classifier interprets the spread of messages on the network, crossed paths and types of links. We tested our classifier on a real word network that we collected from Twitter, and our experiments show the performance of our belief classifier

Dynamic Bayesian Combination of Multiple Imperfect Classifiers

Classifier combination methods need to make best use of the outputs of multiple, imperfect classifiers to enable higher accuracy classifications. In many situations, such as when human decisions need to be combined, the base decisions can vary enormously in reliability. A Bayesian approach to such uncertain combination allows us to infer the differences in performance between individuals and to incorporate any available prior knowledge about their abilities when training data is sparse. In this paper we explore Bayesian classifier combination, using the computationally efficient framework of variational Bayesian inference. We apply the approach to real data from a large citizen science project, Galaxy Zoo Supernovae, and show that our method far outperforms other established approaches to imperfect decision combination. We go on to analyse the putative community structure of the decision makers, based on their inferred decision making strategies, and show that natural groupings are formed. Finally we present a dynamic Bayesian classifier combination approach and investigate the changes in base classifier performance over time.Comment: 35 pages, 12 figure