Search results for "Computational Mathematic"

Textual data compression in computational biology: a synopsis.

2009

Abstract Motivation: Textual data compression, and the associated techniques coming from information theory, are often perceived as being of interest for data communication and storage. However, they are also deeply related to classification and data mining and analysis. In recent years, a substantial effort has been made for the application of textual data compression techniques to various computational biology tasks, ranging from storage and indexing of large datasets to comparison and reverse engineering of biological networks. Results: The main focus of this review is on a systematic presentation of the key areas of bioinformatics and computational biology where compression has been use…

Stochastic Learning for SAT- Encoded Graph Coloring Problems

2010

The graph coloring problem (GCP) is a widely studied combinatorial optimization problem due to its numerous applications in many areas, including time tabling, frequency assignment, and register allocation. The need for more efficient algorithms has led to the development of several GC solvers. In this paper, the authors introduce a team of Finite Learning Automata, combined with the random walk algorithm, using Boolean satisfiability encoding for the GCP. The authors present an experimental analysis of the new algorithm’s performance compared to the random walk technique, using a benchmark set containing SAT-encoding graph coloring test sets.

Mean-field games and dynamic demand management in power grids

2013

This paper applies mean-field game theory to dynamic demand management. For a large population of electrical heating or cooling appliances (called agents), we provide a mean-field game that guarantees desynchronization of the agents thus improving the power network resilience. Second, for the game at hand, we exhibit a mean-field equilibrium, where each agent adopts a bang-bang switching control with threshold placed at a nominal temperature. At equilibrium, through an opportune design of the terminal penalty, the switching control regulates the mean temperature (computed over the population) and the mains frequency around the nominal value. To overcome Zeno phenomena we also adjust the ban…

Reducing the effect of the data order in algorithms for constructing phylogenetic trees.

1988

Modeling and predicting the Spanish Bachillerato academic results over the next few years using a random network model

2016

[EN] Academic performance is a concern of paramount importance in Spain, where around of 30% of the students in the last two courses in high school, before to access to the labor market or to the university, do not achieve the minimum knowledge required according to the Spanish educational law in force. In order to analyze this problem, we propose a random network model to study the dynamics of the academic performance in Spain. Our approach is based on the idea that both, good and bad study habits, are a mixture of personal decisions and influence of classmates. Moreover, in order to consider the uncertainty in the estimation of model parameters, we perform a lot of simulations taking as t…

Visualizing parameters from loglinear models

2004

This paper presents a graphical display for the parameters resulting from loglinear models. Loglinear models provide a method for analyzing associations between two or several categorical variables and have become widely accepted as a tool for researchers during the last two decades. An important part of the output of any computer program focused on loglinear models is that devoted to estimation of parameters in the model. Traditionally, this output has been presented using tables that indicate the values of the coefficients, the associated standard errors and other related information. Evaluation of these tables can be rather tedious because of the number of values shown as well as their r…

Introducing libeemd: a program package for performing the ensemble empirical mode decomposition

2016

The ensemble empirical mode decomposition (EEMD) and its complete variant (CEEMDAN) are adaptive, noise-assisted data analysis methods that improve on the ordinary empirical mode decomposition (EMD). All these methods decompose possibly nonlinear and/or nonstationary time series data into a finite amount of components separated by instantaneous frequencies. This decomposition provides a powerful method to look into the different processes behind a given time series data, and provides a way to separate short time-scale events from a general trend. We present a free software implementation of EMD, EEMD and CEEMDAN and give an overview of the EMD methodology and the algorithms used in the deco…

Adaptive reference-free compression of sequence quality scores

2014

Motivation: Rapid technological progress in DNA sequencing has stimulated interest in compressing the vast datasets that are now routinely produced. Relatively little attention has been paid to compressing the quality scores that are assigned to each sequence, even though these scores may be harder to compress than the sequences themselves. By aggregating a set of reads into a compressed index, we find that the majority of bases can be predicted from the sequence of bases that are adjacent to them and hence are likely to be less informative for variant calling or other applications. The quality scores for such bases are aggressively compressed, leaving a relatively small number at full reso…

Fitting generalized linear models with unspecified link function: A P-spline approach

2008

Generalized linear models (GLMs) outline a wide class of regression models where the effect of the explanatory variables on the mean of the response variable is modelled throughout the link function. The choice of the link function is typically overlooked in applications and the canonical link is commonly used. The estimation of GLMs with unspecified link function is discussed, where the linearity assumption between the link and the linear predictor is relaxed and the unspecified relationship is modelled flexibly by means of P-splines. An estimating algorithm is presented, alternating estimation of two working GLMs up to convergence. The method is applied to the analysis of quit behavior of…

Metagenomics reveals our incomplete knowledge of global diversity

2008

Metagenomic sequencing obtains huge amounts of sequences from environmental and clinical samples, thus providing a glimpse of the global prokaryotic diversity of both species and genes in these sources. The current trend in metagenomic analysis follows the so-called gene-centric approach, focused on describing the environments by the study of the functional roles of the proteins encoded in the sequenced genes. In this way, it is clear that metagenomic analysis relies heavily on the accurate knowledge of the universe of proteins stored in the databases. Nevertheless, it is known that some biases exist in the composition of databases (which are rich in sequences from common, cultivable and ea…