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Subjects / keywords: Computer science; Mathematics; Set theory; Problems, exercises, etc; Algorithms; Logic, Symbolic and mathematical; Problems and exercises; Electronic books

PhyML is a phylogeny software based on the maximum-likelihood principle. Early PhyML versions used a fast algorithm performing nearest neighbor interchanges to improve a reasonable starting tree topology. Since the origi...

Macromolecular X-ray crystallography is routinely applied to understand biological processes at a molecular level. However, significant time and effort are still required to solve and complete many of these structures be...

Many problems of recent interest in statistics and machine learning can be posed in the framework of convex optimization. Due to the explosion in size and complexity of modern datasets, it is increasingly important to be...

Extended-connectivity fingerprints (ECFPs) are a novel class of topological fingerprints for molecular characterization. Historically, topological fingerprints were developed for substructure and similarity searching. EC...

BACKGROUND: We recently described FastTree, a tool for inferring phylogenies for alignments with up to hundreds of thousands of sequences. Here, we describe improvements to FastTree that improve its accuracy without sacr...

During the last decade, the data sizes have grown faster than the speed of processors. In this context, the capabilities of statistical machine learning methods is limited by the computing time rather than the sample siz...

A variant of the popular nonparametric nonuniform intensity normalization (N3) algorithm is proposed for bias field correction. Given the superb performance of N3 and its public availability, it has been the subject of s...

Subjects / keywords: TREMBLAY, JEAN-PAUL; MCGRAW-HILL; 005.113 T789in

Subjects / keywords: Python (Computer program language); Data structures (Computer science); Computer algorithms

Subjects / keywords: Text processing (Computer science); Genetic algorithms; Computational linguistics

Subjects / keywords: Computer algorithms; Databases; Data structures (Computer science); Structured programming

Abstract The main purpose of this research is the survey of the development Block parallel numerical algorithms for solute stiff ordinary differential equations which are suitable for running on MIMD (Multiple instructi...

A transformer less Shunt Active Power Filter (SAPF) for medium voltage distribution networks based on Multilevel Diode Clamped Inverter is presented in this paper. Converter current control is based on a Model Predictive...

Understanding the evolutionary history of living organisms is a central problem in biology. Until recently the ability to infer evolutionary relationships was limited by the amount of DNA sequence data available, but new...

This paper investigates two fundamental problems in computer vision: contour detection and image segmentation. We present state-of-the-art algorithms for both of these tasks. Our contour detector combines multiple local ...

This brief perspective article focuses on the most common errors and pitfalls, as well as the do's and don'ts in drug combination studies, in terms of experimental design, data acquisition, data interpretation, and compu...

"The scientific study of networks, including computer networks, social networks, and biological networks, has received an enormous amount of interest in the last few years. The rise of the Internet and the wide availabil...

Abstract Motivation: Many programs for aligning short sequencing reads to a reference genome have been developed in the last 2 years. Most of them are very efficient for short reads but inefficient or not applicable for ...

This paper describes FieldTrip, an open source software package that we developed for the analysis of MEG, EEG, and other electrophysiological data. The software is implemented as a MATLAB toolbox and includes a complete...

BACKGROUND: The quality of automated gene prediction in microbial organisms has improved steadily over the past decade, but there is still room for improvement. Increasing the number of correct identifications, both of g...

We develop fast algorithms for estimation of generalized linear models with convex penalties. The models include linear regression, two-class logistic regression, and multi- nomial regression problems while the penalties...

MOTIVATION: Biological sequence data is accumulating rapidly, motivating the development of improved high-throughput methods for sequence classification. RESULTS: UBLAST and USEARCH are new algorithms enabling sensitive ...

The electronic properties of ultrathin crystals of molybdenum disulfide consisting of N=1,2,…,6 S-Mo-S monolayers have been investigated by optical spectroscopy. Through characterization by absorption, photoluminescenc...