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The increase in the number of large data sets and the complexity of current probabilistic sequence evolution models necessitates fast and reliable phylogeny reconstruction methods. We describe a new approach, based on th...

Multi-objective evolutionary algorithms (MOEAs) that use non-dominated sorting and sharing have been criticized mainly for: (1) their O(MN/sup 3/) computational complexity (where M is the number of objectives and N is th...

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...

Large phylogenomics data sets require fast tree inference methods, especially for maximum-likelihood (ML) phylogenies. Fast programs exist, but due to inherent heuristics to find optimal trees, it is not clear whether th...

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS whi...

SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over ...

Materias / palabras clave: Extreme learning machine; Computer science; Bottleneck; Generalization; Feedforward neural network; Artificial neural network; Benchmark (surveying); Feed forward; Artificial intelligence; Key (lock); Machine learning; A...

The recent development of various methods of modulation such as PCM and PPM which exchange bandwidth for signal-to-noise ratio has intensified the interest in a general theory of communication. A basis for such a theory ...

Previous article Next article An Algorithm for Least-Squares Estimation of Nonlinear ParametersDonald W. MarquardtDonald W. Marquardthttps://doi.org/10.1137/0111030PDFPDF PLUSBibTexSections ToolsAdd to favoritesExport Ci...

Computational evolutionary biology, statistical phylogenetics and coalescent-based population genetics are becoming increasingly central to the analysis and understanding of molecular sequence data. We present the Bayesi...

Introduction * Information and Likelihood Theory: A Basis for Model Selection and Inference * Basic Use of the Information-Theoretic Approach * Formal Inference From More Than One Model: Multi-Model Inference (MMI) * Mon...

This paper provides a theoretical framework for analysis of consensus algorithms for multi-agent networked systems with an emphasis on the role of directed information flow, robustness to changes in network topology due ...

A comprehensive look at learning and generalization theory. The statistical theory of learning and generalization concerns the problem of choosing desired functions on the basis of empirical data. Highly applicable to a ...

A training algorithm that maximizes the margin between the training patterns and the decision boundary is presented. The technique is applicable to a wide variety of the classification functions, including Perceptrons, p...

Recommender systems apply knowledge discovery techniques to the problem of making personalized recommendations for information, products or services during a liveinteraction. These systems, especially the k-nearest neigh...

Since its introduction in 2001, MrBayes has grown in popularity as a software package for Bayesian phylogenetic inference using Markov chain Monte Carlo (MCMC) methods. With this note, we announce the release of version ...

This paper demonstrates theoretically and empirically that a greedy algorithm called Orthogonal Matching Pursuit (OMP) can reliably recover a signal with $m$ nonzero entries in dimension $d$ given $ {\rm O}(m \ln d)$ ra...

The particle swarm is an algorithm for finding optimal regions of complex search spaces through the interaction of individuals in a population of particles. This paper analyzes a particle's trajectory as it moves in disc...

QUANTUM ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling, based on density-functional theory, plane waves, and pseudopotentials (norm-conserving, ultrasoft, a...

Phylogenies are extremely useful tools, not only for establishing genealogical relationships among a group of organisms or their parts (e.g. genes), but also for a variety of research once the phylogenies are estimated. ...

A structure refinement method is described which does not use integrated neutron powder intensities, single or overlapping, but employs directly the profile intensities obtained from step-scanning measurements of the pow...

Materias / palabras clave: Monte Carlo tree search; Computer science; Champion; Artificial neural network; Reinforcement learning; Artificial intelligence; Game tree; Value (mathematics); Search algorithm; Tree (set theory); Deep neural networks; ...

The new computer program SHELXT employs a novel dual-space algorithm to solve the phase problem for single-crystal reflection data expanded to the space group P1. Missing data are taken into account and the resolution ex...

We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile ...