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The caret package, short for classification and regression training, contains numerous tools for developing predictive models using the rich set of models available in R. The package focuses on simplifying model training...

IQ-TREE (http://www.iqtree.org, last accessed February 6, 2020) is a user-friendly and widely used software package for phylogenetic inference using maximum likelihood. Since the release of version 1 in 2014, we have con...

"This work describes the use of entomological studies combined with in silico models (computer simulations derived from numerical models) to assess the efficacy of a novel device for controlled release of spatial repel...

Se presenta una guía para resolver y estudiar modelos de expectativas racionales dinámicas lineales (LDRE). Luego de codificar el modelo, se aplica una function simple para log-linealizarlo; simular los efectos de seri...

The aqueous solubility of drugs/drug candidates (Sw) is one of the crucial physicochemical parameters in drug discovery studies and any computational method to predict the solubility is highly in demand in the pharmaceut...

To research optimization possibilities in supercritical ORC processes for geothermal power production the Modular low-Temperature Circuit Karlsruhe (MoNiKa) was built at Campus North of the Karlsruhe Institute of Technol...

"The steel industry faces increasing challenges in managing product diversity, maintaining competitiveness, and improving operational efficiency. Within this context, recommendation systems present a promising opportunit...

By decomposing the image formation process into a sequential application of denoising autoencoders, diffusion models (DMs) achieve state-of-the-art synthesis results on image data and beyond. Additionally, their formulat...

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological inte...

A computer is generally considered to be a universal computational device; i.e., it is believed able to simulate any physical computational device with a cost in computation time of at most a polynomial factor: It is not...

Classical Monte Carlo simulations have been carried out for liquid water in the NPT ensemble at 25 °C and 1 atm using six of the simpler intermolecular potential functions for the water dimer: Bernal–Fowler (BF), SPC,...

Comparative analysis of molecular sequence data is essential for reconstructing the evolutionary histories of species and inferring the nature and extent of selective forces shaping the evolution of genes and species. He...

Convolutional networks are at the core of most state of-the-art computer vision solutions for a wide variety of tasks. Since 2014 very deep convolutional networks started to become mainstream, yielding substantial gains ...

Homology modelling has matured into an important technique in structural biology, significantly contributing to narrowing the gap between known protein sequences and experimentally determined structures. Fully automated ...

Scientific collaboration are becoming interdisciplinary, and scientists are working in informal collaboration to solve complex problems that require multiple types of large resources. An option is a computational grid. A...

The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known that more complex evolut...

We describe here a general Amber force field (GAFF) for organic molecules. GAFF is designed to be compatible with existing Amber force fields for proteins and nucleic acids, and has parameters for most organic and pharma...

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, origi...

Since the classical molecular dynamics simulator LAMMPS was released as an open source code in 2004, it has become a widely-used tool for particle-based modeling of materials at length scales ranging from atomic to mesos...

We present Model-based Analysis of ChIP-Seq data, MACS, which analyzes data generated by short read sequencers such as Solexa's Genome Analyzer. MACS empirically models the shift size of ChIP-Seq tags, and uses it to imp...

Genetic algorithms have been used in science and engineering as adaptive algorithms for solving practical problems and as computational models of natural evolutionary systems. This brief, accessible introduction describe...

"The global energy crisis necessitates the development of sustainable energy sources, with nuclear fusion representing a significant long-term opportunity for the future. However, the licensing process for facilities lik...

(NOTE: Each chapter begins with an Introduction, and concludes with Exercises and References.) I. GETTING STARTED. 1. Aspects of Multivariate Analysis. Applications of Multivariate Techniques. The Organization of Data. D...

This paper presents a new vision Transformer, called Swin Transformer, that capably serves as a general-purpose backbone for computer vision. Challenges in adapting Transformer from language to vision arise from differen...