Diffusion is the process by which new products and practices are invented and successfully introduced into a society. This paper presents a possible explanation of this phenomenon in terms of a network of interacting agents whose decisions are determined by the action of their neighbours according to a probabilistic model. It is known that the maximum eigenvalue of the network decides a tipping...

Evolutionary algorithms are general iterative algorithms for combinatorial optimization. The term evolutionary algorithm is used to refer to any probabilistic algorithm whose design is inspired by evolutionary mechanisms found in biological species. These algorithms have been found to be very effective and robust in solving numerous problems from a wide range of application domains. In this pap...

Analyses of virus evolution in known transmission chains have the potential to elucidate the impact of transmission dynamics on the viral evolutionary rate and its difference within and between hosts. Lin et al. (2015, Journal of Virology, 89/7: 3512-22) recently investigated the evolutionary history of hepatitis B virus in a transmission chain and postulated that the 'colonization-adaptation-t...

The evolutionary annealing-simplex algorithm is a probabilistic heuristic global optimisation technique that joins ideas from different methodological approaches, enhancing them with some original elements. The main concept is based on a controlled random search scheme, where a generalised downhill simplex methodology is coupled with a simulated annealing procedure. The algorithm combines the r...

Professional probabilists have long argued over what probability means, with, for example, Bayesians arguing that probabilities refer to subjective degrees of confidence and frequentists arguing that probabilities refer to the frequencies of events in the world. Recently, Gigerenzer and his colleagues have argued that these same distinctions are made by untutored subjects, and that, for many do...

Stochastic optimization by learning and using probabilistic models has received an increasing amount of attention over the last few years. Algorithms within this field estimate the probability distribution of a selection of the available solutions and subsequently draw more samples from the estimated probability distribution. The resulting algorithms have displayed a good performance on a wide ...

Recently, there has been a growing interest in developing evolutionary algorithms based on probabilistic modeling. In this scheme, the offspring population is generated according to the estimated probability density model of the parent instead of using recombination and mutation operators. In this paper, we have proposed probabilistic model-building genetic algorithms (PMBGAs) in permutation re...

The degree of evolutionary conservation of an amino acid in a protein or a nucleic acid in DNA/RNA reflects a balance between its natural tendency to mutate and the overall need to retain the structural integrity and function of the macromolecule. The ConSurf web server (http://consurf.tau.ac.il), established over 15 years ago, analyses the evolutionary pattern of the amino/nucleic acids of the...

Probabilistic evolutionary models revolutionized our capability to extract biological insights from sequence data. While these models accurately describe the stochastic processes of site-specific substitutions, single-base substitutions represent only a fraction of all the events that shape genomes. Specifically, in microbes, events in which entire genes are gained (e.g. via horizontal gene tra...

MOTIVATION We consider models useful for learning an evolutionary or phylogenetic tree from data consisting of DNA sequences corresponding to the leaves of the tree. In particular, we consider a general probabilistic model described in Siepel and Haussler that we call the phylogenetic-HMM model which generalizes the classical probabilistic models of Neyman and Felsenstein. Unfortunately, comput...