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Accurate reconstruction of phylogenies remains a key challenge in evolutionary biology. Most biologically plausible formulations of the problem are formally NP-hard, with no known efficient solution. The standard in practice are fast heuristic methods that are empirically known to work very well in general, but can yield results arbitrarily far from… (More)

Models of reaction chemistry based on the stochastic simulation algorithm (SSA) have become a crucial tool for simulating complicated biological reaction networks due to their ability to handle extremely complicated networks and to represent noise in small-scale chemistry. These methods can, however, become highly inefficient for stiff reaction systems,… (More)

MOTIVATION
Cancer cell genomes acquire several genetic alterations during somatic evolution from a normal cell type. The relative order in which these mutations accumulate and contribute to cell fitness is affected by epistatic interactions. Inferring their evolutionary history is challenging because of the large number of mutations acquired by cancer cells… (More)

Stable random variables are motivated by the central limit theorem for densities with (potentially) unbounded variance and can be thought of as natural generalizations of the Gaussian distribution to skewed and heavy-tailed phenomenon. In this paper, we introduce α-stable graphical (α-SG) models, a class of multivariate stable densities that can also be… (More)

Much modern work in phylogenetics depends on statistical sampling approaches to phylogeny construction to estimate probability distributions of possible trees for any given input data set. Our theoretical understanding of sampling approaches to phylogenetics remains far less developed than that for optimization approaches, however, particularly with regard… (More)

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