Related papers: The shape of the one-dimensional phylogenetic like…
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…
We introduce a new kind of likelihood function based on the sequence of moments of the data distribution. Both binned and unbinned data samples are discussed, and the multivariate case is also derived. Building on this approach we lay out…
We consider a one-dimensional discrete-space birth process with a bounded number of particle per site. Under the assumptions of the finite range of interaction, translation invariance, and non-degeneracy, we prove a shape theorem. We also…
The likelihood function of a finite mixture model is a non-convex function with multiple local maxima and commonly used iterative algorithms such as EM will converge to different solutions depending on initial conditions. In this paper we…
In many applications of computer vision it is important to accurately estimate the trajectory of an object over time by fusing data from a number of sources, of which 2D and 3D imagery is only one. In this paper, we show how to use a deep…
A dynamical picture of phylogenetic evolution is given in terms of Markov models on a state space, comprising joint probability distributions for character types of taxonomic classes. Phylogenetic branching is a process which augments the…
We consider a broadcasting problem on a tree where a binary digit (e.g., a spin or a nucleotide's purine/pyrimidine type) is propagated from the root to the leaves through symmetric noisy channels on the edges that randomly flip the state…
We consider the problem of recovering conditional independence relationships between $p$ jointly distributed Hilbertian random elements given $n$ realizations thereof. We operate in the sparse high-dimensional regime, where $n \ll p$ and no…
Distances between sequences based on their $k$-mer frequency counts can be used to reconstruct phylogenies without first computing a sequence alignment. Past work has shown that effective use of k-mer methods depends on 1) model-based…
We extend the empirical likelihood of Owen [Ann. Statist. 18 (1990) 90-120] by partitioning its domain into the collection of its contours and mapping the contours through a continuous sequence of similarity transformations onto the full…
One of the main aims of phylogenetics is the reconstruction of the correct evolutionary tree when data concerning the underlying species set are given. These data typically come in the form of DNA, RNA or protein alignments, which consist…
Maximum parsimony is one of the most frequently-discussed tree reconstruction methods in phylogenetic estimation. However, in recent years it has become more and more apparent that phylogenetic trees are often not sufficient to describe…
We introduce a general framework for the construction of polynomial frames in $L^2(\mathbb{S}^{d-1})$, $d \geq 3$, where the frame functions are obtained as rotated versions of an initial sequence of polynomials $\Psi^j$, $j\in…
We extend a heuristic method for automatic dimensionality selection, which maximizes a profile likelihood to identify "elbows" in scree plots. Our extension enables researchers to make automatic choices of multiple hyper-parameters…
Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…
The probability density function of the random flight with isotropic initial conditions is obtained by an expansion in the number of collisions and the in the spatial harmonics of the solution, as in a Fourier series. The method holds for…
We present a method of dimensional reduction for the general Markov model of sequence evolution on a phylogenetic tree. We show that taking certain linear combinations of the associated random variables (site pattern counts) reduces the…
Likelihood profiling is an efficient and powerful frequentist approach for parameter estimation, uncertainty quantification and practical identifiablity analysis. Unfortunately, these methods cannot be easily applied for stochastic models…
We propose a framework for 2D shape analysis using positive definite kernels defined on Kendall's shape manifold. Different representations of 2D shapes are known to generate different nonlinear spaces. Due to the nonlinearity of these…