相关论文: Normalizing Kernels in the Billera-Holmes-Vogtmann…

Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…

How a single fertilized cell gives rise to a complex array of specialized cell types in development is a central question in biology. The cells grow, divide, and acquire differentiated characteristics through poorly understood molecular…

Natural systems with emergent behaviors often organize along low-dimensional subsets of high-dimensional spaces. For example, despite the tens of thousands of genes in the human genome, the principled study of genomics is fruitful because…

Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…

Estimation of intracellular gene networks has been a critical component of single-cell transcriptomic data analysis, which can provide crucial insights into the complex interplay between genes, facilitating the discovery of the biological…

We propose a new kernel for biological sequences which borrows ideas and techniques from information theory and data compression. This kernel can be used in combination with any kernel method, in particular Support Vector Machines for…

Many real-world applications generate continuous data streams for regression. Hoeffding trees and their variants have a long-standing tradition due to their effectiveness, either alone or as base models in broader ensembles. Recent…

We propose and study a multi-scale approach to vector quantization. We develop an algorithm, dubbed reconstruction trees, inspired by decision trees. Here the objective is parsimonious reconstruction of unsupervised data, rather than…

Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…

Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…

Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…

Convolutional Neural Networks (CNNs) are known to be significantly over-parametrized, and difficult to interpret, train and adapt. In this paper, we introduce a structural regularization across convolutional kernels in a CNN. In our…

Kernel density estimation is a popular method for estimating unseen probability distributions. However, the convergence of these classical estimators to the true density slows down in high dimensions. Moreover, they do not define meaningful…

We consider the analysis of high dimensional data given in the form of a matrix with columns consisting of observations and rows consisting of features. Often the data is such that the observations do not reside on a regular grid, and the…

In many modern applications, including analysis of gene expression and text documents, the data are noisy, high-dimensional, and unordered--with no particular meaning to the given order of the variables. Yet, successful learning is often…

We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…

This paper provides a short and transparent solution for the covering cost of white-grey trees which play a crucial role in the algorithm of Bergeron {\it et al.}\ to compute the rearrangement distance between two multichromosomal genomes…

The standard approach to estimate species trees is to align a selected set of genes, concatenate the alignments and then estimate a consensus tree. However, individual genes contain differing levels of evolutionary information, either…

Tree kernels have demonstrated their ability to deal with hierarchical data, as the intrinsic tree structure often plays a discriminative role. While such kernels have been successfully applied to various domains such as nature language…

The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…