Related papers: Resampling Residuals on Phylogenetic Trees: Extend…
I propose an approach to identify, among several strategies of phylogenetic analysis, those producing the most accurate results. This approach is based on the hypothesis that the more a result is reproduced from independent data, the more…
UPGMA is a heuristic method identifying the least squares equidistant phylogenetic tree given empirical distance data among $n$ taxa. We study this classic algorithm using the geometry of the space of all equidistant trees with $n$ leaves,…
In phylogenetics, distances are often used to measure the incongruence between a pair of phylogenetic trees that are reconstructed by different methods or using different regions of genome. Motivated by the maximum parsimony principle in…
The development and use of dimension reduction methods is prevalent in modern statistical literature. This paper reviews a class of dimension reduction techniques which aim to simultaneously select relevant predictors and find clusters…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
Within the field of phylogenetics there is growing interest in measures for summarising the dissimilarity, or 'incongruence', of two or more phylogenetic trees. Many of these measures are NP-hard to compute and this has stimulated a…
Random forests construct each tree with a different, randomised representation of the feature space. Their uniform voting cannot correct errors in regions where trees with incorrect representations probabilistically outnumber correct ones,…
Image ranking is to rank images based on some known ranked images. In this paper, we propose an improved linear ordinal distance metric learning approach based on the linear distance metric learning model. By decomposing the distance metric…
Summary: Both theory and empirical evidence indicate that phylogenies (trees) of different genes (loci) do not display precisely matched topologies. This phylogenetic incongruence is attributed to the reticulated evolutionary history of…
This letter provides an adaptive resampling method. It determines the number of particles to resample so that the Kullback-Leibler distance (KLD) between distribution of particles before resampling and after resampling does not exceed a…
We consider the Orthogonal Least-Squares (OLS) algorithm for the recovery of a $m$-dimensional $k$-sparse signal from a low number of noisy linear measurements. The Exact Recovery Condition (ERC) in bounded noisy scenario is established for…
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…
Tree shape statistics quantify some aspect of the shape of a phylogenetic tree. They are commonly used to compare reconstructed trees to evolutionary models and to find evidence of tree reconstruction bias. Historically, to find a useful…
The problem of finding suitable point embedding or geometric configurations given only Euclidean distance information of point pairs arises both as a core task and as a sub-problem in a variety of machine learning applications. In this…
In learning to rank area, industry-level applications have been dominated by gradient boosting framework, which fits a tree using least square error principle. While in classification area, another tree fitting principle, weighted least…
Partial least squares (PLS) is a simple factorisation method that works well with high dimensional problems in which the number of observations is limited given the number of independent variables. In this article, we show that PLS can…
Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and the existence of polynomial time algorithms for their…
We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of…
Though the method of least squares has been used for a long time in solving signal processing problems, in the recent field of sparse recovery from compressed measurements, this method has not been given much attention. In this paper we…
The Random Projection Tree structures proposed in [Freund-Dasgupta STOC08] are space partitioning data structures that automatically adapt to various notions of intrinsic dimensionality of data. We prove new results for both the RPTreeMax…