Related papers: Neighbor joining with phylogenetic diversity estim…
We study the problem of computing similarity joins under edit distance on a set of strings. Edit similarity joins is a fundamental problem in databases, data mining and bioinformatics. It finds important applications in data cleaning and…
K Nearest Neighbor (KNN) joins are used in scientific domains for data analysis, and are building blocks of several well-known algorithms. KNN-joins find the KNN of all points in a dataset. This paper focuses on a hybrid CPU/GPU approach…
Approximate nearest neighbor algorithms are used to speed up nearest neighbor search in a wide array of applications. However, current indexing methods feature several hyperparameters that need to be tuned to reach an acceptable…
Similarity join finds all pairs of close points within a given distance threshold. Many similarity join methods have been proposed, but they are usually not efficient on high-dimensional space due to the curse of dimensionality and…
Rearrangement operations transform a phylogenetic tree into another one and hence induce a metric on the space of phylogenetic trees. Popular operations for unrooted phylogenetic trees are NNI (nearest neighbour interchange), SPR (subtree…
The weighted k-nearest neighbors algorithm is one of the most fundamental non-parametric methods in pattern recognition and machine learning. The question of setting the optimal number of neighbors as well as the optimal weights has…
The class of self-nested trees presents remarkable compression properties because of the systematic repetition of subtrees in their structure. In this paper, we provide a better combinatorial characterization of this specific family of…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…
Comparative analyses of phylogenetic trees typically require identical taxon sets, however, in practice, trees often include distinct but overlapping taxa. Pruning non-shared leaves discards phylogenetic signal, whereas tree completion can…
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…
Join ordering is the NP-hard problem of selecting the most efficient order in which to evaluate joins (conjunctive, binary operators) in a database query. Because query execution performance critically depends on this choice, join ordering…
Agreement forests continue to play a central role in the comparison of phylogenetic trees since their introduction more than 25 years ago. More specifically, they are used to characterise several distances that are based on tree…
We present a method for reconstructing evolutionary trees from high-dimensional data, with a specific application to bird song spectrograms. We address the challenge of inferring phylogenetic relationships from phenotypic traits, like…
K-Nearest Neighbors (KNN) search is a fundamental algorithm in artificial intelligence software with applications in robotics, and autonomous vehicles. These wide-ranging applications utilize KNN either directly for simple classification or…
Regression trees and their ensemble methods are popular methods for nonparametric regression: they combine strong predictive performance with interpretable estimators. To improve their utility for locally smooth response surfaces, we study…
Nearest neighbor search is a basic computational tool used extensively in almost research domains of computer science specially when dealing with large amount of data. However, the use of nearest neighbor search is restricted for the…
We give a 2-approximation algorithm for the Maximum Agreement Forest problem on two rooted binary trees. This NP-hard problem has been studied extensively in the past two decades, since it can be used to compute the rooted Subtree…
We describe a combinatorial approach for investigating properties of rational numbers. The overall approach rests on structural bijections between rational numbers and familiar combinatorial objects, namely rooted trees. We emphasize that…
The nearest neighbor (NN) technique is very simple, highly efficient and effective in the field of pattern recognition, text categorization, object recognition etc. Its simplicity is its main advantage, but the disadvantages can't be…
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…