Related papers: Neighbor joining with phylogenetic diversity estim…
Treewidth is a measure of how tree-like a graph is. It has many important algorithmic applications because many NP-hard problems on general graphs become tractable when restricted to graphs of bounded treewidth. Algorithms for problems on…
Net-trees are a general purpose data structure for metric data that have been used to solve a wide range of algorithmic problems. We give a simple randomized algorithm to construct net-trees on doubling metrics using $O(n\log n)$ time in…
K-Nearest Neighbours (k-NN) is a popular classification and regression algorithm, yet one of its main limitations is the difficulty in choosing the number of neighbours. We present a Bayesian algorithm to compute the posterior probability…
kNN is a very effective Instance based learning method, and it is easy to implement. Due to heterogeneous nature of data, noises from different possible sources are also widespread in nature especially in case of large-scale databases. For…
Similarity search is a fundamental building block for information retrieval on a variety of datasets. The notion of a neighbor is often based on binary considerations, such as the k nearest neighbors. However, considering that data is often…
The forest-of-octrees approach to parallel adaptive mesh refinement and coarsening (AMR) has recently been demonstrated in the context of a number of large-scale PDE-based applications. Although linear octrees, which store only leaf…
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…
In this paper, we lay the groundwork on the comparison of phylogenetic networks based on edge contractions and expansions as edit operations, as originally proposed by Robinson and Foulds to compare trees. We prove that these operations…
We consider the neighborhood tree induced by alternating the use of different neighborhood structures within a local search descent. We investigate the issue of designing a search strategy operating at the neighborhood tree level by…
The reverse $k$ nearest neighbor query finds all points that have the query point as one of their $k$ nearest neighbors, where the $k$NN query finds the $k$ closest points to its query point. Based on conics, we propose an efficent R$k$NN…
Gene tree/species tree reconciliation is a recent decisive progress in phylo-genetic methods, accounting for the possible differences between gene histories and species histories. Reconciliation consists in explaining these differences by…
We introduce our new binary tree code for neighbour search and gravitational force calculations in an N-particle system. The tree is built in a "top-down" fashion by "recursive coordinate bisection" where on each tree level we split the…
In this technical note, we introduce and analyze AWNN: an adaptively weighted nearest neighbor method for performing matrix completion. Nearest neighbor (NN) methods are widely used in missing data problems across multiple disciplines such…
Modern neural network technologies, including large language models, have achieved remarkable success in various applied artificial intelligence applications, however, they face a range of fundamental limitations. Among them are…
Communities play a crucial role to describe and analyse modern networks. However, the size of those networks has grown tremendously with the increase of computational power and data storage. While various methods have been developed to…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
Typing methods are widely used in the surveillance of infectious diseases, outbreaks investigation and studies of the natural history of an infection. And their use is becoming standard, in particular with the introduction of High…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
We present a new algorithm for the approximate near neighbor problem that combines classical ideas from group testing with locality-sensitive hashing (LSH). We reduce the near neighbor search problem to a group testing problem by…
Rotation distance between rooted binary trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. We give an efficient,…