Related papers: Measuring similarity between two mixture trees usi…
We propose a novel technique, termed compact shape trees, for computing correspondences of single-boundary 2-D shapes in O(n2) time. Together with zero or more features defined at each of n sample points on the shape's boundary, the compact…
Cartesian tree pattern matching consists of finding all the factors of a text that have the same Cartesian tree than a given pattern. There already exist theoretical and practical solutions for the exact case. In this paper, we propose the…
In this paper, we present a flexible and probabilistic framework for tracking topological features in time-varying scalar fields using merge trees and partial optimal transport. Merge trees are topological descriptors that record the…
In this paper, we consider the problem of reconstructing trees from traces in the tree edit distance model. Previous work by Davies et al. (2019) analyzed special cases of reconstructing labeled trees. In this work, we significantly expand…
Similarity search is an important problem in information retrieval. This similarity is based on a distance. Symbolic representation of time series has attracted many researchers recently, since it reduces the dimensionality of these high…
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The…
In a population with haploid reproduction any individual has a single parent in the previous generation. If all genealogical distances among pairs of individuals (generations from the closest common ancestor) are known it is possible to…
Understanding the mutational history of tumor cells is a critical endeavor in unraveling the mechanisms underlying cancer. Since the modeling of tumor cell evolution employs labeled trees, researchers are motivated to develop different…
There is a rising interest in mapping trees using satellite or aerial imagery, but there is no standardized evaluation protocol for comparing and enhancing methods. In dense canopy areas, the high variability of tree sizes and their spatial…
Pedigree graphs, or family trees, are typically constructed by an expensive process of examining genealogical records to determine which pairs of individuals are parent and child. New methods to automate this process take as input genetic…
Tree-shaped graphical models are widely used for their tractability. However, they unfortunately lack expressive power as they require committing to a particular sparse dependency structure. We propose a novel class of generative models…
In scientific visualization, scalar fields are often compared through edit distances between their merge trees. Typical tasks include ensemble analysis, feature tracking and symmetry or periodicity detection. Tree edit distances represent…
We consider a random tree and introduce a metric in the space of trees to define the ``mean tree'' as the tree minimizing the average distance to the random tree. When the resulting metric space is compact we have laws of large numbers and…
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…
The graph edit distance is used for comparing graphs in various domains. Due to its high computational complexity it is primarily approximated. Widely-used heuristics search for an optimal assignment of vertices based on the distance…
Fitting distances to tree metrics and ultrametrics are two widely used methods in hierarchical clustering, primarily explored within the context of numerical taxonomy. Given a positive distance function…
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 Subtree…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
A Discriminative Deep Forest (DisDF) as a metric learning algorithm is proposed in the paper. It is based on the Deep Forest or gcForest proposed by Zhou and Feng and can be viewed as a gcForest modification. The case of the fully…
Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Recently, a new distance measure has been proposed: the Maximum Parsimony (MP) distance. This is based on the…