Related papers: Comparing and Aggregating Partially Resolved Trees
Geometry of networks endowed with a causal structure is discussed using the conventional framework of equilibrium statistical mechanics. The popular growing network models appear as particular causal models. We focus on a class of tree…
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…
Evolutionary relationships between species are represented by phylogenetic trees, but these relationships are subject to uncertainty due to the random nature of evolution. A geometry for the space of phylogenetic trees is necessary in order…
We destroy a finite tree of size $n$ by cutting its edges one after the other and in uniform random order. Informally, the associated cut-tree describes the genealogy of the connected components created by this destruction process. We…
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,…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
CONTEXT. Attack treesare a recommended threat modeling tool, but there is no established method to compare them. OBJECTIVE. We aim to establish a method to compare "real" attack trees, based on both the structure of the tree itself and the…
The problem of comparing probability distributions is at the heart of many tasks in statistics and machine learning. Established comparison methods treat the standard setting that the distributions are supported in the same space. Recently,…
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…
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…
Motivation: While the majority of gene histories found in a clade of organisms are expected to be generated by a common process (e.g. the coalescent process), it is well-known that numerous other coexisting processes (e.g. horizontal gene…
In this paper we give some estimates for nonlinear harmonic measures on trees. In particular, we estimate in terms of the size of a set $D$ the value at the origin of the solution to $ u(x)=F((x,0),\dots,(x,m-1))$ for every…
A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the…
We study a model of growing planar tree graphs where in each time step we separate the tree into two components by splitting a vertex and then connect the two pieces by inserting a new link between the daughter vertices. This model…
We determine the tree which maximizes the distance between characteristic set and subtree core over all trees on $n$ vertices. The asymptotic nature of this distance is also discussed. The problem of extremizing the distance between…
We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…
The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…
There is a growing interest in discovery of internet topology at the interface level. A new generation of highly distributed measurement systems is currently being deployed. Unfortunately, the research community has not examined the problem…
We show that the genealogy of any self-similar fragmentation process can be encoded in a compact measured real tree. Under some Malthusian hypotheses, we compute the fractal Hausdorff dimension of this tree through the use of a natural…
Tree perception is an essential building block toward autonomous forestry operations. Current developments generally consider input data from lidar sensors to solve forest navigation, tree detection and diameter estimation problems. Whereas…