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A decision tree looks like a simple directed acyclic computational graph, where only the leaf nodes specify the output values and the non-terminals specify their tests or split conditions. From the numerical perspective, we express decision…
The class of Boolean combinations of tree languages recognized by deterministic top-down tree automata (also known as deterministic root-to-frontier automata) is studied. The problem of determining for a given regular tree language whether…
Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…
Tanglegrams are a special class of graphs appearing in applications concerning cospeciation and coevolution in biology and computer science. They are formed by identifying the leaves of two rooted binary trees. We give an explicit formula…
The class of fighting fish is a recently introduced model of branching surfaces generalizing parallelogram polyominoes. We can alternatively see them as gluings of cells, walks on the square lattice confined to the quadrant or shuffle of…
Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…
An out-branching of a directed graph is a rooted spanning tree with all arcs directed outwards from the root. We consider the problem of deciding whether a given directed graph D has an out-branching with at least k leaves (Directed…
We define simple variants of zip trees, called zip-zip trees, which provide several advantages over zip trees, including overcoming a bias that favors smaller keys over larger ones. We analyze zip-zip trees theoretically and empirically,…
Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…
Here we show that deciding whether two rooted binary phylogenetic trees on the same set of taxa permit a cherry-picking sequence, a special type of elimination order on the taxa, is NP-complete. This improves on an earlier result which…
Let $\Omega_n$ be the family of binary trees on $n$ vertices obtained by identifying the root of an rgood binary tree with a vertex of maximum eccentricity of a binary caterpillar. In the paper titled "On different middle parts of a tree…
It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…
A binary string of length $2^k$ induces the Boolean function of $k$ variables whose Shannon expansion is the given binary string. This Boolean function then is representable via a unique reduced ordered binary decision diagram (ROBDD). The…
We consider drawings of trees in which all edges incident to leaves can be extended to infinite rays without crossing, partitioning the plane into infinite convex polygons. Among all such drawings we seek the one maximizing the angular…
We consider an index data structure for similar strings. The generalized suffix tree can be a solution for this. The generalized suffix tree of two strings $A$ and $B$ is a compacted trie representing all suffixes in $A$ and $B$. It has…
Reachability is the problem of deciding whether there is a path from one vertex to the other in the graph. Standard graph traversal algorithms such as DFS and BFS take linear time to decide reachability however their space complexity is…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Probabilistic programming languages and other machine learning applications often require samples to be generated from a categorical distribution where the probability of each one of $n$ categories is specified as a parameter. If the…
Consider the Aldous Markov chain on the space of rooted binary trees with $n$ labeled leaves in which at each transition a uniform random leaf is deleted and reattached to a uniform random edge. Now, fix $1\le k < n$ and project the leaf…
We study a general procedure that builds random $\mathbb R$-trees by gluing recursively a new branch on a uniform point of the pre-existing tree. The aim of this paper is to see how the asymptotic behavior of the sequence of lengths of…