Related papers: Isomorphic unordered labeled trees up to substitut…
We consider the NP-hard Tree Containment problem that has important applications in phylogenetics. The problem asks if a given leaf-labeled network contains a subdivision of a given leaf-labeled tree. We develop a fast algorithm for the…
We investigate the problem of sequentially predicting the binary labels on the nodes of an arbitrary weighted graph. We show that, under a suitable parametrization of the problem, the optimal number of prediction mistakes can be…
In this paper we investigate undirected discrete graphical tree models when all the variables in the system are binary, where leaves represent the observable variables and where all the inner nodes are unobserved. A novel approach based on…
Algorithms to find optimal alignments among strings, or to find a parsimonious summary of a collection of strings, are well studied in a variety of contexts, addressing a wide range of interesting applications. In this paper, we consider…
As part of work to connect phylogenetics with machine learning, there has been considerable recent interest in vector encodings of phylogenetic trees. We present a simple new "ordered leaf attachment" (OLA) method for uniquely encoding a…
An L(2,1)-labeling of a graph $G$ is an assignment $f$ from the vertex set $V(G)$ to the set of nonnegative integers such that $|f(x)-f(y)|\ge 2$ if $x$ and $y$ are adjacent and $|f(x)-f(y)|\ge 1$ if $x$ and $y$ are at distance 2, for all…
Generating trees are a useful technique in the enumeration of various combinatorial objects, particularly restricted permutations. Quite often the generating tree for the set of permutations avoiding a set of patterns requires infinitely…
We give a representation for labeled ordered trees that supports labeled queries such as finding the i-th ancestor of a node with a given label. Our representation is succinct, namely the redundancy is small-o of the optimal space for…
We present an algorithm for computing a maximum agreement subtree of two unrooted evolutionary trees. It takes O(n^{1.5} log n) time for trees with unbounded degrees, matching the best known time complexity for the rooted case. Our…
We present a new probabilistic proof of Otter's asymptotic formula for the number of unlabelled trees with a given number of vertices. We additionally prove a new approximation result, showing that the total variation distance between…
Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…
Binary classification problems can be naturally modeled as bipartite graphs, where we attempt to classify right nodes based on their left adjacencies. We consider the case of labeled bipartite graphs in which some labels and edges are not…
We define a mapping from transition-based parsing algorithms that read sentences from left to right to sequence labeling encodings of syntactic trees. This not only establishes a theoretical relation between transition-based parsing and…
Alphabetic codes and binary search trees are combinatorial structures that abstract search procedures in ordered sets endowed with probability distributions. In this paper, we design new linear-time algorithms to construct alphabetic codes,…
We consider labelings of a finite regular tree by a finite alphabet subject to restrictions specified by a nonnegative transition matrix, propose an algorithm for determining whether the set of possible configurations on the last row of the…
LRM-Trees are an elegant way to partition a sequence of values into sorted consecutive blocks, and to express the relative position of the first element of each block within a previous block. They were used to encode ordinal trees and to…
We investigate the structural relationship between prefix-free codes over the binary alphabet and a class of unlabeled rooted trees, which we call \emph{symmetric} trees. We establish a canonical correspondence between prefix-free codes and…
Geometric trees are characterized by their tree-structured layout and spatially constrained nodes and edges, which significantly impacts their topological attributes. This inherent hierarchical structure plays a crucial role in domains such…
We show that the equivalence of deterministic linear top-down tree-to-word transducers is decidable in polynomial time. Linear tree-to-word transducers are non-copying but not necessarily order-preserving and can be used to express XML and…
We study the distribution and the popularity of left children on sets of treeshelves avoiding a pattern of size three. (Treeshelves are ordered binary increasing trees where every child is connected to its parent by a left or a right link.)…