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Many common sequential data sources, such as source code and natural language, have a natural tree-structured representation. These trees can be generated by fitting a sequence to a grammar, yielding a hierarchical ordering of the tokens in…
The context tree source is a source model in which the occurrence probability of symbols is determined from a finite past sequence, and is a broader class of sources that includes i.i.d. and Markov sources. The proposed source model in this…
Supertree construction is the process by which a set of phylogenetic trees, each on a subset of the overall set X of species, is combined into a tree on the full set S. The traditional use of supertree methods is the assembly of a large…
For every natural number $n\geq 2$ and every finite sequence $L$ of natural numbers, we consider the set $UD_n(L)$ of all uniquely decodable codes over an $n$-letter alphabet with the sequence $L$ as the sequence of code word lengths, as…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
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…
Suppose $G$ is a tree. Graham's "Tree Reconstruction Conjecture" states that $G$ is uniquely determined by the integer sequence $|G|$, $|L(G)|$, $|L(L(G))|$, $|L(L(L(G)))|$, $\ldots$, where $L(H)$ denotes the line graph of the graph $H$.…
We present here a new and universal approach for the study of random and/or trees, unifying in one framework many different models, including some novel ones not yet understood in the literature. An and/or tree is a Boolean expression…
We prove that if a unimodular random rooted graph is recurrent, the number of ends of its uniform spanning tree is almost surely equal to the number of ends of the graph. Together with previous results in the transient case, this completely…
We prove that in both the free and the wired uniform spanning forest (FUSF and WUSF) of any unimodular random rooted network (in particular, of any Cayley graph), it is impossible to distinguish the connected components of the forest from…
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…
Automatic tree density estimation and counting using single aerial and satellite images is a challenging task in photogrammetry and remote sensing, yet has an important role in forest management. In this paper, we propose the first…
Algorithms for deriving Huffman codes and the recently developed algorithm for compiling PIFO trees to trees of fixed shape (Mohan et al. 2022) are similar, but work with different underlying algebraic operations. In this paper, we exploit…
We give a short and direct proof of a remarkable identity that arises in the enumeration of labeled trees with respect to their indegree sequence, where all edges are oriented from the vertex with lower label towards the vertex with higher…
Building on work by Desjarlais, Molina, Faase, and others, a general method is obtained for counting the number of spanning trees of graphs that are a product of an arbitrary graph and either a path or a cycle, of which grid graphs are a…
A symbolic-computational algorithm, fully implemented in Maple, is described, that computes explicit expressions for generating functions that enable the efficient computations of the expectation, variance, and higher moments, of the random…
The number of "nonequivalent" Huffman codes of length r over an alphabet of size t has been studied frequently. Equivalently, the number of "nonequivalent" complete t-ary trees has been examined. We first survey the literature, unifying…
Efficient methods for storing and querying are critical for scaling high-order n-gram language models to large corpora. We propose a language model based on compressed suffix trees, a representation that is highly compact and can be easily…
We use a sign-reversing involution to show that trees on the vertex set [n], considered to be rooted at 1, in which no vertex has exactly one child are counted by 1/n sum_{k=1}^{n} (-1)^(n-k) {n}-choose-{k} (n-1)!/(k-1)! k^(k-1). This…
An $r$-uniform hypergraph $H$ consists of a set of vertices $V$ and a set of edges whose elements are $r$-subsets of $V$. We define a hypertree to be a connected hypergraph which contains no cycles. A hypertree spans a hypergraph $H$ if it…