Related papers: Entropy Bounds for Grammar-Based Tree Compressors
In analogy to other concepts of a similar nature, we define the inducibility of a rooted binary tree. Given a fixed rooted binary tree $B$ with $k$ leaves, we let $\gamma(B,T)$ be the proportion of all subsets of $k$ leaves in $T$ that…
We describe general approach to classification of character sequences (texts, DNA) using relative entropy estimated by off-the-shelf compression and Markov Chains and find them precise enough. We also notice that the method for estimating…
We study compact straight-line embeddings of trees. We show that perfect binary trees can be embedded optimally: a tree with $n$ nodes can be drawn on a $\sqrt n$ by $\sqrt n$ grid. We also show that testing whether a given binary tree has…
A relaxed $k$-ary tree is an ordered directed acyclic graph with a unique source and sink in which every node has out-degree $k$. These objects arise in the compression of trees in which some repeated subtrees are factored and repeated…
We argue that Bekenstein entropy can be interpreted as the entropy of an effective string with a rescaled tension. Using the AdS/CFT correspondence we show that the Bekenstein entropy on the boundary CFT is given by the entropy of a string…
Topologically constrained genome-like polymers often double-fold into tree-like configurations. Here we calculate the exact number of tightly double-folded configurations available to a ring polymer in ideal conditions. For this purpose, we…
Treebanks, such as the Penn Treebank (PTB), offer a simple approach to obtaining a broad coverage grammar: one can simply read the grammar off the parse trees in the treebank. While such a grammar is easy to obtain, a square-root rate of…
The aim of this paper is to provide upper bounds for the entropy numbers of summation operators on trees in a critical case. In a recent paper [10] we elaborated a framework of weighted summation operators on general trees where we related…
An order-theoretic forest is a countable partial order such that the set of elements larger than any element is linearly ordered. It is an order-theoretic tree if any two elements have an upper-bound. The order type of a branch can be any…
A language L over a finite alphabet is growth-sensitive (or entropy sensitive) if forbidding any set of subwords F yields a sub-language L^F whose exponential growth rate (entropy) is smaller than that of L. Let (X, E, l) be an infinite,…
A well-known but rarely used approach to text categorization uses conditional entropy estimates computed using data compression tools. Text affinity scores derived from compressed sizes can be used for classification and ranking tasks, but…
Suffix trees are one of the most versatile data structures in stringology, with many applications in bioinformatics. Their main drawback is their size, which can be tens of times larger than the input sequence. Much effort has been put into…
This paper deals with the two fundamental problems concerning the handling of large n-gram language models: indexing, that is compressing the n-gram strings and associated satellite data without compromising their retrieval speed; and…
Traditional language models treat language as a finite state automaton on a probability space over words. This is a very strong assumption when modeling something inherently complex such as language. In this paper, we challenge this by…
I give a simple proof for the fact that positive entropy subshifts contain infinite binary trees where branching happens synchronously in each branch, and that the branching times form a set with positive lower asymptotic density.
We study the design of efficient algorithms for combinatorial pattern matching. More concretely, we study algorithms for tree matching, string matching, and string matching in compressed texts.
Motivated by the approach of random linear codes, a new distance in the vector space over a finite field is defined as the logarithm of the "surface area" of a Hamming ball with radius being the corresponding Hamming distance. It is named…
Pairwise ordered tree alignment are combinatorial objects that appear in RNA secondary structure comparison. However, the usual representation of tree alignments as supertrees is ambiguous, i.e. two distinct supertrees may induce identical…
In this experimental study we consider Steiner tree approximations that guarantee a constant approximation of ratio smaller than $2$. The considered greedy algorithms and approaches based on linear programming involve the incorporation of…
A pattern of a sequence is a sequence of integer indices with each index describing the order of first occurrence of the respective symbol in the original sequence. In a recent paper, tight general bounds on the block entropy of patterns of…