Related papers: Average Size of a Suffix Tree for Markov Sources
A suffix tree is a data structure used mainly for pattern matching. It is known that the space complexity of simple suffix trees is quadratic in the length of the string. By a slight modification of the simple suffix trees one gets the…
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…
Suffix trees are a fundamental data structure in stringology, but their space usage, though linear, is an important problem for its applications. We design and implement a new compressed suffix tree targeted to highly repetitive texts, such…
Common assumptions on the source producing the words inserted in a suffix trie with $n$ leaves lead to a $\log n$ height and saturation level. We provide an example of a suffix trie whose height increases faster than a power of $n$ and…
The precise analysis of the variance of the profile of a suffix tree has been a longstanding open problem. We analyze three regimes of the asymptotic growth of the variance of the profile of a suffix tree built from a randomly generated…
We define a new quantitative measure for an arbitrary factorial language: the entropy of a random walk in the prefix tree associated with the language; we call it Markov entropy. We relate Markov entropy to the growth rate of the language…
Graph tries are a new and interesting data structure proposed by Jacquet in 2014. They generalize the classical trie data structure which has found many applications in computer science and is one of the most popular data structure on…
Recently introduced and studied in arXiv:2407.07888, a self-similar Markov tree (ssMt) is a random decorated tree that vastly generalises the fragmentation tree. We study here the critical case that was left aside in arXiv:2407.07888.…
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…
Prediction suffix trees (PST) provide an effective tool for sequence modelling and prediction. Current prediction techniques for PSTs rely on exact matching between the suffix of the current sequence and the previously observed sequence. We…
We consider the problem of uniformly generating a spanning tree, of a connected undirected graph. This process is useful to compute statistics, namely for phylogenetic trees. We describe a Markov chain for producing these trees. For cycle…
Self-similar Markov trees constitute a remarkable family of random compact real trees carrying a decoration function that is positive on the skeleton. As the terminology suggests, they are self-similar objects that further satisfy a Markov…
Recently Kubica et al. (Inf. Process. Let., 2013) and Kim et al. (submitted to Theor. Comp. Sci.) introduced order-preserving pattern matching. In this problem we are looking for consecutive substrings of the text that have the same "shape"…
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…
This work builds upon the recent monograph [5] on self-similar Markov trees. A self-similar Markov tree is a random real tree equipped with a function from the tree to $[0,\infty)$ that we call the decoration. Here, we construct local time…
We introduce a new metric of match, called Cartesian tree matching, which means that two strings match if they have the same Cartesian trees. Based on Cartesian tree matching, we define single pattern matching for a text of length n and a…
Suffix trees are key and efficient data structure for solving string problems. A suffix tree is a compressed trie containing all the suffixes of a given text of length $n$ with a linear construction cost. In this work, we introduce an…
In this paper we study the structure of suffix trees. Given an unlabeled tree $\tau$ on $n$ nodes and suffix links of its internal nodes, we ask the question "Is $\tau$ a suffix tree?", i.e., is there a string $S$ whose suffix tree has the…
Traditional studies of memory for meaningful narratives focus on specific stories and their semantic structures but do not address common quantitative features of recall across different narratives. We introduce a statistical ensemble of…
We solve the problem of finding interspersed maximal repeats using a suffix array construction. As it is well known, all the functionality of suffix trees can be handled by suffix arrays, gaining practicality. Our solution improves the…