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We consider the problem of designing an overlay network and routing mechanism that permits finding resources efficiently in a peer-to-peer system. We argue that many existing approaches to this problem can be modeled as the construction of…
We present new algorithms for the problem of multiple string matching of gapped patterns, where a gapped pattern is a sequence of strings such that there is a gap of fixed length between each two consecutive strings. The problem has…
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"…
We present an online algorithm to deal with pattern matching in strings. The problem we investigate is commonly known as string matching with mismatches in which the objective is to report the number of characters that match when a pattern…
The weighted ancestor problem is a well-known generalization of the predecessor problem to trees. It is known to require $\Omega(\log\log n)$ time for queries provided $O(n\mathop{\mathrm{polylog}} n)$ space is available and weights are…
Reverse search is a convenient method for enumerating structured objects, that can be used both to address theoretical issues and to solve data mining problems. This method has already been successfully developed to handle unordered trees.…
Temporal graphs are a special class of graphs for which a temporal component is added to edges, that is, each edge possesses a set of times at which it is available and can be traversed. Many classical problems on graphs can be translated…
A linear arrangement is a mapping $\pi$ from the $n$ vertices of a graph $G$ to $n$ distinct consecutive integers. Linear arrangements can be represented by drawing the vertices along a horizontal line and drawing the edges as semicircles…
We introduce a new string matching problem called order-preserving matching on numeric strings where a pattern matches a text if the text contains a substring whose relative orders coincide with those of the pattern. Order-preserving…
Large-alphabet strings are common in scenarios such as information retrieval and natural-language processing. The efficient storage and processing of such strings usually introduces several challenges that are not witnessed in…
Positional Encodings (PEs) are used to inject word-order information into transformer-based language models. While they can significantly enhance the quality of sentence representations, their specific contribution to language models is not…
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…
We concern the problem of modifying the edge lengths of a tree in minimum total cost so that the prespecified $p$ vertices become the $p$-maxian with respect to the new edge lengths. This problem is called the inverse $p$-maxian problem on…
Most of the fastest-growing string collections today are repetitive, that is, most of the constituent documents are similar to many others. As these collections keep growing, a key approach to handling them is to exploit their…
Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…
In many real-world database systems, a large fraction of the data is represented by strings: sequences of letters over some alphabet. This is because strings can easily encode data arising from different sources. It is often crucial to…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
Tanglegrams are formed by taking two rooted binary trees $T$ and $S$ with the same number of leaves and uniquely matching each leaf in $T$ with a leaf in $S$. They are usually represented using layouts, which embed the trees and the…
Motivated by studies of data retrieval in polymer-based storage systems, we consider the problem of reconstructing a multiset of binary strings that have the same length and the same weight from the compositions of their prefixes and…
The problem of finding factors of a text string which are identical or similar to a given pattern string is a central problem in computer science. A generalised version of this problem consists in implementing an index over the text to…