Related papers: Summarizing Diverging String Sequences, with Appli…
Mixed-integer optimisation problems can be computationally challenging. Here, we introduce and analyse two efficient algorithms with a specific sequential design that are aimed at dealing with sampled problems within this class. At each…
We study the problem of learning a hierarchical tree representation of data from labeled samples, taken from an arbitrary (and possibly adversarial) distribution. Consider a collection of data tuples labeled according to their hierarchical…
Tanglegrams are a special class of graphs appearing in applications concerning cospeciation and coevolution in biology and computer science. They are formed by identifying the leaves of two rooted binary trees. We give an explicit formula…
We present a new efficient method for approximate search in electronic lexica. Given an input string (the pattern) and a similarity threshold, the algorithm retrieves all entries of the lexicon that are sufficiently similar to the pattern.…
We study distributed optimization problems over a network when the communication between the nodes is constrained, and so information that is exchanged between the nodes must be quantized. This imperfect communication poses a fundamental…
In this note, we first introduce a new problem called the longest common subsequence and substring problem. Let $X$ and $Y$ be two strings over an alphabet $\Sigma$. The longest common subsequence and substring problem for $X$ and $Y$ is to…
A string matching -- and more generally, sequence matching -- algorithm is presented that has a linear worst-case computing time bound, a low worst-case bound on the number of comparisons (2n), and sublinear average-case behavior that is…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
Tasks that model the relation between pairs of tokens in a string are a vital part of understanding natural language. Such tasks, in general, require exhaustive pair-wise comparisons of tokens, thus having a quadratic runtime complexity in…
Single-level density-based approach has long been widely acknowledged to be a conceptually and mathematically convincing clustering method. In this paper, we propose an algorithm called "best-scored clustering forest" that can obtain the…
The binary string matching problem consists in finding all the occurrences of a pattern in a text where both strings are built on a binary alphabet. This is an interesting problem in computer science, since binary data are omnipresent in…
Based on the Breslauer-Italiano online suffix tree construction algorithm (2013) with double logarithmic worst-case guarantees on the update time per letter, we develop near-real-time algorithms for several classical problems on strings,…
The past decade has witnessed substantial developments in string solving. Motivated by the complexity of string solving strategies adopted in existing string solvers, we investigate a simple and generic method for solving string…
Widespread use of string solvers in formal analysis of string-heavy programs has led to a growing demand for more efficient and reliable techniques which can be applied in this context, especially for real-world cases. Designing an…
Given a set of strings over a specified alphabet, identifying a median or consensus string that minimizes the total distance to all input strings is a fundamental data aggregation problem. When the Hamming distance is considered as the…
In the field of algorithmic analysis, one of the more well-known exercises is the subset sum problem. That is, given a set of integers, determine whether one or more integers in the set can sum to a target value. Aside from the brute-force…
Wavelet trees are widely used in the representation of sequences, permutations, text collections, binary relations, discrete points, and other succinct data structures. We show, however, that this still falls short of exploiting all of the…
String data are often disseminated to support applications such as location-based service provision or DNA sequence analysis. This dissemination, however, may expose sensitive patterns that model confidential knowledge. In this paper, we…
DNA sequence alignment is important today as it is usually the first step in finding gene mutation, evolutionary similarities, protein structure, drug development and cancer treatment. Covid-19 is one recent example. There are many…
In this short note we present a comprehensive bibliography for the online exact string matching problem. The problem consists in finding all occurrences of a given pattern in a text. It is an extensively studied problem in computer science,…