Related papers: Assessing the best edit in perturbation-based iter…
Given a static reference string $R$ and a source string $S$, a relative compression of $S$ with respect to $R$ is an encoding of $S$ as a sequence of references to substrings of $R$. Relative compression schemes are a classic model of…
We consider compact representations of collections of similar strings that support random access queries. The collection of strings is given by a rooted tree where edges are labeled by an edit operation (inserting, deleting, or replacing a…
Real-world data often comes in compressed form. Analyzing compressed data directly (without decompressing it) can save space and time by orders of magnitude. In this work, we focus on fundamental sequence comparison problems and try to…
String constraint solving refers to solving combinatorial problems involving constraints over string variables. String solving approaches have become popular over the last years given the massive use of strings in different application…
Iterative pruning is one of the most effective compression methods for pre-trained language models. We discovered that finding the optimal pruning decision is an equality-constrained 0-1 Integer Linear Programming problem. The solution to…
Approximate string matching is the problem of finding all factors of a text t of length n that are at a distance at most k from a pattern x of length m. Approximate circular string matching is the problem of finding all factors of t that…
Motivated by mass-spectrometry protein sequencing, we consider a simply-stated problem of reconstructing a string from the multiset of its substring compositions. We show that all strings of length 7, one less than a prime, or one less than…
Bayesian Optimization is ubiquitous in experimental design and black-box optimization for improving search efficiency. However, most existing approaches rely on regression models which are limited to fixed search spaces and structured,…
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…
Data represented as strings abounds in biology, linguistics, document mining, web search and many other fields. Such data often have a hierarchical structure, either because they were artificially designed and composed in a hierarchical…
We revisit classic string problems considered in the area of parameterized complexity, and study them through the lens of dynamic data structures. That is, instead of asking for a static algorithm that solves the given instance efficiently,…
Edit distance is a fundamental measure of distance between strings and has been widely studied in computer science. While the problem of estimating edit distance has been studied extensively, the equally important question of actually…
String matching is the problem of finding all the substrings of a text which match a given pattern. It is one of the most investigated problems in computer science, mainly due to its very diverse applications in several fields. Recently,…
The problem called "String reconstruction from substrings" is a mathematical model of sequencing by hybridization that plays an important role in DNA sequencing. In this problem, we are given a blackbox oracle holding an unknown string…
String kernels are typically used to compare genome-scale sequences whose length makes alignment impractical, yet their computation is based on data structures that are either space-inefficient, or incur large slowdowns. We show that a…
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…
Sparse coding consists in representing signals as sparse linear combinations of atoms selected from a dictionary. We consider an extension of this framework where the atoms are further assumed to be embedded in a tree. This is achieved…
Exact string matching has been a fundamental problem in computer science for decades because of many practical applications. Some are related to common procedures, such as searching in files and text editors, or, more recently, to more…
The normalized edit distance is one of the distances derived from the edit distance. It is useful in some applications because it takes into account the lengths of the two strings compared. The normalized edit distance is not defined in…
When eating spaghetti, one should have the sauce and noodles mixed instead of eating them separately. We argue that also in string solving, word equations and regular constraints are better mixed together than approached separately as in…