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Grammar-based compression, where one replaces a long string by a small context-free grammar that generates the string, is a simple and powerful paradigm that captures many popular compression schemes. Given a grammar, the random access…

Pseudo-Boolean constraints, also known as 0-1 Integer Linear Constraints, are used to model many real-world problems. A common approach to solve these constraints is to encode them into a SAT formula. The runtime of the SAT solver on such…

The problem of finding a center string that is `close' to every given string arises and has many applications in computational biology and coding theory. This problem has two versions: the Closest String problem and the Closest Substring…

Tries are popular data structures for storing a set of strings, where common prefixes are represented by common root-to-node paths. Over fifty years of usage have produced many variants and implementations to overcome some of their…

In this paper, we consider a generalized longest common subsequence problem, the string-excluding constrained LCS problem. For the two input sequences $X$ and $Y$ of lengths $n$ and $m$, and a constraint string $P$ of length $r$, the…

In this paper, we study the generalization properties of neural networks under input perturbations and show that minimal training data corruption by a few pixel modifications can cause drastic overfitting. We propose an evolutionary…

Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…

Compressed indexing is a powerful technique that enables efficient querying over data stored in compressed form, significantly reducing memory usage and often accelerating computation. While extensive progress has been made for…

Given a string $S$ of length $n$, the classic string indexing problem is to preprocess $S$ into a compact data structure that supports efficient subsequent pattern queries. In the \emph{deterministic} variant the goal is to solve the string…

Given a regular expression $R$ and a string $Q$, the regular expression parsing problem is to determine if $Q$ matches $R$ and if so, determine how it matches, e.g., by a mapping of the characters of $Q$ to the characters in $R$. Regular…

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…

Using electrocardiograms as an example, we demonstrate the characteristic problems that arise when modeling one-dimensional signals containing inaccurate repeating pattern by means of standard convolutional networks. We show that these…

Deep neural networks (DNN) have been used successfully in many scientific problems for their high prediction accuracy, but their application to genetic studies remains challenging due to their poor interpretability. In this paper, we…

The generalization mystery in deep learning is the following: Why do over-parameterized neural networks trained with gradient descent (GD) generalize well on real datasets even though they are capable of fitting random datasets of…

Machine learning has made tremendous progress in recent years, with models matching or even surpassing humans on a series of specialized tasks. One key element behind the progress of machine learning in recent years has been the ability to…

The approximate string matching is a fundamental and recurrent problem that arises in most computer science fields. This problem can be defined as follows: Let $D=\{x_1,x_2,\ldots x_d\}$ be a set of $d$ words defined on an alphabet…

The problem of matching a query string to a directed graph, whose vertices are labeled by strings, has application in different fields, from data mining to computational biology. Several variants of the problem have been considered,…

We consider string matching with variable length gaps. Given a string $T$ and a pattern $P$ consisting of strings separated by variable length gaps (arbitrary strings of length in a specified range), the problem is to find all ending…

We consider the Consensus Patterns problem, where, given a set of input strings, one is asked to extract a long-enough pattern which appears (with some errors) in all strings. We prove that this problem is W[1]-hard when parameterized by…

For a fixed property (graph class) ${\Pi}$, given a graph G and an integer k, the ${\Pi}$-deletion problem consists in deciding if we can turn $G$ into a graph with the property ${\Pi}$ by deleting at most $k$ edges. The ${\Pi}$-deletion…