Related papers: A New Approach to Regular & Indeterminate Strings
In this paper we study the fundamental problem of maintaining a dynamic collection of strings under the following operations: concat - concatenates two strings, split - splits a string into two at a given position, compare - finds the…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
We explore the notion of degree of asymmetry for integer sequences and related combinatorial objects. The degree of asymmetry is a new combinatorial statistic that measures how far an object is from being symmetric. We define this notion…
A string graph is an intersection graph of curves in the plane. A $k$-string graph is a graph with a string representation in which every pair of curves intersects in at most $k$ points. We introduce the class of $(=k)$-string graphs as a…
A degenerate string is a sequence of sets of characters. A generalized degenerate (GD) string extends this notion to the sequence of sets of strings, where strings of the same set are of equal length. Finding an exact match for a pattern…
An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all…
One cannot yet point to any firm string prediction. While many approximate string ground states are known with interesting properties, we do not have any argument that one or another describes what we observe around us, and for reasons…
We discuss different formulations and approaches to string theory and $ 2d$ quantum gravity. The generic idea to get a unique description of {\it many} different string vacua altogether is demonstrated on the examples in $ 2d$ conformal,…
An indexed sequence of strings is a data structure for storing a string sequence that supports random access, searching, range counting and analytics operations, both for exact matches and prefix search. String sequences lie at the core of…
Given a pattern $p = s_1x_1s_2x_2\cdots s_{r-1}x_{r-1}s_r$ such that $x_1,x_2,\ldots,x_{r-1}\in\{x,\overset{{}_{\leftarrow}}{x}\}$, where $x$ is a variable and $\overset{{}_{\leftarrow}}{x}$ its reversal, and $s_1,s_2,\ldots,s_r$ are…
A superstring of a set of strings correspond to a string which contains all the other strings as substrings. The problem of finding the Shortest Linear Superstring is a well-know and well-studied problem in stringology. We present here a…
Information valuable words are the strings with the significant deviation of real frequency from the expected one. The expected frequency is determined through the maximum entropy principle of the reconstructed (extended) frequency…
Flexible sparsity regularization means stably approximating sparse solutions of operator equations by using coefficient-dependent penalizations. We propose and analyse a general nonconvex approach in this respect, from both theoretical and…
We present a new data structure called the \emph{Compressed Random Access Memory} (CRAM) that can store a dynamic string $T$ of characters, e.g., representing the memory of a computer, in compressed form while achieving asymptotically…
In this paper, we present a novel approach to synthesize invariant clusters for polynomial programs. An invariant cluster is a set of program invariants that share a common structure, which could, for example, be used to save the needs for…
Detecting and measuring repetitiveness of strings is a problem that has been extensively studied in data compression and text indexing. However, when the data are structured in a non-linear way, like in the context of two-dimensional…
We define the parametric closure problem, in which the input is a partially ordered set whose elements have linearly varying weights and the goal is to compute the sequence of minimum-weight lower sets of the partial order as the weights…
An infinite number of distinct $d=1$ matrix models reproduce the perturbation theory of $d=2$ string theory. Due to constraints of causality, however, we argue that none of the existing constructions gives a consistent nonperturbative…
We consider the longest common subsequence (LCS) problem with the restriction that the common subsequence is required to consist of at least $k$ length substrings. First, we show an $O(mn)$ time algorithm for the problem which gives a…
In ongoing work to define a principled method for syntenic block discovery and structuring, work based on homology-derived constraints and a generalization of common intervals, we faced a fundamental computational problem: how to determine…