Related papers: String Reconstruction from Substring Compositions
We study the following substring suffix selection problem: given a substring of a string T of length n, compute its k-th lexicographically smallest suffix. This a natural generalization of the well-known question of computing the maximal…
Two strings are considered to have parameterized matching when there exists a bijection of the parameterized alphabet onto itself such that it transforms one string to another. Parameterized matching has application in software duplication…
Computing the {\em matching statistics} of a string $P[1..m]$ with respect to a text $T[1..n]$ is a fundamental problem which has application to genome sequence comparison. In this paper, we study the problem of computing the matching…
Motivated by applications to DNA storage, we study reconstruction and list-reconstruction schemes for integer vectors that suffer from limited-magnitude errors. We characterize the asymptotic size of the intersection of error balls in…
It is shown that from two strings that are partially random and independent (in the sense of Kolmogorov complexity) it is possible to effectively construct polynomially many strings that are random and pairwise independent. If the two…
Numbers and numerical vectors account for a large portion of data. However, recently the amount of string data generated has increased dramatically. Consequently, classifying string data is a common problem in many fields. The most widely…
Palindromes are strings that read the same forward and backward. The computation of palindromic structures within strings is a fundamental problem in string algorithms, being motivated by potential applications in formal language theory and…
We show that Closest Substring, one of the most important problems in the field of biological sequence analysis, is W[1]-hard when parameterized by the number k of input strings (and remains so, even over a binary alphabet). This problem is…
A graph is reconstructible if it is determined up to isomorphism by the multiset of its proper induced subgraphs. The reconstruction conjecture postulates that every graph of order at least 3 is reconstructible. We show that interval graphs…
In this paper we develop combinatorial techniques for the case of string algebras with the aim to give a characterization of string complexes with infinite minimal projective resolution. These complexes will be called \textit{periodic…
In the Shortest Common Superstring problem, one needs to find the shortest superstring for a set of strings. This problem is APX-hard, and many approximation algorithms were proposed, with the current best approximation factor of 2.466.…
In the paper, the Levenshtein's sequence reconstruction problem is considered in the case where at most $t$ substitution errors occur in each of the $N$ channels and the decoder outputs a list of length $\mathcal{L}$. Moreover, it is…
A method to construct and count all the linear codes (of arbitrary length) in $\mathbb{F}_{4}$ that are invariant under reverse permutation and that contain the repetition code is presented. These codes are suitable for constructing DNA…
There are at present two known string theories in $(2,2)$ dimensions. One of them is the well known $N=2$ string, and the other one is a more recently constructed $N=1$ spacetime supersymmetric string. They are both based on certain…
These lectures present some topics of string phenomenology and contain two parts. In the first part, I review the possibility of lowering the string scale in the TeV region, that provides a theoretical framework for solving the mass…
The coded trace reconstruction problem asks to construct a code $C\subset \{0,1\}^n$ such that any $x\in C$ is recoverable from independent outputs ("traces") of $x$ from a binary deletion channel (BDC). We present binary codes of rate…
The population recovery problem asks one to recover an unknown distribution over $n$-bit strings given access to independent noisy samples of strings drawn from the distribution. Recently, Ban et al. [BCF+19] studied the problem where the…
The theory of sequences, supported by many SMT solvers, can model program data types including bounded arrays and lists. Sequences are parameterized by the element data type and provide operations such as accessing elements, concatenation,…
In the Shortest Superstring problem, we are given a set of strings and we are asking for a common superstring, which has the minimum number of characters. The Shortest Superstring problem is NP-hard and several constant-factor approximation…
The present paper deals with the discrete inverse problem of reconstructing binary matrices from their row and column sums under additional constraints on the number and pattern of entries in specified minors. While the classical…