Related papers: A New Algebraic Approach for String Reconstruction…
In the beautifully simple-to-state problem of trace reconstruction, the goal is to reconstruct an unknown binary string $x$ given random "traces" of $x$ where each trace is generated by deleting each coordinate of $x$ independently with…
Abelian string matching problems are becoming an object of considerable interest in last years. Very recently, Alatabbi et al. \cite{AILR2015} presented the first solution for the longest common Abelian factor problem for a pair of strings,…
In this paper, an exact algorithm in polynomial time is developed to solve unrestricted binary quadratic programs. The computational complexity is $O\left( n^{\frac{15}{2}}\right) $, although very conservative, it is sufficient to prove…
We investigate the structure and reconstruction complexity of Manacher arrays. First, we establish a combinatorial lower bound, proving that the number of rooted tandem repeat trees with $n+1$ genes exceeds the number of distinct Manacher…
Reconstruction codes are generalizations of error-correcting codes that can correct errors by a given number of noisy reads. The study of such codes was initiated by Levenshtein in 2001 and developed recently due to applications in modern…
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…
We revisit the classic combinatorial pattern matching problem of finding a longest common subsequence (LCS). For strings $x$ and $y$ of length $n$, a textbook algorithm solves LCS in time $O(n^2)$, but although much effort has been spent,…
Finding an Approximate Longest Common Substring (ALCS) within a given set $S=\{s_1,s_2,\ldots,s_m\}$ of $m \ge 2$ strings is a key problem in computational biology, such as identifying related mutations across multiple genetic sequences. We…
The problem of approximate string matching is important in many different areas such as computational biology, text processing and pattern recognition. A great effort has been made to design efficient algorithms addressing several variants…
Higher-dimensional rewriting is founded on a duality of rewrite systems and cell complexes, connecting computational mathematics to higher categories and homotopy theory: the two sides of a rewrite rule are two halves of the boundary of an…
The genome rearrangement problem computes the minimum number of operations that are required to sort all elements of a permutation. A block-interchange operation exchanges two blocks of a permutation which are not necessarily adjacent and…
Motivated by applications in DNA-based storage, we study explicit encoding and decoding schemes of binary strings satisfying locally balanced constraints, where the $(\ell,\delta)$-locally balanced constraint requires that the weight of any…
We consider the complexities of substitutive sequences over a binary alphabet. By studying various types of special words, we show that, knowing some initial values, its complexity can be completely formulated via a recurrence formula…
We study the problem of learning a node-labeled tree given independent traces from an appropriately defined deletion channel. This problem, tree trace reconstruction, generalizes string trace reconstruction, which corresponds to the tree…
In any string theory there is a hidden, twisted superconformal symmetry algebra, part of which is made up by the BRST current and the anti-ghost. We investigate how this algebra can be systematically constructed for strings with $N\!-\!2$…
String matching is a fundamental problem in algorithm. This study examines the development and construction of two reversible string-matching algorithms: a naive string-matching algorithm and the Rabin-Karp algorithm. The algorithms are…
Sublinear time quantum algorithms have been established for many fundamental problems on strings. This work demonstrates that new, faster quantum algorithms can be designed when the string is highly compressible. We focus on two popular and…
We study the problem of cutting a length-$n$ string of positive real numbers into $k$ pieces so that every piece has sum at least $b$. The problem can also be phrased as transforming such a string into a new one by merging adjacent numbers.…
Grammar compression is a general compression framework in which a string $T$ of length $N$ is represented as a context-free grammar of size $n$ whose language contains only $T$. In this paper, we focus on studying the limitations of…
Bit retrieval is the problem of reconstructing a binary sequence from its periodic autocorrelation, with applications in cryptography and x-ray crystallography. After defining the problem, with and without noise, we describe and compare…