Related papers: Matching Patterns with Variables under Hamming Dis…
This paper extends the problem of 2-dimensional palindrome search into the area of approximate matching. Using the Hamming distance as the measure, we search for 2D palindromes that allow up to $k$ mismatches. We consider two different…
In this paper we consider the Nonnegative Matrix Factorization (NMF) problem: given an (elementwise) nonnegative matrix $V \in \R_+^{m\times n}$ find, for assigned $k$, nonnegative matrices $W\in\R_+^{m\times k}$ and $H\in\R_+^{k\times n}$…
We study the complexity of approximating solution structure of the bijective weighted sentence alignment problem of DeNero and Klein (2008). In particular, we consider the complexity of finding an alignment that has a significant overlap…
Given a set of strings over a specified alphabet, identifying a median or consensus string that minimizes the total distance to all input strings is a fundamental data aggregation problem. When the Hamming distance is considered as the…
We study the Closest Pair Problem in Hamming metric, which asks to find the pair with the smallest Hamming distance in a collection of binary vectors. We give a new randomized algorithm for the problem on uniformly random input…
Following (Kolpakov et al., 2013; Gawrychowski and Manea, 2015), we continue the study of {\em $\alpha$-gapped repeats} in strings, defined as factors $uvu$ with $|uv|\leq \alpha |u|$. Our main result is the $O(\alpha n)$ bound on the…
In this paper, we study the pattern occurrence in $k$-ary words. We prove an explicit upper bound on the number of $k$-ary words avoiding any given pattern using a random walk argument. Additionally, we reproduce several already known…
A constant weight binary code consists of $n$-bit binary codewords, each with exactly $w$ bits equal to 1, such that any two codewords are at least Hamming distance $d$ apart. $A(n,d,w)$ is the maximum size of a constant weight binary code…
We report (to our knowledge) the first evaluation of Constraint Satisfaction as a computational framework for solving closest string problems. We show that careful consideration of symbol occurrences can provide search heuristics that…
A covering code is a set of codewords with the property that the union of balls, suitably defined, around these codewords covers an entire space. Generally, the goal is to find the covering code with the minimum size codebook. While most…
In the area of pattern avoidability the central role is played by special words called Zimin patterns. The symbols of these patterns are treated as variables and the rank of the pattern is its number of variables. Zimin type of a word $x$…
Weighted low rank approximation is a fundamental problem in numerical linear algebra, and it has many applications in machine learning. Given a matrix $M \in \mathbb{R}^{n \times n}$, a non-negative weight matrix $W \in \mathbb{R}_{\geq…
Pattern matching is a powerful tool which is part of many functional programming languages as well as computer algebra systems such as Mathematica. Among the existing systems, Mathematica offers the most expressive pattern matching.…
In this paper we consider stable matchings subject to assignment constraints. These are matchings that require certain assigned pairs to be included, insist that some other assigned pairs are not, and, importantly, are stable. Our main…
The idea that many important classes of signals can be well-represented by linear combinations of a small set of atoms selected from a given dictionary has had dramatic impact on the theory and practice of signal processing. For practical…
We consider a range of simply stated dynamic data structure problems on strings. An update changes one symbol in the input and a query asks us to compute some function of the pattern of length $m$ and a substring of a longer text. We give…
We find generating functions for the number of words avoiding certain patterns or sets of patterns on at most 2 distinct letters and determine which of them are equally avoided. We also find the exact number of words avoiding certain…
Let $W^{(n)}$ be the $n$-letter word obtained by repeating a fixed word $W$, and let $R_n$ be a random $n$-letter word over the same alphabet. We show several results about the length of the longest common subsequence (LCS) between…
The abelian pattern matching problem consists in finding all substrings of a text which are permutations of a given pattern. This problem finds application in many areas and can be solved in linear time by a naive sliding window approach.…
The classical pattern matching paradigm is that of seeking occurrences of one string - the pattern, in another - the text, where both strings are drawn from an alphabet set $\Sigma$. Assuming the text length is $n$ and the pattern length is…