Related papers: Cell-Probe Bounds for Online Edit Distance and Oth…
Dot plots are a standard method for local comparison of biological sequences. In a dot plot, a substring to substring distance is computed for all pairs of fixed-size windows in the input strings. Commonly, the Hamming distance is used…
The decades-old Pattern Matching with Edits problem, given a length-$n$ string $T$ (the text), a length-$m$ string $P$ (the pattern), and a positive integer $k$ (the threshold), asks to list all fragments of $T$ that are at edit distance at…
A pattern $\alpha$ is a string of variables and terminal letters. We say that $\alpha$ matches a word $w$, consisting only of terminal letters, if $w$ can be obtained by replacing the variables of $\alpha$ by terminal words. The matching…
Sum-rank Hamming codes are introduced in this work. They are essentially defined as the longest codes (thus of highest information rate) with minimum sum-rank distance at least $ 3 $ (thus one-error-correcting) for a fixed redundancy $ r $,…
We examine the complexity of the online Dictionary Matching with One Gap Problem (DMOG) which is the following. Preprocess a dictionary $D$ of $d$ patterns, where each pattern contains a special gap symbol that can match any string, so that…
We consider computing a longest palindrome in the streaming model, where the symbols arrive one-by-one and we do not have random access to the input. While computing the answer exactly using sublinear space is not possible in such a…
This paper develops a new technique for proving amortized, randomized cell-probe lower bounds on dynamic data structure problems. We introduce a new randomized nondeterministic four-party communication model that enables "accelerated",…
In the online sorting problem, we have an array $A$ of $n$ cells, and receive a stream of $n$ items $x_1,\dots,x_n\in [0,1]$. When an item arrives, we need to immediately and irrevocably place it into an empty cell. The goal is to minimize…
In the online sorting problem, a sequence of $n$ numbers in $[0, 1]$ (including $\{0,1\}$) have to be inserted in an array of size $m \ge n$ so as to minimize the sum of absolute differences between pairs of numbers occupying consecutive…
In this paper, we design new sublinear-time algorithms for solving the gap edit distance problem and for embedding edit distance to Hamming distance. For the gap edit distance problem, we give an $\tilde{O}(\frac{n}{k}+k^2)$-time greedy…
We present a near-linear time algorithm that approximates the edit distance between two strings within a polylogarithmic factor; specifically, for strings of length n and every fixed epsilon>0, it can compute a (log n)^O(1/epsilon)…
The edit distance is a way of quantifying how similar two strings are to one another by counting the minimum number of character insertions, deletions, and substitutions required to transform one string into the other. In this paper we…
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 develop a new technique for constructing sparse graphs that allow us to prove near-linear lower bounds on the round complexity of computing distances in the CONGEST model. Specifically, we show an $\widetilde{\Omega}(n)$ lower bound for…
We consider the classic Set Cover problem in the data stream model. For $n$ elements and $m$ sets ($m\geq n$) we give a $O(1/\delta)$-pass algorithm with a strongly sub-linear $\tilde{O}(mn^{\delta})$ space and logarithmic approximation…
The edit distance problem is a classical fundamental problem in computer science in general, and in combinatorial pattern matching in particular. The standard dynamic programming solution for this problem computes the edit-distance between…
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…
Although real-world text datasets, such as DNA sequences, are far from being uniformly random, average-case string searching algorithms perform significantly better than worst-case ones in most applications of interest. In this paper, we…
The edit distance between strings classically assigns unit cost to every character insertion, deletion, and substitution, whereas the Hamming distance only allows substitutions. In many real-life scenarios, insertions and deletions…
We study the power of Arthur-Merlin probabilistic proof systems in the data stream model. We show a canonical $\mathcal{AM}$ streaming algorithm for a wide class of data stream problems. The algorithm offers a tradeoff between the length of…