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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)…
A Random Access query to a string $T\in [0..\sigma)^n$ asks for the character $T[i]$ at a given position $i\in [0..n)$. In $O(n\log\sigma)$ bits of space, this fundamental task admits constant-time queries. While this is optimal in the…
We consider the problem of encoding a string of length $n$ from an integer alphabet of size $\sigma$ so that access and substring equality queries (that is, determining the equality of any two substrings) can be answered efficiently. Any…
Monolingual word alignment is crucial to model semantic interactions between sentences. In particular, null alignment, a phenomenon in which words have no corresponding counterparts, is pervasive and critical in handling semantically…
Genetic algorithms have been used in recent decades to solve a broad variety of search problems. These algorithms simulate natural selection to explore a parameter space in search of solutions for a broad variety of problems. In this paper,…
The {\em longest common subsequence (LCS)} problem is a classic and well-studied problem in computer science. LCS is a central problem in stringology and finds broad applications in text compression, error-detecting codes and biological…
Motivated by the imminent growth of massive, highly redundant genomic databases, we study the problem of compressing a string database while simultaneously supporting fast random access, substring extraction and pattern matching to the…
We revisit Matrix Balancing, a pre-conditioning task used ubiquitously for computing eigenvalues and matrix exponentials. Since 1960, Osborne's algorithm has been the practitioners' algorithm of choice and is now implemented in most…
Random graph matching refers to recovering the underlying vertex correspondence between two random graphs with correlated edges; a prominent example is when the two random graphs are given by Erd\H{o}s-R\'{e}nyi graphs $G(n,\frac{d}{n})$.…
In this paper we consider graph algorithms in models of computation where the space usage (random accessible storage, in addition to the read only input) is sublinear in the number of edges $m$ and the access to input data is constrained.…
The problem of constructing optimal factoring automata arises in the context of unification factoring for the efficient execution of logic programs. Given an ordered set of $n$ strings of length $m$, the problem is to construct a trie-like…
We have attempted in this paper to reduce the number of checked condition through saving frequency of the tandem replicated words, and also using non-overlapping iterative neighbor intervals on plane sweep algorithm. The essential idea of…
Exchange type chromosome aberrations (ETCAs) are rearrangements of the genome that occur when chromosomes break and the resulting fragments rejoin with other fragments from other chromosomes. ETCAs are commonly observed in cancer cells and…
We study approximation algorithms for variants of the \emph{median string} problem, which asks for a string that minimizes the sum of edit distances from a given set of $m$ strings of length $n$. Only the straightforward $2$-approximation…
Sorting by reversals is an important problem in inferring the evolutionary relationship between two genomes. The problem of sorting unsigned permutation has been proven to be NP-hard. The best guaranteed error bounded is the 3/2-…
In 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), the task is to list the $k$-error occurrences of $P$ in…
In this paper, we reduce the complexity of approximating the correlation clustering problem from $O(m\times\left( 2+ \alpha (G) \right)+n)$ to $O(m+n)$ for any given value of $\varepsilon$ for a complete signed graph with $n$ vertices and…
In this paper, we propose a new feature selection method for unsupervised domain adaptation based on the emerging optimal transportation theory. We build upon a recent theoretical analysis of optimal transport in domain adaptation and show…
We develop a randomized approximation algorithm for the classical maximum coverage problem, which given a list of sets $A_1,A_2,\cdots, A_m$ and integer parameter $k$, select $k$ sets $A_{i_1}, A_{i_2},\cdots, A_{i_k}$ for maximum union…
Tandem duplication is the process of inserting a copy of a segment of DNA adjacent to the original position. Motivated by applications that store data in living organisms, Jain et al. (2017) proposed the study of codes that correct tandem…