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We consider the following model for sampling pairs of strings: $s_1$ is a uniformly random bitstring of length $n$, and $s_2$ is the bitstring arrived at by applying substitutions, insertions, and deletions to each bit of $s_1$ with some…
In the Pattern Masking for Dictionary Matching (PMDM) problem, we are given a dictionary $\mathcal{D}$ of $d$ strings, each of length $\ell$, a query string $q$ of length $\ell$, and a positive integer $z$, and we are asked to compute a…
We consider geometric instances of the Maximum Weighted Matching Problem (MWMP) and the Maximum Traveling Salesman Problem (MTSP) with up to 3,000,000 vertices. Making use of a geometric duality relationship between MWMP, MTSP, and the…
Multiple sequence alignment (MSA) has been one of the most important problems in bioinformatics for more decades and it is still heavily examined by many mathematicians and biologists. However, mostly because of the practical motivation of…
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…
We study a combinatorial problem arising from microarrays synthesis. The synthesis is done by a light-directed chemical process. The objective is to minimize unintended illumination that may contaminate the quality of experiments.…
In the Demand Strip Packing problem (DSP), we are given a time interval and a collection of tasks, each characterized by a processing time and a demand for a given resource (such as electricity, computational power, etc.). A feasible…
Given a pattern x of length m and a text y of length n, both over an ordered alphabet, the order-preserving pattern matching problem consists in finding all substrings of the text with the same relative order as the pattern. It is an…
Genome rearrangements are events in which large blocks of DNA exchange pieces during evolution. The analysis of such events is a tool for understanding evolutionary genomics, based on finding the minimum number of rearrangements to…
Since the Bin Packing Problem (BPP) is one of the main NP-hard problems, a lot of approximation algorithms have been suggested for it. It has been proven that the best algorithm for BPP has the approximation ratio of 3/2 and the time order…
This paper develops a new storage-optimal algorithm that provably solves generic semidefinite programs (SDPs) in standard form. This method is particularly effective for weakly constrained SDPs. The key idea is to formulate an approximate…
Most existing text-to-image person retrieval methods usually assume that the training image-text pairs are perfectly aligned; however, the noisy correspondence(NC) issue (i.e., incorrect or unreliable alignment) exists due to poor image…
Similarity matching and join of time series data streams has gained a lot of relevance in today's world that has large streaming data. This process finds wide scale application in the areas of location tracking, sensor networks, object…
Given a vertex-weighted connected graph $G = (V, E)$, the maximum weight internal spanning tree (MwIST for short) problem asks for a spanning tree $T$ of $G$ such that the total weight of the internal vertices in $T$ is maximized. The…
Symbol-pair codes introduced by Cassuto and Blaum in 2010 are designed to protect against the pair errors in symbol-pair read channels. One of the central themes in symbol-error correction is the construction of maximal distance separable…
We present experimental work on a primal-dual framework simultaneously approximating maximum cut and weighted fractional cut-covering instances. In this primal-dual framework, we solve a semidefinite programming (SDP) relaxation to either…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
In the Minimum Common String Partition Problem (MCSP), we are given two strings on input, and we want to partition both into the same collection of substrings, minimizing the number of the substrings in the partition. This combinatorial…
In the Shortest-Superstring problem, we are given a set of strings S and want to find a string that contains all strings in S as substrings and has minimum length. This is a classical problem in approximation and the best known…
Dynamic Time Warping (DTW) is a widely used similarity measure for comparing strings that encode time series data, with applications to areas including bioinformatics, signature verification, and speech recognition. The standard…