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The randomized coordinate descent (RCD) method is a classical algorithm with simple, lightweight iterations that is widely used for various optimization problems, including the solution of positive semidefinite linear systems. As a linear…
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…
For a set of mulitple sequences, their patterns,Longest Common Subsequences (LCS) and Shortest Common Supersequences (SCS) represent different aspects of these sequences profile, and they can all be used for biological sequence comparisons…
Two strings of the same length are said to Cartesian-tree match (CT-match) if their Cartesian-trees are isomorphic [Park et al., TCS 2020]. Cartesian-tree matching is a natural model that allows for capturing similarities of numerical…
The Average Common Substring (ACS) is a popular alignment-free distance measure for phylogeny reconstruction. The ACS can be computed in O(n) space and time, where n=x+y is the input size. The compressed string matching is the study of…
In comparative genomic, the first step of sequence analysis is usually to decompose two or more genomes into syntenic blocks that are segments of homologous chromosomes. For the reliable recovery of syntenic blocks, noise and ambiguities in…
Longest Run Subsequence is a problem introduced recently in the context of the scaffolding phase of genome assembly (Schrinner et al., WABI 2020). The problem asks for a maximum length subsequence of a given string that contains at most one…
Unbalanced translocations are among the most frequent chromosomal alterations, accounted for 30\% of all losses of heterozygosity, a major genetic event causing inactivation of tumor suppressor genes. Despite of their central role in…
The minimum-weight $2$-edge-connected spanning subgraph (2-ECSS) problem is a natural generalization of the well-studied minimum-weight spanning tree (MST) problem, and it has received considerable attention in the area of network design.…
Multi-criteria decision-making often requires finding a small representative set from the database. A recently proposed method is the regret minimization set (RMS) query. RMS returns a size $r$ subset $S$ of dataset $D$ that minimizes the…
The Single Cut or Join (SCJ) operation on genomes, generalizing chromosome evolution by fusions and fissions, is the computationally simplest known model of genome rearrangement. While most genome rearrangement problems are already hard…
We study sketching and streaming algorithms for the Longest Common Subsequence problem (LCS) on strings of small alphabet size $|\Sigma|$. For the problem of deciding whether the LCS of strings $x,y$ has length at least $L$, we obtain a…
The efficient sparse coding and reconstruction of signal vectors via linear observations has received a tremendous amount of attention over the last decade. In this context, the automated learning of a suitable basis or overcomplete…
The problem of string reconstruction based on its substrings spectrum has received significant attention recently due to its applicability to DNA data storage and sequencing. In contrast to previous works, we consider in this paper a setup…
Truncated singular value decomposition (SVD), also known as the best low-rank matrix approximation, has been successfully applied to many domains such as biology, healthcare, and others, where high-dimensional datasets are prevalent. To…
Traditionally, data compression deals with the problem of concisely representing a data source, e.g. a sequence of letters, for the purpose of eventual reproduction (either exact or approximate). In this work we are interested in the case…
Compressed sensing (CS) provides an elegant framework for recovering sparse signals from compressed measurements. For example, CS can exploit the structure of natural images and recover an image from only a few random measurements. CS is…
We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly…
We consider a variety of NP-Complete network connectivity problems. We introduce a novel dual-based approach to approximating network design problems with cut-based linear programming relaxations. This approach gives a $3/2$-approximation…
In many real-world problems, we are dealing with collections of high-dimensional data, such as images, videos, text and web documents, DNA microarray data, and more. Often, high-dimensional data lie close to low-dimensional structures…