Related papers: Improved Approximation Algorithms and Hardness Res…
In this paper we study the fine-grained complexity of finding exact and approximate solutions to problems in P. Our main contribution is showing reductions from exact to approximate solution for a host of such problems. As one (notable)…
A critical problem in the emerging high-throughput genotyping protocols is to minimize the number of polymerase chain reaction (PCR) primers required to amplify the single nucleotide polymorphism loci of interest. In this paper we study PCR…
Consider two independent random strings having same length and taking values uniformly in a common finite alphabet. We study the order of the variance of the length of the longest common subsequences (LCS) of these strings when long blocks,…
We study the problem of approximating the cone of positive semidefinite (PSD) matrices with a cone that can be described by smaller-sized PSD constraints. Specifically, we ask the question: "how closely can we approximate the set of…
The problem of finding a longest common subsequence of two main sequences with some constraint that must be a substring of the result (STR-IC-LCS) was formulated recently. It is a variant of the constrained longest common subsequence…
Compressed sensing (CS) demonstrates that a sparse, or compressible signal can be acquired using a low rate acquisition process below the Nyquist rate, which projects the signal onto a small set of vectors incoherent with the sparsity…
We study quantum algorithms for several fundamental string problems, including Longest Common Substring, Lexicographically Minimal String Rotation, and Longest Square Substring. These problems have been widely studied in the stringology…
Compressed sensing (CS) is a promising tool for reducing sampling costs. Current deep neural network (NN)-based CS methods face the challenges of collecting labeled measurement-ground truth (GT) data and generalizing to real applications.…
We study the fundamental problem of finding the best string to represent a given set, in the form of the Closest String problem: Given a set $X \subseteq \Sigma^d$ of $n$ strings, find the string $x^*$ minimizing the radius of the smallest…
We revisit the exact shortest unique substring (SUS) finding problem, and propose its approximate version where mismatches are allowed, due to its applications in subfields such as computational biology. We design a generic in-place…
In the 2-Vertex-Connected Spanning Subgraph problem (2-VCSS), we are given an undirected graph $G$, and the objective is to find a 2-vertex-connected spanning subgraph $S$ of $G$ with the minimum number of edges. In the context of…
Low rank matrix approximation is an important tool in machine learning. Given a data matrix, low rank approximation helps to find factors, patterns and provides concise representations for the data. Research on low rank approximation…
One of the most fundamental method for comparing two given strings $A$ and $B$ is the longest common subsequence (LCS), where the task is to find (the length) of an LCS of $A$ and $B$. In this paper, we deal with the STR-IC-LCS problem…
Strings are a natural representation of biological data such as DNA, RNA and protein sequences. The problem of finding a string that summarizes a set of sequences has direct application in relative compression algorithms for genome and…
In the recent years, DNA has emerged as a potentially viable storage technology. DNA synthesis, which refers to the task of writing the data into DNA, is perhaps the most costly part of existing storage systems. Accordingly, this high cost…
Relative compression, where a set of similar strings are compressed with respect to a reference string, is a very effective method of compressing DNA datasets containing multiple similar sequences. Relative compression is fast to perform…
Covers are a kind of quasiperiodicity in strings. A string $C$ is a cover of another string $T$ if any position of $T$ is inside some occurrence of $C$ in $T$. The shortest and longest cover arrays of $T$ have the lengths of the shortest…
In this paper we present $LCSk$++: a new metric for measuring the similarity of long strings, and provide an algorithm for its efficient computation. With ever increasing size of strings occuring in practice, e.g. large genomes of plants…
We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous…
A class of recovering algorithms for 1-bit compressive sensing (CS) named Soft Consistency Reconstructions (SCRs) are proposed. Recognizing that CS recovery is essentially an optimization problem, we endeavor to improve the characteristics…