Related papers: Deterministic Polynomial-Time Algorithms for Desig…
In this paper, we construct linear codes over $\mathbb{Z}_4$ with bounded $GC$-content. The codes are obtained using a greedy algorithm over $\mathbb{Z}_4$. Further, upper and lower bounds are derived for the maximum size of DNA codes of…
Genome sequencing is the basis for many modern biological and medicinal studies. With recent technological advances, metagenomics has become a problem of interest. This problem entails the analysis and reconstruction of multiple DNA…
We present a polynomial-time pseudo-deterministic algorithm for constructing irreducible polynomial of degree $d$ over finite field $\mathbb{F}_q$. A pseudo-deterministic algorithm is allowed to use randomness, but with high probability it…
The dispersion of a point set $P\subset[0,1]^d$ is the volume of the largest box with sides parallel to the coordinate axes, which does not intersect $P$. Here, we show a construction of low-dispersion point sets, which can be deduced from…
We prove that, unless $\mathrm{P}=\mathrm{NP}$, no polynomial algorithm can approximate the minimum length of \sws for a given \san within a constant factor.
Protein structure prediction can be shown to be an NP-hard problem; the number of conformations grows exponentially with the number of residues. The native conformations of proteins occupy a very small subset of these, hence an exploratory,…
We consider an assortment optimization problem under the multinomial logit choice model with general covering constraints. In this problem, the seller offers an assortment that should contain a minimum number of products from multiple…
Due to its high data density and longevity, DNA is considered a promising medium for satisfying ever-increasing data storage needs. However, the diversity of errors that occur in DNA sequences makes efficient error-correction a challenging…
In this paper, we present a novel design strategy of DNA codes with length $3n$ over the non-chain ring $R=\mathbb{Z}_4+u\mathbb{Z}_4+u^2\mathbb{Z}_4$ with $64$ elements and $u^3=1$, where $n$ denotes the length of a code over $R$. We first…
We show how to determine whether a given pattern p of length m occurs in a given text t of length n in ${\tilde O}(\sqrt{n}+\sqrt{m})$\footnote{${\tilde O}$ allows for logarithmic factors in m and $n/m$} time, with inverse polynomial…
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…
Deep neural network-based architectures give promising results in various domains including pattern recognition. Finding the optimal combination of the hyper-parameters of such a large-sized architecture is tedious and requires a large…
We study the classical approximate string matching problem, that is, given strings $P$ and $Q$ and an error threshold $k$, find all ending positions of substrings of $Q$ whose edit distance to $P$ is at most $k$. Let $P$ and $Q$ have…
We consider the problem of deterministically enumerating all minimum $k$-cut-sets in a given hypergraph for any fixed $k$. The input here is a hypergraph $G = (V, E)$ with non-negative hyperedge costs. A subset $F$ of hyperedges is a…
The deviation of the observed frequency of a word $w$ from its expected frequency in a given sequence $x$ is used to determine whether or not the word is avoided. This concept is particularly useful in DNA linguistic analysis. The value of…
In [20] Goldwasser, Grossman and Holden introduced pseudo-deterministic interactive proofs for search problems where a powerful prover can convince a probabilistic polynomial time verifier that a solution to a search problem is canonical.…
The 0/1 knapsack problem is weakly NP-hard in that there exist pseudo-polynomial time algorithms based on dynamic programming that can solve it exactly. There are also the core branch and bound algorithms that can solve large randomly…
We study the integer minimization of a quasiconvex polynomial with quasiconvex polynomial constraints. We propose a new algorithm that is an improvement upon the best known algorithm due to Heinz (Journal of Complexity, 2005). This…
We consider a new family of codes, termed asymmetric Lee distance codes, that arise in the design and implementation of DNA-based storage systems and systems with parallel string transmission protocols. The codewords are defined over a…
Generalizations of plain strings have been proposed as a compact way to represent a collection of nearly identical sequences or to express uncertainty at specific text positions by enumerating all possibilities. While a plain string stores…