Related papers: Deterministic Polynomial-Time Algorithms for Desig…
We study the problem of estimating the number of defective items $d$ within a pile of $n$ elements up to a multiplicative factor of $\Delta>1$, using deterministic group testing algorithms. We bring lower and upper bounds on the number of…
Given a DNF formula on n variables, the two natural size measures are the number of terms or size s(f), and the maximum width of a term w(f). It is folklore that short DNF formulas can be made narrow. We prove a converse, showing that…
In this paper, we give a matrix construction method for designing DNA codes that come from group matrix rings. We show that with our construction one can obtain reversible $G^k$-codes of length $kn,$ where $k, n \in \mathbb{N},$ over the…
DNA codes have garnered significant interest due to their utilization in digital media storage, cryptography, and DNA computing. In this paper, we first extend the results of constructing reversible group codes \cite{Cengellenmis} and…
We give efficient deterministic algorithms for converting randomized query algorithms into deterministic ones. We first give an algorithm that takes as input a randomized $q$-query algorithm $R$ with description length $N$ and a parameter…
In this paper, we consider the problem of constructing optimal average-length binary codes under the constraint that each codeword must contain at most $D$ ones, where $D$ is a given input parameter. We provide an $O(n^2D)$-time complexity…
In this work, we consider the Combinatorial RNA Design problem, a minimal instance of the RNA design problem which aims at finding a sequence that admits a given target as its unique base pair maximizing structure. We provide complete…
We present a polynomial time algorithm that constructs a deterministic parity automaton (DPA) from a given set of positive and negative ultimately periodic example words. We show that this algorithm is complete for the class of…
As a medium for cold data storage, DNA stands out as it promises significant gains in storage capacity and lifetime. However, it comes with its own data processing challenges to overcome. Constrained codes over the DNA alphabet…
In this work, we investigate a challenging problem, which has been considered to be an important criterion in designing codewords for DNA computing purposes, namely secondary structure avoidance in single-stranded DNA molecules. In short,…
The family of codeword stabilized codes encompasses the stabilizer codes as well as many of the best known nonadditive codes. However, constructing optimal $n$-qubit codeword stabilized codes is made difficult by two main factors. The first…
A method to construct and count all the linear codes (of arbitrary length) in $\mathbb{F}_{4}$ that are invariant under reverse permutation and that contain the repetition code is presented. These codes are suitable for constructing DNA…
Genomes may be analyzed from an information viewpoint as very long strings, containing functional elements of variable length, which have been assembled by evolution. In this work an innovative information theory based algorithm is…
A characteristic sample for a language $L$ and a learning algorithm $\textbf{L}$ is a finite sample of words $T_L$ labeled by their membership in $L$ such that for any sample $T \supseteq T_L$ consistent with $L$, on input $T$ the learning…
To ensure that text generated by large language models (LLMs) is in an expected format, constrained decoding proposes to enforce strict formal language constraints during generation. However, as we show in this work, not only do such…
Locally Decodable Codes (LDCs) are error-correcting codes $C:\Sigma^n\rightarrow \Sigma^m$ with super-fast decoding algorithms. They are important mathematical objects in many areas of theoretical computer science, yet the best…
We consider the fundamental derandomization problem of deterministically finding a satisfying assignment to a CNF formula that has many satisfying assignments. We give a deterministic algorithm which, given an $n$-variable…
In the distributed setting, the only existing constructions of \textit{sparse skeletons}, (i.e., subgraphs with $O(n)$ edges) either use randomization or large messages, or require $\Omega(D)$ time, where $D$ is the hop-diameter of the…
We give an $\mathcal{O}(n \log n)$-time, $\mathcal{O}(n)$-space algorithm for factoring a string into the minimum number of palindromic substrings. That is, given a string $S [1..n]$, in $\mathcal{O}(n \log n)$ time our algorithm returns…
We present a deterministic $(1+o(1))$-approximation $(n^{1/2+o(1)}+D^{1+o(1)})$-time algorithm for solving the single-source shortest paths problem on distributed weighted networks (the CONGEST model); here $n$ is the number of nodes in the…