Related papers: Deterministic Polynomial-Time Algorithms for Desig…
Suppose we have n keys, n access probabilities for the keys, and n+1 access probabilities for the gaps between the keys. Let h_min(n) be the minimal height of a binary search tree for n keys. We consider the problem to construct an optimal…
We investigate the complexity of several fundamental polynomial-time solvable problems on graphs and on matrices, when the given instance has low treewidth; in the case of matrices, we consider the treewidth of the graph formed by non-zero…
Given a string $s$ of length $n$ over a general alphabet and an integer $k$, the problem is to decide whether $s$ is a concatenation of $k$ nonempty palindromes. Two previously known solutions for this problem work in time $O(kn)$ and…
We develop catalytic algorithms for fundamental problems in algorithm design that run in polynomial time, use only $\mathcal{O}(\log(n))$ workspace, and use sublinear catalytic space matching the best-known space bounds of non-catalytic…
Given n elements with nonnegative integer weights w1,..., wn and an integer capacity C, we consider the counting version of the classic knapsack problem: find the number of distinct subsets whose weights add up to at most the given…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…
We consider the fundamental problems of size discovery and topology recognition in radio networks modeled by simple undirected connected graphs. Size discovery calls for all nodes to output the number of nodes in the graph, called its size,…
Due to its higher data density, longevity, energy efficiency, and ease of generating copies, DNA is considered a promising storage technology for satisfying future needs. However, a diverse set of errors including deletions, insertions,…
The Closest String Problem is an NP-hard problem that aims to find a string that has the minimum distance from all sequences that belong to the given set of strings. Its applications can be found in coding theory, computational biology, and…
We present the first optimal randomized algorithm for constructing the order-$k$ Voronoi diagram of $n$ points in two dimensions. The expected running time is $O(n\log n + nk)$, which improves the previous, two-decades-old result of Ramos…
We investigate the construction of prefix-free and fix-free codes with specified codeword compositions. We present a polynomial time algorithm which constructs a fix-free code with the same codeword compositions as a given code for a…
DNA, with remarkable properties of high density, durability, and replicability, is one of the most appealing storage media. Emerging DNA storage technologies use composite DNA letters, where information is represented by probability…
An elastic-degenerate string is a sequence of $n$ finite sets of strings of total length $N$, introduced to represent a set of related DNA sequences, also known as a pangenome. The ED string matching (EDSM) problem consists in reporting all…
In this paper, we consider two versions of the Text Assembling problem. We are given a sequence of strings $s^1,\dots,s^n$ of total length $L$ that is a dictionary, and a string $t$ of length $m$ that is texts. The first version of the…
We give a polynomial time algorithm to decode multivariate polynomial codes of degree $d$ up to half their minimum distance, when the evaluation points are an arbitrary product set $S^m$, for every $d < |S|$. Previously known algorithms can…
We tackle the problem of the randomized generation of slowly synchronizing deterministic automata (DFAs) by generating random primitive sets of matrices. We show that when the randomized procedure is too simple the exponent of the generated…
We give a deterministic polynomial space construction for nearly optimal eps-nets with respect to any input n-dimensional convex body K and norm |.|. More precisely, our algorithm can build and iterate over an eps-net of K with respect to…
Given a hierarchical plan (or schedule) with uncertain task times, we propose a deterministic polynomial (time and memory) algorithm for estimating the probability that its meets a deadline, or, alternately, that its {\em makespan} is less…
DNA sequences are prone to creating secondary structures by folding back on themselves by non-specific hybridization among its nucleotides. The formation of secondary structures makes the sequences chemically inactive towards synthesis and…
In modern age, the increasing complexity of computation and communication technology is leading us towards the necessity of new paradigm. As a result, unconventional approach like DNA coding theory is gaining considerable attention. The…