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In the small phylogeny problem we, are given a phylogenetic tree and gene orders of the extant species and our goal is to reconstruct all of the ancestral genomes so that the number of evolutionary operations is minimized. Algorithms for…
There is a huge difference in techniques and runtimes of distributed algorithms for problems that can be solved by a sequential greedy algorithm and those that cannot. A prime example of this contrast appears in the edge coloring problem:…
Pedigrees, or family trees, are graphs of family relationships that are used to study inheritance. A fundamental problem in computational biology is to find, for a pedigree with $n$ individuals genotyped at every site, a set of…
A run in a string is a maximal periodic substring. For example, the string $\texttt{bananatree}$ contains the runs $\texttt{anana} = (\texttt{an})^{3/2}$ and $\texttt{ee} = \texttt{e}^2$. There are less than $n$ runs in any length-$n$…
The Binary Jumbled String Matching problem is defined as: Given a string $s$ over $\{a,b\}$ of length $n$ and a query $(x,y)$, with $x,y$ non-negative integers, decide whether $s$ has a substring $t$ with exactly $x$ $a$'s and $y$ $b$'s.…
In the 60's, Knuth introduced stack-sorting and serial compositions of stacks. In particular, one significant question arise out of the work of Knuth: how to decide efficiently if a given permutation is sortable with 2 stacks in series?…
We show that any permutation of ${1,2,...,N}$ can be written as the product of two involutions. As a consequence, any permutation of the elements of an array can be performed in-place in parallel in time O(1). In the case where the…
In this paper, we study the following problem of reconstructing a simple polygon: Given a cyclically ordered vertex sequence of an unknown simple polygon P of n vertices and, for each vertex v of P, the sequence of angles defined by all the…
The proliferation of number of processing elements (PEs) in parallel computer systems, along with the use of more extensive parallelization of algorithms causes the interprocessor communications dominate VLSI chip space. This paper proposes…
Synthesis of DNA molecules offers unprecedented advances in storage technology. Yet, the microscopic world in which these molecules reside induces error patterns that are fundamentally different from their digital counterparts. Hence, to…
It is an open question whether there exists a polynomial-time algorithm for computing the rotation distances between pairs of extended ordered binary trees. The problem of computing the rotation distance between an arbitrary pair of trees,…
The {\em longest common subsequence (LCS)} problem is a classic and well-studied problem in computer science. LCS is a central problem in stringology and finds broad applications in text compression, error-detecting codes and biological…
We study variable time search, a form of quantum search where queries to different items take different time. Our first result is a new quantum algorithm that performs variable time search with complexity $O(\sqrt{T}\log n)$ where…
In 1969, Strassen shocked the world by showing that two n x n matrices could be multiplied in time asymptotically less than $O(n^3)$. While the recursive construction in his algorithm is very clear, the key gain was made by showing that 2 x…
We study the following rearrangement problem: Given $n$ words, rearrange and concatenate them so that the obtained string is lexicographically smallest (or largest, respectively). We show that this problem reduces to sorting the given words…
Consider an n-vertex graph G = (V,E) of maximum degree Delta, and suppose that each vertex v \in V hosts a processor. The processors are allowed to communicate only with their neighbors in G. The communication is synchronous, i.e., it…
The backwards diffusion equation is one of the classical ill-posed inverse problems, related to a wide range of applications, and has been extensively studied over the last 50 years. One of the first methods was that of {\it…
We give a positive answer to a question raised by Davis et al. ({\em Discrete Mathematics} 341, 2018), concerning permutations with the same pinnacle set. Given $\pi\in S_n$, a {\em pinnacle} of $\pi$ is an element $\pi_i$ ($i\neq 1,n$)…
We prove a theorem that reduces bounding the mixing time of a card shuffle to verifying a condition that involves only pairs of cards, then we use it to obtain improved bounds for two previously studied models. E. Thorp introduced the…
An iterative decoding algorithm for convolutional codes is presented. It successively processes $N$ consecutive blocks of the received word in order to decode the first block. A bound is presented showing which error configurations can be…