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An orientable sequence of order $n$ is a cyclic binary sequence such that each length-$n$ substring appears at most once \emph{in either direction}. Maximal length orientable sequences are known only for $n\leq 7$, and a trivial upper bound…
The problem of assembling DNA fragments starting from imperfect strings given by a sequencer, classified as NP hard when trying to get perfect answers, has a huge importance in several fields, because of its relation with the possibility of…
The change-making problem consists of representing a certain amount of money with the least possible number of coins, from a given, pre-established set of denominations. The greedy algorithm works by choosing the coins of largest possible…
In graph theory, the longest path problem is the problem of finding a simple path of maximum length in a given graph. For some small classes of graphs, the problem can be solved in polynomial time [2, 4], but it remains NP-hard on general…
In a classical scheduling problem, we are given a set of $n$ jobs of unit length along with precedence constraints and the goal is to find a schedule of these jobs on $m$ identical machines that minimizes the makespan. This problem is…
De novo DNA assembly is a fundamental task in Bioinformatics, and finding Eulerian paths on de Bruijn graphs is one of the dominant approaches to it. In most of the cases, there may be no one order for the de Bruijn graph that works well…
De Bruijn graph is one of the most important data structures used in de-novo genome assembly algorithms, especially for NGS data. There is a growing need for parallel data structures and algorithms due to the increasing number of cores in…
De Brujin graphs are widely used in bioinformatics for processing next-generation sequencing data. Due to a very large size of NGS datasets, it is essential to represent de Bruijn graphs compactly, and several approaches to this problem…
To our knowledge, there are only two known algorithms for constructing sparse and light spanners for general graphs. One of them is the greedy algorithm of Alth$\ddot{o}$fer et al. \cite{ADDJS93}, analyzed by Chandra et al. in SoCG'92. The…
The greedy spanner is the highest quality geometric spanner (in e.g. edge count and weight, both in theory and practice) known to be computable in polynomial time. Unfortunately, all known algorithms for computing it take Omega(n^2) time,…
Aligning a sequence to a walk in a labeled graph is a problem of fundamental importance to Computational Biology. For finding a walk in an arbitrary graph with $|E|$ edges that exactly matches a pattern of length $m$, a lower bound based on…
One of the main problems in all-optical packet-switched networks is the lack of optical buffers, and one feasible technology for the constructions of optical buffers is to use optical crossbar Switches and fiber Delay Lines (SDL). In this…
We study a construction published by Donald Knuth in 1965 yielding a completely uniformly distributed sequence of real numbers. Knuth's work is based on de Bruijn sequences of increasing orders and alphabet sizes, which grow exponentially…
Preferential attachment lies at the heart of many network models aiming to replicate features of real world networks. To simulate the attachment process, conduct statistical tests, or obtain input data for benchmarks, efficient algorithms…
Classic cycle-joining techniques have found widespread application in creating universal cycles for a diverse range of combinatorial objects, such as shorthand permutations, weak orders, orientable sequences, and various subsets of $k$-ary…
Binary time series data are very common in many applications, and are typically modelled independently via a Bernoulli process with a single probability of success. However, the probability of a success can be dependent on the outcome…
Permutation patterns and pattern avoidance have been intensively studied in combinatorics and computer science, going back at least to the seminal work of Knuth on stack-sorting (1968). Perhaps the most natural algorithmic question in this…
Finding efficient tensor contraction paths is essential for a wide range of problems, including model counting, quantum circuits, graph problems, and language models. There exist several approaches to find efficient paths, such as the…
The method of alternating projections involves projecting an element of a Hilbert space cyclically onto a collection of closed subspaces. It is known that the resulting sequence always converges in norm and that one can obtain estimates for…
The binary heap of Williams (1964) is a simple priority queue characterized by only storing an array containing the elements and the number of elements $n$ - here denoted a strictly implicit priority queue. We introduce two new strictly…