Related papers: Extending Common Intervals Searching from Permutat…
The scheduling problem consists of finding a common 1 in two remotely located N bit strings. Denote the number of 1s in the string with the fewer 1s by epsilon*N. Classically, it needs at least O(epsilon*N) bits of communication to find the…
This paper extends the foundational work of Dollma \emph{et al}. on codes for ordered composite DNA sequences. We consider the general setting with an alphabet of size $q$ and a resolution parameter $k$, moving beyond the binary ($q=2$)…
The move structure represents permutations with long contiguously permuted intervals in compressed space with optimal query time. They have become an important feature of compressed text indexes using space proportional to the number of…
Motivated by the problem of the definition of a distance between two sequences of characters, we investigate the so-called learning process of typical sequential data compression schemes. We focus on the problem of how a compression…
Finding the minimum distance of linear codes is an NP-hard problem. Traditionally, this computation has been addressed by means of the design of algorithms that find, by a clever exhaustive search, a linear combination of some generating…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realised by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
In the recent research of data mining, frequent structures in a sequence of graphs have been studied intensively, and one of the main concern is changing structures along a sequence of graphs that can capture dynamic properties of data. On…
Indexing intervals is a fundamental problem, finding a wide range of applications. Recent work on managing large collections of intervals in main memory focused on overlap joins and temporal aggregation problems. In this paper, we propose…
The interval graph for a set of intervals on a line consists of one vertex for each interval, and an edge for each intersecting pair of intervals. A probe interval graph is a variant that is motivated by an application to genomics, where…
Permutation entropy measures the complexity of deterministic time series via a data symbolic quantization consisting of rank vectors called ordinal patterns or just permutations. The reasons for the increasing popularity of this entropy in…
An algorithm for the generation of shuttling sequences is necessary for the operation of a linear segmented ion-trap quantum computer. The present work provides an implementation of an algorithm that produces sequences proved to be optimal…
What advantage do \emph{sequential} procedures provide over batch algorithms for testing properties of unknown distributions? Focusing on the problem of testing whether two distributions $\mathcal{D}_1$ and $\mathcal{D}_2$ on $\{1,\dots,…
To analyze the worst-case running time of branching algorithms, the majority of work in exponential time algorithms focuses on designing complicated branching rules over developing better analysis methods for simple algorithms. In the…
Quadratic Unconstrained Binary Optimization (QUBO) is a standard NP-hard optimization problem. Recently, it has gained renewed interest through quantum computing, as QUBOs directly reduce to the Ising model, on which quantum annealing…
The problem of sequentially finding an independent and identically distributed (i.i.d.) sequence that is drawn from a probability distribution $f_1$ by searching over multiple sequences, some of which are drawn from $f_1$ and the others of…
Sequences have become first class citizens in supervised learning thanks to the resurgence of recurrent neural networks. Many complex tasks that require mapping from or to a sequence of observations can now be formulated with the…
Sequence Alignment is the process of aligning biological sequences in order to identify similarities between multiple sequences. In this paper, a Quantum Algorithm for finding the optimal alignment between DNA sequences has been…
In this paper we give a definition of "algorithm," "finite algorithm," "equivalent algorithms," and what it means for a single algorithm to dominate a set of algorithms. We define a derived algorithm which may have a smaller mean execution…
Quantum-inspired classical algorithms has received much attention due to its exponential speedup compared to existing algorithms, under certain data storage assumptions. The improvements are noticeable in fundamental linear algebra tasks.…
We present methods for implementing arbitrary permutations of qubits under interaction constraints. Our protocols make use of previous methods for rapidly reversing the order of qubits along a path. Given nearest-neighbor interactions on a…