Related papers: A Linear Time Quantum Algorithm for Pairwise Seque…
The alignment of biological networks has the potential to teach us as much about biology and disease as has sequence alignment. Sequence alignment can be optimally solved in polynomial time. In contrast, network alignment is $NP$-hard,…
Quantum algorithms for searching one or more marked items on a d-dimensional lattice provide an extension of Grover's search algorithm including a spatial component. We demonstrate that these lattice search algorithms can be viewed in terms…
De novo DNA sequence assembly is based on finding paths in overlap graphs, which is a NP-hard problem. We developed a quantum algorithm for de novo assembly based on quantum walks in graphs. The overlap graph is partitioned repeatedly to…
Quantum computing has noteworthy speedup over classical computing by taking advantage of quantum parallelism, i.e., the superposition of states. In particular, quantum search is widely used in various computationally hard problems. Grover's…
The main approach to hybrid quantum-classical neural networks (QNN) is employing quantum computing to build a neural network (NN) that has quantum features, which is then optimized classically. Here, we propose a different strategy: to use…
The statistical properties of local alignment algorithms with gaps are analyzed theoretically for uncorrelated and correlated DNA sequences. In the vicinity of the log-linear phase transition, the statistics of alignment with gaps is shown…
Sequence comparison is a prerequisite to virtually all comparative genomic analyses. It is often realized by sequence alignment techniques, which are computationally expensive. This has led to increased research into alignment-free…
This paper describes a linear-time algorithm that finds the longest stretch in a sequence of real numbers (``scores'') in which the sum exceeds an input parameter. The algorithm also solves the problem of finding the longest interval in…
We present QCAM, a quantum analogue of Content-Addressable Memory (CAM), useful for finding matches in two sequences of bit-strings. Our QCAM implementation takes advantage of Grover's search algorithm and proposes a highly-optimized…
Since Grover's seminal work, quantum search has been studied in great detail. In the usual search problem, we have a collection of n items and we would like to find a marked item. We consider a new variant of this problem in which…
It has recently been shown that starting with a classical query algorithm (decision tree) and a guessing algorithm that tries to predict the query answers, we can design a quantum algorithm with query complexity $O(\sqrt{GT})$ where $T$ is…
DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
Dynamic programming is a cornerstone of graph-based optimization. While effective, it scales unfavorably with problem size. In this work, we present QuantGraph, a two-stage quantum-enhanced framework that casts local and global…
Grover's database search algorithm is the optimal algorithm for finding a desired object from an unsorted collection of items. Although it was discovered in the context of quantum computation, it is simple and versatile enough to be…
Ordered search is the task of finding an item in an ordered list using comparison queries. The best exact classical algorithm for this fundamental problem uses $\lceil \log_{2}{n}\rceil$ queries for a list of length $n$. Quantum computers…
Pairwise alignment of DNA sequencing data is a ubiquitous task in bioinformatics and typically represents a heavy computational burden. A standard approach to speed up this task is to compute "sketches" of the DNA reads (typically via…
Quantum computation has attracted much attention since it was shown by Shor and Grover the possibility to implement quantum algorithms able to realize, respectively, factoring and searching in a faster way than any other known classical…
The task of finding an entry in an unsorted list of $N$ elements famously takes $O(N)$ queries to an oracle for a classical computer and $O(\sqrt{N})$ queries for a quantum computer using Grover's algorithm. Reformulated as a spatial search…
A quantum walk on a lattice is a paradigm of a quantum search in a database. The database qubit strings are the lattice sites, qubit rotations are tunneling events, and the target site is tagged by an energy shift. For quantum walks on a…