Related papers: A Linear Time Quantum Algorithm for Pairwise Seque…
The graph isomorphism problem asks whether two graphs are identical up to vertex relabeling. While the exact problem admits quasi-polynomial-time classical algorithms, many applications in molecular comparison, noisy network analysis, and…
In this paper, we present an optical computing method for string data alignment applicable to genome information analysis. By applying moire technique to spatial encoding patterns of deoxyribonucleic acid (DNA) sequences, association…
Quantum computing can empower machine learning models by enabling kernel machines to leverage quantum kernels for representing similarity measures between data. Quantum kernels are able to capture relationships in the data that are not…
Generic quantum search algorithm searches for target entity in an unsorted database by repeatedly applying canonical Grover's quantum rotation transform to reach near the vicinity of the target entity. Thus, upon measurement, there is a…
In the paper, we investigate Two Sets Intersection problem. Assume that we have two sets that are subsets of n objects. Sets are presented by two predicates that show which of n objects belong to these sets. We present a quantum algorithm…
The classical Sankoff algorithm for the simultaneous folding and alignment of homologous RNA sequences is highly influential, but it suffers from two major limitations in efficiency and modeling power. First, it takes $O(n^6)$ for two…
We proposed a probabilistic algorithm to solve the Multiple Sequence Alignment problem. The algorithm is a Simulated Annealing (SA) that exploits the representation of the Multiple Alignment between $D$ sequences as a directed polymer in…
One of the most important algorithmic applications of quantum walks is to solve spatial search problems. A widely used quantum algorithm for this problem, introduced by Childs and Goldstone [Phys. Rev. A 70, 022314 (2004)], finds a marked…
Sequence segmentation is a well-studied problem, where given a sequence of elements, an integer K, and some measure of homogeneity, the task is to split the sequence into K contiguous segments that are maximally homogeneous. A classic…
The paper considers the problem of finding a given substring in a text. It is known that the complexity of a classical search query in an unordered database is linear in the length of the text and a given substring. At the same time,…
We design quantum algorithms for maximum matching. Working in the query model, in both adjacency matrix and adjacency list settings, we improve on the best known algorithms for general graphs, matching previously obtained results for…
Graph matching, also known as network alignment, refers to finding a bijection between the vertex sets of two given graphs so as to maximally align their edges. This fundamental computational problem arises frequently in multiple fields…
Graph coloring is a computationally difficult problem, and currently the best known classical algorithm for $k$-coloring of graphs on $n$ vertices has runtimes $\Omega(2^n)$ for $k\ge 5$. The list coloring problem asks the following more…
We propose a couple of oracle construction methods for quantum pattern matching. We in turn show that one of the construct can be used with the Grover's search algorithm for exact and partial pattern matching, deterministically. The other…
In this paper we will present a quantum algorithm which works very efficiently in case of multiple matches within the search space and in the case of few matches, the algorithm performs classically. This allows us to propose a hybrid…
Grover's algorithm achieves a quadratic speedup over classical algorithms, but it is considered necessary to know the value of $\lambda$ exactly [Phys. Rev. Lett. 95, 150501 (2005); Phys. Rev. Lett. 113, 210501 (2014)], where $\lambda$ is…
Search-base algorithms have widespread applications in different scenarios. Grover's quantum search algorithms and its generalization, amplitude amplification, provide a quadratic speedup over classical search algorithms for unstructured…
Computational methods for discovering patterns of local correlations in sequences are important in computational biology. Here we show how to determine the optimal partitioning of aligned sequences into non-overlapping segments such that…
Drug discovery has become a main challenge in our society, following the Covid-19 pandemic. Even pharmaceutical companies are already using computing to accelerate drug discovery. They are increasingly interested in Quantum Computing with a…
We introduce an iterative method to search for time-optimal Hamiltonians that drive a quantum system between two arbitrary, and in general mixed, quantum states. The method is based on the idea of progressively improving the efficiency of…