Quantum Computing Approach for Alignment-Free Sequence Search and Classification

2012 ◽  
pp. 279-300
Author(s):  
Rao M. Kotamarti ◽  
Mitchell A. Thornton ◽  
Margaret H. Dunham
Keyword(s):  
Quantum Computing ◽  
Quantum Algorithms ◽  
Quantum Algorithm ◽  
Search Space ◽  
Classification Problem ◽  
Sequence Classification ◽  
Sequence Search ◽  
Quantum Version ◽  
Computing Approach ◽  
Candidate Set

Many classes of algorithms that suffer from large complexities when implemented on conventional computers may be reformulated resulting in greatly reduced complexity when implemented on quantum computers. The dramatic reductions in complexity for certain types of quantum algorithms coupled with the computationally challenging problems in some bioinformatics problems motivates researchers to devise efficient quantum algorithms for sequence (DNA, RNA, protein) analysis. This chapter shows that the important sequence classification problem in bioinformatics is suitable for formulation as a quantum algorithm. This chapter leverages earlier research for sequence classification based on Extensible Markov Model (EMM) and proposes a quantum computing alternative. The authors utilize sequence family profiles built using EMM methodology which is based on using pre-counted word data for each sequence. Then a new method termed quantum seeding is proposed for generating a key based on high frequency words. The key is applied in a quantum search based on Grover algorithm to determine a candidate set of models resulting in a significantly reduced search space. Given Z as a function of M models of size N, the quantum version of the seeding algorithm has a time complexity in the order of as opposed to O(Z) for the standard classic version for large values of Z.

Quantum Computing Approach for Alignment-Free Sequence Search and Classification

2013 ◽  
pp. 1705-1726
Author(s):  
Rao M. Kotamarti ◽  
Mitchell A. Thornton ◽  
Margaret H. Dunham
Keyword(s):  
Quantum Computing ◽  
Quantum Algorithms ◽  
Quantum Algorithm ◽  
Search Space ◽  
Classification Problem ◽  
Sequence Classification ◽  
Sequence Search ◽  
Quantum Version ◽  
Computing Approach ◽  
Candidate Set

Many classes of algorithms that suffer from large complexities when implemented on conventional computers may be reformulated resulting in greatly reduced complexity when implemented on quantum computers. The dramatic reductions in complexity for certain types of quantum algorithms coupled with the computationally challenging problems in some bioinformatics problems motivates researchers to devise efficient quantum algorithms for sequence (DNA, RNA, protein) analysis. This chapter shows that the important sequence classification problem in bioinformatics is suitable for formulation as a quantum algorithm. This chapter leverages earlier research for sequence classification based on Extensible Markov Model (EMM) and proposes a quantum computing alternative. The authors utilize sequence family profiles built using EMM methodology which is based on using pre-counted word data for each sequence. Then a new method termed quantum seeding is proposed for generating a key based on high frequency words. The key is applied in a quantum search based on Grover algorithm to determine a candidate set of models resulting in a significantly reduced search space. Given Z as a function of M models of size N, the quantum version of the seeding algorithm has a time complexity in the order of as opposed to O(Z) for the standard classic version for large values of Z.

scholarly journals Quantum computation of Groebner basis

2021 ◽  
Author(s):  
Ichio Kikuchi ◽  
Akihito Kikuchi
Keyword(s):  
Algebraic Geometry ◽  
Quantum Computation ◽  
Classical Method ◽  
Quantum Algorithms ◽  
Quantum Algorithm ◽  
Full Rank ◽  
Groebner Basis ◽  
Linear Solvers ◽  
Regular Sequences ◽  
Quantum Version

In this essay, we examine the feasibility of quantum computation of Groebner basis which is a fundamental tool of algebraic geometry. The classical method for computing Groebner basis is based on Buchberger's algorithm, and our question is how to adopt quantum algorithm there. A Quantum algorithm for finding the maximum is usable for detecting head terms of polynomials, which are required for the computation of S-polynomials. The reduction of S-polynomials with respect to a Groebner basis could be done by the quantum version of Gauss-Jordan elimination of echelon which represents polynomials. However, the frequent occurrence of zero-reductions of polynomials is an obstacle to the effective application of quantum algorithms. This is because zero-reductions of polynomials occur in non-full-rank echelons, for which quantum linear systems algorithms (through the inversion of matrices) are inadequate, as ever-known quantum linear solvers (such as Harrow-Hassidim-Lloyd) require the clandestine computations of the inverses of eigenvalues. Hence, for the quantum computation of the Groebner basis, the schemes to suppress the zero-reductions are necessary. To this end, the F5 algorithm or its variant (F5C) would be the most promising, as these algorithms have countermeasures against the occurrence of zero-reductions and can construct full-rank echelons whenever the inputs are regular sequences. Between these two algorithms, the F5C is the better match for algorithms involving the inversion of matrices.

scholarly journals AN OBSERVER-BASED DE-QUANTISATION OF DEUTSCH'S ALGORITHM

2011 ◽  
Vol 22 (01) ◽  
pp. 191-201
Author(s):  
CRISTIAN S. CALUDE ◽  
MATTEO CAVALIERE ◽  
RADU MARDARE
Keyword(s):  
Quantum Computing ◽  
Quantum Measurement ◽  
Quantum Algorithms ◽  
Quantum Algorithm ◽  
Classical Solutions ◽  
Finite State Automata ◽  
Computational Problem ◽  
Classical Simulation ◽  
Finite State ◽  
Classical Computing

Deutsch's problem is the simplest and most frequently examined example of computational problem used to demonstrate the superiority of quantum computing over classical computing. Deutsch's quantum algorithm has been claimed to be faster than any classical ones solving the same problem, only to be discovered later that this was not the case. Various de-quantised solutions for Deutsch's quantum algorithm—classical solutions which are as efficient as the quantum one—have been proposed in the literature. These solutions are based on the possibility of classically simulating "superpositions", a key ingredient of quantum algorithms, in particular, Deutsch's algorithm. The de-quantisation proposed in this note is based on a classical simulation of the quantum measurement achieved with a model of observed system. As in some previous de-quantisations of Deutsch's quantum algorithm, the resulting de-quantised algorithm is deterministic. Finally, we classify observers (as finite state automata) that can solve the problem in terms of their "observational power".

QUANTUM COMPUTING, GROVER'S SEARCH ALGORITHM AND ITS APPLICATIONS IN BIOINFORMATICS

COSMOS ◽  
2006 ◽  
Vol 02 (01) ◽  
pp. 71-80
Author(s):  
K. W. CHOO
Keyword(s):  
Quantum Computing ◽  
Mass Spectra ◽  
Search Algorithm ◽  
Quantum Algorithms ◽  
Quantum Algorithm ◽  
Protein Mass ◽  
Quantum Counting ◽  
Grover’S Search Algorithm ◽  
Counting Algorithm

This article reviews quantum computing and quantum algorithms. Some insights into its potential in speeding up computations are covered, with emphasis on the use of Grover's Search. In the last section, we discuss applications of quantum algorithm to bioinformatics. In particular, the extension of quantum counting algorithm to protein mass spectra counting is proposed.

scholarly journals qRobot: A Quantum Computing Approach in Mobile Robot Order Picking and Batching Problem Solver Optimization

Algorithms ◽  
2021 ◽  
Vol 14 (7) ◽  
pp. 194
Author(s):  
Parfait Atchade-Adelomou ◽  
Guillermo Alonso-Linaje ◽  
Jordi Albo-Canals ◽  
Daniel Casado-Fauli
Keyword(s):  
Quantum Computing ◽  
Quantum Algorithms ◽  
Quantum Algorithm ◽  
Order Picking ◽  
Public Access ◽  
Raspberry Pi ◽  
Problem Solver ◽  
Proof Of Concept ◽  
Distribution Centers ◽  
D Wave

This article aims to bring quantum computing to robotics. A quantum algorithm is developed to minimize the distance traveled in warehouses and distribution centers where order picking is applied. For this, a proof of concept is proposed through a Raspberry Pi 4, generating a quantum combinatorial optimization algorithm that saves the distance travelled and the batch of orders to be made. In case of computational need, the robot will be able to parallelize part of the operations in hybrid computing (quantum + classical), accessing CPUs and QPUs distributed in a public or private cloud. We developed a stable environment (ARM64) inside the robot (Raspberry) to run gradient operations and other quantum algorithms on IBMQ, Amazon Braket (D-Wave), and Pennylane locally or remotely. The proof of concept, when run in the above stated quantum environments, showed the execution time of our algorithm with different public access simulators on the market, computational results of our picking and batching algorithm, and analyze the quantum real-time execution. Our findings are that the behavior of the Amazon Braket D-Wave is better than Gate-based Quantum Computing over 20 qubits, and that AWS-Braket has better time performance than Qiskit or Pennylane.

The Essence of Quantum Computing

2018 ◽  
Author(s):  
Rajendra K. Bera
Keyword(s):  
Hilbert Space ◽  
Quantum Computing ◽  
Quantum Physics ◽  
Quantum Algorithms ◽  
Quantum Computers ◽  
Turing Machines ◽  
Classical Physics ◽  
Core Set ◽  
The World ◽  
Subordinate Role

It now appears that quantum computers are poised to enter the world of computing and establish its dominance, especially, in the cloud. Turing machines (classical computers) tied to the laws of classical physics will not vanish from our lives but begin to play a subordinate role to quantum computers tied to the enigmatic laws of quantum physics that deal with such non-intuitive phenomena as superposition, entanglement, collapse of the wave function, and teleportation, all occurring in Hilbert space. The aim of this 3-part paper is to introduce the readers to a core set of quantum algorithms based on the postulates of quantum mechanics, and reveal the amazing power of quantum computing.

scholarly journals Practical Security of RSA Against NTC-Architecture Quantum Computing Attacks

2021 ◽  
Author(s):  
Kai Li ◽  
Qing-yu Cai
Keyword(s):  
Quantum Computing ◽  
Ion Trap ◽  
Quantum Algorithms ◽  
Coherence Time ◽  
Quantum Computers ◽  
Quantum Time ◽  
Speed Up ◽  
Key Length ◽  
Concurrent Architecture ◽  
Qubit Gate

AbstractQuantum algorithms can greatly speed up computation in solving some classical problems, while the computational power of quantum computers should also be restricted by laws of physics. Due to quantum time-energy uncertainty relation, there is a lower limit of the evolution time for a given quantum operation, and therefore the time complexity must be considered when the number of serial quantum operations is particularly large. When the key length is about at the level of KB (encryption and decryption can be completed in a few minutes by using standard programs), it will take at least 50-100 years for NTC (Neighbor-only, Two-qubit gate, Concurrent) architecture ion-trap quantum computers to execute Shor’s algorithm. For NTC architecture superconducting quantum computers with a code distance 27 for error-correcting, when the key length increased to 16 KB, the cracking time will also increase to 100 years that far exceeds the coherence time. This shows the robustness of the updated RSA against practical quantum computing attacks.

scholarly journals Practical Quantum Computing

2021 ◽  
Vol 2 (1) ◽  
pp. 1-35
Author(s):  
Adrien Suau ◽  
Gabriel Staffelbach ◽  
Henri Calandra
Keyword(s):  
Wave Equation ◽  
Quantum Computer ◽  
Quantum Algorithms ◽  
Quantum Algorithm ◽  
Quantum Circuit ◽  
Equation Solving ◽  
Small Quantum ◽  
Quantum Wave ◽  
Variational Algorithms ◽  
The One

In the last few years, several quantum algorithms that try to address the problem of partial differential equation solving have been devised: on the one hand, “direct” quantum algorithms that aim at encoding the solution of the PDE by executing one large quantum circuit; on the other hand, variational algorithms that approximate the solution of the PDE by executing several small quantum circuits and making profit of classical optimisers. In this work, we propose an experimental study of the costs (in terms of gate number and execution time on a idealised hardware created from realistic gate data) associated with one of the “direct” quantum algorithm: the wave equation solver devised in [32]. We show that our implementation of the quantum wave equation solver agrees with the theoretical big-O complexity of the algorithm. We also explain in great detail the implementation steps and discuss some possibilities of improvements. Finally, our implementation proves experimentally that some PDE can be solved on a quantum computer, even if the direct quantum algorithm chosen will require error-corrected quantum chips, which are not believed to be available in the short-term.

scholarly journals Deep neural networks for quantum circuit mapping

2021 ◽  
Author(s):  
Giovanni Acampora ◽  
Roberto Schiattarella
Keyword(s):  
Neural Networks ◽  
Deep Neural Networks ◽  
Quantum Algorithms ◽  
Quantum Algorithm ◽  
Quantum Circuit ◽  
Machine Learning Techniques ◽  
Quantum Computers ◽  
Physical Constraints ◽  
Proper Mapping ◽  
Correct Execution

AbstractQuantum computers have become reality thanks to the effort of some majors in developing innovative technologies that enable the usage of quantum effects in computation, so as to pave the way towards the design of efficient quantum algorithms to use in different applications domains, from finance and chemistry to artificial and computational intelligence. However, there are still some technological limitations that do not allow a correct design of quantum algorithms, compromising the achievement of the so-called quantum advantage. Specifically, a major limitation in the design of a quantum algorithm is related to its proper mapping to a specific quantum processor so that the underlying physical constraints are satisfied. This hard problem, known as circuit mapping, is a critical task to face in quantum world, and it needs to be efficiently addressed to allow quantum computers to work correctly and productively. In order to bridge above gap, this paper introduces a very first circuit mapping approach based on deep neural networks, which opens a completely new scenario in which the correct execution of quantum algorithms is supported by classical machine learning techniques. As shown in experimental section, the proposed approach speeds up current state-of-the-art mapping algorithms when used on 5-qubits IBM Q processors, maintaining suitable mapping accuracy.

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