Development of quantum machine learning for protein structure prediction

Authors

  • Nimbe Qureshi Bianco University of Kansas, USA
  • Sierra-Sosa Miyashita University of Kansas, USA
  • Pathak Pathak University of Kansas, USA

Keywords:

Hybrid Quantum-Classical Models, Protein Structure Prediction, Quantum Computing, Quantum Error Correction, Quantum Machine Learning

Abstract

Quantum Machine Learning (QML) holds immense potential in revolutionizing the prediction of protein structures, a critical challenge in computational biology. This research explores the application of quantum states, including superposition and entanglement, to capture the intricate and uncertain nature of protein conformations. Quantum gates and Fourier transforms are investigated as tools to manipulate and enhance quantum states, showcasing their ability to discern features essential for accurate predictions. The integration of hybrid quantum-classical models addresses the current limitations of quantum hardware, combining classical and quantum computing strengths. Quantum error correction is identified as a pivotal aspect for ensuring the reliability of predictions in the quantum domain. A numerical example is presented to illustrate the probabilistic nature of quantum states and the potential for obtaining optimized outcomes through quantum machine learning. The findings highlight the need for continued interdisciplinary collaboration between quantum physicists, computer scientists, and computational biologists to advance the field. While the exploration of QML for Protein Structure Prediction is in its early stages, the research emphasizes the transformative potential of quantum computing in unraveling the complexities of molecular structures.

References

N. Kitadai and S. Maruyama, “Origins of building blocks of life: A review,” Geosci. Front., vol. 9, no. 4, pp. 1117–1153, 2018.

S. Y. Liaw et al., “Wow, woo, win"-Healthcare students’ and facilitators’ experiences of interprofessional simulation in three-dimensional virtual world: A qualitative evaluation study,” Nurse Educ. Today, vol. 105, p. 105018, 2021.

B. Kuhlman and P. Bradley, “Advances in protein structure prediction and design,” Nat. Rev. Mol. Cell Biol., vol. 20, no. 11, pp. 681–697, 2019.

T. Siebenmorgen and M. Zacharias, “Computational prediction of protein–protein binding affinities,” Wiley Interdiscip. Rev. Comput. Mol. Sci., vol. 10, no. 3, p. e1448, 2020.

V. A. Jisna and P. B. Jayaraj, “Protein structure prediction: conventional and deep learning perspectives,” Protein J., vol. 40, no. 4, pp. 522–544, 2021.

A. Srivastava, T. Nagai, A. Srivastava, O. Miyashita, and F. Tama, “Role of computational methods in going beyond X-ray crystallography to explore protein structure and dynamics,” Int. J. Mol. Sci., vol. 19, no. 11, p. 3401, 2018.

C. Outeiral, M. Strahm, J. Shi, G. M. Morris, S. C. Benjamin, and C. M. Deane, “The prospects of quantum computing in computational molecular biology,” Wiley Interdiscip. Rev. Comput. Mol. Sci., vol. 11, no. 1, p. e1481, 2021.

L. Marchetti et al., “Quantum computing algorithms: getting closer to critical problems in computational biology,” Brief. Bioinform., vol. 23, no. 6, p. bbac437, 2022.

E. National Academies of Sciences and Medicine, “Quantum computing: progress and prospects,” 2019.

Y. Cao, J. Romero, and A. Aspuru-Guzik, “Potential of quantum computing for drug discovery,” IBM J. Res. Dev., vol. 62, no. 6, pp. 1–6, 2018.

T. Nguyen and N. T. Anh, “How Quantum Mechanics and Machine Learning Could Collaboratively Advance the Field of Pharmaceutical Research,” Eig. Rev. Sci. Technol., vol. 7, no. 1, pp. 266–276, 2023.

K. Egon, J. ROSINSKI, and L. KARL, “Quantum Machine Learning: The Confluence of Quantum Computing and AI,” 2023.

S. Bhuvaneswari, R. Deepakraj, S. Urooj, N. Sharma, and N. Pathak, “Computational Analysis: Unveiling the Quantum Algorithms for Protein Analysis and Predictions,” IEEE Access, 2023.

M. Avramouli, I. K. Savvas, A. Vasilaki, and G. Garani, “Unlocking the Potential of Quantum Machine Learning to Advance Drug Discovery,” Electronics, vol. 12, no. 11, p. 2402, 2023.

S. McWeeney et al., “Quantum Computing for Biomedical Computational and Data Sciences: A Joint DOE-NIH Roundtable,” USDOE Office of Science (SC)(United States), 2023.

R. Pearce and Y. Zhang, “Deep learning techniques have significantly impacted protein structure prediction and protein design,” Curr. Opin. Struct. Biol., vol. 68, pp. 194–207, 2021.

A. Ecoffet, J. Huizinga, J. Lehman, K. O. Stanley, and J. Clune, “First return, then explore,” Nature, vol. 590, no. 7847, pp. 580–586, 2021.

V. Dunjko and H. J. Briegel, “Machine learning & artificial intelligence in the quantum domain: a review of recent progress,” Reports Prog. Phys., vol. 81, no. 7, p. 74001, 2018.

C. Ciliberto et al., “Quantum machine learning: a classical perspective,” Proc. R. Soc. A Math. Phys. Eng. Sci., vol. 474, no. 2209, p. 20170551, 2018.

M. H. Ullah, R. Eskandarpour, H. Zheng, and A. Khodaei, “Quantum computing for smart grid applications,” IET Gener. Transm. Distrib., vol. 16, no. 21, pp. 4239–4257, 2022.

M. Kim, D. Venturelli, and K. Jamieson, “Towards hybrid classical-quantum computation structures in wirelessly-networked systems,” in Proceedings of the 19th ACM Workshop on Hot Topics in Networks, 2020, pp. 110–116.

P. Adebayo, F. Basaky, and E. Osaghae, “Variational Quantum-Classical Algorithms: A Review of Theory, Applications, and Opportunities,” UMYU Sci., vol. 2, no. 4, pp. 65–75, 2023.

R. K. Jha, “From Quantum Computing to Quantum-inspired Computation for Neuromorphic Advancement--A Survey,” Authorea Prepr., 2023.

A. Jacquier, O. Kondratyev, A. Lipton, and M. L. de Prado, Quantum Machine Learning and Optimisation in Finance: On the Road to Quantum Advantage. Packt Publishing Ltd, 2022.

T. Morawietz and N. Artrith, “Machine learning-accelerated quantum mechanics-based atomistic simulations for industrial applications,” J. Comput. Aided. Mol. Des., vol. 35, no. 4, pp. 557–586, 2021.

T. F. G. G. Cova and A. A. C. C. Pais, “Deep learning for deep chemistry: optimizing the prediction of chemical patterns,” Front. Chem., vol. 7, p. 809, 2019.

S. Pal, M. Bhattacharya, S. Dash, S.-S. Lee, and C. Chakraborty, “Future Potential of Quantum Computing and Simulations in Biological Science,” Mol. Biotechnol., pp. 1–18, 2023.

J. Tilly et al., “The variational quantum eigensolver: a review of methods and best practices,” Phys. Rep., vol. 986, pp. 1–128, 2022.

D. Maheshwari, B. Garcia-Zapirain, and D. Sierra-Sosa, “Quantum machine learning applications in the biomedical domain: A systematic review,” Ieee Access, 2022.

Y. Han et al., “Machine learning accelerates quantum mechanics predictions of molecular crystals,” Phys. Rep., vol. 934, pp. 1–71, 2021.

A. Baiardi, M. Christandl, and M. Reiher, “Quantum computing for molecular biology,” ChemBioChem, vol. 24, no. 13, p. e202300120, 2023.

J. Biamonte, P. Wittek, N. Pancotti, P. Rebentrost, N. Wiebe, and S. Lloyd, “Quantum machine learning,” Nature, vol. 549, no. 7671, pp. 195–202, 2017.

M. Rupp, A. Tkatchenko, K.-R. Müller, and O. A. Von Lilienfeld, “Fast and accurate modeling of molecular atomization energies with machine learning,” Phys. Rev. Lett., vol. 108, no. 5, p. 58301, 2012.

G. Montavon et al., “Learning invariant representations of molecules for atomization energy prediction,” Adv. Neural Inf. Process. Syst., vol. 25, 2012.

J. R. McClean, J. Romero, R. Babbush, and A. Aspuru-Guzik, “The theory of variational hybrid quantum-classical algorithms,” New J. Phys., vol. 18, no. 2, p. 23023, 2016.

P. J. J. O’Malley et al., “Scalable quantum simulation of molecular energies,” Phys. Rev. X, vol. 6, no. 3, p. 31007, 2016.

L. Alchieri, D. Badalotti, P. Bonardi, and S. Bianco, “An introduction to quantum machine learning: from quantum logic to quantum deep learning,” Quantum Mach. Intell., vol. 3, pp. 1–30, 2021.

A. Robert, P. K. Barkoutsos, S. Woerner, and I. Tavernelli, “Resource-efficient quantum algorithm for protein folding,” npj Quantum Inf., vol. 7, no. 1, p. 38, 2021.

Y. Zhang, H. Deng, Q. Li, H. Song, and L. Nie, “Optimizing quantum programs against decoherence: Delaying qubits into quantum superposition,” in 2019 International Symposium on Theoretical Aspects of Software Engineering (TASE), IEEE, 2019, pp. 184–191.

F. R. Cardoso, D. Z. Rossatto, G. P. L. M. Fernandes, G. Higgins, and C. J. Villas-Boas, “Superposition of two-mode squeezed states for quantum information processing and quantum sensing,” Phys. Rev. A, vol. 103, no. 6, p. 62405, 2021.

D. Paneru, E. Cohen, R. Fickler, R. W. Boyd, and E. Karimi, “Entanglement: quantum or classical?,” Reports Prog. Phys., vol. 83, no. 6, p. 64001, 2020.

A. Holmes, S. Johri, G. G. Guerreschi, J. S. Clarke, and A. Y. Matsuura, “Impact of qubit connectivity on quantum algorithm performance,” Quantum Sci. Technol., vol. 5, no. 2, p. 25009, 2020.

A. Shukla and P. Vedula, “A quantum approach for digital signal processing,” Eur. Phys. J. Plus, vol. 138, no. 12, pp. 1–24, 2023.

M. Mastriani, “Quantum-classical algorithm for an instantaneous spectral analysis of signals: a complement to Fourier Theory,” 2018.

P. Nimbe, B. A. Weyori, and A. F. Adekoya, “Models in quantum computing: a systematic review,” Quantum Inf. Process., vol. 20, no. 2, p. 80, 2021.

A. Ajagekar, T. Humble, and F. You, “Quantum computing based hybrid solution strategies for large-scale discrete-continuous optimization problems,” Comput. Chem. Eng., vol. 132, p. 106630, 2020.

S. S. Tannu and M. Qureshi, “Ensemble of diverse mappings: Improving reliability of quantum computers by orchestrating dissimilar mistakes,” in Proceedings of the 52nd Annual IEEE/ACM International Symposium on Microarchitecture, 2019, pp. 253–265.

M. Swathi and B. Rudra, “A novel approach for asymmetric quantum error correction with syndrome measurement,” IEEE Access, vol. 10, pp. 44669–44676, 2022.

P. Fuentes-Ugartemendia, “Error correction for reliable quantum computing,” 2022.

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Published

2023-11-30

How to Cite

Bianco, N. Q., Miyashita, S.-S., & Pathak, P. (2023). Development of quantum machine learning for protein structure prediction . Journal of Computer Science and Research (JoCoSiR), 1(4), 125–131. Retrieved from http://journal.aptikomsumut.org/index.php/jocosir/article/view/31