Quantum computing at the frontiers of biological sciences

Prashant S Emani^#^{1

2}, Jonathan Warrell^#^{1

2}, Alan Anticevic³, Stefan Bekiranov⁴, Michael Gandal⁵, Michael J McConnell⁶, Guillermo Sapiro⁷, Alán Aspuru-Guzik^{8

9

10

11}, Justin T Baker^{12

13}, Matteo Bastiani^{14

15}, John D Murray^{16

17}, Stamatios N Sotiropoulos^{14

18}, Jacob Taylor^{19

20}, Geetha Senthil²¹, Thomas Lehner^{22

23

24}, Mark B Gerstein^{25

26

27

28}, Aram W Harrow²⁹

Affiliations

¹ Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.
² Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
³ Yale School of Medicine, Department of Psychiatry, New Haven, CT, USA.
⁴ Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
⁵ Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA.
⁶ Lieber Institute for Brain Development, Baltimore, MD, USA.
⁷ Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA.
⁸ Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
⁹ Canadian Institute for Advanced Research (CIFAR) Artificial Intelligence Research Chair, Toronto, Ontario, Canada.
¹⁰ Vector Institute, Toronto, Ontario, Canada.
¹¹ Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
¹² Institute for Technology in Psychiatry, McLean Hospital, Belmont, MA, USA.
¹³ Department of Psychiatry, Harvard Medical School, Boston, MA, USA.
¹⁴ Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham, UK.
¹⁵ Wellcome Centre for Integrative Neuroimaging, FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, UK.
¹⁶ Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.
¹⁷ Department of Physics, Yale University, New Haven, CT, USA.
¹⁸ NIHR Nottingham Biomedical Research Centre, Queen's Medical Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK.
¹⁹ Joint Center for Quantum Information and Computer Science, University of Maryland, College Park, MD, USA.
²⁰ National Institute of Standards and Technology, Gaithersburg, MD, USA.
²¹ New York Genome Center, New York, NY, USA.
²² New York Genome Center, New York, NY, USA. tlehner@gmail.com.
²³ National Institute of Mental Health, Bethesda, MD, USA. tlehner@gmail.com.
²⁴ Neuropsychiatric Disease Genomics, New York Genome Center, New York, NY, USA. tlehner@gmail.com.
²⁵ Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA. mark@gersteinlab.org.
²⁶ Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. mark@gersteinlab.org.
²⁷ Department of Computer Science, Yale University, New Haven, CT, USA. mark@gersteinlab.org.
²⁸ Department of Statistics and Data Science, Yale University, New Haven, CT, USA. mark@gersteinlab.org.
²⁹ Center for Theoretical Physics, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA. aram@mit.edu.

^# Contributed equally.

PMID: 33398186
PMCID: PMC8254820
DOI: 10.1038/s41592-020-01004-3

Quantum computing at the frontiers of biological sciences

Prashant S Emani et al. Nat Methods. 2021 Jul.

. 2021 Jul;18(7):701-709.

doi: 10.1038/s41592-020-01004-3.

Authors

Affiliations

¹ Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA.
² Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA.
³ Yale School of Medicine, Department of Psychiatry, New Haven, CT, USA.
⁴ Department of Biochemistry and Molecular Genetics, University of Virginia School of Medicine, Charlottesville, VA, USA.
⁵ Department of Psychiatry, Semel Institute, David Geffen School of Medicine, University of California-Los Angeles, Los Angeles, CA, USA.
⁶ Lieber Institute for Brain Development, Baltimore, MD, USA.
⁷ Department of Electrical and Computer Engineering, Duke University, Durham, NC, USA.
⁸ Department of Chemistry, University of Toronto, Toronto, Ontario, Canada.
⁹ Canadian Institute for Advanced Research (CIFAR) Artificial Intelligence Research Chair, Toronto, Ontario, Canada.
¹⁰ Vector Institute, Toronto, Ontario, Canada.
¹¹ Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
¹² Institute for Technology in Psychiatry, McLean Hospital, Belmont, MA, USA.
¹³ Department of Psychiatry, Harvard Medical School, Boston, MA, USA.
¹⁴ Sir Peter Mansfield Imaging Centre, School of Medicine, University of Nottingham, Nottingham, UK.
¹⁵ Wellcome Centre for Integrative Neuroimaging, FMRIB Centre, Nuffield Department of Clinical Neurosciences, University of Oxford, John Radcliffe Hospital, Oxford, UK.
¹⁶ Department of Psychiatry, Yale University School of Medicine, New Haven, CT, USA.
¹⁷ Department of Physics, Yale University, New Haven, CT, USA.
¹⁸ NIHR Nottingham Biomedical Research Centre, Queen's Medical Centre, Nottingham University Hospitals NHS Trust, Nottingham, UK.
¹⁹ Joint Center for Quantum Information and Computer Science, University of Maryland, College Park, MD, USA.
²⁰ National Institute of Standards and Technology, Gaithersburg, MD, USA.
²¹ New York Genome Center, New York, NY, USA.
²² New York Genome Center, New York, NY, USA. tlehner@gmail.com.
²³ National Institute of Mental Health, Bethesda, MD, USA. tlehner@gmail.com.
²⁴ Neuropsychiatric Disease Genomics, New York Genome Center, New York, NY, USA. tlehner@gmail.com.
²⁵ Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT, USA. mark@gersteinlab.org.
²⁶ Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT, USA. mark@gersteinlab.org.
²⁷ Department of Computer Science, Yale University, New Haven, CT, USA. mark@gersteinlab.org.
²⁸ Department of Statistics and Data Science, Yale University, New Haven, CT, USA. mark@gersteinlab.org.
²⁹ Center for Theoretical Physics, Department of Physics, Massachusetts Institute of Technology, Cambridge, MA, USA. aram@mit.edu.

^# Contributed equally.

PMID: 33398186
PMCID: PMC8254820
DOI: 10.1038/s41592-020-01004-3

Abstract

Computing plays a critical role in the biological sciences but faces increasing challenges of scale and complexity. Quantum computing, a computational paradigm exploiting the unique properties of quantum mechanical analogs of classical bits, seeks to address many of these challenges. We discuss the potential for quantum computing to aid in the merging of insights across different areas of biological sciences.

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Conflict of interest statement

Competing interests

A.A. serves as a member of the Scientific Advisory Board of, consults for, has received grants from, and holds equity in BlackThorn Therapeutics. G. Sapiro consulted for Apple, Volvo, Restore3D and SIS, and has received speaking fees from Johnson & Johnson. J.T.B. has received consulting fees from BlackThorn Therapeutics, Niraxx Therapeutics, Verily Life Sciences, AbleTo Inc. and Pear Therapeutics, and has received consulting fees and equity from Mindstrong Inc. J.D.M. consults for, has received grants from, and holds equity in BlackThorn Therapeutics. A.W.H. has recently joined the Scientific Advisory Board of Zapata Computing, from which he expects income and equity.

Figures

**Fig. 1 |. Concepts in quantum computing.**
a, Conceptual illustration of bit versus qubit. The state of a qubit can be represented by a point on the unit sphere with the north and south poles corresponding to the states 0 and 1 of a classical bit. b, The state space of 3 qubits is a 2³-dimensional complex vector. c, Classical (number field sieve (NFS) algorithm) and quantum (Beckman–Chari–Devabhaktuni–Preskill (BCDP) implementation of Shor’s algorithm) run times for factoring integers. Shor’s algorithm for quantum computers yields an exponential speedup over the best known classical algorithm (panel c adapted with permission from ref. , R. Van Meter et al.).

**Fig. 2 |. Complexity of linking levels of analyses from genetics to human behavior.**
The challenge consists, in part, of the need to interrogate the enormous search space for determining the mapping across levels, which constitutes a many-to-many probabilistic problem. Computational innovation will be a key effort to help close these gaps. Portion of figure adapted with permission from ref. , Elsevier. Also shown are some of the ways in which QC can aid in the interrogation of these levels.

See this image and copyright information in PMC

References

1. Mohseni M et al. Nature 543, 171–174 (2017). - PubMed
1. Arute F et al. Nature 574, 505–510 (2019). - PubMed
1. U.S. House of Representatives. 115th Congress H.R. 6227, U.S. National Quantum Initiative Act (Government Printing Office, 2018).
1. Monroe C, Raymer MG & Taylor J Science 364, 440–442 (2019). - PubMed
1. Thew R, Jennewein T & Sasaki M Quantum Sci. Technol 5, 010201 (2019).

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Quantum computing at the frontiers of biological sciences

Affiliations

Quantum computing at the frontiers of biological sciences

Authors

Affiliations

Abstract

Conflict of interest statement

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources