Peer-Reviewed Publication
J R Soc Interface2018;15(141)April 1, 2018Journal Article
Opportunities and obstacles for deep learning in biology and medicine.
Travers Ching1, Daniel S Himmelstein2, Brett K Beaulieu-Jones3, Alexandr A Kalinin4, Brian T Do5, Gregory P Way2, Enrico Ferrero6, Paul-Michael Agapow7, Michael Zietz2, Michael M Hoffman8,9,10, Wei Xie11, Gail L Rosen12, Benjamin J Lengerich13, Johnny Israeli14, Jack Lanchantin15, Stephen Woloszynek12, Anne E Carpenter16, Avanti Shrikumar17, Jinbo Xu18, Evan M Cofer19,20, Christopher A Lavender21, Srinivas C Turaga22, Amr M Alexandari17, Zhiyong Lu23, David J Harris24, Dave DeCaprio25, Yanjun Qi15, Anshul Kundaje17,26, Yifan Peng23, Laura K Wiley27, Marwin H S Segler28, Simina M Boca29, S Joshua Swamidass30, Austin Huang31, Anthony Gitter32,33, Casey S Greene34
1Molecular Biosciences and Bioengineering Graduate Program, University of Hawaii at Manoa, Honolulu, HI, USA.
2Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
3Genomics and Computational Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
4Department of Computational Medicine and Bioinformatics, University of Michigan Medical School, Ann Arbor, MI, USA.
5Harvard Medical School, Boston, MA, USA.
6Computational Biology and Stats, Target Sciences, GlaxoSmithKline, Stevenage, UK.
7Data Science Institute, Imperial College London, London, UK.
8Princess Margaret Cancer Centre, Toronto, Ontario, Canada.
9Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.
10Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.
11Electrical Engineering and Computer Science, Vanderbilt University, Nashville, TN, USA.
12Ecological and Evolutionary Signal-processing and Informatics Laboratory, Department of Electrical and Computer Engineering, Drexel University, Philadelphia, PA, USA.
13Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA.
14Biophysics Program, Stanford University, Stanford, CA, USA.
15Department of Computer Science, University of Virginia, Charlottesville, VA, USA.
16Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
17Department of Computer Science, Stanford University, Stanford, CA, USA.
18Toyota Technological Institute at Chicago, Chicago, IL, USA.
19Department of Computer Science, Trinity University, San Antonio, TX, USA.
20Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ, USA.
21Integrative Bioinformatics, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.
22Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, USA.
23National Center for Biotechnology Information and National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
24Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, USA.
25ClosedLoop.ai, Austin, TX, USA.
26Department of Genetics, Stanford University, Stanford, CA, USA.
27Division of Biomedical Informatics and Personalized Medicine, University of Colorado School of Medicine, Aurora, CO, USA.
28Institute of Organic Chemistry, Westfälische Wilhelms-Universität Münster, Münster, Germany.
29Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC, USA.
30Department of Pathology and Immunology, Washington University in Saint Louis, St Louis, MO, USA.
31Department of Medicine, Brown University, Providence, RI, USA.
32Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA gitter@biostat.wisc.edu.
33Morgridge Institute for Research, Madison, WI, USA.
34Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA greenescientist@gmail.com.
Abstract
Deep learning describes a class of machine learning algorithms that are capable of combining raw inputs into layers of intermediate features. These algorithms have recently shown impressive results across a variety of domains. Biology and medicine are data-rich disciplines, but the data are complex and often ill-understood. Hence, deep learning techniques may be particularly well suited to solve p…
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