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Opportunities and obstacles for deep learning in biology and medicine. 2018
Travers Ching, and
Daniel S Himmelstein, and
Brett K Beaulieu-Jones, and
Alexandr A Kalinin, and
Brian T Do, and
Gregory P Way, and
Enrico Ferrero, and
Paul-Michael Agapow, and
Michael Zietz, and
Michael M Hoffman, and
Wei Xie, and
Gail L Rosen, and
Benjamin J Lengerich, and
Johnny Israeli, and
Jack Lanchantin, and
Stephen Woloszynek, and
Anne E Carpenter, and
Avanti Shrikumar, and
Jinbo Xu, and
Evan M Cofer, and
Christopher A Lavender, and
Srinivas C Turaga, and
Amr M Alexandari, and
Zhiyong Lu, and
David J Harris, and
Dave DeCaprio, and
Yanjun Qi, and
Anshul Kundaje, and
Yifan Peng, and
Laura K Wiley, and
Marwin H S Segler, and
Simina M Boca, and
S Joshua Swamidass, and
Austin Huang, and
Anthony Gitter, and
Casey S Greene
Molecular Biosciences and Bioengineering Graduate Program, University of Hawaii at Manoa, Honolulu, HI, USA.
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 problems of these fields. We examine applications of deep learning to a variety of biomedical problems-patient classification, fundamental biological processes and treatment of patients-and discuss whether deep learning will be able to transform these tasks or if the biomedical sphere poses unique challenges. Following from an extensive literature review, we find that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art. Even though improvements over previous baselines have been modest in general, the recent progress indicates that deep learning methods will provide valuable means for speeding up or aiding human investigation. Though progress has been made linking a specific neural network's prediction to input features, understanding how users should interpret these models to make testable hypotheses about the system under study remains an open challenge. Furthermore, the limited amount of labelled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning enabling changes at both bench and bedside with the potential to transform several areas of biology and medicine.
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