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A call for deep-learning healthcare

Here we argue that now is the time to create smarter healthcare systems in which the best treatment decisions are computationally learned from electronic health record data by deep-learning methodologies.

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Fig. 1: A deep-learning healthcare system.


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Correspondence to Atul J. Butte.

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A.J.B. reports grants and non-financial support from Progenity, personal fees from NuMedii, personal fees from Personalis, grants and personal fees from NIH (multiple institutes), grants from L'Oreal, grants and personal fees from Genentech, personal fees from Merck, personal fees from Lilly, personal fees from Assay Depot, personal fees from Geisinger Health, personal fees from GNS Healthcare, personal fees from uBiome, personal fees from Roche, personal fees from Wilson Sonsini Goodrich & Rosati, personal fees from Orrick, Herrington & Sutcliffe, personal fees from Verinata, personal fees from 10x Genomics, personal fees from Pathway Genomics, personal fees from Guardant Health, personal fees from Gerson Lehrman Group, personal fees from Nuna Health, personal fees from Samsung, personal fees from Milken Institute, personal fees from Brown University, personal fees from Oregon Health Sciences University Knight Cancer Center, personal fees from Vermont Oxford Network, personal fees from University of Chicago, personal fees from Mount Sinai School of Medicine, personal fees from University of Pittsburgh School of Medicine, personal fees from Capital Royalty Group, personal fees from Champalimaud Foundation, personal fees from Scripps Translational Science Institute, personal fees from Washington University in St. Louis, personal fees from University of Maryland, personal fees from HIMSS, personal fees from Federation of Clinical Immunology Societies (FOCIS), personal fees from Kansas City Area Life Sciences Institute, personal fees from Association for Molecular Pathology, personal fees from TEDMED, personal fees from Physician’s Education Resource, personal fees from Optum Labs, personal fees from National Jewish Health, personal fees from Federation of the Israeli Societies for Experimental Biology (FISEB), personal fees from Pfizer, personal fees from Bayer, personal fees from Fusion Conferences, personal fees from Accelerating Biopharmaceutical Development (AccBio), personal fees from Three Lakes Partners, personal fees from Pediatric Academic Societies, personal fees from Korean Society for Biochemistry and Molecular Biology, personal fees from Human Proteomics Organization (HUPO), personal fees from HudsonAlpha, personal fees from Tensegrity, grants from Intervalien Foundation, personal fees from Association for Academic Health Sciences Libraries, personal fees from Westat, personal fees from FH Foundation, personal fees from University of Kentucky, personal fees from University of Pennsylvania, personal fees from The Transplantation Society, personal fees from California Office of Planning and Research, personal fees from WuXi, personal fees from University of Arkansas, personal fees from FlareCapital, personal fees from National Academies, personal fees from Helix, personal fees from American Urological Association, personal fees from Association for American Medical Colleges, personal fees from Roam Insights, personal fees from United Network for Organ Sharing, personal fees from American Association of Allergy Asthma and Immunology, personal fees from University of Michigan, personal fees from Autodesk, personal fees from Regenstrief Institute, personal fees from American Medical Association, personal fees from Precision Medicine World Conference, personal fees from University of Chicago, personal fees from Mars, and personal fees from Kneed Media. In addition, A.J.B. has a patent Atul Butte, Isaac Kohane. A system and method for mining data from a database using relevance networks. Published March 8, 2001. WO2001016805 and US2000024257. pending, a patent Atul Butte. Relevance networks for visualizing clusters in gene expression data. Published May 16, 2002. WO2002039214 and US2001043604. pending, a patent Atul Butte. Method and apparatus for determining fold difference significance. Published November 20, 2003. WO2002059820. pending, a patent “Atul J. Butte, Isaac Kohane. Method and system for identifying time-series relationships of gene expression level using signal processing metrics. Published November 14, 2002. WO2002046474.” pending, a patent “Atul Butte, Ronald Kahn, Yu-Hua Tseng. Methods and compositions for modulating adipocyte function. Published April 28, 2005. WO2005037232 and US20050187154.“ pending, a patent “Atul Butte, Rong Chen. Methods for monitoring allograft rejection. Published August 19, 2010. WO 2010093869 and US20120165207.” pending, a patent “Minnie M. Sarwal, Atul Butte. Compartment-specific non-HLA targets for diagnosis and prediction of graft outcome. Published March 29, 2012. WO2010096160 and US20120077689.” pending, a patent “Atul Butte, Keiichi Kodama. Methods for diagnosis and treatment of non-insulin dependent diabetes mellitus. Published August 4, 2011. WO2011094731 and US20130071408.” pending, a patent “Minnie M. Sarwal, Li Li, Tara Sigdel, Amit Kaushal, Wenzhong Xiao, Atul J. Butte, Purvesh Khatri. Protein and gene biomarkers for rejection of organ transplants. Published September 29, 2011. WO2011119980 and US20130143755.” pending, a patent “Shai S. Shen-Orr, Atul J. Butte, Mark M. Davis, David Furman, Brian A. Kidd. Diagnostic markers of immunosenescence and methods of use thereof. Published January 26, 2012. US20120021414.” issued, a patent “Atul J. Butte, Kenneth Weinberg, Shivkumar Venkatasubrahmanyam, Maheswaran Mani. Modulation of kit signaling and hematopoietic cell development by IL-4 receptor modulation. Published March 29, 2012. US20120076797.” pending, a patent “Joel T. Dudley, Atul J. Butte. Method and System for Computing and Integrating Genetic and Environmental Health Risks for a Personal Genome. Published April 26, 2012. US20120101736.” with royalties paid to Personalis, a patent “Yannick Pouliot, Annie P. Chiang, Atul J. Butte. Method and System for Predicting Adverse Drug Reactions Using BioAssay Data. Published June 6, 2013. US20130144636.” pending, a patent “Joel T. Dudley, Atul J. Butte. Method And System For Functional Evolutionary Assessment Of Genetic Variants. Published April 11, 2013. US20130090909.” with royalties paid to Personalis, a patent “Konrad Karczewski, Michael Snyder, Atul J. Butte, Joel T. Dudley, Eurie Hong, Alan Boyle, J. Michael Cherry. Method and System for Assessment of Regulatory Variants in a Genome. Published May 9, 2013. US20130116931.” with royalties paid to Personalis, a patent “Frederick Dewey, Euan Ashley, Carlos Daniel Bustamante, Atul Butte, Jake Byrnes, Rong Chen. Phased Whole Genome Genetic Risk In A Family Quartet. Published March 28, 2013. US20130080068.” with royalties paid to Personalis, a patent “Purvesh Khatri, Atul J. Butte, Minnie M. Sarwal. Identification of new therapeutic uses for known therapeutic agents. Published August 1, 2013. WO2013112933 and US20150133390.” pending, a patent “Atul J. Butte, Bruce Xuefeng Ling, Linda Liu Miller, Alexander A. Morgan, Gongxing Chen, Jun Ji, Ting Yang. Methods and compositions for providing a preeclampsia assessment. Published November 14, 2013. WO2013169751 and US2013039918.” with royalties paid to Carmenta, a patent “Julien Sage, Atul J. Butte, Joel T. Dudley, Nadine Jahchan. Methods for the treatment of cancer. Published January 30, 2014. WO2014018563.” pending, a patent “Bruce Xuefeng Ling, Ting Yang, Atul J. Butte, Linda Liu Miller, Qiaojun Wen, Guojun Sheng, Cantas Alev. Methods of Prognosing Preeclampsia. Published January 21, 2016. US20160018413.” pending, a patent “Atul J. Butte, Linda Anne Szabo, Purvesh Khatri, Bruce Xuefeng Ling. Biomarkers for Ovarian Cancer. Published October 6, 2016. US20160291024.” pending, a patent “M. Peter Marinkovich, Atul J. Butte, Mazen Nasrallah, Carl Gustaf, Maarten Winge. Epithelial ion channel (ENAC) blockers to treat psoriasis. Published June 29, 2017. US20170182040.” pending, a patent “Hua Fan-Minogue, Atul J. Butte, Jason Wheeler. Methods and Compositions for Modulating Lung Cancer Tumor Initiating Cells (TIC), and Oxytocin Receptor (OXTR) Modulatory Agents for Use in Practicing the Same. Published July 13, 2017. US20170198292.” pending, and a patent “M. Peter Marinkovich, Carl Gustaf, Maarten Winge, Atul J. Butte, Mazen Nasrallah. Treatment of melanoma by blocking benzamil sensitive ion channels/exchangers. Published August 10, 2017. US20170224683.” pending, and Stanford University pays royalties each year on licensed intellectual property. MIT Press pays royalties each year on book sales.

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Norgeot, B., Glicksberg, B.S. & Butte, A.J. A call for deep-learning healthcare. Nat Med 25, 14–15 (2019).

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