. 2018 Apr; 15(141):20170387.
doi: 10.1098/rsif.2017.0387.

Opportunities and obstacles for deep learning in biology and medicine

Travers Ching 1 Daniel S Himmelstein 2 Brett K Beaulieu-Jones 3 Alexandr A Kalinin 4 Brian T Do 5 Gregory P Way 2 Enrico Ferrero 6 Paul-Michael Agapow 7 Michael Zietz 2 Michael M Hoffman 8 Wei Xie 9 Gail L Rosen 10 Benjamin J Lengerich 11 Johnny Israeli 12 Jack Lanchantin 13 Stephen Woloszynek 10 Anne E Carpenter 14 Avanti Shrikumar 15 Jinbo Xu 16 Evan M Cofer 17 Christopher A Lavender 18 Srinivas C Turaga 19 Amr M Alexandari 15 Zhiyong Lu 20 David J Harris 21 Dave DeCaprio 22 Yanjun Qi 13 Anshul Kundaje 15 Yifan Peng 20 Laura K Wiley 23 Marwin H S Segler 24 Simina M Boca 25 S Joshua Swamidass 26 Austin Huang 27 Anthony Gitter 28 Casey S Greene 29 
  • PMID: 29618526
  •     274 References
  •     245 citations


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.

Keywords: deep learning; genomics; machine learning; precision medicine.

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Proc Conf, 2016 Nov 26; 2016. PMID: 27885364    Free PMC article.
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Realizing the full potential of electronic health records: the role of natural language processing.
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TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions.
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Sex bias in neuroscience and biomedical research.
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Highly Cited. Review.
Convolutional neural network architectures for predicting DNA-protein binding.
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Cytometry A, 2016 Jul 20; 91(2). PMID: 27434125
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Bioinformatics, 2017 Apr 27; 33(17). PMID: 28444127
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Genome Med, 2016 Apr 01; 8(1). PMID: 27029192    Free PMC article.
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Boosting Docking-Based Virtual Screening with Deep Learning.
Janaina Cruz Pereira, Ernesto Raúl Caffarena, Cicero Nogueira Dos Santos.
J Chem Inf Model, 2016 Dec 28; 56(12). PMID: 28024405
Molecular graph convolutions: moving beyond fingerprints.
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J Comput Aided Mol Des, 2016 Aug 26; 30(8). PMID: 27558503    Free PMC article.
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Improving chemical disease relation extraction with rich features and weakly labeled data.
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Machines that learn to segment images: a crucial technology for connectomics.
Viren Jain, H Sebastian Seung, Srinivas C Turaga.
Curr Opin Neurobiol, 2010 Aug 31; 20(5). PMID: 20801638    Free PMC article.
Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks.
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Genome Res, 2016 May 20; 26(7). PMID: 27197224    Free PMC article.
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The state of the art of mammalian promoter recognition.
Thomas Werner.
Brief Bioinform, 2003 Apr 29; 4(1). PMID: 12715831
Accurate phylogenetic classification of variable-length DNA fragments.
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Nat Methods, 2006 Dec 21; 4(1). PMID: 17179938
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Learning the sequence determinants of alternative splicing from millions of random sequences.
Alexander B Rosenberg, Rupali P Patwardhan, Jay Shendure, Georg Seelig.
Cell, 2015 Oct 27; 163(3). PMID: 26496609
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RNA mis-splicing in disease.
Marina M Scotti, Maurice S Swanson.
Nat Rev Genet, 2015 Nov 26; 17(1). PMID: 26593421    Free PMC article.
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Accurate and efficient target prediction using a potency-sensitive influence-relevance voter.
Alessandro Lusci, Michael Browning, +2 authors, Pierre Baldi.
J Cheminform, 2016 Jan 01; 7. PMID: 26719774    Free PMC article.
Drug drug interaction extraction from biomedical literature using syntax convolutional neural network.
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Bioinformatics, 2016 Jul 29; 32(22). PMID: 27466626    Free PMC article.
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis.
Riu Yamashita, Nuankanya P Sathira, +7 authors, Yutaka Suzuki.
Genome Res, 2011 Mar 05; 21(5). PMID: 21372179    Free PMC article.
A neural joint model for entity and relation extraction from biomedical text.
Fei Li, Meishan Zhang, Guohong Fu, Donghong Ji.
BMC Bioinformatics, 2017 Apr 01; 18(1). PMID: 28359255    Free PMC article.
MEME SUITE: tools for motif discovery and searching.
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Nucleic Acids Res, 2009 May 22; 37(Web Server issue). PMID: 19458158    Free PMC article.
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A Shortest Dependency Path Based Convolutional Neural Network for Protein-Protein Relation Extraction.
Lei Hua, Chanqin Quan.
Biomed Res Int, 2016 Aug 06; 2016. PMID: 27493967    Free PMC article.
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Michael A Lodato, Mollie B Woodworth, +11 authors, Christopher A Walsh.
Science, 2015 Oct 03; 350(6256). PMID: 26430121    Free PMC article.
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The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease.
Justin Lamb, Emily D Crawford, +17 authors, Todd R Golub.
Science, 2006 Sep 30; 313(5795). PMID: 17008526
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Deep learning in neural networks: an overview.
Jürgen Schmidhuber.
Neural Netw, 2014 Dec 03; 61. PMID: 25462637
Highly Cited. Review.
Fizzy: feature subset selection for metagenomics.
Gregory Ditzler, J Calvin Morrison, Yemin Lan, Gail L Rosen.
BMC Bioinformatics, 2015 Nov 06; 16. PMID: 26538306    Free PMC article.
RNA-protein binding motifs mining with a new hybrid deep learning based cross-domain knowledge integration approach.
Xiaoyong Pan, Hong-Bin Shen.
BMC Bioinformatics, 2017 Mar 02; 18(1). PMID: 28245811    Free PMC article.
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Children of the 90s: Coming of age.
Helen Pearson.
Nature, 2012 Apr 14; 484(7393). PMID: 22498607
Hit and lead generation: beyond high-throughput screening.
Konrad H Bleicher, Hans-Joachim Böhm, Klaus Müller, Alexander I Alanine.
Nat Rev Drug Discov, 2003 May 17; 2(5). PMID: 12750740
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A Deep Learning Network Approach to ab initio Protein Secondary Structure Prediction.
Matt Spencer, Jesse Eickholt, Jianlin Cheng.
IEEE/ACM Trans Comput Biol Bioinform, 2015 Mar 10; 12(1). PMID: 25750595    Free PMC article.
Predicting effective microRNA target sites in mammalian mRNAs.
Vikram Agarwal, George W Bell, Jin-Wu Nam, David P Bartel.
Elife, 2015 Aug 13; 4. PMID: 26267216    Free PMC article.
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Machine learning and computer vision approaches for phenotypic profiling.
Ben T Grys, Dara S Lo, +4 authors, Brenda J Andrews.
J Cell Biol, 2016 Dec 13; 216(1). PMID: 27940887    Free PMC article.
The Novel Roles of Connexin Channels and Tunneling Nanotubes in Cancer Pathogenesis.
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Int J Mol Sci, 2018 Apr 27; 19(5). PMID: 29695070    Free PMC article.
Deep learning in pharmacogenomics: from gene regulation to patient stratification.
Alexandr A Kalinin, Gerald A Higgins, +5 authors, Brian D Athey.
Pharmacogenomics, 2018 Apr 27; 19(7). PMID: 29697304    Free PMC article.
Patient-Centered Mobile Health Data Management Solution for the German Health Care System (The DataBox Project).
Titus Josef Brinker, Stefanie Rudolph, Daniela Richter, Christof von Kalle.
JMIR Cancer, 2018 May 13; 4(1). PMID: 29752255    Free PMC article.
Opportunities and challenges in developing deep learning models using electronic health records data: a systematic review.
Cao Xiao, Edward Choi, Jimeng Sun.
J Am Med Inform Assoc, 2018 Jun 13; 25(10). PMID: 29893864    Free PMC article.
Highly Cited. Systematic Review.
Extracting chemical-protein relations with ensembles of SVM and deep learning models.
Yifan Peng, Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu.
Database (Oxford), 2018 Jul 19; 2018. PMID: 30020437    Free PMC article.
Rise of Deep Learning for Genomic, Proteomic, and Metabolomic Data Integration in Precision Medicine.
Dmitry Grapov, Johannes Fahrmann, Kwanjeera Wanichthanarak, Sakda Khoomrung.
OMICS, 2018 Aug 21; 22(10). PMID: 30124358    Free PMC article.
Systems Medicine Disease: Disease Classification and Scalability Beyond Networks and Boundary Conditions.
Richard Berlin, Russell Gruen, James Best.
Front Bioeng Biotechnol, 2018 Aug 23; 6. PMID: 30131956    Free PMC article.
Deep learning in biomedicine.
Michael Wainberg, Daniele Merico, Andrew Delong, Brendan J Frey.
Nat Biotechnol, 2018 Sep 07; 36(9). PMID: 30188539
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3D Shape Modeling for Cell Nuclear Morphological Analysis and Classification.
Alexandr A Kalinin, Ari Allyn-Feuer, +15 authors, Ivo D Dinov.
Sci Rep, 2018 Sep 14; 8(1). PMID: 30209281    Free PMC article.
The Human Interface of Biomedical Informatics.
Edward C Klatt.
J Pathol Inform, 2018 Sep 22; 9. PMID: 30237909    Free PMC article.
Multi-omic and multi-view clustering algorithms: review and cancer benchmark.
Nimrod Rappoport, Ron Shamir.
Nucleic Acids Res, 2018 Oct 09; 46(20). PMID: 30295871    Free PMC article.
Highly Cited. Review.
Universal cancer screening: revolutionary, rational, and realizable.
David A Ahlquist.
NPJ Precis Oncol, 2018 Nov 06; 2. PMID: 30393772    Free PMC article.
A reference set of curated biomedical data and metadata from clinical case reports.
J Harry Caufield, Yijiang Zhou, +13 authors, Peipei Ping.
Sci Data, 2018 Nov 21; 5. PMID: 30457569    Free PMC article.
The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.
Žiga Avsec, Roman Kreuzhuber, +10 authors, Julien Gagneur.
Nat Biotechnol, 2019 May 30; 37(6). PMID: 31138913    Free PMC article.
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Computational pathology definitions, best practices, and recommendations for regulatory guidance: a white paper from the Digital Pathology Association.
Esther Abels, Liron Pantanowitz, +9 authors, Cleopatra Kozlowski.
J Pathol, 2019 Jul 30; 249(3). PMID: 31355445    Free PMC article.
Artificial intelligence in digital pathology - new tools for diagnosis and precision oncology.
Kaustav Bera, Kurt A Schalper, +2 authors, Anant Madabhushi.
Nat Rev Clin Oncol, 2019 Aug 11; 16(11). PMID: 31399699    Free PMC article.
Highly Cited. Review.
Learning Drug Functions from Chemical Structures with Convolutional Neural Networks and Random Forests.
Jesse G Meyer, Shengchao Liu, +2 authors, Anthony Gitter.
J Chem Inf Model, 2019 Sep 14; 59(10). PMID: 31518132    Free PMC article.
Inferring Disease-Associated MicroRNAs Using Semi-supervised Multi-Label Graph Convolutional Networks.
Xiaoyong Pan, Hong-Bin Shen.
iScience, 2019 Oct 13; 20. PMID: 31605942    Free PMC article.
DeepImpute: an accurate, fast, and scalable deep neural network method to impute single-cell RNA-seq data.
Cédric Arisdakessian, Olivier Poirion, +2 authors, Lana X Garmire.
Genome Biol, 2019 Oct 20; 20(1). PMID: 31627739    Free PMC article.
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Trends and Focus of Machine Learning Applications for Health Research.
Brett Beaulieu-Jones, Samuel G Finlayson, +7 authors, Tristan Naumann.
JAMA Netw Open, 2019 Oct 28; 2(10). PMID: 31651969    Free PMC article.
The second information revolution: digitalization brings opportunities and concerns for public health.
Martin McKee, May C I van Schalkwyk, David Stuckler.
Eur J Public Health, 2019 Nov 19; 29(Supplement_3). PMID: 31738440    Free PMC article.
Deep spectral learning for label-free optical imaging oximetry with uncertainty quantification.
Rongrong Liu, Shiyi Cheng, Lei Tian, Ji Yi.
Light Sci Appl, 2019 Nov 23; 8. PMID: 31754429    Free PMC article.
Extracting a biologically latent space of lung cancer epigenetics with variational autoencoders.
Zhenxing Wang, Yadong Wang.
BMC Bioinformatics, 2019 Nov 26; 20(Suppl 18). PMID: 31760935    Free PMC article.
From Genotype to Phenotype: Augmenting Deep Learning with Networks and Systems Biology.
Vahid H Gazestani, Nathan E Lewis.
Curr Opin Syst Biol, 2019 Nov 30; 15. PMID: 31777764    Free PMC article.
tRNA functional signatures classify plastids as late-branching cyanobacteria.
Travis J Lawrence, Katherine Ch Amrine, Wesley D Swingley, David H Ardell.
BMC Evol Biol, 2019 Dec 11; 19(1). PMID: 31818253    Free PMC article.
Graph Embedding Deep Learning Guides Microbial Biomarkers' Identification.
Qiang Zhu, Xingpeng Jiang, +2 authors, Tingting He.
Front Genet, 2019 Dec 12; 10. PMID: 31824573    Free PMC article.
A Deep Learning Approach for Meibomian Gland Atrophy Evaluation in Meibography Images.
Jiayun Wang, Thao N Yeh, +2 authors, Meng C Lin.
Transl Vis Sci Technol, 2019 Dec 24; 8(6). PMID: 31867138    Free PMC article.
Digital Health and the State of Interoperable Electronic Health Records.
Jessica Germaine Shull.
JMIR Med Inform, 2019 Nov 05; 7(4). PMID: 31682583    Free PMC article.
Evolving the pulmonary nodules diagnosis from classical approaches to deep learning-aided decision support: three decades' development course and future prospect.
Bo Liu, Wenhao Chi, +5 authors, Jianxing He.
J Cancer Res Clin Oncol, 2019 Dec 02; 146(1). PMID: 31786740
Brain Imaging Genomics: Integrated Analysis and Machine Learning.
Li Shen, Paul M Thompson.
Proc IEEE Inst Electr Electron Eng, 2020 Jan 07; 108(1). PMID: 31902950    Free PMC article.
Co-expression Networks Identify DHX15 RNA Helicase as a B Cell Regulatory Factor.
Thiago Detanico, Richard Virgen-Slane, +8 authors, Carl F Ware.
Front Immunol, 2020 Jan 11; 10. PMID: 31921164    Free PMC article.
Applications of Machine Learning Using Electronic Medical Records in Spine Surgery.
John T Schwartz, Michael Gao, +3 authors, Samuel K Cho.
Neurospine, 2020 Jan 07; 16(4). PMID: 31905452    Free PMC article.
Multiset sparse partial least squares path modeling for high dimensional omics data analysis.
Attila Csala, Aeilko H Zwinderman, Michel H Hof.
BMC Bioinformatics, 2020 Jan 11; 21(1). PMID: 31918677    Free PMC article.
deepDR: a network-based deep learning approach to in silico drug repositioning.
Xiangxiang Zeng, Siyi Zhu, +3 authors, Feixiong Cheng.
Bioinformatics, 2019 May 23; 35(24). PMID: 31116390    Free PMC article.
Highly Cited.
Cloud bursting galaxy: federated identity and access management.
Vahid Jalili, Enis Afgan, James Taylor, Jeremy Goecks.
Bioinformatics, 2019 Jun 15; 36(1). PMID: 31197310    Free PMC article.
Dynamic distribution decomposition for single-cell snapshot time series identifies subpopulations and trajectories during iPSC reprogramming.
Jake P Taylor-King, Asbjørn N Riseth, Will Macnair, Manfred Claassen.
PLoS Comput Biol, 2020 Jan 11; 16(1). PMID: 31923173    Free PMC article.
Knowledge Generation with Rule Induction in Cancer Omics.
Giovanni Scala, Antonio Federico, +2 authors, Barbara Majello.
Int J Mol Sci, 2019 Dec 22; 21(1). PMID: 31861438    Free PMC article.
Molecular Insights from Conformational Ensembles via Machine Learning.
Oliver Fleetwood, Marina A Kasimova, Annie M Westerlund, Lucie Delemotte.
Biophys J, 2020 Jan 19; 118(3). PMID: 31952811    Free PMC article.
ORSO (Online Resource for Social Omics): A data-driven social network connecting scientists to genomics datasets.
Christopher A Lavender, Andrew J Shapiro, Frank S Day, David C Fargo.
PLoS Comput Biol, 2020 Jan 25; 16(1). PMID: 31978042    Free PMC article.
Deep learning in clinical natural language processing: a methodical review.
Stephen Wu, Kirk Roberts, +9 authors, Hua Xu.
J Am Med Inform Assoc, 2019 Dec 04; 27(3). PMID: 31794016    Free PMC article.
Deep learning cardiac motion analysis for human survival prediction.
Ghalib A Bello, Timothy J W Dawes, +8 authors, Declan P O'Regan.
Nat Mach Intell, 2019 Feb 26; 1. PMID: 30801055    Free PMC article.
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Privacy-Preserving Generative Deep Neural Networks Support Clinical Data Sharing.
Brett K Beaulieu-Jones, Zhiwei Steven Wu, +4 authors, Casey S Greene.
Circ Cardiovasc Qual Outcomes, 2019 Jul 10; 12(7). PMID: 31284738    Free PMC article.
Neural computational model GrowthEstimate: A model for studying living resources through digestive efficiency.
Krisna Rungruangsak-Torrissen, Poramate Manoonpong.
PLoS One, 2019 Aug 29; 14(8). PMID: 31461459    Free PMC article.
The discovery BPD (D-BPD) program: study protocol of a prospective translational multicenter collaborative study to investigate determinants of chronic lung disease in very low birth weight infants.
Gaston Ofman, Mauricio T Caballero, +22 authors, Fernando P Polack.
BMC Pediatr, 2019 Jul 08; 19(1). PMID: 31279333    Free PMC article.
Characterization of a novel cotton MYB gene, GhMYB108-like responsive to abiotic stresses.
Abid Ullah, Muhammad Tahir Ul Qamar, +8 authors, Xiyan Yang.
Mol Biol Rep, 2020 Jan 15; 47(3). PMID: 31933260
Learning to predict the cosmological structure formation.
Siyu He, Yin Li, +4 authors, Barnabás Póczos.
Proc Natl Acad Sci U S A, 2019 Jun 27; 116(28). PMID: 31235606    Free PMC article.
Comparative performances of machine learning methods for classifying Crohn Disease patients using genome-wide genotyping data.
Alberto Romagnoni, Simon Jégou, +3 authors, International Inflammatory Bowel Disease Genetics Consortium (IIBDGC).
Sci Rep, 2019 Jul 19; 9(1). PMID: 31316157    Free PMC article.
Technical considerations of multi-parametric tissue outcome prediction methods in acute ischemic stroke patients.
Anthony J Winder, Susanne Siemonsen, +3 authors, Nils D Forkert.
Sci Rep, 2019 Sep 15; 9(1). PMID: 31519923    Free PMC article.
Latent Risk Intrahepatic Cholangiocarcinoma Susceptible to Adjuvant Treatment After Resection: A Clinical Deep Learning Approach.
Seogsong Jeong, Yang Ge, +11 authors, Lei Chen.
Front Oncol, 2020 Mar 07; 10. PMID: 32140448    Free PMC article.
Evolving systems biology approaches to understanding non-coding RNAs in pulmonary hypertension.
Lloyd D Harvey, Stephen Y Chan.
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How to rekindle drug discovery process through integrative therapeutic targeting?
Ashok Vaidya, Anuradha Roy, Rathnam Chaguturu.
Expert Opin Drug Discov, 2018 Aug 28; 13(10). PMID: 30146919    Free PMC article.
DeepSeeNet: A Deep Learning Model for Automated Classification of Patient-based Age-related Macular Degeneration Severity from Color Fundus Photographs.
Yifan Peng, Shazia Dharssi, +5 authors, Zhiyong Lu.
Ophthalmology, 2018 Nov 25; 126(4). PMID: 30471319    Free PMC article.
Practical Model Selection for Prospective Virtual Screening.
Shengchao Liu, Moayad Alnammi, +6 authors, Anthony Gitter.
J Chem Inf Model, 2018 Dec 01; 59(1). PMID: 30500183    Free PMC article.
Deep Learning in Image Cytometry: A Review.
Anindya Gupta, Philip J Harrison, +9 authors, Carolina Wählby.
Cytometry A, 2018 Dec 20; 95(4). PMID: 30565841    Free PMC article.
Single cell RNA-sequencing: replicability of cell types.
Megan Crow, Jesse Gillis.
Curr Opin Neurobiol, 2019 Jan 18; 56. PMID: 30654233    Free PMC article.
Unsupervised classification of multi-omics data during cardiac remodeling using deep learning.
Neo Christopher Chung, Bilal Mirza, +4 authors, Wei Wang.
Methods, 2019 Mar 12; 166. PMID: 30853547    Free PMC article.
Assessment of a Deep Learning Model Based on Electronic Health Record Data to Forecast Clinical Outcomes in Patients With Rheumatoid Arthritis.
Beau Norgeot, Benjamin S Glicksberg, +6 authors, Atul J Butte.
JAMA Netw Open, 2019 Mar 16; 2(3). PMID: 30874779    Free PMC article.
MetaPheno: A critical evaluation of deep learning and machine learning in metagenome-based disease prediction.
Nathan LaPierre, Chelsea J-T Ju, Guangyu Zhou, Wei Wang.
Methods, 2019 Mar 20; 166. PMID: 30885720    Free PMC article.
Artificial intelligence in reproductive medicine.
Renjie Wang, Wei Pan, +7 authors, Shujie Liao.
Reproduction, 2019 Apr 11; 158(4). PMID: 30970326    Free PMC article.
A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action.
Jason H Yang, Sarah N Wright, +9 authors, James J Collins.
Cell, 2019 May 14; 177(6). PMID: 31080069    Free PMC article.
Highly Cited.
A Brief History of Protein Sorting Prediction.
Henrik Nielsen, Konstantinos D Tsirigos, Søren Brunak, Gunnar von Heijne.
Protein J, 2019 May 24; 38(3). PMID: 31119599    Free PMC article.
Reproduction study using public data of: Development and validation of a deep learning algorithm for detection of diabetic retinopathy in retinal fundus photographs.
Mike Voets, Kajsa Møllersen, Lars Ailo Bongo.
PLoS One, 2019 Jun 07; 14(6). PMID: 31170223    Free PMC article.
Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays.
Rajiv Movva, Peyton Greenside, +3 authors, Anshul Kundaje.
PLoS One, 2019 Jun 18; 14(6). PMID: 31206543    Free PMC article.
Open collaborative writing with Manubot.
Daniel S Himmelstein, Vincent Rubinetti, +4 authors, Anthony Gitter.
PLoS Comput Biol, 2019 Jun 25; 15(6). PMID: 31233491    Free PMC article.
Machine and deep learning meet genome-scale metabolic modeling.
Guido Zampieri, Supreeta Vijayakumar, Elisabeth Yaneske, Claudio Angione.
PLoS Comput Biol, 2019 Jul 12; 15(7). PMID: 31295267    Free PMC article.
Prediction of regulatory motifs from human Chip-sequencing data using a deep learning framework.
Jinyu Yang, Anjun Ma, +6 authors, Qin Ma.
Nucleic Acids Res, 2019 Aug 03; 47(15). PMID: 31372637    Free PMC article.
Designing combination therapies with modeling chaperoned machine learning.
Yin Zhang, Julie M Huynh, +4 authors, Tongli Zhang.
PLoS Comput Biol, 2019 Sep 10; 15(9). PMID: 31498788    Free PMC article.
DeepSynth: Three-dimensional nuclear segmentation of biological images using neural networks trained with synthetic data.
Kenneth W Dunn, Chichen Fu, +4 authors, Edward J Delp.
Sci Rep, 2019 Dec 05; 9(1). PMID: 31797882    Free PMC article.
Precision Psychiatry Applications with Pharmacogenomics: Artificial Intelligence and Machine Learning Approaches.
Eugene Lin, Chieh-Hsin Lin, Hsien-Yuan Lane.
Int J Mol Sci, 2020 Feb 07; 21(3). PMID: 32024055    Free PMC article.
Predicting or Pretending: Artificial Intelligence for Protein-Ligand Interactions Lack of Sufficiently Large and Unbiased Datasets.
Jincai Yang, Cheng Shen, Niu Huang.
Front Pharmacol, 2020 Mar 13; 11. PMID: 32161539    Free PMC article.
Classifying T cell activity in autofluorescence intensity images with convolutional neural networks.
Zijie J Wang, Alex J Walsh, Melissa C Skala, Anthony Gitter.
J Biophotonics, 2019 Oct 30; 13(3). PMID: 31661592    Free PMC article.
MethylNet: an automated and modular deep learning approach for DNA methylation analysis.
Joshua J Levy, Alexander J Titus, +3 authors, Brock C Christensen.
BMC Bioinformatics, 2020 Mar 19; 21(1). PMID: 32183722    Free PMC article.
The Roles of the NLRP3 Inflammasome in Neurodegenerative and Metabolic Diseases and in Relevant Advanced Therapeutic Interventions.
Rameez Hassan Pirzada, Nasir Javaid, Sangdun Choi.
Genes (Basel), 2020 Feb 06; 11(2). PMID: 32012695    Free PMC article.
Standard machine learning approaches outperform deep representation learning on phenotype prediction from transcriptomics data.
Aaron M Smith, Jonathan R Walsh, +9 authors, Charles K Fisher.
BMC Bioinformatics, 2020 Mar 22; 21(1). PMID: 32197580    Free PMC article.
Prediction of the miRNA interactome - Established methods and upcoming perspectives.
Moritz Schäfer, Constance Ciaudo.
Comput Struct Biotechnol J, 2020 Mar 27; 18. PMID: 32211130    Free PMC article.
Technical and imaging factors influencing performance of deep learning systems for diabetic retinopathy.
Michelle Y T Yip, Gilbert Lim, +16 authors, Daniel S W Ting.
NPJ Digit Med, 2020 Mar 29; 3. PMID: 32219181    Free PMC article.
How Machine Learning Will Transform Biomedicine.
Jeremy Goecks, Vahid Jalili, Laura M Heiser, Joe W Gray.
Cell, 2020 Apr 04; 181(1). PMID: 32243801    Free PMC article.
Selene: a PyTorch-based deep learning library for sequence data.
Kathleen M Chen, Evan M Cofer, Jian Zhou, Olga G Troyanskaya.
Nat Methods, 2019 Mar 30; 16(4). PMID: 30923381    Free PMC article.
Tyrosine Kinase Inhibitors in Cancer: Breakthrough and Challenges of Targeted Therapy.
Charles Pottier, Margaux Fresnais, +3 authors, Nor Eddine Sounni.
Cancers (Basel), 2020 Apr 05; 12(3). PMID: 32244867    Free PMC article.
Emerging role of deep learning-based artificial intelligence in tumor pathology.
Yahui Jiang, Meng Yang, +2 authors, Yan Sun.
Cancer Commun (Lond), 2020 Apr 12; 40(4). PMID: 32277744    Free PMC article.
Brain Morphometry Estimation: From Hours to Seconds Using Deep Learning.
Michael Rebsamen, Yannick Suter, +2 authors, Christian Rummel.
Front Neurol, 2020 Apr 24; 11. PMID: 32322235    Free PMC article.
Molecular Generation for Desired Transcriptome Changes With Adversarial Autoencoders.
Rim Shayakhmetov, Maksim Kuznetsov, +4 authors, Daniil Polykovskiy.
Front Pharmacol, 2020 May 05; 11. PMID: 32362822    Free PMC article.
Discovering the hidden messages within cell trajectories using a deep learning approach for in vitro evaluation of cancer drug treatments.
A Mencattini, D Di Giuseppe, +8 authors, E Martinelli.
Sci Rep, 2020 May 08; 10(1). PMID: 32376840    Free PMC article.
Predicting cancer origins with a DNA methylation-based deep neural network model.
Chunlei Zheng, Rong Xu.
PLoS One, 2020 May 10; 15(5). PMID: 32384093    Free PMC article.
MOLI: multi-omics late integration with deep neural networks for drug response prediction.
Hossein Sharifi-Noghabi, Olga Zolotareva, Colin C Collins, Martin Ester.
Bioinformatics, 2019 Sep 13; 35(14). PMID: 31510700    Free PMC article.
Artificial intelligence in oncology.
Hideyuki Shimizu, Keiichi I Nakayama.
Cancer Sci, 2020 Mar 07; 111(5). PMID: 32133724    Free PMC article.
Specific histone modifications associate with alternative exon selection during mammalian development.
Qiwen Hu, Casey S Greene, Elizabeth A Heller.
Nucleic Acids Res, 2020 Apr 23; 48(9). PMID: 32319526    Free PMC article.
Automated abnormality classification of chest radiographs using deep convolutional neural networks.
Yu-Xing Tang, You-Bao Tang, +8 authors, Ronald M Summers.
NPJ Digit Med, 2020 May 22; 3. PMID: 32435698    Free PMC article.
Developing Real-world Evidence-Ready Datasets: Time for Clinician Engagement.
James M Snyder, Jacob A Pawloski, Laila M Poisson.
Curr Oncol Rep, 2020 Apr 17; 22(5). PMID: 32297007
Automated quantitative analysis of Ki-67 staining and HE images recognition and registration based on whole tissue sections in breast carcinoma.
Min Feng, Yang Deng, +10 authors, Hong Bu.
Diagn Pathol, 2020 May 31; 15(1). PMID: 32471471    Free PMC article.
Assistant diagnosis with Chinese electronic medical records based on CNN and BiLSTM with phrase-level and word-level attentions.
Tong Wang, Ping Xuan, Zonglin Liu, Tiangang Zhang.
BMC Bioinformatics, 2020 Jun 07; 21(1). PMID: 32503424    Free PMC article.
An image-based data-driven analysis of cellular architecture in a developing tissue.
Jonas Hartmann, Mie Wong, Elisa Gallo, Darren Gilmour.
Elife, 2020 Jun 06; 9. PMID: 32501214    Free PMC article.
HISTOBREAST, a collection of brightfield microscopy images of Haematoxylin and Eosin stained breast tissue.
Roxana M Buga, Tiberiu Totu, +4 authors, Stefan G Stanciu.
Sci Data, 2020 Jun 07; 7(1). PMID: 32503988    Free PMC article.
Drug Resistance Prediction Using Deep Learning Techniques on HIV-1 Sequence Data.
Margaret C Steiner, Keylie M Gibson, Keith A Crandall.
Viruses, 2020 May 23; 12(5). PMID: 32438586    Free PMC article.
Integrative computational epigenomics to build data-driven gene regulation hypotheses.
Tyrone Chen, Sonika Tyagi.
Gigascience, 2020 Jun 17; 9(6). PMID: 32543653    Free PMC article.
Enhanced Integrated Gradients: improving interpretability of deep learning models using splicing codes as a case study.
Anupama Jha, Joseph K Aicher, +2 authors, Yoseph Barash.
Genome Biol, 2020 Jun 21; 21(1). PMID: 32560708    Free PMC article.
Putting deep learning in perspective for pest management scientists.
Robert D Clark.
Pest Manag Sci, 2020 Mar 17; 76(7). PMID: 32173969    Free PMC article.
Don't dismiss logistic regression: the case for sensible extraction of interactions in the era of machine learning.
Joshua J Levy, A James O'Malley.
BMC Med Res Methodol, 2020 Jul 01; 20(1). PMID: 32600277    Free PMC article.
An artificial neural network approach for predicting hypertension using NHANES data.
Fernando López-Martínez, Edward Rolando Núñez-Valdez, Rubén González Crespo, Vicente García-Díaz.
Sci Rep, 2020 Jul 02; 10(1). PMID: 32606434    Free PMC article.
Links between Nutrition, Infectious Diseases, and Microbiota: Emerging Technologies and Opportunities for Human-Focused Research.
Manuela Cassotta, Tamara Yuliett Forbes-Hernández, +4 authors, Maurizio Battino.
Nutrients, 2020 Jun 25; 12(6). PMID: 32575399    Free PMC article.
Deep in the Bowel: Highly Interpretable Neural Encoder-Decoder Networks Predict Gut Metabolites from Gut Microbiome.
Vuong Le, Thomas P Quinn, Truyen Tran, Svetha Venkatesh.
BMC Genomics, 2020 Jul 22; 21(Suppl 4). PMID: 32689932    Free PMC article.
Methodological Challenges of Deep Learning in Optical Coherence Tomography for Retinal Diseases: A Review.
Ryan T Yanagihara, Cecilia S Lee, Daniel Shu Wei Ting, Aaron Y Lee.
Transl Vis Sci Technol, 2020 Jul 25; 9(2). PMID: 32704417    Free PMC article.
Convolutional Neural Networks Can Predict Retinal Differentiation in Retinal Organoids.
Evgenii Kegeles, Anton Naumov, +2 authors, Petr Baranov.
Front Cell Neurosci, 2020 Jul 29; 14. PMID: 32719585    Free PMC article.
Artificial intelligence in digital breast pathology: Techniques and applications.
Asmaa Ibrahim, Paul Gamble, +4 authors, Emad A Rakha.
Breast, 2020 Jan 15; 49. PMID: 31935669    Free PMC article.
A refined cell-of-origin classifier with targeted NGS and artificial intelligence shows robust predictive value in DLBCL.
Zijun Y Xu-Monette, Hongwei Zhang, +25 authors, Ken H Young.
Blood Adv, 2020 Jul 30; 4(14). PMID: 32722783    Free PMC article.
Relevant Applications of Generative Adversarial Networks in Drug Design and Discovery: Molecular De Novo Design, Dimensionality Reduction, and De Novo Peptide and Protein Design.
Eugene Lin, Chieh-Hsin Lin, Hsien-Yuan Lane.
Molecules, 2020 Jul 28; 25(14). PMID: 32708785    Free PMC article.
Artificial Intelligence and Health Technology Assessment: Anticipating a New Level of Complexity.
Hassane Alami, Pascale Lehoux, +7 authors, Jean-Paul Fortin.
J Med Internet Res, 2020 May 15; 22(7). PMID: 32406850    Free PMC article.
Knowledge-primed neural networks enable biologically interpretable deep learning on single-cell sequencing data.
Nikolaus Fortelny, Christoph Bock.
Genome Biol, 2020 Aug 05; 21(1). PMID: 32746932    Free PMC article.
A hybrid unsupervised-Deep learning tandem for electrooculography time series analysis.
Ruxandra Stoean, Catalin Stoean, +5 authors, Gonzalo Joya.
PLoS One, 2020 Jul 22; 15(7). PMID: 32692779    Free PMC article.
A Review on the Challenges in Indian Genomics Research for Variant Identification and Interpretation.
Sandhya Kiran Pemmasani, Rasika Raman, +2 authors, Anuradha Acharya.
Front Genet, 2020 Aug 15; 11. PMID: 32793285    Free PMC article.
An annotated fluorescence image dataset for training nuclear segmentation methods.
Florian Kromp, Eva Bozsaky, +11 authors, Sabine Taschner-Mandl.
Sci Data, 2020 Aug 13; 7(1). PMID: 32782410    Free PMC article.
Investigation on the impacts of COVID-19 quarantine on society and environment: Preventive measures and supportive technologies.
Santhosh Kumar Kumaravel, Ranjith Kumar Subramani, +4 authors, Umashankar Subramaniam.
3 Biotech, 2020 Aug 22; 10(9). PMID: 32821645    Free PMC article.
Integrative Methods and Practical Challenges for Single-Cell Multi-omics.
Anjun Ma, Adam McDermaid, +2 authors, Qin Ma.
Trends Biotechnol, 2020 Aug 21; 38(9). PMID: 32818441    Free PMC article.
Futuristic CRISPR-based biosensing in the cloud and internet of things era: an overview.
Abdullahi Umar Ibrahim, Fadi Al-Turjman, Zubaida Sa'id, Mehmet Ozsoz.
Multimed Tools Appl, 2020 Aug 25;. PMID: 32837247    Free PMC article.
Towards Building a Plant Cell Atlas.
Seung Y Rhee, Kenneth D Birnbaum, David W Ehrhardt.
Trends Plant Sci, 2019 Feb 20; 24(4). PMID: 30777643    Free PMC article.
Deep learning and feature based medication classifications from EEG in a large clinical data set.
David O Nahmias, Eugene F Civillico, Kimberly L Kontson.
Sci Rep, 2020 Aug 28; 10(1). PMID: 32848165    Free PMC article.
Using Deep Learning with Convolutional Neural Network Approach to Identify the Invasion Depth of Endometrial Cancer in Myometrium Using MR Images: A Pilot Study.
Hsiang-Chun Dong, Hsiang-Kai Dong, +2 authors, Cheng-Chang Chang.
Int J Environ Res Public Health, 2020 Aug 23; 17(16). PMID: 32824765    Free PMC article.
Histopathological Classification of Breast Cancer Images Using a Multi-Scale Input and Multi-Feature Network.
Taimoor Shakeel Sheikh, Yonghee Lee, Migyung Cho.
Cancers (Basel), 2020 Jul 30; 12(8). PMID: 32722111    Free PMC article.
Predicting risk of late age-related macular degeneration using deep learning.
Yifan Peng, Tiarnan D Keenan, +5 authors, Zhiyong Lu.
NPJ Digit Med, 2020 Sep 10; 3. PMID: 32904246    Free PMC article.
Deep learning with noisy labels: Exploring techniques and remedies in medical image analysis.
Davood Karimi, Haoran Dou, Simon K Warfield, Ali Gholipour.
Med Image Anal, 2020 Jul 06; 65. PMID: 32623277    Free PMC article.
Conditional antagonism in co-cultures of Pseudomonas aeruginosa and Candida albicans: An intersection of ethanol and phosphate signaling distilled from dual-seq transcriptomics.
Georgia Doing, Katja Koeppen, +2 authors, Deborah A Hogan.
PLoS Genet, 2020 Aug 20; 16(8). PMID: 32813693    Free PMC article.
Objective assessment of stored blood quality by deep learning.
Minh Doan, Joseph A Sebastian, +16 authors, Anne E Carpenter.
Proc Natl Acad Sci U S A, 2020 Aug 26; 117(35). PMID: 32839303    Free PMC article.
Breast cancer detection using deep convolutional neural networks and support vector machines.
Dina A Ragab, Maha Sharkas, Stephen Marshall, Jinchang Ren.
PeerJ, 2019 Feb 05; 7. PMID: 30713814    Free PMC article.
Artificial intelligence systems for complex decision-making in acute care medicine: a review.
Lawrence A Lynn.
Patient Saf Surg, 2019 Feb 09; 13. PMID: 30733829    Free PMC article.
Artificial intelligence for precision oncology: beyond patient stratification.
Francisco Azuaje.
NPJ Precis Oncol, 2019 Mar 02; 3. PMID: 30820462    Free PMC article.
Embedded deep learning in ophthalmology: making ophthalmic imaging smarter.
Petteri Teikari, Raymond P Najjar, Leopold Schmetterer, Dan Milea.
Ther Adv Ophthalmol, 2019 Mar 27; 11. PMID: 30911733    Free PMC article.
Translating the hemodynamic response: why focused interdisciplinary integration should matter for the future of functional neuroimaging.
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PeerJ, 2019 Apr 04; 7. PMID: 30941269    Free PMC article.
Recent Advances of Deep Learning in Bioinformatics and Computational Biology.
Binhua Tang, Zixiang Pan, Kang Yin, Asif Khateeb.
Front Genet, 2019 Apr 12; 10. PMID: 30972100    Free PMC article.
Introduction to Digital Image Analysis in Whole-slide Imaging: A White Paper from the Digital Pathology Association.
Famke Aeffner, Mark D Zarella, +11 authors, Douglas Bowman.
J Pathol Inform, 2019 Apr 16; 10. PMID: 30984469    Free PMC article.
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A roadmap for semi-automatically extracting predictive and clinically meaningful temporal features from medical data for predictive modeling.
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Glob Transit, 2019 Apr 30; 1. PMID: 31032483    Free PMC article.
Natural Language Processing of Clinical Notes on Chronic Diseases: Systematic Review.
Seyedmostafa Sheikhalishahi, Riccardo Miotto, +3 authors, Venet Osmani.
JMIR Med Inform, 2019 May 09; 7(2). PMID: 31066697    Free PMC article.
Deep Learning Methods for Predicting Disease Status Using Genomic Data.
Qianfan Wu, Adel Boueiz, +5 authors, Weiliang Qiu.
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Shihab Sarwar, Anglin Dent, +4 authors, Phedias Diamandis.
NPJ Digit Med, 2019 Jul 16; 2. PMID: 31304375    Free PMC article.
Machine Learning Approaches for the Estimation of Biological Aging: The Road Ahead for Population Studies.
Alessandro Gialluisi, Augusto Di Castelnuovo, +3 authors, Moli-sani Study Investigators.
Front Med (Lausanne), 2019 Jul 25; 6. PMID: 31338367    Free PMC article.
Convolutional Neural Networks for the Automatic Identification of Plant Diseases.
Justine Boulent, Samuel Foucher, Jérôme Théau, Pierre-Luc St-Charles.
Front Plant Sci, 2019 Aug 10; 10. PMID: 31396250    Free PMC article.
Machine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks.
Baiba Vilne, Irēna Meistere, Lelde Grantiņa-Ieviņa, Juris Ķibilds.
Front Microbiol, 2019 Aug 27; 10. PMID: 31447800    Free PMC article.
A machine-learning algorithm for neonatal seizure recognition: a multicentre, randomised, controlled trial.
Andreea M Pavel, Janet M Rennie, +17 authors, Geraldine B Boylan.
Lancet Child Adolesc Health, 2020 Aug 31; 4(10). PMID: 32861271    Free PMC article.
Clinical features of COVID-19 mortality: development and validation of a clinical prediction model.
Arjun S Yadaw, Yan-Chak Li, +3 authors, Gaurav Pandey.
Lancet Digit Health, 2020 Sep 29; 2(10). PMID: 32984797    Free PMC article.
Enhancing scientific discoveries in molecular biology with deep generative models.
Romain Lopez, Adam Gayoso, Nir Yosef.
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A bird's-eye view of deep learning in bioimage analysis.
Erik Meijering.
Comput Struct Biotechnol J, 2020 Oct 01; 18. PMID: 32994890    Free PMC article.
Minimum information about clinical artificial intelligence modeling: the MI-CLAIM checklist.
Beau Norgeot, Giorgio Quer, +10 authors, Atul J Butte.
Nat Med, 2020 Sep 11; 26(9). PMID: 32908275    Free PMC article.
Preparing next-generation scientists for biomedical big data: artificial intelligence approaches.
Jason H Moore, Mary Regina Boland, +9 authors, John H Holmes.
Per Med, 2019 Feb 15; 16(3). PMID: 30760118    Free PMC article.
Accelerated knowledge discovery from omics data by optimal experimental design.
Xiaokang Wang, Navneet Rai, +2 authors, Ilias Tagkopoulos.
Nat Commun, 2020 Oct 08; 11(1). PMID: 33024104    Free PMC article.
Sequence-to-function deep learning frameworks for engineered riboregulators.
Jacqueline A Valeri, Katherine M Collins, +4 authors, Diogo M Camacho.
Nat Commun, 2020 Oct 09; 11(1). PMID: 33028819    Free PMC article.
Codon optimization with deep learning to enhance protein expression.
Hongguang Fu, Yanbing Liang, +6 authors, Zhong Liu.
Sci Rep, 2020 Oct 21; 10(1). PMID: 33077783    Free PMC article.
Pattern recognition based on machine learning identifies oil adulteration and edible oil mixtures.
Kevin Lim, Kun Pan, Zhe Yu, Rong Hui Xiao.
Nat Commun, 2020 Oct 25; 11(1). PMID: 33097723    Free PMC article.
Analyzing Malaria Disease Using Effective Deep Learning Approach.
Krit Sriporn, Cheng-Fa Tsai, Chia-En Tsai, Paohsi Wang.
Diagnostics (Basel), 2020 Sep 30; 10(10). PMID: 32987888    Free PMC article.
Deep metabolome: Applications of deep learning in metabolomics.
Yotsawat Pomyen, Kwanjeera Wanichthanarak, +3 authors, Sakda Khoomrung.
Comput Struct Biotechnol J, 2020 Nov 03; 18. PMID: 33133423    Free PMC article.
Adversarial attacks on medical machine learning.
Samuel G Finlayson, John D Bowers, +3 authors, Isaac S Kohane.
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Designing accurate emulators for scientific processes using calibration-driven deep models.
Jayaraman J Thiagarajan, Bindya Venkatesh, +4 authors, Brian Spears.
Nat Commun, 2020 Nov 08; 11(1). PMID: 33159053    Free PMC article.
Direct cortical thickness estimation using deep learning-based anatomy segmentation and cortex parcellation.
Michael Rebsamen, Christian Rummel, +2 authors, Richard McKinley.
Hum Brain Mapp, 2020 Aug 14; 41(17). PMID: 32786059    Free PMC article.
A Review of Integrative Imputation for Multi-Omics Datasets.
Meng Song, Jonathan Greenbaum, +6 authors, Hong-Wen Deng.
Front Genet, 2020 Nov 17; 11. PMID: 33193667    Free PMC article.
Neuromorphic on-chip recognition of saliva samples of COPD and healthy controls using memristive devices.
Pouya Soltani Zarrin, Finn Zahari, +3 authors, Christian Wenger.
Sci Rep, 2020 Nov 14; 10(1). PMID: 33184439    Free PMC article.
Repositioning microbial biotechnology against COVID-19: the case of microbial production of flavonoids.
Tobias Goris, Álvaro Pérez-Valero, +7 authors, Juan Nogales.
Microb Biotechnol, 2020 Oct 14; 14(1). PMID: 33047877    Free PMC article.
Automatic Grading of Individual Knee Osteoarthritis Features in Plain Radiographs Using Deep Convolutional Neural Networks.
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Diagnostics (Basel), 2020 Nov 14; 10(11). PMID: 33182830    Free PMC article.
Machine Learning Methods in Drug Discovery.
Lauv Patel, Tripti Shukla, +2 authors, Shanzhi Wang.
Molecules, 2020 Nov 18; 25(22). PMID: 33198233    Free PMC article.
Rethinking glottal midline detection.
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Sci Rep, 2020 Nov 28; 10(1). PMID: 33244031    Free PMC article.
Multi-omics integration in biomedical research - A metabolomics-centric review.
Maria A Wörheide, Jan Krumsiek, Gabi Kastenmüller, Matthias Arnold.
Anal Chim Acta, 2020 Nov 30; 1141. PMID: 33248648    Free PMC article.
PASNet: pathway-associated sparse deep neural network for prognosis prediction from high-throughput data.
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BMC Bioinformatics, 2018 Dec 19; 19(1). PMID: 30558539    Free PMC article.
An integrative approach for building personalized gene regulatory networks for precision medicine.
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Genome Med, 2018 Dec 21; 10(1). PMID: 30567569    Free PMC article.
Application of machine learning in rheumatic disease research.
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Detecting Adverse Drug Events with Rapidly Trained Classification Models.
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A deep learning method to more accurately recall known lysine acetylation sites.
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BMC Bioinformatics, 2019 Jan 25; 20(1). PMID: 30674277    Free PMC article.
16S rRNA sequence embeddings: Meaningful numeric feature representations of nucleotide sequences that are convenient for downstream analyses.
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PLoS Comput Biol, 2019 Feb 27; 15(2). PMID: 30807567    Free PMC article.
Learning Contextual Hierarchical Structure of Medical Concepts with Poincairé Embeddings to Clarify Phenotypes.
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Pac Symp Biocomput, 2019 Mar 14; 24. PMID: 30864306    Free PMC article.
Systems biology intertwines with single cell and AI.
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BMC Bioinformatics, 2019 May 11; 20(Suppl 7). PMID: 31074375    Free PMC article.
Genomic data mining for functional annotation of human long noncoding RNAs.
Brian L Gudenas, Jun Wang, +3 authors, Liang-Jiang Wang.
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ProteinNet: a standardized data set for machine learning of protein structure.
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BMC Bioinformatics, 2019 Jun 13; 20(1). PMID: 31185886    Free PMC article.
Applications, promises, and pitfalls of deep learning for fluorescence image reconstruction.
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Nat Methods, 2019 Jul 10; 16(12). PMID: 31285623
Region Extraction and Classification of Skin Cancer: A Heterogeneous framework of Deep CNN Features Fusion and Reduction.
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J Med Syst, 2019 Jul 22; 43(9). PMID: 31327058
HetEnc: a deep learning predictive model for multi-type biological dataset.
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BMC Genomics, 2019 Aug 10; 20(1). PMID: 31395005    Free PMC article.
Joint Banknote Recognition and Counterfeit Detection Using Explainable Artificial Intelligence.
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Sensors (Basel), 2019 Aug 23; 19(16). PMID: 31430971    Free PMC article.
Identifying Methylation Pattern and Genes Associated with Breast Cancer Subtypes.
Lei Chen, Tao Zeng, +3 authors, Yu-Dong Cai.
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Deep learning predicts short non-coding RNA functions from only raw sequence data.
Teresa Maria Rosaria Noviello, Francesco Ceccarelli, Michele Ceccarelli, Luigi Cerulo.
PLoS Comput Biol, 2020 Nov 12; 16(11). PMID: 33175836    Free PMC article.
The impact of different negative training data on regulatory sequence predictions.
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PLoS One, 2020 Dec 02; 15(12). PMID: 33259518    Free PMC article.
Deep Learning in LncRNAome: Contribution, Challenges, and Perspectives.
Tanvir Alam, Hamada R H Al-Absi, Sebastian Schmeier.
Noncoding RNA, 2020 Dec 04; 6(4). PMID: 33266128    Free PMC article.
Identifying Mouse Autoimmune Uveitis from Fundus Photographs Using Deep Learning.
Jian Sun, Xiaoqin Huang, +4 authors, Siamak Yousefi.
Transl Vis Sci Technol, 2020 Dec 10; 9(2). PMID: 33294300    Free PMC article.
Predicting Drug Response and Synergy Using a Deep Learning Model of Human Cancer Cells.
Brent M Kuenzi, Jisoo Park, +5 authors, Trey Ideker.
Cancer Cell, 2020 Oct 24; 38(5). PMID: 33096023    Free PMC article.
Identifying Ethical Considerations for Machine Learning Healthcare Applications.
Danton S Char, Michael D Abràmoff, Chris Feudtner.
Am J Bioeth, 2020 Oct 27; 20(11). PMID: 33103967    Free PMC article.
Methods for correcting inference based on outcomes predicted by machine learning.
Siruo Wang, Tyler H McCormick, Jeffrey T Leek.
Proc Natl Acad Sci U S A, 2020 Nov 20; 117(48). PMID: 33208538    Free PMC article.
Axes of a revolution: challenges and promises of big data in healthcare.
Smadar Shilo, Hagai Rossman, Eran Segal.
Nat Med, 2020 Jan 15; 26(1). PMID: 31932803
Machine learning-enabled multiplexed microfluidic sensors.
Sajjad Rahmani Dabbagh, Fazle Rabbi, +2 authors, Savas Tasoglu.
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Augmented Realities, Artificial Intelligence, and Machine Learning: Clinical Implications and How Technology Is Shaping the Future of Medicine.
Gaby N Moawad, Jad Elkhalil, +3 authors, Ibrahim Alkatout.
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Learning to detect the onset of slow activity after a generalized tonic-clonic seizure.
Carroll Vance, Yejin Kim, +5 authors, Xiaoqian Jiang.
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Deep Learning in Proteomics.
Bo Wen, Wen-Feng Zeng, +4 authors, Bing Zhang.
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State of the Field in Multi-Omics Research: From Computational Needs to Data Mining and Sharing.
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Front Genet, 2020 Dec 29; 11. PMID: 33362867    Free PMC article.
Applications of machine learning methods in kidney disease: hope or hype?
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Application of deep learning in genomics.
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Molecular Sets (MOSES): A Benchmarking Platform for Molecular Generation Models.
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Front Pharmacol, 2021 Jan 05; 11. PMID: 33390943    Free PMC article.
Teasing out Artificial Intelligence in Medicine: An Ethical Critique of Artificial Intelligence and Machine Learning in Medicine.
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Pneumonia Classification Using Deep Learning from Chest X-ray Images During COVID-19.
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DeepGraphMolGen, a multi-objective, computational strategy for generating molecules with desirable properties: a graph convolution and reinforcement learning approach.
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Extraction of Family History Information From Clinical Notes: Deep Learning and Heuristics Approach.
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Artificial intelligence and computational pathology.
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Multi-classifier-based identification of COVID-19 from chest computed tomography using generalizable and interpretable radiomics features.
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Single-cell cytometry via multiplexed fluorescence prediction by label-free reflectance microscopy.
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Translating research findings into clinical practice: a systematic and critical review of neuroimaging-based clinical tools for brain disorders.
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The physician-scientist, 75 years after Vannevar Bush-rethinking the 'bench' and 'bedside' dichotomy.
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Nat Med, 2020 Apr 11; 26(4). PMID: 32273602
Unraveling the deep learning gearbox in optical coherence tomography image segmentation towards explainable artificial intelligence.
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Artificial intelligence for good health: a scoping review of the ethics literature.
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Prevalence of low high-density lipoprotein among young adults receiving antiretroviral therapy in Zambia: An opportunity to consider non-communicable diseases in resource-limited settings.
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Rethinking drug design in the artificial intelligence era.
Petra Schneider, W Patrick Walters, +15 authors, Gisbert Schneider.
Nat Rev Drug Discov, 2019 Dec 06; 19(5). PMID: 31801986
Machine Learning to Predict Delayed Cerebral Ischemia and Outcomes in Subarachnoid Hemorrhage.
Jude P J Savarraj, Georgene W Hergenroeder, +7 authors, H Alex Choi.
Neurology, 2020 Nov 14; 96(4). PMID: 33184232    Free PMC article.
A deep learning algorithm using CT images to screen for Corona virus disease (COVID-19).
Shuai Wang, Bo Kang, +8 authors, Bo Xu.
Eur Radiol, 2021 Feb 26;. PMID: 33629156    Free PMC article.
TranSynergy: Mechanism-driven interpretable deep neural network for the synergistic prediction and pathway deconvolution of drug combinations.
Qiao Liu, Lei Xie.
PLoS Comput Biol, 2021 Feb 13; 17(2). PMID: 33577560    Free PMC article.
SynTEG: a framework for temporal structured electronic health data simulation.
Ziqi Zhang, Chao Yan, +2 authors, Bradley A Malin.
J Am Med Inform Assoc, 2020 Dec 06; 28(3). PMID: 33277896    Free PMC article.
Deep learning-based high-throughput phenotyping can drive future discoveries in plant reproductive biology.
Cedar Warman, John E Fowler.
Plant Reprod, 2021 Mar 17; 34(2). PMID: 33725183    Free PMC article.
Artificial Intelligence Based Approaches to Identify Molecular Determinants of Exceptional Health and Life Span-An Interdisciplinary Workshop at the National Institute on Aging.
Jason H Moore, Nalini Raghavachari, Workshop Speakers.
Front Artif Intell, 2019 Aug 06; 2. PMID: 33733101    Free PMC article.
Biological network analysis with deep learning.
Giulia Muzio, Leslie O'Bray, Karsten Borgwardt.
Brief Bioinform, 2020 Nov 11; 22(2). PMID: 33169146    Free PMC article.
Human-interpretable image features derived from densely mapped cancer pathology slides predict diverse molecular phenotypes.
James A Diao, Jason K Wang, +19 authors, Amaro Taylor-Weiner.
Nat Commun, 2021 Mar 14; 12(1). PMID: 33712588    Free PMC article.
Complementary performances of convolutional and capsule neural networks on classifying microfluidic images of dividing yeast cells.
Mehran Ghafari, Justin Clark, +4 authors, Hong Qin.
PLoS One, 2021 Mar 18; 16(3). PMID: 33730031    Free PMC article.
Executable cancer models: successes and challenges.
Matthew A Clarke, Jasmin Fisher.
Nat Rev Cancer, 2020 Apr 29; 20(6). PMID: 32341552
Review of deep learning: concepts, CNN architectures, challenges, applications, future directions.
Laith Alzubaidi, Jinglan Zhang, +7 authors, Laith Farhan.
J Big Data, 2021 Apr 06; 8(1). PMID: 33816053    Free PMC article.
Genome annotation across species using deep convolutional neural networks.
Ghazaleh Khodabandelou, Etienne Routhier, Julien Mozziconacci.
PeerJ Comput Sci, 2021 Apr 06; 6. PMID: 33816929    Free PMC article.
Helixer: Cross-species gene annotation of large eukaryotic genomes using deep learning.
Felix Stiehler, Marvin Steinborn, +3 authors, Alisandra K Denton.
Bioinformatics, 2020 Dec 17;. PMID: 33325516    Free PMC article.
Artificial intelligence and leukocyte epigenomics: Evaluation and prediction of late-onset Alzheimer's disease.
Ray O Bahado-Singh, Sangeetha Vishweswaraiah, +11 authors, Uppala Radhakrishna.
PLoS One, 2021 Apr 01; 16(3). PMID: 33788842    Free PMC article.
Typing methods based on whole genome sequencing data.
Laura Uelze, Josephine Grützke, +5 authors, Burkhard Malorny.
One Health Outlook, 2020 Feb 18; 2. PMID: 33829127    Free PMC article.
A large-scale internal validation study of unsupervised virtual trichrome staining technologies on nonalcoholic steatohepatitis liver biopsies.
Joshua J Levy, Nasim Azizgolshani, +7 authors, Louis J Vaickus.
Mod Pathol, 2020 Dec 11; 34(4). PMID: 33299110    Free PMC article.
Artificial intelligence in cancer research: learning at different levels of data granularity.
Davide Cirillo, Iker Núñez-Carpintero, Alfonso Valencia.
Mol Oncol, 2021 Feb 04; 15(4). PMID: 33533192    Free PMC article.
Machine learning, the kidney, and genotype-phenotype analysis.
Rachel S G Sealfon, Laura H Mariani, Matthias Kretzler, Olga G Troyanskaya.
Kidney Int, 2020 May 04; 97(6). PMID: 32359808    Free PMC article.
Machine learning for patient risk stratification: standing on, or looking over, the shoulders of clinicians?
Brett K Beaulieu-Jones, William Yuan, +4 authors, Isaac S Kohane.
NPJ Digit Med, 2021 Apr 01; 4(1). PMID: 33785839    Free PMC article.
Automated detection and segmentation of thoracic lymph nodes from CT using 3D foveal fully convolutional neural networks.
Andra-Iza Iuga, Heike Carolus, +6 authors, Michael Püsken.
BMC Med Imaging, 2021 Apr 15; 21(1). PMID: 33849483    Free PMC article.
Action detection using a neural network elucidates the genetics of mouse grooming behavior.
Brian Q Geuther, Asaf Peer, +3 authors, Vivek Kumar.
Elife, 2021 Mar 18; 10. PMID: 33729153    Free PMC article.
Machine learning analysis to predict the need for ankle foot orthosis in patients with stroke.
Yoo Jin Choo, Jeoung Kun Kim, +2 authors, Donghwi Park.
Sci Rep, 2021 Apr 21; 11(1). PMID: 33875716    Free PMC article.
Opportunities and challenges for the computational interpretation of rare variation in clinically important genes.
Gregory McInnes, Andrew G Sharo, +11 authors, Russ B Altman.
Am J Hum Genet, 2021 Apr 03; 108(4). PMID: 33798442    Free PMC article.
Pretreatment MRI Radiomics Based Response Prediction Model in Locally Advanced Cervical Cancer.
Benedetta Gui, Rosa Autorino, +15 authors, Giovanni Scambia.
Diagnostics (Basel), 2021 Apr 04; 11(4). PMID: 33807494    Free PMC article.
G2S: A New Deep Learning Tool for Predicting Stool Microbiome Structure From Oral Microbiome Data.
Simone Rampelli, Marco Fabbrini, +3 authors, Silvia Turroni.
Front Genet, 2021 Apr 27; 12. PMID: 33897763    Free PMC article.
Machine learning-based investigation of the cancer protein secretory pathway.
Rasool Saghaleyni, Azam Sheikh Muhammad, +2 authors, Jonathan L Robinson.
PLoS Comput Biol, 2021 Apr 06; 17(4). PMID: 33819271    Free PMC article.
Single-cell transcriptomics in cancer: computational challenges and opportunities.
Jean Fan, Kamil Slowikowski, Fan Zhang.
Exp Mol Med, 2020 Sep 16; 52(9). PMID: 32929226    Free PMC article.
Multi-Layer Picture of Neurodegenerative Diseases: Lessons from the Use of Big Data through Artificial Intelligence.
Andrea Termine, Carlo Fabrizio, +5 authors, Raffaella Cascella.
J Pers Med, 2021 May 01; 11(4). PMID: 33917161    Free PMC article.
The pursuit of mechanism of action: uncovering drug complexity in TB drug discovery.
Tianao Yuan, Joshua M Werman, Nicole S Sampson.
RSC Chem Biol, 2021 May 01; 2(2). PMID: 33928253    Free PMC article.
Deep generative model embedding of single-cell RNA-Seq profiles on hyperspheres and hyperbolic spaces.
Jiarui Ding, Aviv Regev.
Nat Commun, 2021 May 07; 12(1). PMID: 33953202    Free PMC article.
Text mining for modeling of protein complexes enhanced by machine learning.
Varsha D Badal, Petras J Kundrotas, Ilya A Vakser.
Bioinformatics, 2020 Sep 23; 37(4). PMID: 32960948    Free PMC article.
The Importance of Image Resolution in Building Deep Learning Models for Medical Imaging.
Paras Lakhani.
Radiol Artif Intell, 2020 Jan 22; 2(1). PMID: 33939779    Free PMC article.
Deep learning methods allow fully automated segmentation of metacarpal bones to quantify volumetric bone mineral density.
Lukas Folle, Timo Meinderink, +5 authors, Andreas Maier.
Sci Rep, 2021 May 08; 11(1). PMID: 33958664    Free PMC article.
CIRFESS: An Interactive Resource for Querying the Set of Theoretically Detectable Peptides for Cell Surface and Extracellular Enrichment Proteomic Studies.
Matthew Waas, Jack Littrell, Rebekah L Gundry.
J Am Soc Mass Spectrom, 2020 Mar 28; 31(7). PMID: 32212654    Free PMC article.
Smart Video Surveillance System Based on Edge Computing.
Antonio Carlos Cob-Parro, Cristina Losada-Gutiérrez, +2 authors, Ignacio Bravo-Muñoz.
Sensors (Basel), 2021 May 01; 21(9). PMID: 33922548    Free PMC article.
Machine learning for sperm selection.
Jae Bem You, Christopher McCallum, +3 authors, David Sinton.
Nat Rev Urol, 2021 May 19;. PMID: 34002070
Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator.
Adrian L Sanborn, Benjamin T Yeh, +5 authors, Roger D Kornberg.
Elife, 2021 Apr 28; 10. PMID: 33904398    Free PMC article.
Hybrid modelling for stroke care: Review and suggestions of new approaches for risk assessment and simulation of scenarios.
Tilda Herrgårdh, Vince I Madai, +5 authors, Gunnar Cedersund.
Neuroimage Clin, 2021 May 18; 31. PMID: 34000646    Free PMC article.
Dual-scale categorization based deep learning to evaluate programmed cell death ligand 1 expression in non-small cell lung cancer.
Xiangyun Wang, Peilin Chen, +5 authors, Qiang Fu.
Medicine (Baltimore), 2021 May 21; 100(20). PMID: 34011092    Free PMC article.
Predicting youth diabetes risk using NHANES data and machine learning.
Nita Vangeepuram, Bian Liu, +2 authors, Gaurav Pandey.
Sci Rep, 2021 May 29; 11(1). PMID: 34045491    Free PMC article.
Translational precision medicine: an industry perspective.
Dominik Hartl, Valeria de Luca, +11 authors, Adrian Roth.
J Transl Med, 2021 Jun 07; 19(1). PMID: 34090480    Free PMC article.