Journal Article
. 2019 May;4(2).
doi: 10.1080/23808993.2019.1585805.

Deep learning and radiomics in precision medicine

Vishwa S Parekh 1 Michael A Jacobs 1 
  • PMID: 31080889
  •     33 References
  •     19 citations


Introduction: The radiological reading room is undergoing a paradigm shift to a symbiosis of computer science and radiology using artificial intelligence integrated with machine and deep learning with radiomics to better define tissue characteristics. The goal is to use integrated deep learning and radiomics with radiological parameters to produce a personalized diagnosis for a patient.

Areas Covered: This review provides an overview of historical and current deep learning and radiomics methods in the context of precision medicine in radiology. A literature search for 'Deep Learning', 'Radiomics', 'Machine learning', 'Artificial Intelligence', 'Convolutional Neural Network', 'Generative Adversarial Network', 'Autoencoders', Deep Belief Networks", Reinforcement Learning", and 'Multiparametric MRI' was performed in PubMed, ArXiv, Scopus, CVPR, SPIE, IEEE Xplore, and NIPS to identify articles of interest.

Expert Opinion: In conclusion, both deep learning and radiomics are two rapidly advancing technologies that will unite in the future to produce a single unified framework for clinical decision support with a potential to completely revolutionize the field of precision medicine.

Keywords: Deep learning networks; machine learning; multiparametric radiomics.

New variants of a method of MRI scale standardization.
L G Nyúl, J K Udupa, X Zhang.
IEEE Trans Med Imaging, 2000 Apr 28; 19(2). PMID: 10784285
Highly Cited.
The perceptron: a probabilistic model for information storage and organization in the brain.
Psychol Rev, 1958 Nov 01; 65(6). PMID: 13602029
Highly Cited.
A fast learning algorithm for deep belief nets.
Geoffrey E Hinton, Simon Osindero, Yee-Whye Teh.
Neural Comput, 2006 Jun 13; 18(7). PMID: 16764513
Highly Cited.
Selforganization in molecular and cellular networks.
M Eigen.
Neurochem Int, 1980 Jan 01; 2C. PMID: 20487767
Mayo clinical Text Analysis and Knowledge Extraction System (cTAKES): architecture, component evaluation and applications.
Guergana K Savova, James J Masanz, +4 authors, Christopher G Chute.
J Am Med Inform Assoc, 2010 Sep 08; 17(5). PMID: 20819853    Free PMC article.
Highly Cited.
An automated model to identify heart failure patients at risk for 30-day readmission or death using electronic medical record data.
Ruben Amarasingham, Billy J Moore, +7 authors, Ethan A Halm.
Med Care, 2010 Oct 14; 48(11). PMID: 20940649
Highly Cited.
A logical calculus of the ideas immanent in nervous activity. 1943.
W S McCulloch, W Pitts.
Bull Math Biol, 1990 Jan 01; 52(1-2). PMID: 2185863
Highly Cited.
Use of diverse electronic medical record systems to identify genetic risk for type 2 diabetes within a genome-wide association study.
Abel N Kho, M Geoffrey Hayes, +17 authors, William L Lowe.
J Am Med Inform Assoc, 2011 Nov 22; 19(2). PMID: 22101970    Free PMC article.
Highly Cited.
Radiomics: extracting more information from medical images using advanced feature analysis.
Philippe Lambin, Emmanuel Rios-Velazquez, +8 authors, Hugo J W L Aerts.
Eur J Cancer, 2012 Jan 20; 48(4). PMID: 22257792    Free PMC article.
Highly Cited. Review.
Radiomics: the process and the challenges.
Virendra Kumar, Yuhua Gu, +13 authors, Robert J Gillies.
Magn Reson Imaging, 2012 Aug 18; 30(9). PMID: 22898692    Free PMC article.
Highly Cited. Review.
Decoding tumour phenotype by noninvasive imaging using a quantitative radiomics approach.
Hugo J W L Aerts, Emmanuel Rios Velazquez, +15 authors, Philippe Lambin.
Nat Commun, 2014 Jun 04; 5. PMID: 24892406    Free PMC article.
Highly Cited.
Deep learning in neural networks: an overview.
Jürgen Schmidhuber.
Neural Netw, 2014 Dec 03; 61. PMID: 25462637
Highly Cited. Review.
Human-level control through deep reinforcement learning.
Volodymyr Mnih, Koray Kavukcuoglu, +16 authors, Demis Hassabis.
Nature, 2015 Feb 27; 518(7540). PMID: 25719670
Highly Cited.
Deep learning.
Yann LeCun, Yoshua Bengio, Geoffrey Hinton.
Nature, 2015 May 29; 521(7553). PMID: 26017442
Highly Cited. Review.
Mastering the game of Go with deep neural networks and tree search.
David Silver, Aja Huang, +17 authors, Demis Hassabis.
Nature, 2016 Jan 29; 529(7587). PMID: 26819042
Highly Cited.
Applications and limitations of radiomics.
Stephen S F Yip, Hugo J W L Aerts.
Phys Med Biol, 2016 Jun 09; 61(13). PMID: 27269645    Free PMC article.
Highly Cited. Review.
Radiomics: a new application from established techniques.
Vishwa Parekh, Michael A Jacobs.
Expert Rev Precis Med Drug Dev, 2017 Jan 04; 1(2). PMID: 28042608    Free PMC article.
Highly Cited.
SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation.
Vijay Badrinarayanan, Alex Kendall, Roberto Cipolla.
IEEE Trans Pattern Anal Mach Intell, 2017 Jan 07; 39(12). PMID: 28060704
Highly Cited.
Intrinsic dependencies of CT radiomic features on voxel size and number of gray levels.
Muhammad Shafiq-Ul-Hassan, Geoffrey G Zhang, +10 authors, Eduardo Gerardo Moros.
Med Phys, 2017 Jan 24; 44(3). PMID: 28112418    Free PMC article.
Highly Cited.
Deep Learning for Brain MRI Segmentation: State of the Art and Future Directions.
Zeynettin Akkus, Alfiia Galimzianova, +2 authors, Bradley J Erickson.
J Digit Imaging, 2017 Jun 04; 30(4). PMID: 28577131    Free PMC article.
Highly Cited. Review.
A survey on deep learning in medical image analysis.
Geert Litjens, Thijs Kooi, +6 authors, Clara I Sánchez.
Med Image Anal, 2017 Aug 05; 42. PMID: 28778026
Highly Cited. Review.
Deep reinforcement learning for automated radiation adaptation in lung cancer.
Huan-Hsin Tseng, Yi Luo, +3 authors, Issam El Naqa.
Med Phys, 2017 Oct 17; 44(12). PMID: 29034482    Free PMC article.
Integrated radiomic framework for breast cancer and tumor biology using advanced machine learning and multiparametric MRI.
Vishwa S Parekh, Michael A Jacobs.
NPJ Breast Cancer, 2017 Nov 21; 3. PMID: 29152563    Free PMC article.
Deep Learning and Its Applications in Biomedicine.
Chensi Cao, Feng Liu, +6 authors, Zhi Xie.
Genomics Proteomics Bioinformatics, 2018 Mar 10; 16(1). PMID: 29522900    Free PMC article.
Survey on deep learning for radiotherapy.
Philippe Meyer, Vincent Noblet, Christophe Mazzara, Alex Lallement.
Comput Biol Med, 2018 May 23; 98. PMID: 29787940
Multi-Scale Deep Reinforcement Learning for Real-Time 3D-Landmark Detection in CT Scans.
Florin-Cristian Ghesu, Bogdan Georgescu, +4 authors, Dorin Comaniciu.
IEEE Trans Pattern Anal Mach Intell, 2018 Jul 11; 41(1). PMID: 29990011
Voxel size and gray level normalization of CT radiomic features in lung cancer.
Muhammad Shafiq-Ul-Hassan, Kujtim Latifi, +3 authors, Eduardo Moros.
Sci Rep, 2018 Jul 14; 8(1). PMID: 30002441    Free PMC article.
Medical Image Synthesis with Context-Aware Generative Adversarial Networks.
Dong Nie, Roger Trullo, +4 authors, Dinggang Shen.
Med Image Comput Comput Assist Interv, 2018 Jul 17; 10435. PMID: 30009283    Free PMC article.
Highly Cited.
StackGAN++: Realistic Image Synthesis with Stacked Generative Adversarial Networks.
Han Zhang, Tao Xu, +4 authors, Dimitris N Metaxas.
IEEE Trans Pattern Anal Mach Intell, 2018 Jul 17; 41(8). PMID: 30010548
Continual lifelong learning with neural networks: A review.
German I Parisi, Ronald Kemker, +2 authors, Stefan Wermter.
Neural Netw, 2019 Feb 20; 113. PMID: 30780045
Neural networks and physical systems with emergent collective computational abilities.
J J Hopfield.
Proc Natl Acad Sci U S A, 1982 Apr 01; 79(8). PMID: 6953413    Free PMC article.
Highly Cited.
Neocognitron: a self organizing neural network model for a mechanism of pattern recognition unaffected by shift in position.
K Fukushima.
Biol Cybern, 1980 Jan 01; 36(4). PMID: 7370364
Highly Cited.
Long short-term memory.
S Hochreiter, J Schmidhuber.
Neural Comput, 1997 Oct 23; 9(8). PMID: 9377276
Highly Cited.
Deep Learning: A Review for the Radiation Oncologist.
Luca Boldrini, Jean-Emmanuel Bibault, +2 authors, Martin-Immanuel Bittner.
Front Oncol, 2019 Oct 22; 9. PMID: 31632910    Free PMC article.
Role of Complex Networks for Integrating Medical Images and Radiomic Features of Intracranial Ependymoma Patients in Response to Proton Radiotherapy.
Marco Dominietto, Alessia Pica, +3 authors, Enrico Capobianco.
Front Med (Lausanne), 2020 Feb 06; 6. PMID: 32010703    Free PMC article.
Multiparametric deep learning tissue signatures for a radiological biomarker of breast cancer: Preliminary results.
Vishwa S Parekh, Katarzyna J Macura, +4 authors, Michael A Jacobs.
Med Phys, 2019 Oct 11; 47(1). PMID: 31598978    Free PMC article.
In vivo magnetic resonance imaging and spectroscopy. Technological advances and opportunities for applications continue to abound.
Peter van Zijl, Linda Knutsson.
J Magn Reson, 2019 Aug 05; 306. PMID: 31377150    Free PMC article.
Retrospective imaging studies of gastric cancer: Study protocol clinical trial (SPIRIT Compliant).
Zixing Huang, Dan Liu, +5 authors, Bing Wu.
Medicine (Baltimore), 2020 Feb 23; 99(8). PMID: 32080093    Free PMC article.
Artificial intelligence with multi-functional machine learning platform development for better healthcare and precision medicine.
Zeeshan Ahmed, Khalid Mohamed, Saman Zeeshan, XinQi Dong.
Database (Oxford), 2020 Mar 19; 2020. PMID: 32185396    Free PMC article.
Multiparametric radiomics methods for breast cancer tissue characterization using radiological imaging.
Vishwa S Parekh, Michael A Jacobs.
Breast Cancer Res Treat, 2020 Feb 06; 180(2). PMID: 32020435    Free PMC article.
A low-cost texture-based pipeline for predicting myocardial tissue remodeling and fibrosis using cardiac ultrasound.
Nobuyuki Kagiyama, Sirish Shrestha, +5 authors, Partho P Sengupta.
EBioMedicine, 2020 Apr 09; 54. PMID: 32268274    Free PMC article.
Longitudinal functional and imaging outcome measures in FKRP limb-girdle muscular dystrophy.
Doris G Leung, Alex E Bocchieri, +9 authors, Kathryn R Wagner.
BMC Neurol, 2020 May 21; 20(1). PMID: 32429923    Free PMC article.
erbB in NSCLC as a molecular target: current evidences and future directions.
Marzia Del Re, Federico Cucchiara, +7 authors, Romano Danesi.
ESMO Open, 2020 Aug 21; 5(4). PMID: 32820012    Free PMC article.
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.
Introduction to Special Issue of Radiology and Imaging of Cancer.
Roberta Fusco, Vincenza Granata, Antonella Petrillo.
Cancers (Basel), 2020 Sep 24; 12(9). PMID: 32961946    Free PMC article.
Radiomics at a Glance: A Few Lessons Learned from Learning Approaches.
Enrico Capobianco, Jun Deng.
Cancers (Basel), 2020 Sep 03; 12(9). PMID: 32872466    Free PMC article.
Integrated Multiparametric Radiomics and Informatics System for Characterizing Breast Tumor Characteristics with the OncotypeDX Gene Assay.
Michael A Jacobs, Christopher B Umbricht, +5 authors, Antonio C Wolff.
Cancers (Basel), 2020 Oct 01; 12(10). PMID: 32992569    Free PMC article.
Progress of Artificial Intelligence in Gynecological Malignant Tumors.
Jie Zhou, Zhi Ying Zeng, Li Li.
Cancer Manag Res, 2020 Dec 29; 12. PMID: 33364831    Free PMC article.
Toward radiomics for assessment of response to systemic therapies in lung cancer.
Shawn Sun, Florent L Besson, +2 authors, Laurent Dercle.
Oncotarget, 2021 Jan 22; 11(51). PMID: 33473253    Free PMC article.
Standardization of imaging methods for machine learning in neuro-oncology.
Xiao Tian Li, Raymond Y Huang.
Neurooncol Adv, 2021 Feb 02; 2(Suppl 4). PMID: 33521640    Free PMC article.
Radiomics of hepatocellular carcinoma.
Sara Lewis, Stefanie Hectors, Bachir Taouli.
Abdom Radiol (NY), 2020 Jan 12; 46(1). PMID: 31925492
Comparison of Intraoperative Ultrasound B-Mode and Strain Elastography for the Differentiation of Glioblastomas From Solitary Brain Metastases. An Automated Deep Learning Approach for Image Analysis.
Santiago Cepeda, Sergio García-García, +5 authors, Rosario Sarabia.
Front Oncol, 2021 Feb 20; 10. PMID: 33604286    Free PMC article.