. 2019 Sep; 6:2374289519873088.
doi: 10.1177/2374289519873088.

Artificial Intelligence and Machine Learning in Pathology: The Present Landscape of Supervised Methods

Hooman H Rashidi 1 Nam K Tran 1 Elham Vali Betts 1 Lydia P Howell 1 Ralph Green 1 
  • PMID: 31523704
  •     19 References
  •     34 citations


Increased interest in the opportunities provided by artificial intelligence and machine learning has spawned a new field of health-care research. The new tools under development are targeting many aspects of medical practice, including changes to the practice of pathology and laboratory medicine. Optimal design in these powerful tools requires cross-disciplinary literacy, including basic knowledge and understanding of critical concepts that have traditionally been unfamiliar to pathologists and laboratorians. This review provides definitions and basic knowledge of machine learning categories (supervised, unsupervised, and reinforcement learning), introduces the underlying concept of the bias-variance trade-off as an important foundation in supervised machine learning, and discusses approaches to the supervised machine learning study design along with an overview and description of common supervised machine learning algorithms (linear regression, logistic regression, Naive Bayes, k-nearest neighbor, support vector machine, random forest, convolutional neural networks).

Keywords: algorithms; artificial intelligence; convolutional neural network; deep learning; k-nearest neighbor; machine learning; random forest; supervised learning; supervised methods; support vector machine; unsupervised learning.

Prognostic factors for mortality in left colonic peritonitis: a new scoring system.
S Biondo, E Ramos, +5 authors, E Jaurrieta.
J Am Coll Surg, 2000 Dec 29; 191(6). PMID: 11129812
Information management: moving from test results to clinical information.
M J Becich.
Clin Leadersh Manag Rev, 2001 Feb 24; 14(6). PMID: 11210218
Multiple additive regression trees with application in epidemiology.
Jerome H Friedman, Jacqueline J Meulman.
Stat Med, 2003 Apr 22; 22(9). PMID: 12704603
Tumor classification by tissue microarray profiling: random forest clustering applied to renal cell carcinoma.
Tao Shi, David Seligson, +2 authors, Steve Horvath.
Mod Pathol, 2004 Nov 06; 18(4). PMID: 15529185
Melting point prediction employing k-nearest neighbor algorithms and genetic parameter optimization.
Florian Nigsch, Andreas Bender, +3 authors, John B O Mitchell.
J Chem Inf Model, 2006 Nov 28; 46(6). PMID: 17125183
A working guide to boosted regression trees.
J Elith, J R Leathwick, T Hastie.
J Anim Ecol, 2008 Apr 10; 77(4). PMID: 18397250
Highly Cited.
Common pitfalls in statistical analysis: Odds versus risk.
Priya Ranganathan, Rakesh Aggarwal, C S Pramesh.
Perspect Clin Res, 2015 Dec 02; 6(4). PMID: 26623395    Free PMC article.
Medical big data: promise and challenges.
Choong Ho Lee, Hyung-Jin Yoon.
Kidney Res Clin Pract, 2017 Apr 11; 36(1). PMID: 28392994    Free PMC article.
Highly Cited.
Common pitfalls in statistical analysis: Logistic regression.
Priya Ranganathan, C S Pramesh, Rakesh Aggarwal.
Perspect Clin Res, 2017 Aug 23; 8(3). PMID: 28828311    Free PMC article.
Classification and mutation prediction from non-small cell lung cancer histopathology images using deep learning.
Nicolas Coudray, Paolo Santiago Ocampo, +6 authors, Aristotelis Tsirigos.
Nat Med, 2018 Sep 19; 24(10). PMID: 30224757
Highly Cited.
Interpretation and Impact of Real-World Clinical Data for the Practicing Clinician.
Lawrence Blonde, Kamlesh Khunti, +2 authors, Neil S Skolnik.
Adv Ther, 2018 Oct 26; 35(11). PMID: 30357570    Free PMC article.
Machine learning in medicine: Addressing ethical challenges.
Effy Vayena, Alessandro Blasimme, I Glenn Cohen.
PLoS Med, 2018 Nov 07; 15(11). PMID: 30399149    Free PMC article.
Highly Cited.
Impact of pre-analytical variables on deep learning accuracy in histopathology.
Andrew D Jones, John Paul Graff, +8 authors, Hooman H Rashidi.
Histopathology, 2019 Feb 26; 75(1). PMID: 30801768    Free PMC article.
A comparative study on machine learning based algorithms for prediction of motorcycle crash severity.
Lukuman Wahab, Haobin Jiang.
PLoS One, 2019 Apr 05; 14(4). PMID: 30947250    Free PMC article.
Review of Machine Learning Algorithms for Diagnosing Mental Illness.
Gyeongcheol Cho, Jinyeong Yim, +2 authors, Seoung-Hwan Lee.
Psychiatry Investig, 2019 Apr 06; 16(4). PMID: 30947496    Free PMC article.
Artificial intelligence and machine learning for predicting acute kidney injury in severely burned patients: A proof of concept.
Nam K Tran, Soman Sen, +4 authors, Hooman H Rashidi.
Burns, 2019 Jun 25; 45(6). PMID: 31230801
Studies in the history of probability and statistics. XV. The historical velopment of the Gauss linear model.
H L Seal.
Biometrika, 1967 Jun 01; 54(1). PMID: 4860564
Estimation of the probability of an event as a function of several independent variables.
S H Walker, D B Duncan.
Biometrika, 1967 Jun 01; 54(1). PMID: 6049533
Highly Cited.
A comparison of goodness-of-fit tests for the logistic regression model.
D W Hosmer, T Hosmer, S Le Cessie, S Lemeshow.
Stat Med, 1997 May 15; 16(9). PMID: 9160492
Highly Cited. Review.
Artificial intelligence and radiomics in nuclear medicine: potentials and challenges.
Cumali Aktolun.
Eur J Nucl Med Mol Imaging, 2019 Nov 02; 46(13). PMID: 31673788
Early Recognition of Burn- and Trauma-Related Acute Kidney Injury: A Pilot Comparison of Machine Learning Techniques.
Hooman H Rashidi, Soman Sen, +3 authors, Nam K Tran.
Sci Rep, 2020 Jan 16; 10(1). PMID: 31937795    Free PMC article.
Limited Number of Cases May Yield Generalizable Models, a Proof of Concept in Deep Learning for Colon Histology.
Lorne Holland, Dongguang Wei, +6 authors, Hooman H Rashidi.
J Pathol Inform, 2020 Mar 17; 11. PMID: 32175170    Free PMC article.
Random Forest Classification of Alcohol Use Disorder Using fMRI Functional Connectivity, Neuropsychological Functioning, and Impulsivity Measures.
Chella Kamarajan, Babak A Ardekani, +8 authors, Bernice Porjesz.
Brain Sci, 2020 Feb 26; 10(2). PMID: 32093319    Free PMC article.
Introduction to digital pathology and computer-aided pathology.
Soojeong Nam, Yosep Chong, +5 authors, Heounjeong Go.
J Pathol Transl Med, 2020 Feb 13; 54(2). PMID: 32045965    Free PMC article.
An App Developed for Detecting Nurse Burnouts Using the Convolutional Neural Networks in Microsoft Excel: Population-Based Questionnaire Study.
Yi-Lien Lee, Willy Chou, +3 authors, Huan-Fang Lee.
JMIR Med Inform, 2020 May 08; 8(5). PMID: 32379050    Free PMC article.
An App for Detecting Bullying of Nurses Using Convolutional Neural Networks and Web-Based Computerized Adaptive Testing: Development and Usability Study.
Shu-Ching Ma, Willy Chou, +4 authors, Huan-Fang Lee.
JMIR Mhealth Uhealth, 2020 May 21; 8(5). PMID: 32432557    Free PMC article.
Novel application of an automated-machine learning development tool for predicting burn sepsis: proof of concept.
Nam K Tran, Samer Albahra, +5 authors, Hooman H Rashidi.
Sci Rep, 2020 Jul 25; 10(1). PMID: 32704168    Free PMC article.
An App for Classifying Personal Mental Illness at Workplace Using Fit Statistics and Convolutional Neural Networks: Survey-Based Quantitative Study.
Yu-Hua Yan, Tsair-Wei Chien, +2 authors, Shu-Chen Hsing.
JMIR Mhealth Uhealth, 2020 Aug 01; 8(7). PMID: 32735232    Free PMC article.
Head-tracking as an interface device for image control in digital pathology: a comparative study.
Eduardo Alcaraz-Mateos, Iva Turic, +2 authors, Enrique Poblet.
Rev Esp Patol, 2020 Oct 06; 53(4). PMID: 33012490    Free PMC article.
A Regulatory Science Initiative to Harmonize and Standardize Digital Pathology and Machine Learning Processes to Speed up Clinical Innovation to Patients.
Hetal Desai Marble, Richard Huang, +14 authors, Jochen K Lennerz.
J Pathol Inform, 2020 Oct 13; 11. PMID: 33042601    Free PMC article.
Leveraging Data Science for a Personalized Haemodialysis.
Miguel Hueso, Lluís de Haro, +5 authors, Alfredo Vellido.
Kidney Dis (Basel), 2020 Dec 15; 6(6). PMID: 33313059    Free PMC article.
Predicting the Response of High Frequency Spinal Cord Stimulation in Patients with Failed Back Surgery Syndrome: A Retrospective Study with Machine Learning Techniques.
Lisa Goudman, Jean-Pierre Van Buyten, +4 authors, Maarten Moens.
J Clin Med, 2020 Dec 30; 9(12). PMID: 33371497    Free PMC article.
Early lung cancer diagnostic biomarker discovery by machine learning methods.
Ying Xie, Wei-Yu Meng, +14 authors, Elaine Lai-Han Leung.
Transl Oncol, 2020 Nov 21; 14(1). PMID: 33217646    Free PMC article.
Artificial intelligence and computational pathology.
Miao Cui, David Y Zhang.
Lab Invest, 2021 Jan 18; 101(4). PMID: 33454724    Free PMC article.
Artificial Intelligence for Histology-Based Detection of Microsatellite Instability and Prediction of Response to Immunotherapy in Colorectal Cancer.
Lindsey A Hildebrand, Colin J Pierce, +2 authors, Asaf Maoz.
Cancers (Basel), 2021 Jan 27; 13(3). PMID: 33494280    Free PMC article.
Robotics, microfluidics, nanotechnology and AI in the synthesis and evaluation of liposomes and polymeric drug delivery systems.
Egor Egorov, Calvin Pieters, +2 authors, Avi Schroeder.
Drug Deliv Transl Res, 2021 Feb 16; 11(2). PMID: 33585972    Free PMC article.
Artificial Intelligence-related Literature in Transplantation: A Practical Guide.
Sook Hyeon Park, Nikhilesh R Mazumder, +3 authors, Daniela P Ladner.
Transplantation, 2020 Aug 23; 105(4). PMID: 32826800    Free PMC article.
Has the Flood Entered the Basement? A Systematic Literature Review about Machine Learning in Laboratory Medicine.
Luca Ronzio, Federico Cabitza, Alessandro Barbaro, Giuseppe Banfi.
Diagnostics (Basel), 2021 Mar 07; 11(2). PMID: 33671623    Free PMC article.
Application of Single-Cell Approaches to Study Myeloproliferative Neoplasm Biology.
Daniel Royston, Adam J Mead, Bethan Psaila.
Hematol Oncol Clin North Am, 2021 Mar 02; 35(2). PMID: 33641869    Free PMC article.
Evolution of the liver biopsy and its future.
Dhanpat Jain, Richard Torres, +3 authors, Vasilis Vasiliou.
Transl Gastroenterol Hepatol, 2021 Apr 08; 6. PMID: 33824924    Free PMC article.
Novel application of automated machine learning with MALDI-TOF-MS for rapid high-throughput screening of COVID-19: a proof of concept.
Nam K Tran, Taylor Howard, +5 authors, Hooman H Rashidi.
Sci Rep, 2021 Apr 17; 11(1). PMID: 33859233    Free PMC article.
Artificial intelligence and capsule endoscopy: unravelling the future.
Miguel Mascarenhas, João Afonso, +2 authors, Guilherme Macedo.
Ann Gastroenterol, 2021 May 06; 34(3). PMID: 33948053    Free PMC article.
Effects of Image Quantity and Image Source Variation on Machine Learning Histology Differential Diagnosis Models.
Elham Vali-Betts, Kevin J Krause, +10 authors, Hooman H Rashidi.
J Pathol Inform, 2021 May 21; 12. PMID: 34012709    Free PMC article.
Requirements for implementation of artificial intelligence in the practice of gastrointestinal pathology.
Hiroshi Yoshida, Tomoharu Kiyuna.
World J Gastroenterol, 2021 Jun 18; 27(21). PMID: 34135556    Free PMC article.
Application of the random forest algorithm to Streptococcus pyogenes response regulator allele variation: from machine learning to evolutionary models.
Sean J Buckley, Robert J Harvey, Zack Shan.
Sci Rep, 2021 Jun 18; 11(1). PMID: 34135390    Free PMC article.
Independent real-world application of a clinical-grade automated prostate cancer detection system.
Leonard M da Silva, Emilio M Pereira, +18 authors, Jorge S Reis-Filho.
J Pathol, 2021 Apr 28; 254(2). PMID: 33904171    Free PMC article.
Application of Raman spectroscopy for detection of histologically distinct areas in formalin-fixed paraffin-embedded glioblastoma.
Gilbert Georg Klamminger, Jean-Jacques Gérardy, +7 authors, Felix B Kleine-Borgmann.
Neurooncol Adv, 2021 Aug 07; 3(1). PMID: 34355170    Free PMC article.
Experimental Models of Hepatocellular Carcinoma-A Preclinical Perspective.
Alexandru Blidisel, Iasmina Marcovici, +3 authors, Octavian Marius Cretu.
Cancers (Basel), 2021 Aug 08; 13(15). PMID: 34359553    Free PMC article.
The Emerging Role of Long Non-Coding RNAs and MicroRNAs in Neurodegenerative Diseases: A Perspective of Machine Learning.
Ángela García-Fonseca, Cynthia Martin-Jimenez, +2 authors, Janneth González.
Biomolecules, 2021 Aug 28; 11(8). PMID: 34439798    Free PMC article.
Automated machine learning for endemic active tuberculosis prediction from multiplex serological data.
Hooman H Rashidi, Luke T Dang, +2 authors, Imran H Khan.
Sci Rep, 2021 Sep 11; 11(1). PMID: 34504228    Free PMC article.
A Comprehensive Review on Radiomics and Deep Learning for Nasopharyngeal Carcinoma Imaging.
Song Li, Yu-Qin Deng, +2 authors, Ze-Zhang Tao.
Diagnostics (Basel), 2021 Sep 29; 11(9). PMID: 34573865    Free PMC article.
Machine Learning in Modeling of Mouse Behavior.
Marjan Gharagozloo, Abdelaziz Amrani, +2 authors, Denis Gris.
Front Neurosci, 2021 Oct 02; 15. PMID: 34594182    Free PMC article.
Artificial Intelligence and Cellular Segmentation in Tissue Microscopy Images.
Madeleine S Durkee, Rebecca Abraham, Marcus R Clark, Maryellen L Giger.
Am J Pathol, 2021 Jun 16; 191(10). PMID: 34129842    Free PMC article.