Machine learning in the prognostic appraisal of Class III growth

Abstract Machine Learning (ML) is an emerging subfield of artificial intelligence with significant resources being applied to connect computer science, statistics, and medical problems. Currently, and even more so in the future, ML algorithms applied to the orthodontic specialty will offer sophisticated and automatic models able to process and synthesize data in ways orthodontists could never do themselves, and ultimately convert data into intelligent treatment actions. This work focuses on the usefulness of two ML methodologies, LASSO networks (Ln), and Boruta selection (Ba), to simplify information from different types of pathogenic processes leading to the worsening of skeletal Class III malocclusion. Cephalometric analyses of 144 Class III untreated subjects followed longitudinally during the growth process (4–19 years) were performed. After separating subjects into two subgroups of 116 with mild (M) and 28 with very serious (VS) unfavorable growth, cephalometric features were processed using Ba and Ln algorithms for feature selection and regularization. The selection procedure revealed the unexpected predictive importance of the combination of two often overlooked craniofacial variables, SN-PP and L1-MP angles. Ln regularization highlighted additional feature interactions between M and VS growing subjects. Thus, the appropriate removal of redundant cephalometric features from the dataset contributed to the detection of subjects affected by serious unfavorable craniofacial progression and revealed the unexpected prognostic value of some skeletal feature interactions.

[1]  Duncan Fyfe Gillies,et al.  A Review of Feature Selection and Feature Extraction Methods Applied on Microarray Data , 2015, Adv. Bioinformatics.

[2]  Benedikt Hallgrímsson,et al.  Variation , 2006, Keywords and Concepts in Evolutionary Developmental Biology.

[3]  Wray L. Buntine Myths and Legends in Learning Classification Rules , 1990, AAAI.

[4]  B Solow,et al.  The Dentoalveolar Compensatory Mechanism: Background and Clinical Implications * , 1980, British journal of orthodontics.

[5]  Fotios Petropoulos,et al.  Golden Rule of Forecasting : Be Conservative , 2015 .

[6]  Pedro Larrañaga,et al.  A review of feature selection techniques in bioinformatics , 2007, Bioinform..

[7]  Anne-Laure Boulesteix,et al.  Ten Simple Rules for Reducing Overoptimistic Reporting in Methodological Computational Research , 2015, PLoS Comput. Biol..

[8]  Isabelle Guyon,et al.  An Introduction to Variable and Feature Selection , 2003, J. Mach. Learn. Res..

[9]  S. Adams,et al.  Clinical prediction rules , 2012, BMJ : British Medical Journal.

[10]  Witold R. Rudnicki,et al.  Feature Selection with the Boruta Package , 2010 .

[11]  Tulips Angel Thankachan A Survey on Classification and Rule Extraction Techniques for Datamining , 2013 .

[12]  Davide Castelvecchi,et al.  Can we open the black box of AI? , 2016, Nature.

[13]  J. McNamara,et al.  Growth in the Untreated Class III Subject , 2007 .

[14]  Wei-Yin Loh,et al.  Classification and regression trees , 2011, WIREs Data Mining Knowl. Discov..

[15]  Peter H. Buschang,et al.  Applications of artificial intelligence and machine learning in orthodontics , 2020 .

[16]  J. McNamara,et al.  A multilevel analysis of craniofacial growth in subjects with untreated Class III malocclusion. , 2020, Orthodontics & craniofacial research.

[17]  Abraham Silberschatz,et al.  What Makes Patterns Interesting in Knowledge Discovery Systems , 1996, IEEE Trans. Knowl. Data Eng..

[18]  Daniel B. Mark,et al.  TUTORIAL IN BIOSTATISTICS MULTIVARIABLE PROGNOSTIC MODELS: ISSUES IN DEVELOPING MODELS, EVALUATING ASSUMPTIONS AND ADEQUACY, AND MEASURING AND REDUCING ERRORS , 1996 .

[19]  S. Sultan,et al.  Environmentally Contingent Variation: Phenotypic Plasticity and Norms of Reaction , 2005 .

[20]  Casey S. Greene,et al.  Incorporating biological structure into machine learning models in biomedicine , 2019, Current opinion in biotechnology.

[21]  F L Bookstein,et al.  The concept of pattern in craniofacial growth. , 1979, American journal of orthodontics.

[22]  H. Zou The Adaptive Lasso and Its Oracle Properties , 2006 .

[23]  David J. Hand,et al.  Classifier Technology and the Illusion of Progress , 2006, math/0606441.

[24]  A Ziegler,et al.  Data Analysis and Data Mining: Current Issues in Biomedical Informatics , 2011, Methods of Information in Medicine.

[25]  Pat Langley,et al.  Selection of Relevant Features and Examples in Machine Learning , 1997, Artif. Intell..

[26]  J. McNamara,et al.  Short-term and long-term treatment outcomes with the FR-3 appliance of Fränkel. , 2008, American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics.

[27]  G. Caldarelli,et al.  Using Networks To Understand Medical Data: The Case of Class III Malocclusions , 2012, PloS one.

[28]  R. Dawes,et al.  Heuristics and Biases: Clinical versus Actuarial Judgment , 2002 .

[29]  R. Dawes Statistical Prediction versus Clinical Prediction : Improving What Works , 2016 .

[30]  S. Jackson,et al.  Machine learning and complex biological data , 2019, Genome Biology.

[31]  G. Gigerenzer,et al.  The bias bias , 2015 .

[32]  Shulin Wang,et al.  Feature selection in machine learning: A new perspective , 2018, Neurocomputing.

[33]  Claude Sammut,et al.  Extracting Hidden Context , 1998, Machine Learning.

[34]  Dennis Bray,et al.  Limits of computational biology , 2015, In silico biology.

[35]  Yvonne Vergouwe,et al.  Prognosis and prognostic research: what, why, and how? , 2009, BMJ : British Medical Journal.

[36]  Pascal Vincent,et al.  Representation Learning: A Review and New Perspectives , 2012, IEEE Transactions on Pattern Analysis and Machine Intelligence.

[37]  A. Barabasi,et al.  Network medicine : a network-based approach to human disease , 2010 .

[38]  B. Liebgott Factors of human skeletal craniofacial morphology. , 1977, The Angle orthodontist.

[39]  Edward R. Dougherty,et al.  What should be expected from feature selection in small-sample settings , 2006, Bioinform..

[40]  A. Laupacis,et al.  Clinical prediction rules. A review and suggested modifications of methodological standards. , 1997, JAMA.

[41]  Le Thi Hoai An,et al.  Feature selection in machine learning: an exact penalty approach using a Difference of Convex function Algorithm , 2014, Machine Learning.

[42]  Witold R. Rudnicki,et al.  Boruta - A System for Feature Selection , 2010, Fundam. Informaticae.

[43]  Alejandro Martínez-Abraín,et al.  Statistical significance and biological relevance: A call for a more cautious interpretation of results in ecology , 2008 .

[44]  E. Steyerberg Clinical Prediction Models , 2008, Statistics for Biology and Health.

[45]  Ulisses Braga-Neto,et al.  Impact of error estimation on feature selection , 2005, Pattern Recognit..

[46]  J. McNamara,et al.  Semilongitudinal cephalometric study of craniofacial growth in untreated Class III malocclusion. , 2009, American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics.

[47]  Lorenzo Franchi,et al.  Forecasting craniofacial growth in individuals with class III malocclusion by computational modelling. , 2014, European journal of orthodontics.

[48]  Frank Davidoff,et al.  Predicting Clinical States in Individual Patients , 1996, Annals of Internal Medicine.

[49]  Kesten C. Green,et al.  Golden Rule of Forecasting: Be Conservative , 2015 .

[50]  J. Sawyer,et al.  Measurement and prediction, clinical and statistical. , 1966, Psychological bulletin.

[51]  N. Meinshausen,et al.  High-dimensional graphs and variable selection with the Lasso , 2006, math/0608017.

[52]  Steven Finlay,et al.  Predictive Analytics, Data Mining and Big Data: Myths, Misconceptions and Methods , 2014 .

[53]  Balaji Padmanabhan,et al.  Unexpectedness as a Measure of Interestingness in Knowledge Discovery , 1999, Decis. Support Syst..

[54]  Su-In Lee,et al.  Learning graphical models with hubs , 2014, J. Mach. Learn. Res..

[55]  W. Grobman,et al.  Methods of clinical prediction. , 2006, American journal of obstetrics and gynecology.

[56]  Paul Sajda,et al.  Machine learning for detection and diagnosis of disease. , 2006, Annual review of biomedical engineering.