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Cleophas Ton J. M. - Machine Learning in Medicine

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Cleophas Ton J. M. Machine Learning in Medicine

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V.1. Introduction to machine learning -- Logistic regression for health profiling -- Optimal scaling: discretization -- Optimal scaling: regulaization including ridge, lasso, and elastic net regression -- Partial correlations -- Mixed linear models -- Binary partitioning -- Item response modeling -- Time-dependent predictor modeling -- Seasonality assessments -- Non-linear modeling -- Artificial intelligence, multilayer perceptron modeling -- Artificial intelligence, radial basis functions -- Factor analysis -- Hierarchical cluster analysis for unsupervised data -- Partial least squares -- Discriminant analysis for supervised data -- Canonical regression -- Fuzzy modeling -- Conclusions--;Machine learning is a novel discipline concerned with the analysis of large and multiple variables data. It involves computationally intensive methods, like factor analysis, cluster analysis, and discriminant analysis. It is currently mainly the domain of computer scientists, and is already commonly used in social sciences, marketing research, operational research and applied sciences. It is virtually unused in clinical research. This is probably due to the traditional belief of clinicians in clinical trials where multiple variables are equally balanced by the randomization process and are not further taken into account. In contrast, modern computer data files often involve hundreds of variables like genes and other laboratory values, and computationally intensive methods are required. This book was written as a hand-hold presentation accessible to clinicians, and as a must-read publication for those new to the methods--Publishers description.;v. 2. Introduction to machine learning part two -- Two-stage least squares -- Multiple imputations -- Bhattacharya analysis -- Quality-of-life (QOL) assessments with odds ratios -- Logistic regression for assessing novel diagnostic tests against control -- validating surrogate endpoints -- Two-dimensional clustering -- Multidimensional clustering -- Anomaly detection -- Association rule analysis -- Multidimensional scaling -- Correspondence analysis -- Multivariate analysis of time series -- Support vector machines -- Bayesian networks -- Protein and DNA sequence mining -- Continuous sequential techniques -- Discrete wavelet analysis -- Machine learning and common sense.;v. 3. Introduction to Machine learning part three -- Evolutionary operations -- Multiple treatments -- Multiple endpoints -- Optimal binning -- Exact p-values -- Probit regression -- Over-dispersion -- Random effects -- Weighted least squares -- Multiple response sets -- Complex samples -- Runs tests -- Decision trees -- Spectral plots -- Newtons methods -- Stochastic processes, stationary Markov chains -- Stochastic processes, absorbing Markov chains -- Conjoint models -- Machine learning and unsolved questions.

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Ton J. Cleophas and Aeilko H. Zwinderman Machine Learning in Medicine 2013 10.1007/978-94-007-5824-7_1 Springer Science+Business Media Dordrecht 2013
1. Introduction to Machine Learning
Ton J. Cleophas 1 and Aeilko H. Zwinderman 2
(1)
European College Pharmaceutical Medicine, Lyon, France
(2)
Department of Epidemiology and Biostatistics, Academic Medical Center, Amsterdam, Netherlands
Abstract
Traditional statistical tests are unable to handle large numbers of variables. The simplest method to reduce large numbers of variables is the use of add-up scores. But add-up scores do not account the relative importance of the separate variables, their interactions and differences in units. Machine learning can be defined as knowledge for making predictions as obtained from processing training data through a computer. If data sets involve multiple variables, data analyses will be complex, and modern computationally intensive methods will have to be applied for analysis.
Summary
Background
Traditional statistical tests are unable to handle large numbers of variables. The simplest method to reduce large numbers of variables is the use of add-up scores. But add-up scores do not account the relative importance of the separate variables, their interactions and differences in units. Machine learning can be defined as knowledge for making predictions as obtained from processing training data through a computer. If data sets involve multiple variables, data analyses will be complex, and modern computationally intensive methods will have to be applied for analysis.
Objective and Methods
The current book, using real data examples as well as simulated data, reviews important methods relevant for health care and research, although little used in the field so far.
Results and Conclusions
One of the first machine learning methods used in health research is logistic regression for health profiling where single combinations of x-variables are used to predict the risk of a medical event in single persons ).
A wonderful method for analyzing imperfect data with multiple variables is optimal scaling ().
Partial correlations analysis is the best method for removing interaction effects from large clinical data sets).
Mixed linear modeling (1), binary partitioning (2), item response modeling (3), time dependent predictor analysis (4) and autocorrelation (5) are linear or loglinear regression methods suitable for assessing data with respectively repeated measures (1), binary decision trees (2), exponential exposure-response relationships (3), different values at different periods (4) and those with seasonal differences (5), ().
Clinical data sets with non-linear relationships between exposure and outcome variables require special analysis methods, and can usually also be adequately analyzed with neural networks methods like multi layer perceptron networks, and radial basis functions networks ().
Clinical data with multiple exposure variables are usually analyzed using analysis of (co-) variance (AN(C)OVA), but this method does not adequately account the relative importance of the variables and their interactions. Factor analysis and hierarchical cluster analysis account for all of these limitations ().
Data with multiple outcome variables are usually analyzed with multivariate analysis of (co-) variance (MAN(C)OVA). However, this has the same limitations as ANOVA. Partial least squares analysis, discriminant analysis, and canonical regression account all of these limitations ().
Fuzzy modeling is a method suitable for modeling soft data, like data that are partially true or response patterns that are different at different times ).
Introduction
Traditional statistical tests are unable to handle large numbers of variables. The simplest method to reduce large numbers of variables is the use of add-up scores. But add-up scores do not account the relative importance of the separate variables, their interactions and differences in units.
Principal components analysis and partial least square analysis, hierarchical cluster analysis, optimal scaling and canonical regression are modern computationally intensive methods, currently often listed as machine learning methods. This is because the computations they make are far too complex to perform without the help of a computer, and because they turn imputed information into knowledge, which is in human terms a kind of learning process.
An additional advantage is that the novel methods are able to account all of the limitations of the traditional methods. Although widely used in the fields of behavioral sciences, social sciences, marketing, operational research and applied sciences, they are virtually unused in medicine. This is a pity given the omnipresence of large numbers of variables in this field of research. However, this is probably just a matter of time, now that the methods are increasingly available in SPSS statistical software and many other packages.
We will start with logistic regression for health profiling where single combinations of x-variables are used to predict the risk of a medical event in single persons explains fuzzy modeling as a method for modeling soft data, like data that are partially true or response patterns that are different at different times.
A nice thing about the novel methodologies, thus, is that, unlike the traditional methods like ANOVA and MANOVA, they not only can handle large data files with numerous exposure and outcome variables, but also can do it in a relatively unbiased way.
The current book serves as an introduction to machine learning methods in clinical research, and was written as a hand-hold presentation accessible to clinicians, and as a must-read publication for those new to the methods. It is the authors experience, as master class professors, that students are eager to master adequate command of statistical software. For their benefit all of the steps of the novel methods from logging in to the final result using SPSS statistical software will be given in most of the chapters. We will end up this initial chapter with some machine learning terminology.
Machine Learning Terminology
Artificial Intelligence
Engineering method that simulates the structures and operating principles of the human brain.
Bootstraps
Machine learning methods are computationally intensive. Computers make use of bootstraps, otherwise called random sampling from the data with replacement, in order to facilitate the calculations. Bootstraps is a Monte Carlo method.
Canonical Regression
Multivariate method. ANOVA / ANCOVA (analysis of (co)variance) and MANOVA / MANCOVA (multivariate analysis of (co)variance) are the standard methods for the analysis of data with respectively multiple independent and dependent variables. A problem with these methods is, that they rapidly lose statistical power with increasing numbers of variables, and that computer commands may not be executed due to numerical problems with higher order calculations among components. Also, clinically, we are often more interested in the combined effects of the clusters of variables than in the separate effects of the different variables. As a simple solution composite variables can be used as add-up sums of separate variables, but add-up sums do not account the relative importance of the separate variables, their interactions, and differences in units. Canonical analysis can account all of that, and, unlike MANCOVA, gives, in addition to test statistics of the separate variables, overall test statistics of entire sets of variables.
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