Extreme learning machine Cox model for high‐dimensional survival analysis

Some interesting recent studies have shown that neural network models are useful alternatives in modeling survival data when the assumptions of a classical parametric or semiparametric survival model such as the Cox (1972) model are seriously violated. However, to the best of our knowledge, the plausibility of adapting the emerging extreme learning machine (ELM) algorithm for single-hidden-layer feedforward neural networks to survival analysis has not been explored. In this paper, we present a kernel ELM Cox model regularized by an L0 -based broken adaptive ridge (BAR) penalization method. Then, we demonstrate that the resulting method, referred to as ELMCoxBAR, can outperform some other state-of-art survival prediction methods such as L1 - or L2 -regularized Cox regression, random survival forest with various splitting rules, and boosted Cox model, in terms of its predictive performance using both simulated and real world datasets. In addition to its good predictive performance, we illustrate that the proposed method has a key computational advantage over the above competing methods in terms of computation time efficiency using an a real-world ultra-high-dimensional survival data.

[1]  Harald Binder,et al.  Allowing for mandatory covariates in boosting estimation of sparse high-dimensional survival models , 2008, BMC Bioinformatics.

[2]  Allan Pinkus,et al.  Multilayer Feedforward Networks with a Non-Polynomial Activation Function Can Approximate Any Function , 1991, Neural Networks.

[3]  W. Weichert,et al.  A prognostic gene expression index in ovarian cancer—validation across different independent data sets , 2009, The Journal of pathology.

[4]  Grégory Nuel,et al.  An Adaptive Ridge Procedure for L0 Regularization , 2015, PloS one.

[5]  Harald Binder,et al.  Partitioned Learning of Deep Boltzmann Machines for SNP Data , 2016, bioRxiv.

[6]  Chee Kheong Siew,et al.  Universal Approximation using Incremental Constructive Feedforward Networks with Random Hidden Nodes , 2006, IEEE Transactions on Neural Networks.

[7]  Jooyoung Park,et al.  Universal Approximation Using Radial-Basis-Function Networks , 1991, Neural Computation.

[8]  Benjamin Haibe-Kains,et al.  Angiogenic mRNA and microRNA Gene Expression Signature Predicts a Novel Subtype of Serous Ovarian Cancer , 2012, PloS one.

[9]  E Biganzoli,et al.  Feed forward neural networks for the analysis of censored survival data: a partial logistic regression approach. , 1998, Statistics in medicine.

[10]  David E. Misek,et al.  Gene-expression profiles predict survival of patients with lung adenocarcinoma , 2002, Nature Medicine.

[11]  Hongming Zhou,et al.  Extreme Learning Machine for Regression and Multiclass Classification , 2012, IEEE Transactions on Systems, Man, and Cybernetics, Part B (Cybernetics).

[12]  Axel Benner,et al.  High‐Dimensional Cox Models: The Choice of Penalty as Part of the Model Building Process , 2010, Biometrical journal. Biometrische Zeitschrift.

[13]  Marvin N. Wright,et al.  Unbiased split variable selection for random survival forests using maximally selected rank statistics , 2017, Statistics in medicine.

[14]  M. Ebell Artificial neural networks for predicting failure to survive following in-hospital cardiopulmonary resuscitation. , 1993, The Journal of family practice.

[15]  Matthias Schmid,et al.  On the use of Harrell's C for clinical risk prediction via random survival forests , 2015, Expert Syst. Appl..

[16]  Hemant Ishwaran,et al.  Random Survival Forests , 2008, Wiley StatsRef: Statistics Reference Online.

[17]  Elia Biganzoli,et al.  A general framework for neural network models on censored survival data , 2002, Neural Networks.

[18]  Leo Breiman,et al.  Random Forests , 2001, Machine Learning.

[19]  Jiang Gui,et al.  Penalized Cox regression analysis in the high-dimensional and low-sample size settings, with applications to microarray gene expression data , 2005, Bioinform..

[20]  Guang-Bin Huang,et al.  Extreme learning machine: a new learning scheme of feedforward neural networks , 2004, 2004 IEEE International Joint Conference on Neural Networks (IEEE Cat. No.04CH37541).

[21]  D Faraggi,et al.  A neural network model for survival data. , 1995, Statistics in medicine.

[22]  Joshua E. Lewis,et al.  Predicting clinical outcomes from large scale cancer genomic profiles with deep survival models , 2017, Scientific Reports.

[23]  Guang-Bin Huang,et al.  Extreme Learning Machine for Multilayer Perceptron , 2016, IEEE Transactions on Neural Networks and Learning Systems.

[24]  H. Müller,et al.  Hazard rate estimation under random censoring with varying kernels and bandwidths. , 1994, Biometrics.

[25]  Elia Biganzoli,et al.  Selection of artificial neural network models for survival analysis with Genetic Algorithms , 2007, Comput. Stat. Data Anal..

[26]  T Cai,et al.  Regularized Estimation for the Accelerated Failure Time Model , 2009, Biometrics.

[27]  Guang-Bin Huang,et al.  Learning to Rank with Extreme Learning Machine , 2013, Neural Processing Letters.

[28]  Chee Kheong Siew,et al.  Extreme learning machine: Theory and applications , 2006, Neurocomputing.

[29]  Yutaka Shimada,et al.  Prediction of survival in patients with esophageal carcinoma using artificial neural networks , 2005, Cancer.

[30]  R. Tibshirani The lasso method for variable selection in the Cox model. , 1997, Statistics in medicine.

[31]  Elia Biganzoli,et al.  Artificial neural network for the joint modelling of discrete cause-specific hazards , 2006, Artif. Intell. Medicine.

[32]  Paulo J. G. Lisboa,et al.  Partial Logistic Artificial Neural Network for Competing Risks Regularized With Automatic Relevance Determination , 2009, IEEE Transactions on Neural Networks.

[33]  Georg Heinze,et al.  Validating the impact of a molecular subtype in ovarian cancer on outcomes: A study of the OVCAD Consortium , 2012, Cancer science.

[34]  R. Tibshirani,et al.  Repeated observation of breast tumor subtypes in independent gene expression data sets , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[35]  Tatsuhiko Tsunoda,et al.  High-Risk Ovarian Cancer Based on 126-Gene Expression Signature Is Uniquely Characterized by Downregulation of Antigen Presentation Pathway , 2012, Clinical Cancer Research.

[36]  J. Tu,et al.  Use of a neural network as a predictive instrument for length of stay in the intensive care unit following cardiac surgery. , 1993, Computers and biomedical research, an international journal.

[37]  Benjamin J. Raphael,et al.  Integrated Genomic Analyses of Ovarian Carcinoma , 2011, Nature.

[38]  G. Clark,et al.  A practical application of neural network analysis for predicting outcome of individual breast cancer patients , 2005, Breast Cancer Research and Treatment.

[39]  K. Liestøl,et al.  Survival analysis and neural nets. , 1994, Statistics in medicine.

[40]  Anil Potti,et al.  An integrated genomic-based approach to individualized treatment of patients with advanced-stage ovarian cancer. , 2007, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.

[41]  Geoffrey E. Hinton,et al.  Deep Learning , 2015, Nature.

[42]  F. Markowetz,et al.  The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups , 2012, Nature.

[43]  David Madigan,et al.  High-dimensional, massive sample-size Cox proportional hazards regression for survival analysis. , 2014, Biostatistics.

[44]  Lei Wang,et al.  Multiple kernel extreme learning machine , 2015, Neurocomputing.

[45]  Yew-Soon Ong,et al.  A Fast Reduced Kernel Extreme Learning Machine , 2016, Neural Networks.

[46]  E Graf,et al.  Assessment and comparison of prognostic classification schemes for survival data. , 1999, Statistics in medicine.

[47]  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 .

[48]  Ying Huang,et al.  A Novel Extreme Learning Machine Classification Model for e-Nose Application Based on the Multiple Kernel Approach , 2017, Sensors.

[49]  Trevor Hastie,et al.  Regularization Paths for Cox's Proportional Hazards Model via Coordinate Descent. , 2011, Journal of statistical software.

[50]  Lili Guo,et al.  Extreme learning machine with kernel model based on deep learning , 2017, Neural Computing and Applications.

[51]  Chih-Jen Lin,et al.  A Practical Guide to Support Vector Classication , 2008 .