Recent studies have adopted an approach of selecting accurate and diverse trees based on individual or collective performance within an ensemble for classification and regression problems. This work follows in the wake of these investigations and considers the possibility of growing a forest of optimal survival trees. Initially, a large set of survival trees are grown using the method of random survival forest. The grown trees are then ranked from smallest to highest value of their prediction error using out-of-bag observations for each respective survival tree. The top ranked survival trees are then assessed for their collective performance as an ensemble. This ensemble is initiated with the survival tree which stands first in rank, then further trees are tested one by one by adding them to the ensemble in order of rank. A survival tree is selected for the resultant ensemble if the performance improves after an assessment using independent training data. This ensemble is called an optimal trees ensemble (OSTE). The proposed method is assessed using 17 benchmark datasets and the results are compared with those of random survival forest, conditional inference forest, bagging and a non tree based method, the Cox proportional hazard model. In addition to improve predictive performance, the proposed method reduces the number of survival trees in the ensemble as compared to the other tree based methods. The method is implemented in an R package called "OSTE".
In this paper we utilize a survival analysis methodology incorporating Bayesian additive regression trees to account for nonlinear and additive covariate effects. We compare the performance of Bayesian additive regression trees, Cox proportional hazards and random survival forests models for censored survival data, using simulation studies and survival analysis for breast cancer with U.S. SEER database for the year 2005. In simulation studies, we compare the three models across varying sample sizes and censoring rates on the basis of bias and prediction accuracy. In survival analysis for breas…
Background: Many authors have described MELD as a predictor of short-term mortality in the liver transplantation waiting list. However MELD score accuracy to predict long term mortality has not been statistically evaluated. Objective: The aim of this study is to analyze the MELD score as well as other variables as a predictor of long-term mortality using a new model: the Survival Tree analysis. Study Design and Setting: The variables obtained at the time of liver transplantation list enrollment and considered in this study are: sex, age, blood type, body mass index, etiology of liver disease, …
In this paper we describe a novel implementation of adaboost for prediction of survival function. We take different variations of the algorithm and compare the algorithms based on system run time and root mean square error. Our construction includes right censoring data and competing risk data too. We take different data set to illustrate the performance of the algorithms.
Survival data with time-varying covariates are common in practice. If relevant, they can improve on the estimation of survival function. However, the traditional survival forests - conditional inference forest, relative risk forest and random survival forest - have accommodated only time-invariant covariates. We generalize the conditional inference and relative risk forests to allow time-varying covariates. We also propose a general framework for estimation of a survival function in the presence of time-varying covariates. We compare their performance with that of the Cox model and transformat…
Popular parametric and semiparametric hazards regression models for clustered survival data are inappropriate and inadequate when the unknown effects of different covariates and clustering are complex. This calls for a flexible modeling framework to yield efficient survival prediction. Moreover, for some survival studies involving time to occurrence of some asymptomatic events, survival times are typically interval censored between consecutive clinical inspections. In this article, we propose a robust semiparametric model for clustered interval-censored survival data under a paradigm of Bayesi…
With the availability of massive amounts of data from electronic health records and registry databases, incorporating time-varying patient information to improve risk prediction has attracted great attention. To exploit the growing amount of predictor information over time, we develop a unified framework for landmark prediction using survival tree ensembles, where an updated prediction can be performed when new information becomes available. Compared to conventional landmark prediction with fixed landmark times, our methods allow the landmark times to be subject-specific and triggered by an in…
Quantifying uncertainty of individualized treatment effects in right-censored survival data: A comparison of Bayesian additive regression trees and causal survival forest
Lung cancer is among the most common cancers in the United States, in terms of incidence and mortality. In 2009, it is estimated that more than 150,000 deaths will result from lung cancer alone. Genetic information is an extremely valuable data source in characterizing the personal nature of cancer. Over the past several years, investigators have conducted numerous association studies where intensive genetic data is collected on relatively few patients compared to the numbers of gene predictors, with one scientific goal being to identify genetic features associated with cancer recurrence or su…
Yokozuna Data, a Keywords Studio（Yokozuna Data（Keywords Studio旗下公司））；Dpto. Física Fundamental, UNED（西班牙国家远程教育大学基础物理系）
Retaining premium players is key to the success of free-to-play games, but most of them do not start purchasing right after joining the game. By exploiting the exceptionally rich datasets recorded by modern video games--which provide information on the individual behavior of each and every player--survival analysis techniques can be used to predict what players are more likely to become paying (or even premium) users and when, both in terms of time and game level, the conversion will take place. Here we show that a traditional semi-parametric model (Cox regression), a random survival forest (R…
Spatio temporal data are more ubiquitous and richer than even before and the availability of such data poses great challenges in data analytics. Ecological facilitation, the positive effect of density of individuals on the individual's survival across a stress gradient, is a complex phenomenon. A large number of tree individuals coupled with soil moisture, temperature, and water stress data across a long temporal period were followed. Data driven analysis in the absence of hypothesis was performed. Information theoretic analysis of multiple statistical models was employed in order to quantify …
University of California, Los Angeles（加州大学洛杉矶分校）；Nuffield College, Oxford University（牛津大学纳菲尔德学院）；Oxford Man Institute, Oxford University（牛津大学牛津曼研究所）；Alan Turing Institute（艾伦·图灵研究所）
Given the limited pool of donor organs, accurate predictions of survival on the wait list and post transplantation are crucial for cardiac transplantation decisions and policy. However, current clinical risk scores do not yield accurate predictions. We develop a new methodology (ToPs, Trees of Predictors) built on the principle that specific predictors should be used for specific clusters within the target population. ToPs discovers these specific clusters of patients and the specific predictor that perform best for each cluster. In comparison with current clinical risk scoring systems, our me…
The instability in the selection of models is a major concern with data sets containing a large number of covariates. This paper deals with variable selection methodology in the case of high-dimensional problems where the response variable can be right censored. We focuse on new stable variable selection methods based on bootstrap for two methodologies: the Cox proportional hazard model and survival trees. As far as the Cox model is concerned, we investigate the bootstrapping applied to two variable selection techniques: the stepwise algorithm based on the AIC criterion and the L1-penalization…
We introduce random survival forests, a random forests method for the analysis of right-censored survival data. New survival splitting rules for growing survival trees are introduced, as is a new missing data algorithm for imputing missing data. A conservation-of-events principle for survival forests is introduced and used to define ensemble mortality, a simple interpretable measure of mortality that can be used as a predicted outcome. Several illustrative examples are given, including a case study of the prognostic implications of body mass for individuals with coronary artery disease. Comput…
EPFL（洛桑联邦理工学院）；IBM Research Lab, Zurich（IBM苏黎世研究实验室）
We study the effectiveness of non-uniform randomized feature selection in decision tree classification. We experimentally evaluate two feature selection methodologies, based on information extracted from the provided dataset: $(i)$ \emph{leverage scores-based} and $(ii)$ \emph{norm-based} feature selection. Experimental evaluation of the proposed feature selection techniques indicate that such approaches might be more effective compared to naive uniform feature selection and moreover having comparable performance to the random forest algorithm [3]
Optimizing Prognostic Biomarker Discovery in Pancreatic Cancer Through Hybrid Ensemble Feature Selection and Multi-Omics Data
Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway（癌症遗传学系，癌症研究所，奥斯陆大学医院，奥斯陆，挪威）；Oslo Centre for Biostatistics and Epidemiology (OCBE), Department of Biostatistics, University of Oslo, Oslo, Norway（奥斯陆生物统计与流行病学中心（OCBE），生物统计学系，奥斯陆大学，奥斯陆，挪威）；Department of Informatics, University of Oslo, Oslo, Norway（信息学系，奥斯陆大学，奥斯陆，挪威）；Department of Statistics, Ludwig Maximilian University of Munich, Munich, Germany（统计学系，慕尼黑路德维希-马克西米利安大学，慕尼黑，德国）；Munich Center for Machine Learning (MCML)（慕尼黑机器学习中心（MCML））
