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. Computations for all examples were implemented using the freely available R-software package, randomSurvivalForest.
We investigate the effect of the proportional hazards assumption on prognostic and predictive models of the survival time of patients suffering from amyotrophic lateral sclerosis (ALS). We theoretically compare the underlying model formulations of several variants of survival forests and implementations thereof, including random forests for survival, conditional inference forests, Ranger, and survival forests with $L_1$ splitting, with two novel variants, namely distributional and transformation survival forests. Theoretical considerations explain the low power of log-rank-based splitting in d…
Time-varying covariates are often available in survival studies and estimation of the hazard function needs to be updated as new information becomes available. In this paper, we investigate several different easy-to-implement ways that random forests can be used for dynamic estimation of the survival or hazard function from discrete-time survival data. The results from a simulation study indicate that all methods can perform well, and that none dominates the others. In general, situations that are more difficult from an estimation point of view (such as weaker signals and less data) favour a g…
Peter the Great St.Petersburg Polytechnic University (SPbPU)（圣彼得堡彼得大帝理工大学）；St.Petersburg Clinical Research Center for Special Types of Medical Care (Oncology-oriented)（圣彼得堡特殊医疗类型临床研究中心（肿瘤方向））
A weighted random survival forest is presented in the paper. It can be regarded as a modification of the random forest improving its performance. The main idea underlying the proposed model is to replace the standard procedure of averaging used for estimation of the random survival forest hazard function by weighted avaraging where the weights are assigned to every tree and can be veiwed as training paremeters which are computed in an optimal way by solving a standard quadratic optimization problem maximizing Harrell's C-index. Numerical examples with real data illustrate the outperformance of…
Random forest (Leo Breiman 2001a) (RF) is a non-parametric statistical method requiring no distributional assumptions on covariate relation to the response. RF is a robust, nonlinear technique that optimizes predictive accuracy by fitting an ensemble of trees to stabilize model estimates. Random survival forests (RSF) (Ishwaran and Kogalur 2007; Ishwaran et al. 2008) are an extension of Breimans RF techniques allowing efficient nonparametric analysis of time to event data. The randomForestSRC package (Ishwaran and Kogalur 2014) is a unified treatment of Breimans random forest for survival, reg…
Survival random forest is a popular machine learning tool for modeling censored survival data. However, there is currently no statistically valid and computationally feasible approach for estimating its confidence band. This paper proposes an unbiased confidence band estimation by extending recent developments in infinite-order incomplete U-statistics. The idea is to estimate the variance-covariance matrix of the cumulative hazard function prediction on a grid of time points. We then generate the confidence band by viewing the cumulative hazard function estimation as a Gaussian process whose d…
Random survival forest and survival trees are popular models in statistics and machine learning. However, there is a lack of general understanding regarding consistency, splitting rules and influence of the censoring mechanism. In this paper, we investigate the statistical properties of existing methods from several interesting perspectives. First, we show that traditional splitting rules with censored outcomes rely on a biased estimation of the within-node failure distribution. To exactly quantify this bias, we develop a concentration bound of the within-node estimation based on non i.i.d. sa…
Breiman's random forest (RF) can be interpreted as an implicit kernel generator,where the ensuing proximity matrix represents the data-driven RF kernel. Kernel perspective on the RF has been used to develop a principled framework for theoretical investigation of its statistical properties. However, practical utility of the links between kernels and the RF has not been widely explored and systematically evaluated.Focus of our work is investigation of the interplay between kernel methods and the RF. We elucidate the performance and properties of the data driven RF kernels used by regularized lin…
In oncology clinical trials, characterizing the long-term overall survival (OS) benefit for an experimental drug or treatment regimen (experimental group) is often unobservable if some patients in the control group switch to drugs in the experimental group and/or other cancer treatments after disease progression. A key question often raised by payers and reimbursement agencies is how to estimate the true benefit of the experimental drug group on overall survival that would have been estimated if there were no treatment switches. Several commonly used statistical methods are available to estima…
Kidney transplantation is the best treatment for end-stage renal failure patients. The predominant method used for kidney quality assessment is the Cox regression-based, kidney donor risk index. A machine learning method may provide improved prediction of transplant outcomes and help decision-making. A popular tree-based machine learning method, random forest, was trained and evaluated with the same data originally used to develop the risk index (70,242 observations from 1995-2005). The random forest successfully predicted an additional 2,148 transplants than the risk index with equal type II …
We introduce random spatial forests, a method of bagging regression trees allowing for spatial correlation. Our main contribution is the development of a computationally efficient tree building algorithm which selects each split of the tree adjusting for spatial correlation. We evaluate two different approaches for estimation of random spatial forests, a pseudo-likelihood approach combining random forests with kriging and a non-parametric version for a general class of spatial smoothers. We show improved prediction accuracy of our method compared to existing two-step approaches combining rando…
Automated brain tumor segmentation plays an important role in the diagnosis and prognosis of the patient. In addition, features from the tumorous brain help in predicting patients overall survival. The main focus of this paper is to segment tumor from BRATS 2018 benchmark dataset and use age, shape and volumetric features to predict overall survival of patients. The random forest classifier achieves overall survival accuracy of 59% on the test dataset and 67% on the dataset with resection status as gross total resection. The proposed approach uses fewer features but achieves better accuracy th…
Idaho State University（爱达荷州立大学）；Utah State University（犹他州立大学）
Random forests are considered one of the best out-of-the-box classification and regression algorithms due to their high level of predictive performance with relatively little tuning. Pairwise proximities can be computed from a trained random forest and measure the similarity between data points relative to the supervised task. Random forest proximities have been used in many applications including the identification of variable importance, data imputation, outlier detection, and data visualization. However, existing definitions of random forest proximities do not accurately reflect the data ge…
Glioblastoma Multiforme is a very aggressive type of brain tumor. Due to spatial and temporal intra-tissue inhomogeneity, location and the extent of the cancer tissue, it is difficult to detect and dissect the tumor regions. In this paper, we propose survival prognosis models using four regressors operating on handcrafted image-based and radiomics features. We hypothesize that the radiomics shape features have the highest correlation with survival prediction. The proposed approaches were assessed on the Brain Tumor Segmentation (BraTS-2020) challenge dataset. The highest accuracy of image feat…
Comparison of static and dynamic random forests models for EHR data in the presence of competing risks: predicting central line-associated bloodstream infection
KU Leuven（鲁汶大学）；University Hospitals Leuven（鲁汶大学医院）；Maastricht University（马斯特里赫特大学）；Leiden University Medical Center（莱顿大学医学中心）
University College London（伦敦大学学院）；University of Cambridge（剑桥大学）；University of Oxford（牛津大学）
Ensembles of randomized decision trees, usually referred to as random forests, are widely used for classification and regression tasks in machine learning and statistics. Random forests achieve competitive predictive performance and are computationally efficient to train and test, making them excellent candidates for real-world prediction tasks. The most popular random forest variants (such as Breiman's random forest and extremely randomized trees) operate on batches of training data. Online methods are now in greater demand. Existing online random forests, however, require more training data …
Random forests, introduced by Leo Breiman in 2001, are a very effective statistical method. The complex mechanism of the method makes theoretical analysis difficult. Therefore, a simplified version of random forests, called purely random forests, which can be theoretically handled more easily, has been considered. In this paper we introduce a variant of this kind of random forests, that we call purely uniformly random forests. In the context of regression problems with a one-dimensional predictor space, we show that both random trees and random forests reach minimax rate of convergence. In add…
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…
This paper is a comment on the survey paper by Biau and Scornet (2016) about random forests. We focus on the problem of quantifying the impact of each ingredient of random forests on their performance. We show that such a quantification is possible for a simple pure forest , leading to conclusions that could apply more generally. Then, we consider "hold-out" random forests, which are a good middle point between "toy" pure forests and Breiman's original random forests.
We propose random hinge forests, a simple, efficient, and novel variant of decision forests. Importantly, random hinge forests can be readily incorporated as a general component within arbitrary computation graphs that are optimized end-to-end with stochastic gradient descent or variants thereof. We derive random hinge forest and ferns, focusing on their sparse and efficient nature, their min-max margin property, strategies to initialize them for arbitrary network architectures, and the class of optimizers most suitable for optimizing random hinge forest. The performance and versatility of ran…
We introduce the C++ application and R package ranger. The software is a fast implementation of random forests for high dimensional data. Ensembles of classification, regression and survival trees are supported. We describe the implementation, provide examples, validate the package with a reference implementation, and compare runtime and memory usage with other implementations. The new software proves to scale best with the number of features, samples, trees, and features tried for splitting. Finally, we show that ranger is the fastest and most memory efficient implementation of random forests…
Random forests are ensemble methods which grow trees as base learners and combine their predictions by averaging. Random forests are known for their good practical performance, particularly in high dimensional set-tings. On the theoretical side, several studies highlight the potentially fruitful connection between random forests and kernel methods. In this paper, we work out in full details this connection. In particular, we show that by slightly modifying their definition, random forests can be rewrit-ten as kernel methods (called KeRF for Kernel based on Random Forests) which are more interp…
Like many predictive models, random forests provide point predictions for new observations. Besides the point prediction, it is important to quantify the uncertainty in the prediction. Prediction intervals provide information about the reliability of the point predictions. We have developed a comprehensive R package, RFpredInterval, that integrates 16 methods to build prediction intervals with random forests and boosted forests. The set of methods implemented in the package includes a new method to build prediction intervals with boosted forests (PIBF) and 15 method variations to produce predi…
In this paper we propose using the principle of boosting to reduce the bias of a random forest prediction in the regression setting. From the original random forest fit we extract the residuals and then fit another random forest to these residuals. We call the sum of these two random forests a \textit{one-step boosted forest}. We show with simulated and real data that the one-step boosted forest has a reduced bias compared to the original random forest. The paper also provides a variance estimate of the one-step boosted forest by an extension of the infinitesimal Jackknife estimator. Using thi…
Several studies have shown that combining machine learning models in an appropriate way will introduce improvements in the individual predictions made by the base models. The key to make well-performing ensemble model is in the diversity of the base models. Of the most common solutions for introducing diversity into the decision trees are bagging and random forest. Bagging enhances the diversity by sampling with replacement and generating many training data sets, while random forest adds selecting a random number of features as well. This has made the random forest a winning candidate for many…
As a testament to their success, the theory of random forests has long been outpaced by their application in practice. In this paper, we take a step towards narrowing this gap by providing a consistency result for online random forests.
University of Pennsylvania（宾夕法尼亚大学）；Wharton School（沃顿商学院）
A random forest is a popular tool for estimating probabilities in machine learning classification tasks. However, the means by which this is accomplished is unprincipled: one simply counts the fraction of trees in a forest that vote for a certain class. In this paper, we forge a connection between random forests and kernel regression. This places random forest probability estimation on more sound statistical footing. As part of our investigation, we develop a model for the proximity kernel and relate it to the geometry and sparsity of the estimation problem. We also provide intuition and recom…
The last decade has witnessed a growing interest in random forest models which are recognized to exhibit good practical performance, especially in high-dimensional settings. On the theoretical side, however, their predictive power remains largely unexplained, thereby creating a gap between theory and practice. The aim of this paper is twofold. Firstly, we provide theoretical guarantees to link finite forests used in practice (with a finite number M of trees) to their asymptotic counterparts. Using empirical process theory, we prove a uniform central limit theorem for a large class of random fo…
Renmin University of China（中国人民大学）；University of Stuttgart（斯图加特大学）
We propose an algorithm named best-scored random forest for binary classification problems. The terminology "best-scored" means to select the one with the best empirical performance out of a certain number of purely random tree candidates as each single tree in the forest. In this way, the resulting forest can be more accurate than the original purely random forest. From the theoretical perspective, within the framework of regularized empirical risk minimization penalized on the number of splits, we establish almost optimal convergence rates for the proposed best-scored random trees under cert…
The paper demonstrates the use of the fully convolutional neural network for glioma segmentation on the BraTS 2019 dataset. Three-layers deep encoder-decoder architecture is used along with dense connection at encoder part to propagate the information from coarse layer to deep layers. This architecture is used to train three tumor sub-components separately. Subcomponent training weights are initialized with whole tumor weights to get the localization of the tumor within the brain. At the end, three segmentation results were merged to get the entire tumor segmentation. Dice Similarity of traini…
Randomization Can Reduce Both Bias and Variance: A Case Study in Random Forests
Operations Research Center Massachusetts Institute of Technology（麻省理工学院运筹学研究中心）；Sloan School of Management Massachusetts Institute of Technology（麻省理工学院斯隆管理学院）
In this paper we study asymptotic properties of random forests within the framework of nonlinear time series modeling. While random forests have been successfully applied in various fields, the theoretical justification has not been considered for their use in a time series setting. Under mild conditions, we prove a uniform concentration inequality for regression trees built on nonlinear autoregressive processes and, subsequently, we use this result to prove consistency for a large class of random forests. The results are supported by various simulations.
$Q$-learning is the most fundamental model-free reinforcement learning algorithm. Deployment of $Q$-learning requires approximation of the state-action value function (also known as the $Q$-function). In this work, we provide online random forests as $Q$-function approximators and propose a novel method wherein the random forest is grown as learning proceeds (through expanding forests). We demonstrate improved performance of our methods over state-of-the-art Deep $Q$-Networks in two OpenAI gyms (`blackjack' and `inverted pendulum') but not in the `lunar lander' gym. We suspect that the resilie…
University of British Columbia（不列颠哥伦比亚大学）；Oxford University（牛津大学）
Despite widespread interest and practical use, the theoretical properties of random forests are still not well understood. In this paper we contribute to this understanding in two ways. We present a new theoretically tractable variant of random regression forests and prove that our algorithm is consistent. We also provide an empirical evaluation, comparing our algorithm and other theoretically tractable random forest models to the random forest algorithm used in practice. Our experiments provide insight into the relative importance of different simplifications that theoreticians have made to o…
Random forests are a very effective and commonly used statistical method, but their full theoretical analysis is still an open problem. As a first step, simplified models such as purely random forests have been introduced, in order to shed light on the good performance of random forests. In this paper, we study the approximation error (the bias) of some purely random forest models in a regression framework, focusing in particular on the influence of the number of trees in the forest. Under some regularity assumptions on the regression function, we show that the bias of an infinite forest decre…
Random forests are a type of ensemble method which makes predictions by combining the results of several independent trees. However, the theory of random forests has long been outpaced by their application. In this paper, we propose a novel random forests algorithm based on cooperative game theory. Banzhaf power index is employed to evaluate the power of each feature by traversing possible feature coalitions. Unlike the previously used information gain rate of information theory, which simply chooses the most informative feature, the Banzhaf power index can be considered as a metric of the imp…
We propose novel applications of parallel coordinates plots and Sankey diagrams to represent the hierarchies of interacting covariate effects in random forests. Each visualisation summarises the frequencies of all of the paths through all of the trees in a random forest. Visualisations of the roles of covariates in random forests include: ranked bar or dot charts depicting scalar metrics of the contributions of individual covariates to the predictive accuracy of the random forest; line graphs depicting various summaries of the effect of varying a particular covariate on the predictions from th…
We propose a random forest based estimation procedure for Quantile Oriented Sensitivity Analysis-QOSA. In order to be efficient, a cross validation step on the leaf size of trees is required. Our full estimation procedure is tested on both simulated data and a real dataset.
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…
Random forests are ensemble learning methods introduced by Breiman (2001) that operate by averaging several decision trees built on a randomly selected subspace of the data set. Despite their widespread use in practice, the respective roles of the different mechanisms at work in Breiman's forests are not yet fully understood, neither is the tuning of the corresponding parameters. In this paper, we study the influence of two parameters , namely the subsampling rate and the tree depth, on Breiman's forests performance. More precisely, we show that fully developed sub-sampled forests and pruned (…
Due to their long-standing reputation as excellent off-the-shelf predictors, random forests continue remain a go-to model of choice for applied statisticians and data scientists. Despite their widespread use, however, until recently, little was known about their inner-workings and about which aspects of the procedure were driving their success. Very recently, two competing hypotheses have emerged -- one based on interpolation and the other based on regularization. This work argues in favor of the latter by utilizing the regularization framework to reexamine the decades-old question of whether …
As a flexible nonparametric learning tool, the random forests algorithm has been widely applied to various real applications with appealing empirical performance, even in the presence of high-dimensional feature space. Unveiling the underlying mechanisms has led to some important recent theoretical results on the consistency of the random forests algorithm and its variants. However, to our knowledge, almost all existing works concerning random forests consistency in high dimensional setting were established for various modified random forests models where the splitting rules are independent of…
Lassoed Forests: Random Forests with Adaptive Lasso Post-selection
Department of Statistics（统计学系）；Department of Biomedical Data Science（生物医学数据科学系）；Princess Margaret Cancer Centre（荣格癌症中心）；Department of Medical Biophysics（医学生物物理系）
Random Forests are one of the most popular classifiers in machine learning. The larger they are, the more precise is the outcome of their predictions. However, this comes at a cost: their running time for classification grows linearly with the number of trees, i.e. the size of the forest. In this paper, we propose a method to aggregate large Random Forests into a single, semantically equivalent decision diagram. Our experiments on various popular datasets show speed-ups of several orders of magnitude, while, at the same time, also significantly reducing the size of the required data structure.
Random forests are one of the most popular machine learning methods due to their accuracy and variable importance assessment. However, random forests only provide variable importance in a global sense. There is an increasing need for such assessments at a local level, motivated by applications in personalized medicine, policy-making, and bioinformatics. We propose a new nonparametric estimator that pairs the flexible random forest kernel with local sufficient dimension reduction to adapt to a regression function's local structure. This allows us to estimate a meaningful directional local varia…
Shapelet is a discriminative subsequence of time series. An advanced shapelet-based method is to embed shapelet into accurate and fast random forest. However, it shows several limitations. First, random shapelet forest requires a large training cost for split threshold searching. Second, a single shapelet provides limited information for only one branch of the decision tree, resulting in insufficient accuracy and interpretability. Third, randomized ensemble causes interpretability declining. For that, this paper presents Random Pairwise Shapelets Forest (RPSF). RPSF combines a pair of shapelet…
Random forests are a scheme proposed by Leo Breiman in the 2000's for building a predictor ensemble with a set of decision trees that grow in randomly selected subspaces of data. Despite growing interest and practical use, there has been little exploration of the statistical properties of random forests, and little is known about the mathematical forces driving the algorithm. In this paper, we offer an in-depth analysis of a random forests model suggested by Breiman in \cite{Bre04}, which is very close to the original algorithm. We show in particular that the procedure is consistent and adapts…
The issue of estimating residual variance in regression models has experienced relatively little attention in the machine learning community. However, the estimate is of primary interest in many practical applications, e.g. as a primary step towards the construction of prediction intervals. Here, we consider this issue for the random forest. Therein, the functional relationship between covariates and response variable is modeled by a weighted sum of the latter. The dependence structure is, however, involved in the weights that are constructed during the tree construction process making the mod…
The infinitesimal jackknife (IJ) has recently been applied to the random forest to estimate its prediction variance. These theorems were verified under a traditional random forest framework which uses classification and regression trees (CART) and bootstrap resampling. However, random forests using conditional inference (CI) trees and subsampling have been found to be not prone to variable selection bias. Here, we conduct simulation experiments using a novel approach to explore the applicability of the IJ to random forests using variations on the resampling method and base learner. Test data p…
Random Forests [Breiman:2001] (RF) are a fully non-parametric statistical method requiring no distributional assumptions on covariate relation to the response. RF are a robust, nonlinear technique that optimizes predictive accuracy by fitting an ensemble of trees to stabilize model estimates. The randomForestSRC package (http://cran.r-project.org/package=randomForestSRC) is a unified treatment of Breiman's random forests for survival, regression and classification problems. Predictive accuracy make RF an attractive alternative to parametric models, though complexity and interpretability of the…
University of Liège（列日大学）；Aristotle University of Thessaloniki（塞萨洛尼基亚里士多德大学）；Katholieke Universiteit Leuven（鲁汶天主教大学）
Within machine learning, the supervised learning field aims at modeling the input-output relationship of a system, from past observations of its behavior. Decision trees characterize the input-output relationship through a series of nested $if-then-else$ questions, the testing nodes, leading to a set of predictions, the leaf nodes. Several of such trees are often combined together for state-of-the-art performance: random forest ensembles average the predictions of randomized decision trees trained independently in parallel, while tree boosting ensembles train decision trees sequentially to ref…
