Random Forests
01 Oct 2001-Vol. 45, Iss: 1, pp 5-32
TL;DR: Internal estimates monitor error, strength, and correlation and these are used to show the response to increasing the number of features used in the forest, and are also applicable to regression.
Abstract: Random forests are a combination of tree predictors such that each tree depends on the values of a random vector sampled independently and with the same distribution for all trees in the forest. The generalization error for forests converges a.s. to a limit as the number of trees in the forest becomes large. The generalization error of a forest of tree classifiers depends on the strength of the individual trees in the forest and the correlation between them. Using a random selection of features to split each node yields error rates that compare favorably to Adaboost (Y. Freund & R. Schapire, Machine Learning: Proceedings of the Thirteenth International conference, aaa, 148–156), but are more robust with respect to noise. Internal estimates monitor error, strength, and correlation and these are used to show the response to increasing the number of features used in the splitting. Internal estimates are also used to measure variable importance. These ideas are also applicable to regression.
Citations
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TL;DR: The random forest is clearly the best family of classifiers (3 out of 5 bests classifiers are RF), followed by SVM (4 classifiers in the top-10), neural networks and boosting ensembles (5 and 3 members in theTop-20, respectively).
Abstract: We evaluate 179 classifiers arising from 17 families (discriminant analysis, Bayesian, neural networks, support vector machines, decision trees, rule-based classifiers, boosting, bagging, stacking, random forests and other ensembles, generalized linear models, nearest-neighbors, partial least squares and principal component regression, logistic and multinomial regression, multiple adaptive regression splines and other methods), implemented in Weka, R (with and without the caret package), C and Matlab, including all the relevant classifiers available today. We use 121 data sets, which represent the whole UCI data base (excluding the large-scale problems) and other own real problems, in order to achieve significant conclusions about the classifier behavior, not dependent on the data set collection. The classifiers most likely to be the bests are the random forest (RF) versions, the best of which (implemented in R and accessed via caret) achieves 94.1% of the maximum accuracy overcoming 90% in the 84.3% of the data sets. However, the difference is not statistically significant with the second best, the SVM with Gaussian kernel implemented in C using LibSVM, which achieves 92.3% of the maximum accuracy. A few models are clearly better than the remaining ones: random forest, SVM with Gaussian and polynomial kernels, extreme learning machine with Gaussian kernel, C5.0 and avNNet (a committee of multi-layer perceptrons implemented in R with the caret package). The random forest is clearly the best family of classifiers (3 out of 5 bests classifiers are RF), followed by SVM (4 classifiers in the top-10), neural networks and boosting ensembles (5 and 3 members in the top-20, respectively).
2,616 citations
Cites methods from "Random Forests"
...130. rforest R creates a random forest (Breiman, 2001) ensemble, using the R function randomForest in the randomForest package, with parameters ntree = 500 (number of trees in the forest) and mtry= √ #inputs....
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TL;DR: It is shown that random forest has comparable performance to other classification methods, including DLDA, KNN, and SVM, and that the new gene selection procedure yields very small sets of genes (often smaller than alternative methods) while preserving predictive accuracy.
Abstract: Selection of relevant genes for sample classification is a common task in most gene expression studies, where researchers try to identify the smallest possible set of genes that can still achieve good predictive performance (for instance, for future use with diagnostic purposes in clinical practice). Many gene selection approaches use univariate (gene-by-gene) rankings of gene relevance and arbitrary thresholds to select the number of genes, can only be applied to two-class problems, and use gene selection ranking criteria unrelated to the classification algorithm. In contrast, random forest is a classification algorithm well suited for microarray data: it shows excellent performance even when most predictive variables are noise, can be used when the number of variables is much larger than the number of observations and in problems involving more than two classes, and returns measures of variable importance. Thus, it is important to understand the performance of random forest with microarray data and its possible use for gene selection. We investigate the use of random forest for classification of microarray data (including multi-class problems) and propose a new method of gene selection in classification problems based on random forest. Using simulated and nine microarray data sets we show that random forest has comparable performance to other classification methods, including DLDA, KNN, and SVM, and that the new gene selection procedure yields very small sets of genes (often smaller than alternative methods) while preserving predictive accuracy. Because of its performance and features, random forest and gene selection using random forest should probably become part of the "standard tool-box" of methods for class prediction and gene selection with microarray data.
2,610 citations
Cites methods from "Random Forests"
...Using simulated and nine microarray data sets we show that random forest has comparable performance to other classification methods, including DLDA, KNN, and SVM, and that the new gene selection procedure yields very small sets of genes (often smaller than alternative methods) while preserving…...
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TL;DR: A gut-microbiome-brain connection in a mouse model of ASD is supported and a potential probiotic therapy for GI and particular behavioral symptoms in human neurodevelopmental disorders is identified.
2,507 citations
TL;DR: A new, conditional permutation scheme is developed for the computation of the variable importance measure that reflects the true impact of each predictor variable more reliably than the original marginal approach.
Abstract: Random forests are becoming increasingly popular in many scientific fields because they can cope with "small n large p" problems, complex interactions and even highly correlated predictor variables. Their variable importance measures have recently been suggested as screening tools for, e.g., gene expression studies. However, these variable importance measures show a bias towards correlated predictor variables. We identify two mechanisms responsible for this finding: (i) A preference for the selection of correlated predictors in the tree building process and (ii) an additional advantage for correlated predictor variables induced by the unconditional permutation scheme that is employed in the computation of the variable importance measure. Based on these considerations we develop a new, conditional permutation scheme for the computation of the variable importance measure. The resulting conditional variable importance reflects the true impact of each predictor variable more reliably than the original marginal approach.
2,466 citations
Cites background from "Random Forests"
...Results: We identify two mechanisms responsible for this finding: (i) A preference for the selection of correlated predictors in the tree building process and (ii) an additional advantage for correlated predictor variables induced by the unconditional permutation scheme that is employed in the…...
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25 Jun 2006
TL;DR: A large-scale empirical comparison between ten supervised learning methods: SVMs, neural nets, logistic regression, naive bayes, memory-based learning, random forests, decision trees, bagged trees, boosted trees, and boosted stumps is presented.
Abstract: A number of supervised learning methods have been introduced in the last decade. Unfortunately, the last comprehensive empirical evaluation of supervised learning was the Statlog Project in the early 90's. We present a large-scale empirical comparison between ten supervised learning methods: SVMs, neural nets, logistic regression, naive bayes, memory-based learning, random forests, decision trees, bagged trees, boosted trees, and boosted stumps. We also examine the effect that calibrating the models via Platt Scaling and Isotonic Regression has on their performance. An important aspect of our study is the use of a variety of performance criteria to evaluate the learning methods.
2,450 citations
References
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01 Aug 1996
TL;DR: Tests on real and simulated data sets using classification and regression trees and subset selection in linear regression show that bagging can give substantial gains in accuracy.
Abstract: Bagging predictors is a method for generating multiple versions of a predictor and using these to get an aggregated predictor. The aggregation averages over the versions when predicting a numerical outcome and does a plurality vote when predicting a class. The multiple versions are formed by making bootstrap replicates of the learning set and using these as new learning sets. Tests on real and simulated data sets using classification and regression trees and subset selection in linear regression show that bagging can give substantial gains in accuracy. The vital element is the instability of the prediction method. If perturbing the learning set can cause significant changes in the predictor constructed, then bagging can improve accuracy.
16,118 citations
Proceedings Article•
AT&T1
TL;DR: This paper describes experiments carried out to assess how well AdaBoost with and without pseudo-loss, performs on real learning problems and compared boosting to Breiman's "bagging" method when used to aggregate various classifiers.
Abstract: In an earlier paper, we introduced a new "boosting" algorithm called AdaBoost which, theoretically, can be used to significantly reduce the error of any learning algorithm that con- sistently generates classifiers whose performance is a little better than random guessing. We also introduced the related notion of a "pseudo-loss" which is a method for forcing a learning algorithm of multi-label concepts to concentrate on the labels that are hardest to discriminate. In this paper, we describe experiments we carried out to assess how well AdaBoost with and without pseudo-loss, performs on real learning problems. We performed two sets of experiments. The first set compared boosting to Breiman's "bagging" method when used to aggregate various classifiers (including decision trees and single attribute- value tests). We compared the performance of the two methods on a collection of machine-learning benchmarks. In the second set of experiments, we studied in more detail the performance of boosting using a nearest-neighbor classifier on an OCR problem.
7,601 citations
"Random Forests" refers background or methods in this paper
...But none of these these three forests do as well as Adaboost (Freund & Schapire, 1996) or other algorithms that work by adaptive reweighting (arcing) of the training set (see Breiman, 1998b; Dieterrich, 1998; Bauer & Kohavi, 1999)....
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...In its original version, Adaboost (Freund & Schapire, 1996) is a deterministic algorithm that selects the weights on the training set for input to the next classifier based on the misclassifications in the previous classifiers....
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TL;DR: A method to construct a decision tree based classifier is proposed that maintains highest accuracy on training data and improves on generalization accuracy as it grows in complexity.
Abstract: Much of previous attention on decision trees focuses on the splitting criteria and optimization of tree sizes. The dilemma between overfitting and achieving maximum accuracy is seldom resolved. A method to construct a decision tree based classifier is proposed that maintains highest accuracy on training data and improves on generalization accuracy as it grows in complexity. The classifier consists of multiple trees constructed systematically by pseudorandomly selecting subsets of components of the feature vector, that is, trees constructed in randomly chosen subspaces. The subspace method is compared to single-tree classifiers and other forest construction methods by experiments on publicly available datasets, where the method's superiority is demonstrated. We also discuss independence between trees in a forest and relate that to the combined classification accuracy.
5,984 citations
"Random Forests" refers background in this paper
...Ho (1998) has written a number of papers on “the random subspace” method which does a random selection of a subset of features to use to grow each tree....
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...Keywords: classification, regression, ensemble...
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TL;DR: In this article, the authors compared the effectiveness of randomization, bagging, and boosting for improving the performance of the decision-tree algorithm C4.5 and found that in situations with little or no classification noise, randomization is competitive with bagging but not as accurate as boosting.
Abstract: Bagging and boosting are methods that generate a diverse ensemble of classifiers by manipulating the training data given to a “base” learning algorithm. Breiman has pointed out that they rely for their effectiveness on the instability of the base learning algorithm. An alternative approach to generating an ensemble is to randomize the internal decisions made by the base algorithm. This general approach has been studied previously by Ali and Pazzani and by Dietterich and Kong. This paper compares the effectiveness of randomization, bagging, and boosting for improving the performance of the decision-tree algorithm C4.5. The experiments show that in situations with little or no classification noise, randomization is competitive with (and perhaps slightly superior to) bagging but not as accurate as boosting. In situations with substantial classification noise, bagging is much better than boosting, and sometimes better than randomization.
2,919 citations
TL;DR: It is found that Bagging improves when probabilistic estimates in conjunction with no-pruning are used, as well as when the data was backfit, and that Arc-x4 behaves differently than AdaBoost if reweighting is used instead of resampling, indicating a fundamental difference.
Abstract: Methods for voting classification algorithms, such as Bagging and AdaBoost, have been shown to be very successful in improving the accuracy of certain classifiers for artificial and real-world datasets. We review these algorithms and describe a large empirical study comparing several variants in conjunction with a decision tree inducer (three variants) and a Naive-Bayes inducer. The purpose of the study is to improve our understanding of why and when these algorithms, which use perturbation, reweighting, and combination techniques, affect classification error. We provide a bias and variance decomposition of the error to show how different methods and variants influence these two terms. This allowed us to determine that Bagging reduced variance of unstable methods, while boosting methods (AdaBoost and Arc-x4) reduced both the bias and variance of unstable methods but increased the variance for Naive-Bayes, which was very stable. We observed that Arc-x4 behaves differently than AdaBoost if reweighting is used instead of resampling, indicating a fundamental difference. Voting variants, some of which are introduced in this paper, include: pruning versus no pruning, use of probabilistic estimates, weight perturbations (Wagging), and backfitting of data. We found that Bagging improves when probabilistic estimates in conjunction with no-pruning are used, as well as when the data was backfit. We measure tree sizes and show an interesting positive correlation between the increase in the average tree size in AdaBoost trials and its success in reducing the error. We compare the mean-squared error of voting methods to non-voting methods and show that the voting methods lead to large and significant reductions in the mean-squared errors. Practical problems that arise in implementing boosting algorithms are explored, including numerical instabilities and underflows. We use scatterplots that graphically show how AdaBoost reweights instances, emphasizing not only “hard” areas but also outliers and noise.
2,686 citations
"Random Forests" refers background or methods in this paper
...But none of these these three forests do as well as Adaboost (Freund & Schapire, 1996) or other algorithms that work by adaptive reweighting (arcing) of the training set (see Breiman, 1998b; Dieterrich, 1998; Bauer & Kohavi, 1999)....
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...The second is that bagging can be used to give ongoing estimates of the generalization error (PE∗) of the combined ensemble of trees, as well as estimates for the strength and correlation....
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