Geodesic distance is the shortest path between two points in a Riemannian manifold. Manifold learning algorithms, such as Isomap, seek to learn a manifold that preserves geodesic distances. However, such methods operate on the ambient dimensionality, and are therefore fragile to noise dimensions. We developed an unsupervised random forest method (URerF) to approximately learn geodesic distances in linear and nonlinear manifolds with noise. URerF operates on low-dimensional sparse linear combinations of features, rather than the full observed dimensionality. To choose the optimal split in a computationally efficient fashion, we developed a fast Bayesian Information Criterion statistic for Gaussian mixture models. We introduce geodesic precision-recall curves which quantify performance relative to the true latent manifold. Empirical results on simulated and real data demonstrate that URerF is robust to high-dimensional noise, where as other methods, such as Isomap, UMAP, and FLANN, quickly deteriorate in such settings. In particular, URerF is able to estimate geodesic distances on a real connectome dataset better than other approaches.
Finally, most closely related to our method are existing unsupervised random forest methods, the most popular of which is included in Adele Cutler's RandomForest R package @cite_33 . It proceeds by generating a synthetic copy of the data by randomly permuting each feature independently of the others, and then attempts to classify the real versus the synthetic dataset. As will be seen below, this approach leads to missing surprisingly easy latent structures.
@cite_33
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Classification procedures are some of the most widely used statistical methods in ecology. Random forests (RF) is a new and powerful statistical classifier that is well established in other disciplines but is relatively unknown in ecology. Advantages of RF compared to other statistical classifiers include (1) very high classification accuracy; (2) a novel method of determining variable importance; (3) ability to model complex interactions among predictor variables; (4) flexibility to perform several types of statistical data analysis, including regression, classification, survival analysis, and unsupervised learning; and (5) an algorithm for imputing missing values. We compared the accuracies of RF and four other commonly used statistical classifiers using data on invasive plant species presence in Lava Beds National Monument, California, USA, rare lichen species presence in the Pacific Northwest, USA, and nest sites for cavity nesting birds in the Uinta Mountains, Utah, USA. We observed high classification accuracy in all applications as measured by cross-validation and, in the case of the lichen data, by independent test data, when comparing RF to other common classification methods. We also observed that the variables that RF identified as most important for classifying invasive plant species coincided with expectations based on the literature. Random Forest is an ensemble supervised machine learning technique. Based on bagging and random feature selection, number of decision trees (base classifiers) is generated and majority voting is taken for classification. For effective learning and classification of Random Forest, there is need for reducing number of trees (Pruning) in Random Forest. We have presented here systematic survey of pruning efforts of Random Forest classifier along with the required theoretical background. Most of the work for pruning takes static approach while recently dynamic pruning is being targeted. We have also generated a Comparison Chart by taking relevant parameters. There is research scope for analyzing behavior of Random forest, generating accurate and diverse base decision trees, truly dynamic pruning algorithm for Random Forest classifier, and generating optimal subset of Random forest. A new classification and regression tool, Random Forest, is introduced and investigated for predicting a compound's quantitative or categorical biological activity based on a quantitative description of the compound's molecular structure. Random Forest is an ensemble of unpruned classification or regression trees created by using bootstrap samples of the training data and random feature selection in tree induction. Prediction is made by aggregating (majority vote or averaging) the predictions of the ensemble. We built predictive models for six cheminformatics data sets. Our analysis demonstrates that Random Forest is a powerful tool capable of delivering performance that is among the most accurate methods to date. We also present three additional features of Random Forest: built-in performance assessment, a measure of relative importance of descriptors, and a measure of compound similarity that is weighted by the relative importance of descriptors. It is the combination of relatively high prediction accu... 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 (2004), which is very close to the original algorithm. We show in particular that the procedure is consistent and adapts to sparsity, in the sense that its rate of convergence depends only on the number of strong features and not on how many noise variables are present.