Implementation Of Random Forests Research Articles

Tree aggregation for random forest class probability estimation

AbstractIn random forest methodology, an overall prediction or estimate is made by aggregating predictions made by individual decision trees. Popular implementations of random forests rely on different methods for aggregating predictions. In this study, we provide an empirical analysis of the performance of aggregation approaches available for classification and regression problems. We show that while the choice of aggregation scheme usually has little impact in regression, it can have a profound effect on probability estimation in classification problems. Our study illustrates the causes of calibration issues that arise from two popular aggregation approaches and highlights the important role that terminal nodesize plays in the aggregation of tree predictions. We show that optimal choices for random forest tuning parameters depend heavily on the manner in which tree predictions are aggregated.

FPGA-Based Network Traffic Classification Using Machine Learning

Real-time classification of internet traffic is critical for the efficient management of networks. Classification approaches based on machine learning techniques have shown promising results with high levels of accuracy. In this article, the suitability of packet-level and flow-level features is validated using stepwise regression and random forest feature selection. Moreover, the optimal percentage of packets considered within a flow while extracting flow-level features is determined. Several experiments are conducted using naive Bayes, support vector machine, $k$ -nearest neighbor, random forest, and artificial neural networks on the University of Brescia (UNIBS) and the University of New Brunswick (UNB) datasets, which are both publicly available. The performed experiments show that 60% of flow packets are a good compromise that ensures high performance in the least processing time. The results of the conducted experiments indicate that random forest outperforms other algorithms achieving a maximum accuracy of 98.5% and an F-score of 0.932. Further, and since software-based classifiers cannot meet the anticipated real-time requirements, we propose a Field-Programmable Gate Array (FPGA) based random forest implementation that utilizes a highly pipelined architecture to accelerate such a time-consuming task. The proposed design achieves an average throughput of 163.24 Gbps, exceeding throughputs of reported hardware-based classifiers that use comparable approaches, which in turn ensures the continuity of real-time traffic classification at congested data centers.

A Hybrid Set of Handwriting Features for Handwritten Recognition

Handwriting of each person is unique since each person has their own unique and different style of handwriting. Handwriting verification can be performed in two ways, dynamic and static. The dynamic verification process is the writer dependent whereas the static verification process is the writer independent procedure. The features can be spatial, structural, statistical, geometrical, graphological, and from other feature extraction techniques. In this work, we are considering the combination of multilevel feature set for writer recognition and identification purpose. A dataset of different handwriting samples collected from 100 different writers is used for this experiment. A decision tree classifier with random forest implementation is used for recognition and identification of writer with 98.2% accuracy.

Random forest implementation and optimization for Big Data analytics on LexisNexis\u2019s high performance computing cluster platform

In this paper, we comprehensively explain how we built a novel implementation of the Random Forest algorithm on the High Performance Computing Cluster (HPCC) Systems Platform from LexisNexis. The algorithm was previously unavailable on that platform. Random Forest’s learning process is based on the principle of recursive partitioning and although recursion per se is not allowed in ECL (HPCC’s programming language), we were able to implement the recursive partition algorithm as an iterative split/partition process. In addition, we analyze the flaws found in our initial implementation and we thoroughly describe all the modifications required to overcome the bottleneck within the iterative split/partition process, i.e., the optimization of the data gathering of selected independent variables which are used for the node’s best-split analysis. Essentially, we describe how our initial Random Forest implementation has been optimized and has become an efficient distributed machine learning implementation for Big Data. By taking full advantage of the HPCC Systems Platform’s Big Data processing and analytics capabilities, we succeed in enhancing the data gathering method from an inefficient Pass them All and Filter approach into an effective and completely parallelized Fetching on Demand approach. Finally, based upon the results of our learning process runtime comparison between these two approaches, we confirm the speed up of our optimized Random Forest implementation.

The German Minimum Wage and Wage Growth: Heterogeneous Treatment Effects Using Causal Forests

Previous research suggests that minimum wages induce heterogeneous treatment effects on wages across different groups of employees. This research usually defines groups \textit{ex ante}. We analyze to what extent effect heterogeneities can be discerned in a data-driven manner by adapting the generalized random forest implementation of Athey et al (2019) in a difference-in-differences setting. Such a data-driven methodology allows detecting the potentially spurious nature of heterogeneities found in subgroups chosen ex-ante. The 2015 introduction of a minimum wage in Germany is the institutional background, with data of the Socio-economic Panel serving as our empirical basis. Our analysis not only reveals considerable treatment heterogeneities, it also shows that previously documented effect heterogeneities can be explained by interactions of other covariates.

A Brief Review of Random Forests for Water Scientists and Practitioners and Their Recent History in Water Resources

Random forests (RF) is a supervised machine learning algorithm, which has recently started to gain prominence in water resources applications. However, existing applications are generally restricted to the implementation of Breiman’s original algorithm for regression and classification problems, while numerous developments could be also useful in solving diverse practical problems in the water sector. Here we popularize RF and their variants for the practicing water scientist, and discuss related concepts and techniques, which have received less attention from the water science and hydrologic communities. In doing so, we review RF applications in water resources, highlight the potential of the original algorithm and its variants, and assess the degree of RF exploitation in a diverse range of applications. Relevant implementations of random forests, as well as related concepts and techniques in the R programming language, are also covered.

Assessment of Convolution Neural Networks for Wetland Mapping with Landsat in the Central Canadian Boreal Forest Region

Methods for effective wetland monitoring are needed to understand how ecosystem services may be altered from past and present anthropogenic activities and recent climate change. The large extent of wetlands in many regions suggests remote sensing as an effective means for monitoring. Remote sensing approaches have shown good performance in local extent studies, but larger regional efforts have generally produced low accuracies for detailed classes. In this research we evaluate the potential of deep-learning Convolution Neural Networks (CNNs) for wetland classification using Landsat data to bog, fen, marsh, swamp, and water classes defined by the Canada Wetland Classification System (CWCS). The study area is the northern part of the forested region of Alberta where we had access to two reference data sources. We evaluated ResNet CNNs and developed a Multi-Size/Scale ResNet Ensemble (MSRE) approach that exhibited the best performance. For assessment, a spatial extension strategy was employed that separated regions for training and testing. Results were consistent between the two reference sources. The best overall accuracy for the CWCS classes was 62–68%. Compared to a pixel-based random forest implementation this was 5–7% higher depending on the accuracy measure considered. For a parameter-optimized spatial-based implementation this was 2–4% higher. For a reduced set of classes to water, wetland, and upland, overall accuracy was in the range of 86–87%. Assessment for sampling over the entire region instead of spatial extension improved the mean class accuracies (F1-score) by 9% for the CWCS classes and for the reduced three-class level by 6%. The overall accuracies were 69% and 90% for the CWCS and reduced classes respectively with region sampling. Results in this study show that detailed classification of wetland types with Landsat remains challenging, particularly for small wetlands. In addition, further investigation of deep-learning methods are needed to identify CNN configurations and sampling methods better suited to moderate spatial resolution imagery across a range of environments.

Implementation of random forest in geo-acoustic study

The correlation between sediment sound velocity (V) and physical properties has been studied for 60 years using empirical formulas and found to be difficult to predict V accurately. Random forest (RF) is a scientific discipline and a method of data analysis that automates analytical model building. Here, we present the implementation of the RF algorithm in V prediction and sediment classification. The goal of this study is to establish a predictive model based on RF using multiple physical parameters (mean grain size, porosity, wet bulk density, and water content). Compared to empirical formulas, the average error of RF velocity is only 0.95%, ranging from 0.03% to 2.73%, which has improved the accuracy of V prediction. We also used Mean Decrease Impurity importance to evaluate the importance of a variable and found that the most important feature in the predictive model is the mean grain size. The classification model based on RF reaching up to 75% accuracy in the dataset. Multiple features, such as physical properties, sedimentary environment, and sediment source, affect the geo-acoustic properties of sediments. The next goal is to use multiple features to improve the model and further improve the accuracy of sound velocity prediction and sediment classification.

Evaluating parameters for ligand-based modeling with random forest on sparse data sets

Ligand-based predictive modeling is widely used to generate predictive models aiding decision making in e.g. drug discovery projects. With growing data sets and requirements on low modeling time comes the necessity to analyze data sets efficiently to support rapid and robust modeling. In this study we analyzed four data sets and studied the efficiency of machine learning methods on sparse data structures, utilizing Morgan fingerprints of different radii and hash sizes, and compared with molecular signatures descriptor of different height. We specifically evaluated the effect these parameters had on modeling time, predictive performance, and memory requirements using two implementations of random forest; Scikit-learn as well as FEST. We also compared with a support vector machine implementation. Our results showed that unhashed fingerprints yield significantly better accuracy than hashed fingerprints (p le 0.05), with no pronounced deterioration in modeling time and memory usage. Furthermore, the fast execution and low memory usage of the FEST algorithm suggest that it is a good alternative for large, high dimensional sparse data. Both support vector machines and random forest performed equally well but results indicate that the support vector machine was better at using the extra information from larger values of the Morgan fingerprint’s radius.

Random Forest Algorithm for Prediction of Precipitation

Predicting rainfall needs to be done as one of such effort to anticipate water flooding. One of the algorithm that can be used to predict rainfall is random forest. The porpose of the research is to create a model by implementing random forest algorithm. The research method consist of four steps: data collection, data processing, random forest implementation, analysis. Random forest implementation with using training set resulted model that has accurracy 71,09%, precision 0.75, recall 0.85, f-measure 0.79, kappa statistic 0.33, MAE 0.35, RMSE 0.46, ROC Area 0.78. Implementation of random forest algorithm with 10-fold cross validation resulted the output with accurracy 99.45%, precision 0.99, recall 0.99, f-measure 0.99, kappa statistic 0.99, MAE 0,09, RMSE 0.14, ROC area 1.

Tree-based Claims Algorithm for Measuring Pretreatment Quality of Care in Medicare Disabled Hepatitis C Patients.

To help broaden the use of machine-learning approaches in health services research, we provide an easy-to-follow framework on the implementation of random forests and apply it to identify quality of care (QC) patterns correlated with treatment receipt among Medicare disabled patients with hepatitis C virus (HCV). Using Medicare claims 2006-2009, we identified 1936 patients with 6 months continuous enrollment before HCV diagnosis. We ran a random forest on 14 pretreatment QC indicators, extracted the forest's representative tree, and aggregated its terminal nodes into 4 QC groups predictive of treatment. To explore determinants of differential QC receipt, we compared patient-level and county-level (linked AHRF data) characteristics across QC groups. The strongest predictors of treatment included "liver biopsy," "HCV genotype testing," "specialist visit," "HCV viremia confirmation," and "iron overload testing." High QC [n=360, proportion treated (pt)=33.3%] was defined for patients with at least 2 from the above-mentioned metrics. Good QC patients (n=302, pt=12.3%) had either "HCV genotype testing" or "specialist visit," whereas fair QC (n=282, pt=7.1%) only had "HCV viremia confirmation." Low QC patients (n=992, pt=2.5%) had none of the selected metrics. The algorithm accuracy of predicting treatment was 70% sensitivity and 78% specificity. HIV coinfection, drug abuse, and residence in counties with higher supply of hospitals with immunization and AIDS services correlated with lower QC. Machine-learning techniques could be useful in exploring patterns of care. Among Medicare disabled HCV patients, the receipt of more QC indicators was associated with higher treatment rates. Future research is needed to assess determinants of differential QC receipt.

Random Forests for Big Data

Big Data is one of the major challenges of statistical science and has numerous consequences from algorithmic and theoretical viewpoints. Big Data always involve massive data but they also often include online data and data heterogeneity. Recently some statistical methods have been adapted to process Big Data, like linear regression models, clustering methods and bootstrapping schemes. Based on decision trees combined with aggregation and bootstrap ideas, random forests were introduced by Breiman in 2001. They are a powerful nonparametric statistical method allowing to consider in a single and versatile framework regression problems, as well as two-class and multi-class classification problems. Focusing on classification problems, this paper proposes a selective review of available proposals that deal with scaling random forests to Big Data problems. These proposals rely on parallel environments or on online adaptations of random forests. We also describe how out-of-bag error is addressed in these methods. Then, we formulate various remarks for random forests in the Big Data context. Finally, we experiment five variants on two massive datasets (15 and 120 millions of observations), a simulated one as well as real world data. One variant relies on subsampling while three others are related to parallel implementations of random forests and involve either various adaptations of bootstrap to Big Data or “divide-and-conquer” approaches. The fifth variant is related to online learning of random forests. These numerical experiments lead to highlight the relative performance of the different variants, as well as some of their limitations.

Using the 500 m MODIS land cover product to derive a consistent continental scale 30 m Landsat land cover classification

Classification is a fundamental process in remote sensing used to relate pixel values to land cover classes present on the surface. Over large areas land cover classification is challenging particularly due to the cost and difficulty of collecting representative training data that enable classifiers to be consistent and locally reliable. A novel methodology to classify large volume Landsat data using high quality training data derived from the 500m MODIS land cover product is demonstrated and used to generate a 30m land cover classification for all of North America between 20°N and 50°N. Publically available 30m global monthly Web-enabled Landsat Data (GWELD) products generated from every available Landsat 7 ETM+ and Landsat 5 TM image for a three year period, that are defined aligned to the MODIS land products and are consistently pre-processed data (cloud-screened, saturation flagged, atmospherically corrected and normalized to nadir BRDF adjusted reflectance), were classified. The MODIS 500m land cover product was filtered judiciously, using only good quality pixels that did not change land cover class in 2009, 2010 or 2011, followed by automated selection of spatially corresponding 30m GWELD temporal metric values, to define a large training data set sampled across North America. The training data were sampled so that the class proportions were the same as the North America MODIS land cover product class proportions and corresponded to 1% of the 500m and <0.005% of the 30m pixels. Thirty nine GWELD temporal metrics for every 30m North America pixel location were classified using (a) a single random forest, and (b) a locally adaptive method with a random forest classifier derived and applied locally and the classification results spatially mosaicked together. The land cover classification results appeared geographically plausible and at synoptic scale were similar to the MODIS land cover product. Detailed visual inspection revealed that the locally adaptive random forest classifications and associated classification confidences were generally more coherent than the single random forest classification results. The level of agreement between the 30m classifications and the MODIS land cover product derived training data was assessed by bootstrapping the random forest implementation. The locally adaptive random forest classification had higher overall agreement (95.44%, 0.9443 kappa) than the single random forest classification (93.13%, 0.9195 kappa). The paper concludes with a discussion of future research including the potential for automated global land cover classification.

IntegratedMRF: random forest-based framework for integrating prediction from different data types.

IntegratedMRF is an open-source R implementation for integrating drug response predictions from various genomic characterizations using univariate or multivariate random forests that includes various options for error estimation techniques. The integrated framework was developed following superior performance of random forest based methods in NCI-DREAM drug sensitivity prediction challenge. The computational framework can be applied to estimate mean and confidence interval of drug response prediction errors based on ensemble approaches with various combinations of genetic and epigenetic characterizations as inputs. The multivariate random forest implementation included in the package incorporates the correlations between output responses in the modeling and has been shown to perform better than existing approaches when the drug responses are correlated. Detailed analysis of the provided features is included in the Supplementary Material . The framework has been implemented as a package IntegratedMRF , which can be downloaded from https://cran.r-project.org/web/packages/IntegratedMRF/index.html , where further explanation of the package is available. ranadip.pal@ttu.edu. Supplementary data are available at Bioinformatics online.

Ranger: A Fast Implementation of Random Forests for High Dimensional Data in C++ and R

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 to analyze data on the scale of a genome-wide association study.

Practical aspects of gene regulatory inference via conditional inference forests from expression data.

Gene regulatory network (GRN) inference is an active area of research that facilitates understanding the complex interplays between biological molecules. We propose a novel framework to create such GRNs, based on Conditional Inference Forests (CIFs) as proposed by Strobl etal. Our framework consists of using ensembles of Conditional Inference Trees (CITs) and selecting an appropriate aggregation scheme for variant selection prior to network construction. We show on synthetic microarray data that taking the original implementation of CIFs with conditional permutation scheme (CIFcond ) may lead to improved performance compared to Breiman's implementation of Random Forests (RF). Among all newly introduced CIF-based methods and five network scenarios obtained from the DREAM4 challenge, CIFcond performed best. Networks derived from well-tuned CIFs, obtained by simply averaging P-values over tree ensembles (CIFmean ) are particularly attractive, because they combine adequate performance with computational efficiency. Moreover, thresholds for variable selection are based on significance levels for P-values and, hence, do not need to be tuned. From a practical point of view, our extensive simulations show the potential advantages of CIFmean -based methods. Although more work is needed to improve on speed, especially when fully exploiting the advantages of CITs in the context of heterogeneous and correlated data, we have shown that CIF methodology can be flexibly inserted in a framework to infer biological interactions. Notably, we confirmed biologically relevant interaction between IL2RA and FOXP1, linked to the IL-2 signaling pathway and to type 1 diabetes.

CloudForest: A Scalable and Efficient Random Forest Implementation for Biological Data.

Random Forest has become a standard data analysis tool in computational biology. However, extensions to existing implementations are often necessary to handle the complexity of biological datasets and their associated research questions. The growing size of these datasets requires high performance implementations. We describe CloudForest, a Random Forest package written in Go, which is particularly well suited for large, heterogeneous, genetic and biomedical datasets. CloudForest includes several extensions, such as dealing with unbalanced classes and missing values. Its flexible design enables users to easily implement additional extensions. CloudForest achieves fast running times by effective use of the CPU cache, optimizing for different classes of features and efficiently multi-threading. https://github.com/ilyalab/CloudForest.

A random forest approach for competing risks based on pseudo‐values

Random forest is a supervised learning method that combines many classification or regression trees for prediction. Here we describe an extension of the random forest method for building event risk prediction models in survival analysis with competing risks. In case of right-censored data, the event status at the prediction horizon is unknown for some subjects. We propose to replace the censored event status by a jackknife pseudo-value, and then to apply an implementation of random forests for uncensored data. Because the pseudo-responses take on values on a continuous scale, the node variance is chosen as split criterion for growing regression trees. In a simulation study, the pseudo split criterion is compared with the Gini split criterion when the latter is applied to the uncensored event status. To investigate the resulting pseudo random forest method for building risk prediction models, we analyze it in a simulation study of predictive performance where we compare it to Cox regression and random survival forest. The method is further illustrated in two real data sets.

Comparison of the CPU and memory performance of StatPatternRecognitions (SPR) and Toolkit for MultiVariate Analysis (TMVA)

High Energy Physics data sets are often characterized by a huge number of events. Therefore, it is extremely important to use statistical packages able to efficiently analyze these unprecedented amounts of data. We compare the performance of the statistical packages StatPatternRecognition (SPR) and Toolkit for MultiVariate Analysis (TMVA). We focus on how CPU time and memory usage of the learning process scale versus data set size. As classifiers, we consider Random Forests, Boosted Decision Trees and Neural Networks only, each with specific settings. For our tests, we employ a data set widely used in the machine learning community, “Threenorm” data set, as well as data tailored for testing various edge cases. For each data set, we constantly increase its size and check CPU time and memory needed to build the classifiers implemented in SPR and TMVA. We show that SPR is often significantly faster and consumes significantly less memory. For example, the SPR implementation of Random Forest is by an order of magnitude faster and consumes an order of magnitude less memory than TMVA on Threenorm data.

Recursive partitioning on incomplete data using surrogate decisions and multiple imputation

The occurrence of missing data is a major problem in statistical data analysis. All scientific fields and data of all kinds and size are touched by this problem. There is a number of ad-hoc solutions which unfortunately lead to a loss of power, biased inference, underestimation of variability and distorted relationships between variables. A more promising approach of rising popularity is multiple imputation by chained equations (MICE) also known as imputation by full conditional specification (FCS). Alternatives to imputation are given by methods with built-in procedures. These include recursive partitioning by classification and regression trees as well as corresponding Random Forests. However there is only few literature comparing the two approaches. Existing evaluations often lack generalizability due to restrictions on data structure and simulation schemes. The application of both methods to several kinds of data and different simulation settings is meant to improve and extend the comparative analyses. Classification and regression studies are examined. Recursive partitioning is executed by two popular tree and one Random Forest implementation. Findings show that multiple imputation produces ambiguous performance results for both, simulated and real life data. Using surrogates instead is a fast and simple way to achieve performances which are only negligible worse and in many cases even superior.