PBL height from random forest, random forest classifier and lightGBM ML models.
PBL height from random forest, random forest classifier and lightGBM ML models.
LightGBM ML models↗
SEARCH · Engineering Papers
Results for “Random forests”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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FORESTR: Finding, Organizing, Representing, Explaining, Summarizing, and Thinning Random forests
Random forests have become popular models used for data driven predictions. As a result, random forests are currently used or being considered for high-consequence mission applications in national security, such as the prediction of yield from optical signals and malware detection. While random forests may provide accurate predictions, the complexity of the algorithm causes a lack of interpretability. Random forests are an ensemble of regression or decision trees. Individual regression and decision trees are interpretable, but ensembles are inherently difficult to interpret due to the compilation of many models. We aim to increase the interpretability of random forests by finding patterns in the ensemble of trees that can be used to “thin” (or remove) trees. As a starting point, in this report, we develop a new distance metric for quantifying the similarity between trees based on their topologies (i.e., shapes). We base the metric on a novel distance metric for graphs that is a proper mathematical distance, is invariant to transformations, has registration between graphs, and computes topological evolutions between graphs. We use the tree distance metric to compute tree statistics such as a “mean tree” and to identify clusters of trees. We apply the developed methodology to a toy dataset and a mission relevant product inspection dataset to demonstrate how the metric can provide insight into random forests. Furthermore, we discuss the limitations of the approach and ideas for future research into how the metric could be used as a thinning tool to develop less complex models.
97 MATHEMATICS AND COMPUTING↗
Evaluating the performance of random forest and iterative random forest based methods when applied to gene expression data
Gene-to-gene networks, such as Gene Regulatory Networks (GRN) and Predictive Expression Networks (PEN) capture relationships between genes and are beneficial for use in downstream biological analyses. There exists multiple network inference tools to produce these gene-to-gene networks from matrices of gene expression data. Random Forest-Leave One Out Prediction (RF-LOOP) is a method that has been shown to be efficient at producing these gene-to-gene networks, frequently known as GEne Network Inference with Ensemble of trees (GENIE3). Random Forest can be replaced in this process by iterative Random Forest (iRF), which performs variable selection and boosting. Here we validate that iterative Random Forest-Leave One Out Prediction (iRF-LOOP) produces higher quality networks than GENIE3 (RF-LOOP). We use both synthetic and empirical networks from the Dialogue for Reverse Engineering Assessment and Methods (DREAM) Challenges by Sage Bionetworks, as well as two additional empirical networks created from Arabidopsis thaliana and Populus trichocarpa expression data.
59 BASIC BIOLOGICAL SCIENCES↗
Evaluating the Performance of Random Forest and Iterative Random Forest Based Methods when Applied to Gene Expression Data
Gene-to-gene networks, such as Gene Regulatory Networks (GRN) and Predictive Expression Networks (PEN) capture relationships between genes and are beneficial for use in downstream biological analyses. There exists multiple network inference tools to produce these gene-to-gene networks from matrices of gene expression data. Random Forest-Leave One Out Prediction (RF-LOOP) is a method that has been shown to be efficient at producing these gene-to-gene networks, frequently known as GEne Network Inference with Ensemble of trees (GENIE3). Here we validate that iterative Random Forest-Leave One Out Prediction (iRF-LOOP) produces higher quality networks than GENIE3. We use both synthetic and empirical networks from the Dialogue for Reverse Engineering Assessment and Methods (DREAM) Challenges by Sage Bionetworks, as well as two additional empirical networks created from Arabidopsis thaliana and Populus trichocarpa expression data.
iRF-Loop, expression network, Populus Trichocarpa↗
Accelerating Random Forest Classification on GPU and FPGA
Random Forests (RFs) are a commonly used machine learning method for classification and regression tasks spanning a variety of application domains, including bioinformatics, business analytics, and software optimization. While prior work has focused primarily on improving performance of the training of RFs, many applications, such as malware identification, cancer prediction, and banking fraud detection, require fast RF classification. In this work, we accelerate RF classification on GPU and FPGA. In order to provide efficient support for large datasets, we propose a hierarchical memory layout suitable to the GPU/FPGA memory hierarchy. We design three RF classification code variants based on that layout, and we investigate GPU- and FPGA-specific considerations for these kernels. Our experimental evaluation, performed on an Nvidia Xp GPU and on a Xilinx Alveo U250 FPGA accelerator card using publicly available datasets on the scale of millions of samples and tens of features, covers various aspects. First, we evaluate the performance benefits of our hierarchical data structure over the standard compressed sparse row (CSR) format. Second, we compare our GPU implementation with cuML, a machine learning library targeting Nvidia GPUs. Third, we explore the performance/accuracy tradeoff resulting from the use of different tree depths in the RF. Finally, we perform a comparative performance analysis of our GPU and FPGA implementations. Our evaluation shows that for high accuracy targets, our GPU implementation yields 5-9x speedup over CSR, and up to a 2x speedup over cuML.
FPGA, Xilinx FPGA, GPU, Random Forest classificati↗
mcharrison95/RF_for_Yeast_GenSpec: Random forest code for y1000+ paper
Random forest code for predicting generalists and specialists from gene annotations for the paper "Genomic and ecological factors shaping specialism and generalism across an entire subphylum"
ascomycota/genetics/metabolism↗
Data-assisted combustion simulations with dynamic submodel assignment using random forests
This investigation outlines a data-assisted approach that employs random forest classifiers for local and dynamic submodel assignment in turbulent-combustion simulations. This method is demonstrated in simulations of a single-element GOX/GCH4 rocket combustor; a priori as well as a posteriori assessments are conducted to (i) evaluate the accuracy and adjustability of the classifier for targeting different quantities of interest (QoIs), and (ii) assess improvements, resulting from the data-assisted combustion model assignment, in predicting target QoIs during simulation runtime. Results from the a priori study show that random forests, trained with local flow properties as input variables and combustion model errors as training labels, assign three different combustion models – finite-rate chemistry (FRC), flamelet progress variable (FPV) model, and inert mixing (IM) – with reasonable classification performance even when targeting multiple QoIs. Applications in a posteriori studies demonstrate improved predictions from data-assisted simulations, in temperature and CO mass fraction, when compared with monolithic FPV calculations. An additional a posteriori data-assisted simulation of a modified configuration demonstrates that the present approach can be successfully applied to different configurations, as long as thermophysical behavior can be represented by the training data. Furthermore, these results demonstrate that this data-driven framework holds promise for dynamic combustion submodel assignments in reacting flow simulations.
42 ENGINEERING↗
Ch3MS-RF: a random forest model for chemical characterization and improved quantification of unidentified atmospheric organics detected by chromatography–mass spectrometry techniques
Abstract. The chemical composition of ambient organic aerosols plays a critical role in driving their climate and health-relevant properties and holds important clues to the sources and formation mechanisms of secondary aerosol material. In most ambient atmospheric environments, this composition remains incompletely characterized, with the number of identifiable species consistently outnumbered by those that have no mass spectral matches in the literature or the National Institute of Standards and Technology/National Institutes of Health/Environmental Protection Agency (NIST/NIH/EPA) mass spectral databases, making them nearly impossible to definitively identify. This creates significant challenges in utilizing the full analytical capabilities of techniques which separate and generate spectra for complex environmental samples. In this work, we develop the use of machine learning techniques to quantify and characterize novel, or unidentifiable, organic material. This work introduces Ch3MS-RF (Chemical Characterization by Chromatography–Mass Spectrometry Random Forest Modeling), an open-source, R-based software tool, for efficient machine-learning-enabled characterization of compounds separated in chromatography–mass spectrometry applications but not identifiable by comparison to mass spectral databases. A random forest model is trained and tested on a known 130 component representative external standard to predict the response factors of novel environmental organics based on position in volatility–polarity space and mass spectrum, enabling the reproducible, efficient, and optimized quantification of novel environmental species. Quantification accuracy on a reserved 20 % test set randomly split from the external standard compound list indicates that random forest modeling significantly outperforms the commonly used methods in both precision and accuracy, with a median response factor percent error of −2 %, for modeled response factors, compared to > 15 %, for typically used proxy assignment-based methods. Chemical properties modeling, evaluated on the same reserved 20 % test set and an extrapolation set of species identified in ambient organic aerosol samples collected in the Amazon rainforest, also demonstrate robust performance. Extrapolation set property prediction mean absolute errors for carbon number, oxygen to carbon ratio (O : C), average carbon oxidation state (OSc‾), and vapor pressure are 1.8, 0.15, 0.25, and 1.0 (log(atm)), respectively. Extrapolation set out-of-sample R2 for all properties modeled are above 0.75, with the exception of vapor pressure. While predictive performance for vapor pressure is less robust compared to the other chemical properties modeled, random-forest-based modeling was significantly more accurate than other commonly used methods of vapor pressure prediction, decreasing the mean vapor pressure prediction error to 0.24 (log(atm)) from 0.55 (log(atm)) (chromatography-based vapor pressure prediction) and 1.2 (log(atm)) (chemical formula-based vapor pressure prediction). The random forest model significantly advances an untargeted analysis of the full scope of chemical speciation yielded by two-dimensional gas chromatography (GCxGC-MS) techniques and can be applied to gas chromatography coupled with electron ionization mass spectrometry (GC-MS) as well. It enables the accurate estimation of key chemical properties commonly utilized in the atmospheric chemistry community, which may be used to more efficiently identify important tracers for further individual analysis and to characterize compound populations uniquely formed under specific ambient conditions.
54 ENVIRONMENTAL SCIENCES↗
Effects of random forest modeling decisions on biogeochemical time series predictions
Abstract Random forests (RF) are an increasingly popular machine learning approach used to model biogeochemical processes in the Earth system. While RF models are robust to many assumptions that complicate deterministic models, there are several important parameterization decisions for appropriate use and optimal model fit. We explored the role that parameter decisions, including training/testing data splitting strategies, variable selection, and hyperparameters play on RF goodness‐of‐fit by constructing models using 1296 unique parameter combinations to predict concentrations of nitrate, a key nutrient for biogeochemical cycling in aquatic ecosystems. Models were built on long‐term, publicly available water quality and meteorology time series collected by the National Estuarine Research Reserve monitoring network for two contrasting ecosystems representing freshwater and brackish estuaries. We found that accounting for temporal dependence when splitting data into training and testing subsets was key for avoiding over‐estimation of model predictive power. In addition, variable selection, the ratio of training to testing data, and to a lesser degree, variables per split and number of trees, were significant parameters for optimizing RF goodness‐of‐fit. We also explored how model parameter decisions influenced interpretation of the relative importance of predictors to the model, and model predictor‐dependent variable relationships, with results suggesting that both data structure and model parameterization influence these factors. Because much of the current RF literature is written for the computational and statistical science communities, the primary goal of this study is to provide guidelines for aquatic scientists new to machine learning to apply RF techniques appropriately to aquatic biogeochemical datasets.
54 ENVIRONMENTAL SCIENCES↗
Estimating carrying capacity for juvenile salmon using quantile random forest models
Abstract Establishing robust methods and metrics to evaluate habitat quality is critical for the recovery of endangered Pacific salmonids ( Oncorhynchus spp.). A variety of modeling approaches are used for status and trend monitoring of anadromous species throughout the Pacific Northwest, USA, but current methods may fail to capture the complex relationship between fish and habitat and are often limited in predictive power beyond specific watersheds. Further, the focus on species distribution and abundance is not easily manipulated to predict carrying capacity and traditional stock‐recruitment analyses are reliant on long‐term data which are not always available. In this study, we developed a quantile random forest model to provide estimates of habitat carrying capacity for Chinook salmon ( O. tshawytscha ) parr during the summer months, at both the site and watershed scale. Quantile random forest models allow for the consideration of noisy data, correlated variables, and non‐linear relationships: common features in fish–habitat datasets. We leveraged Columbia Habitat Monitoring Program data to select habitat co‐variates and predict capacity at those sites. We also identified a set of globally available attributes to extrapolate capacity estimate predictions throughout wadeable streams within the Columbia River basin. Total capacity estimates for watersheds closely matched estimates from alternative fish productivity models. Carrying capacity estimates based on quantile random forest models, like those presented here, provide managers a framework to guide the identification, prioritization, and development of habitat rehabilitation actions to recover salmon populations.
See, Kevin E.↗
Analysis of Random Forest Modeling Strategies for Multi-Step Wind Speed Forecasting
Although the random forest (RF) model is a powerful machine learning tool that has been utilized in many wind speed/power forecasting studies, there has been no consensus on optimal RF modeling strategies. This study investigates three basic questions which aim to assist in the discernment and quantification of the effects of individual model properties, namely: (1) using a standalone RF model versus using RF as a correction mechanism for the persistence approach, (2) utilizing a recursive versus direct multi-step forecasting strategy, and (3) training data availability on model forecasting accuracy from one to six hours ahead. These questions are investigated utilizing data from the FINO1 offshore platform and Atmospheric Radiation Measurement (ARM) Southern Great Plains (SGP) C1 site, and testing results are compared to the persistence method. At FINO1, due to the presence of multiple wind farms and high inter-annual variability, RF is more effective as an error-correction mechanism for the persistence approach. The direct forecasting strategy is seen to slightly outperform the recursive strategy, specifically for forecasts three or more steps ahead. Finally, increased data availability (up to ~8 equivalent years of hourly training data) appears to continually improve forecasting accuracy, although changing environmental flow patterns have the potential to negate such improvement. We hope that the findings of this study will assist future researchers and industry professionals to construct accurate, reliable RF models for wind speed forecasting.
54 ENVIRONMENTAL SCIENCES↗
Using Random Forest Models to Predict Organizational Violence
We present a methodology to access the proclivity of an organization to commit violence against nongovernment personnel. We fitted a Random Forest model using the Minority at Risk Organizational Behavior (MAROS) dataset. The MAROS data is longitudinal; so, individual observations are not independent. We propose a modification to the standard Random Forest methodology to account for the violation of the independence assumption. We present the results of the model fit, an example of predicting violence for an organization; and finally, we present a summary of the forest in a "meta-tree,"
Levine, Burton↗
Random Forests as a Viable Method to Select and Discover High-redshift Quasars
We present a method of selecting quasars up to redshift ≈6 with random forests, a supervised machine-learning method, applied to Pan-STARRS1 and WISE data. We find that, thanks to the increasing set of known quasars, we can assemble a training set that enables supervised machine-learning algorithms to become a competitive alternative to other methods up to this redshift. We present a candidate set for the redshift range 4.8–6.3, which includes the region around z = 5.5 where selecting quasars is difficult due to their photometric similarity to red and brown dwarfs. We demonstrate that, under our survey restrictions, we can reach a high completeness (66% ± 7% below redshift 5.6/83{sub -9}{sup +6}% above redshift 5.6) while maintaining a high selection efficiency (78{sub -8}{sup +10}%/94{sub -8}{sup +5}%). Our selection efficiency is estimated via a novel method based on the different distributions of quasars and contaminants on the sky. The final catalog of 515 candidates includes 225 known quasars. We predict the candidate catalog to contain additional 148{sub -33}{sup +41} new quasars below redshift 5.6 and 45{sub -8}{sup +5} above, and we make the catalog publicly available. Spectroscopic follow-up observations of 37 candidates led us to discover 20 new high redshift quasars (18 at 4.6 ≤ z ≤ 5.5, 2 z ~ 5.7). These observations are consistent with our predictions on efficiency. We argue that random forests can lead to higher completeness because our candidate set contains a number of objects that would be rejected by common color cuts, including one of the newly discovered redshift 5.7 quasars.
79 ASTRONOMY AND ASTROPHYSICS↗
PlasmidHostFinder: Prediction of Plasmid Hosts Using Random Forest
Plasmids play a major role facilitating the spread of antimicrobial resistance between bacteria. Understanding the host range and dissemination trajectories of plasmids is critical for surveillance and prevention of antimicrobial resistance. Identification of plasmid host ranges could be improved using automated pattern detection methods compared to homology-based methods due to the diversity and genetic plasticity of plasmids. In this study, we developed a method for predicting the host range of plasmids using machine learning—specifically, random forests. We trained the models with 8,519 plasmids from 359 different bacterial species per taxonomic level; the models achieved Matthews correlation coefficients of 0.662 and 0.867 at the species and order levels, respectively. Our results suggest that despite the diverse nature and genetic plasticity of plasmids, our random forest model can accurately distinguish between plasmid hosts. This tool is available online through the Center for Genomic Epidemiology (https://cge.cbs.dtu.dk/services/PlasmidHostFinder/).
59 BASIC BIOLOGICAL SCIENCES↗
Incorporating space and time into random forest models for analyzing geospatial patterns of drug-related crime incidents in a major U.S. metropolitan area
The opioid crisis has hit American cities hard, and research on spatial and temporal patterns of drug-related activities including detecting and predicting clusters of crime incidents involving particular types of drugs is useful for distinguishing hot zones where drugs are present that in turn can further provide a basis for assessing and providing related treatment services. In this study, we investigated spatiotemporal patterns of more than 52,000 reported incidents of drug-related crime at block group granularity in Chicago, IL between 2016 and 2019. We applied a space-time analysis framework and machine learning approaches to build a model using training data that identified whether certain locations and built environment and sociodemographic factors were correlated with drug-related crime incident patterns, and establish the top contributing factors that underlaid the trends. Space and time, together with multiple driving factors, were incorporated into a random forest model to analyze these changing patterns. We accommodated both spatial and temporal autocorrelation in the model learning process to assist with capturing the changes over time and tested the capabilities of the space-time random forest model by predicting drug-related activity hot zones. Overall, we focused particularly on crime incidents that involved heroin and synthetic drugs as these have been key drug types that have highly impacted cities during the opioid crisis in the U.S.
97 MATHEMATICS AND COMPUTING↗
Enhanced Boundary Layer Height Detection Using Ceilometer, Surface Meteorology, and Radiation Products With a Random Forest Ensemble Method
This study develops and evaluates a Random Forest (RF) model for estimating planetary boundary layer height (PBLH) using 9 years of data from the Atmospheric Radiation Measurement Southern Great Plains (ARM SGP) user facility, with potential application in the NOAA Surface Radiation (SURFRAD) Network. The model integrates ceilometer, surface meteorology, and radiation measurements, and is trained using thermodynamic PBLH estimates derived from radiosondes. This approach aims to bridge gaps between aerosol-based and thermodynamic-based PBLH estimates. The RF model outperformed traditional methods during daytime and better captured transition periods, demonstrating improved accuracy and robustness. At ARM SGP, it showed a substantial reduction in both bias and RMSE, with a bias near zero (−4.9 m) compared with traditional Haar Wavelet (HW) (70.9 m) and Vaisala BL-View software (124.1 m), and an RMSE of 303.2 m, lower than both BL-View (566.9 m) and HW (404.6 m). During daytime hours, RF consistently outperformed both alternatives, maintaining lower bias and RMSE across all periods. At a second evaluation site, RF achieved the lowest overall RMSE (323.7 m), similar to HW (326.4 m) and significantly better than BL-View (738.3 m). However, all models showed reduced accuracy under stable nighttime conditions, limiting the reliability of PBLH estimates. Key predictors for the model included the lifting condensation level height (LCLH), aerosol gradients, and month for seasonal variability. The study underscores the potential of integrating machine learning with multiple data sets such as surface energy and thermodynamic data to advance PBLH estimation.
boundary layer height↗
Feature Pathway Graphs using Random Forest Regressors
SAND2025-04671O Feature Pathway Graphs using Random Forest Regressors is a software tool that uses machine learning to determine pathways of influence between features in data sets. It can be used as a surrogate method for casual discovery. The output creates pathway graphs between features of interest. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.
Peterson, Matthew↗
A mathematical assessment of the isolation random forest method for anomaly detection in big data
We present the mathematical analysis of the Isolation Random Forest Method (IRF Method) for anomaly detection, proposed by Liu F.T., Ting K.M. and Zhou Z. H. in their seminal work as a heuristic method for anomaly detection in Big Data. We prove that the IRF space can be endowed with a probability induced by the Isolation Tree algorithm (iTree). In this setting, the convergence of the IRF method is proved, using the Law of Large Numbers. Here, a couple of counterexamples are presented to show that the method is inconclusive and no certificate of quality can be given, when using it as a means to detect anomalies. Hence, an alternative version of the method is proposed whose mathematical foundation is fully justified. Furthermore, a criterion for choosing the number of sampled trees needed to guarantee confidence intervals of the numerical results is presented. Finally, numerical experiments are presented to compare the performance of the classic method with the proposed one.
97 MATHEMATICS AND COMPUTING↗