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DOE OSTI2020

Arctic Tipping Points Triggering Global Change (LDRD Final Report)

The Arctic is warming and feedbacks in the coupled Earth system may be driving the Arctic to tipping events that could have critical downstream impacts for the rest of the globe. In this project we have focused on analyzing sea ice variability and loss in the coupled Earth system Summer sea ice loss is happening rapidly and although the loss may be smooth and reversible, it has significant consequences for other Arctic systems as well as geopolitical and economic implications. Accurate seasonal predictions of sea ice minimum extent and long-term estimates of timing for a seasonally ice-free Arctic depend on a better understanding of the factors influencing sea ice dynamics and variation in this strongly coupled system. Under this project we have investigated the most influential factors in accurate predictions of September Arctic sea ice extent using machine learning models trained separately on observational data and on simulation data from five E3SM historical ensembles. Monthly averaged data from June, July, and August for a selection of ice, ocean, and atmosphere variables were used to train a random forest regression model. Gini importance measures were computed for each input feature with the testing data. We found that sea ice volume is most important earlier in the season (June) and sea ice extent became a more important predictor closer to September. Results from this study provide insight into how feature importance changes with forecast length and illustrates differences between observational data and simulated Earth system data. We have additionally performed a global sensitivity analysis (GSA) using a fully coupled ultra- low resolution configuration E3SM. To our knowledge, this is the first global sensitivity analysis involving the fully-coupled E3SM Earth system model. We have found that parameter variations show significant impact on the Arctic climate state and atmospheric parameters related to cloud parameterizations are the most significant. We also find significant interactions between parameters from different components of E3SM. The results of this study provide invaluable insight into the relative importance of various parameters from the sea ice, atmosphere and ocean components of the E3SM (including cross-component parameter interactions) on various Arctic-focused quantities of interest (QOIs).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Construction of Women’s All-Around Speed Skating Event Performance Prediction Model and Competition Strategy Analysis Based on Machine Learning Algorithms

Introduction Accurately predicting the competitive performance of elite athletes is an essential prerequisite for formulating competitive strategies. Women’s all-around speed skating event consists of four individual subevents, and the competition system is complex and challenging to make accurate predictions on their performance. Objective The present study aims to explore the feasibility and effectiveness of machine learning algorithms for predicting the performance of women’s all-around speed skating event and provide effective training and competition strategies. Methods The data, consisting of 16 seasons of world-class women’s all-around speed skating competition results, used in the present study came from the International Skating Union (ISU). According to the competition rules, distinct features are filtered using lasso regression, and a 5,000 m race model and a medal model are built using a fivefold cross-validation method. Results The results showed that the support vector machine model was the most stable among the 5,000 m race and the medal models, with the highest AUC (0.86, 0.81, respectively). Furthermore, 3,000 m points are the main characteristic factors that decide whether an athlete can qualify for the final. The 11th lap of the 5,000 m, the second lap of the 500 m, and the fourth lap of the 1,500 m are the main characteristic factors that affect the athlete’s ability to win medals. Conclusion Compared with logistic regression, random forest, K-nearest neighbor, naive Bayes, neural network, support vector machine is a more viable algorithm to establish the performance prediction model of women’s all-around speed skating event; excellent performance in the 3,000 m event can facilitate athletes to advance to the final, and athletes with outstanding performance in the 500 m event are more likely competitive for medals.

Liu, Meng↗

DOE OSTI2020

Using machine learning to derive cloud condensation nuclei number concentrations from commonly available measurements

Cloud condensation nuclei (CCN) number concentrations are an important aspect of aerosol–cloud interactions and the subsequent climate effects; however, their measurements are very limited. We use a machine learning tool, random decision forests, to develop a random forest regression model (RFRM) to derive CCN at 0.4 % supersaturation ([CCN0.4]) from commonly available measurements. The RFRM is trained on the long-term simulations in a global size-resolved particle microphysics model. Using atmospheric state and composition variables as predictors, through associations of their variabilities, the RFRM is able to learn the underlying dependence of [CCN0.4] on these predictors, which are as follows: eight fractions of PM 2.5 (NH 4 , SO 4 , NO 3, secondary organic aerosol (SOA), black carbon (BC), primary organic carbon (POC), dust, and salt), seven gaseous species (NO x , NH 3 , O 3 , SO 2 , OH, isoprene, and monoterpene), and four meteorological variables (temperature (T), relative humidity (RH), precipitation, and solar radiation). The RFRM is highly robust: it has a median mean fractional bias (MFB) of 4.4 % with ≈96.33 % of the derived [CCN0.4] within a good agreement range of -60% 2.5 speciation (NH 4 , SO 4 , NO 3 , and organic carbon (OC)), NO x , O 3 , SO 2 , T, and RH, as well as [CCN0.4] are available. We modify, optimize, and retrain the developed RFRM to make predictions from 19 to 9 of these available predictors. This retrained RFRM (RFRM-ShortVars) shows a reduction in performance due to the unavailability and sparsity of measurements (predictors); it captures the [CCN0.4] variability and magnitude at SGP with ≈67.02 % of the derived values in the good agreement range. This work shows the potential of using the more commonly available measurements of PM 2.5 speciation to alleviate the sparsity of CCN number concentrations' measurements.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2022

Correcting for filter-based aerosol light absorption biases at the Atmospheric Radiation Measurement program's Southern Great Plains site using photoacoustic measurements and machine learning

Abstract. Measurement of light absorption of solar radiation by aerosols is vital for assessing direct aerosol radiative forcing, which affects local and global climate. Low-cost and easy-to-operate filter-based instruments, such as the Particle Soot Absorption Photometer (PSAP), that collect aerosols on a filter and measure light attenuation through the filter are widely used to infer aerosol light absorption. However, filter-based absorption measurements are subject to artifacts that are difficult to quantify. These artifacts are associated with the presence of the filter medium and the complex interactions between the filter fibers and accumulated aerosols. Various correction algorithms have been introduced to correct for the filter-based absorption coefficient measurements toward predicting the particle-phase absorption coefficient (Babs). However, the inability of these algorithms to incorporate into their formulations the complex matrix of influencing parameters such as particle asymmetry parameter, particle size, and particle penetration depth results in prediction of particle-phase absorption coefficients with relatively low accuracy. The analytical forms of corrections also suffer from a lack of universal applicability: different corrections are required for rural and urban sites across the world. In this study, we analyzed and compared 3 months of high-time-resolution ambient aerosol absorption data collected synchronously using a three-wavelength photoacoustic absorption spectrometer (PASS) and PSAP. Both instruments were operated on the same sampling inlet at the Department of Energy's Atmospheric Radiation Measurement program's Southern Great Plains (SGP) user facility in Oklahoma. We implemented the two most commonly used analytical correction algorithms, namely, Virkkula (2010) and the average of Virkkula (2010) and Ogren (2010)–Bond et al. (1999) as well as a random forest regression (RFR) machine learning algorithm to predict Babs values from the PSAP's filter-based measurements. The predicted Babs was compared against the reference Babs measured by the PASS. The RFR algorithm performed the best by yielding the lowest root mean square error of prediction. The algorithm was trained using input datasets from the PSAP (transmission and uncorrected absorption coefficient), a co-located nephelometer (scattering coefficients), and the Aerosol Chemical Speciation Monitor (mass concentration of non-refractory aerosol particles). A revised form of the Virkkula (2010) algorithm suitable for the SGP site has been proposed; however, its performance yields approximately 2-fold errors when compared to the RFR algorithm. To generalize the accuracy and applicability of our proposed RFR algorithm, we trained and tested it on a dataset of laboratory measurements of combustion aerosols. Input variables to the algorithm included the aerosol number size distribution from the Scanning Mobility Particle Sizer, absorption coefficients from the filter-based Tricolor Absorption Photometer, and scattering coefficients from a multiwavelength nephelometer. The RFR algorithm predicted Babs values within 5 % of the reference Babs measured by the multiwavelength PASS during the laboratory experiments. Thus, we show that machine learning approaches offer a promising path to correct for biases in long-term filter-based absorption datasets and accurately quantify their variability and trends needed for robust radiative forcing determination.

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2026

Quantifying mean, variability, and uncertainty in indoor radon exposure in Pennsylvania using random forest and quantile regression forest models

Radon is a naturally occurring radioactive gas that poses a serious health risk as the primary cause of lung cancer in non-smokers. Despite the well-known adverse association with health outcomes, current radon exposure assessments are limited to county-level or average-level estimates, which fail to capture regional variability. This study uses Machine Learning models, including Random Forest (RF) and Quantile Regression Forest (QRF), to estimate the indoor radon concentrations at the ZCTA (Zip code tabulation area)-level and characterize uncertainties in model estimates. Incorporating geological, meteorological, and building-specific data, the models aim to improve radon risk assessment by capturing mean exposure, variability, and extreme concentration levels. Processed radon test data (n = 718,111) were analyzed using average, variability, and quantile prediction methods. Models that estimate the average radon exposure at the ZCTA-level can yield promising model-fit results, but they do not capture the underlying variability of indoor radon exposure within a ZCTA. We utilize volatility analyses to identify characteristics indicative of high variability of indoor radon exposure. We also show that a QRF model can be used to estimate upper quantiles of residential radon exposure, thereby uncovering localized areas of elevated exposure that were not apparent in mean estimates. The results highlighted the need for a deep characterization of exposure risk and show that regions with moderate average exposure levels could still harbor extreme outliers with implications for evaluating health risks. Utilizing multiple radon exposure models allows for a deeper characterization of radon risk within a geographic area and can better identify high-risk areas. The results from this study provide a foundation for developing mitigation strategies and examining associations between radon exposure and health outcomes at fine scales. Future research should extend the geographic scope and incorporate additional environmental risk factors to establish a comprehensive framework for risk assessment.

Lee, Heechan [ORNL]↗

DOE OSTI2020

Quantifying Leaf Chlorophyll Concentration of Sorghum from Hyperspectral Data Using Derivative Calculus and Machine Learning

Leaf chlorophyll concentration (LCC) is an important indicator of plant health, vigor, physiological status, productivity, and nutrient deficiencies. Hyperspectral spectroscopy at leaf level has been widely used to estimate LCC accurately and non-destructively. This study utilized leaf-level hyperspectral data with derivative calculus and machine learning to estimate LCC of sorghum. We calculated fractional derivative (FD) orders starting from 0.2 to 2.0 with 0.2 order increments. Additionally, 43 common vegetation indices (VIs) were calculated from leaf spectral reflectance factor to make comparisons with reflectance-based data. Within the modeling pipeline, three feature selection methods were assessed: Pearson’s correlation coefficient (PCC), partial least squares based variable importance in the projection (VIP), and random forest-based mean decrease impurity (MDI). Finally, we used partial least squares regression (PLSR), random forest regression (RFR), support vector regression (SVR), and extreme learning regression (ELR) to estimate the LCC of sorghum. Results showed that: (1) increasing derivative order can show improved model performance until certain order for reflectance-based analysis; however, it is inconclusive to state that a particular order is optimal for estimating LCC of sorghum; (2) VI-based modeling outperformed derivative augmented reflectance factor-based modeling; (3) mean decrease impurity was found effective in selecting sensitive features from large feature space (reflectance-based analysis), whereas simple Pearson’s correlation coefficient worked better with smaller feature space (VI-based analysis); and (4) SVR outperformed all other models within reflectance-based analysis; alternatively, ELR with VIs from original reflectance yielded slightly better results compared to all other models.

47 OTHER INSTRUMENTATION↗

DOE OSTI2024

Evaluating county-level lung cancer incidence from environmental radiation exposure, PM 2.5 , and other exposures with regression and machine learning models

Characterizing the interplay between exposures shaping the human exposome is vital for uncovering the etiology of complex diseases. For example, cancer risk is modified by a range of multifactorial external environmental exposures. Environmental, socioeconomic, and lifestyle factors all shape lung cancer risk. However, epidemiological studies of radon aimed at identifying populations at high risk for lung cancer often fail to consider multiple exposures simultaneously. For example, moderating factors, such as PM 2.5 , may affect the transport of radon progeny to lung tissue. This ecological analysis leveraged a population-level dataset from the National Cancer Institute’s Surveillance, Epidemiology, and End-Results data (2013–17) to simultaneously investigate the effect of multiple sources of low-dose radiation (gross γ activity and indoor radon) and PM 2.5 on lung cancer incidence rates in the USA. County-level factors (environmental, sociodemographic, lifestyle) were controlled for, and Poisson regression and random forest models were used to assess the association between radon exposure and lung and bronchus cancer incidence rates. Tree-based machine learning (ML) method perform better than traditional regression: Poisson regression: 6.29/7.13 (mean absolute percentage error, MAPE), 12.70/12.77 (root mean square error, RMSE); Poisson random forest regression: 1.22/1.16 (MAPE), 8.01/8.15 (RMSE). The effect of PM 2.5 increased with the concentration of environmental radon, thereby confirming findings from previous studies that investigated the possible synergistic effect of radon and PM 2.5 on health outcomes. In summary, the results demonstrated (1) a need to consider multiple environmental exposures when assessing radon exposure’s association with lung cancer risk, thereby highlighting (1) the importance of an exposomics framework and (2) that employing ML models may capture the complex interplay between environmental exposures and health, as in the case of indoor radon exposure and lung cancer incidence.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗

DOE OSTI2023

Machine learning and deep learning for mineralogy interpretation and CO 2 saturation estimation in geological carbon Storage: A case study in the Illinois Basin

Carbon capture and storage (CCS) is a promising approach to simultaneously maintaining energy security and reducing carbon dioxide (CO 2 ) emissions under the current energy portfolio that is dominated by fossil fuel energy. Pre-injection formation characterization and post-injection CO 2 monitoring are two critical tasks to guarantee storage efficiency in CCS. The CCS projects in the Illinois Basin, the first large-scale CO 2 injection into saline aquifers in the United States, employed conventional and the latest pulsed neutron logging (PNL) tools for mineralogy interpretation and CO 2 saturation estimation, which provide valuable references for future CCS projects. Because of the inherent fuzziness of petrophysical measurements and complex subsurface heterogeneity, interpreting well-logging data is time-consuming, and its accuracy can be user-biased. In recent years, data-driven methods have been widely used to capture the non-linear patterns between input features and interpretation results. This work applied and evaluated four commonly used machine learning (ML) models, including ridge regression (RR), random forest (RF), gradient boosting regression (GBR), support vector regression (SVR), and one deep learning (DL) model, the artificial neural network (ANN). We optimized the hyperparameters of the four ML models and the DL model using the simulated annealing algorithm and the grid search strategy, respectively. The input features of the mineralogy interpretation models were eleven conventional well-logging parameters, and the label data (i.e., ground truth) were the porosity and volumetric fractions of six minerals, including quartz, feldspar, dolomite, calcite, clay, and iron minerals. The results demonstrated that the GBR and RF models were superior in predicting volumetric fractions of minerals and porosity; label data with low coefficient of variation (CV) values tended to yield better performance. For CO 2 saturation estimation, the RF was the best-performing model, followed by SVR, ANN, GBR, and RR. Furthermore, we conducted feature importance ranking using the permutation importance algorithm and found that the formation sigma and well pressure were the most important features in this study. In conclusion, the study of CCS projects in the Illinois Basin bridges the gap between the limited knowledge and understanding of geological carbon storage and the increasing demand for reliable, cost-effective, and sustainable energy solutions.

58 GEOSCIENCES↗

DOE OSTI2023

Machine learning assisted phase and size-controlled synthesis of iron oxide particles

Synthesis of iron oxides with specific phases and particle sizes is a crucial challenge in various fields, including materials science, energy storage, biomedical applications, environmental science, and earth science. However, despite significant advances in this area, much of the current palette of particle outcomes has been based on time-consuming trial-and-error exploration of synthesis conditions. The present study was designed to explore a very different approach to 1) predict the outcome of synthesis from specified reaction parameters based on using machine learning (ML) techniques, and 2) correlate sets of parameters to obtain products with desired outcomes by a newly designed recommendation algorithm. To achieve this, four ML algorithms were tested, namely random forest, logistic regression, support vector machine, and k-nearest neighbor. Among the models, random forest outperformed the others, attaining 96% and 81% accuracy when predicting the phase and size of iron oxide particles in the test dataset. Surprisingly, the permutation feature importance analysis revealed that volume, which may strongly relate to pressure, was one of the important features, along with precursor concentration, pH, temperature, and time, influencing the phase and size of iron oxide particles during synthesis. To verify the robustness of the random forest models, prediction and experimental results were compared based on 24 randomly generated methods in additive and non-additive systems not included in the datasets. The predictions of product phase and particle size from the models agreed well with the experimental results. Furthermore, a searching and ranking algorithm was developed to recommend potential synthesis parameters for obtaining iron oxide products with the desired phase and particle size from previous studies in the dataset. Furthermore, this study lays the foundation for a closed-loop approach in materials synthesis and preparation, beginning with suggesting potential reaction parameters from the dataset and predicting potential outcomes, followed by conducting experiments and analyses, and ultimately enriching the dataset.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2026

Uncertainty-Aware Machine Learning for Small-Angle X-ray Scattering Analysis in Autonomous Experimentation

Small-angle X-ray scattering (SAXS) is a powerful high-throughput characterization tool for probing nanoscale structure in native sample environments, providing real-time morphological information such as nanoparticle size and shape during synthesis. However, automated SAXS data analysis for extracting meaningful structural parameters is non-trivial and remains a bottleneck in closed-loop experimentation towards autonomous materials discovery, which demands fast, reliable, and uncertainty-aware data analysis. Here, we develop a machine-learning approach for automated SAXS analysis tailored to closed-loop nanoparticle synthesis. A Random Forest (RF) regression model is trained on 100,000 synthetic SAXS curves generated from polydisperse spherical nanoparticles with realistic background contributions. Using normalized one-dimensional SAXS intensity profiles as input, the RF model directly predicts nanoparticle radius, size polydispersity, and background parameters, while the ensemble standard deviation across trees provides built-in uncertainty quantification (UQ). On synthetic data, we show that combining fit-quality metrics (R 2 , MAE) with thresholds on prediction uncertainty reliably identifies accurate parameter estimates without access to ground truth. We then apply the trained model to 365 experimental SAXS profiles of citrate-reduced gold nanoparticles synthesized using an automated droplet-flow microreactor with in situ SAXS at a synchrotron beamline, classifying the results into high- and low-confidence subsets based on UQ metrics. Finally, we integrate RF-based SAXS analysis into a simulated closed-loop optimization campaign using Gaussian process Bayesian optimization to minimize nanoparticle polydispersity, benchmarking against conventional automated Levenberg–Marquardt fitting. The RF-guided campaign exhibits substantially faster convergence and lower relative opportunity cost (∼0.07 vs ∼0.3), demonstrating that uncertainty-aware machine-learning SAXS analysis significantly enhances the efficiency and robustness of autonomous nanomaterials synthesis workflows.

Bayesian optimization↗

DOE OSTI2022

Deep learning the properties of inorganic perovskites

We report the ability to accurately and quickly predict the stability of materials and their structural and electronic properties remains a grand challenge in materials science. Density functional theory is widely used as a means of predicting these material properties, but is known to be computationally expensive and scales as the cube of the number of electrons in the material’s unit cell. In this article, for a previously published dataset of inorganic perovskites, we show that a single neural network model using only the elemental properties of the compounds’ constituents can predict lattice constants to within 0.1 Å, heat of formation to within 0.2 eV, and band gaps to within 0.7 eV RMSE. We also compare the performance of the trained network to two widely used regression techniques, namely random forest and Kernel ridge regression, and find that the neural network’s predictions are more accurate for each of the properties. The simultaneous accurate prediction of multiple key properties of technologically relevant materials is promising for rational design and optimization in known and novel chemical spaces.

36 MATERIALS SCIENCE↗

DOE OSTI2020

Predicting the Activity and Selectivity of Bimetallic Metal Catalysts for Ethanol Reforming using Machine Learning

Machine learning is ideally suited for the pattern detection in large uniform datasets, but consistent experimental datasets on catalyst studies are often small. Here we demonstrate how a combination of machine learning and first-principles calculations can be used to extract knowledge from a relatively small set of experimental data. The approach is based on combining a complex machine-learning model trained on an extensive computational library of transition-state energies with simple linear regression models of experimental catalytic activities and selectivities from the literature. Using the combined model, we identify the key C–C bond scission reactions involved in ethanol reforming and perform a computational screening for ethanol reforming on monolayer bimetallic catalysts with architectures TM-Pt-Pt(111) and Pt-TM-Pt(111) (TM = 3d transition metals). The model also predicts four promising catalyst compositions for future experimental studies. In conclusion, the approach is not limited to ethanol reforming but is of general use for the interpretation of experimental observations as well as for the computational discovery of novel catalytic materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Decayheatml

This code is designed to predict and analyze the decay heat generated in molten salt reactors (MSRs) using a hybrid approach that combines machine learning and segmented polynomial fitting. The accurate prediction of decay heat is essential for reactor safety and the optimization of spent fuel storage. The code operates through several key components: 1) Data Architecture: It incorporates a modular data architecture that handles various MSR-specific operational parameters such as power density, humidity content, and air ingress. These parameters are sampled using Sobol sequences to ensure comprehensive coverage of operational uncertainties. 2) Machine Learning Framework: The code employs a diverse set of machine learning models, including polynomial regression, decision trees, random forests, gradient boosting, support vector regression, k-nearest neighbors, multi-layer perceptrons, and symbolic regression. These models are trained to predict decay heat over a wide temporal range, from immediate shutdown up to 10,000 years. 3) Region-Optimized Training: The temporal domain is divided into multiple regions, each modeled separately to capture distinct decay heat characteristics across different time scales. This approach significantly improves the accuracy and interpretability of predictions. 4) Segmented Polynomial Interpretation (SPI): The SPI method translates machine learning predictions into piecewise polynomial equations. These equations are physically interpretable and can be directly integrated into existing engineering workflows and safety analyses. 5) Front-End Interfaces: The code includes both a Jupyter notebook interface for research development and a Streamlit web application for operational deployment. These interfaces allow users to interactively explore decay heat predictions, adjust operational parameters, and visualize results in real-time. 6) Applications: The framework supports various applications, including safety system validation and spent fuel container optimization. It enables real-time evaluation of worst-case decay heat scenarios, informing the design of passive safety systems and optimizing container designs for long-term storage. Overall, this code provides a robust, accurate, and user-friendly tool for predicting decay heat in MSRs, enhancing reactor safety, and optimizing spent fuel management.

Retamales, Mauricio Eduardo Tano [Idaho National L↗

DOE OSTI2026

Random forest models accurately classify synthetic opioids using high-dimensionality mass spectrometry datasets

Detection of novel threat agents presents several challenges, a principle one being the development of untargeted methods to screen an increasing number of threat chemicals whose exact structures are unknown. With the use of Machine Learning (ML) tools, we can guide the development of analytical methods for broad-spectrum detection of unbounded threat chemical families in complex mixtures. Toward this goal, we used nominal mass and high-resolution mass spectrometry data for hundreds of synthetic opioids and non-opioid compounds. We tested two ML techniques, logistic regression and random forest, to develop models towards a practical, implementable method for opioid detection. We found that of these tested ML methods, random forest models resulted in the highest validation accuracy (95+%) for both nominal mass and high-resolution classification of opioids versus non-opioids, with low false positive and false negative rates. The RF models were then used to successfully predict the classification of 10 compounds—five opioids and five non-opioids not part of the training and validation analysis. This application of ML is a critical step towards the development of field-deployable nominal mass spectrometers with ML-driven analyses for classification of emergent threats.

Chemistry↗

DOE OSTI2025

Random forest models accurately classify synthetic opioids using high-dimensionality mass spectrometry datasets

Arasteh, Kourosh [Lawrence Livermore National Labo↗

DOE OSTI2022

Classification of bacterial plasmid and chromosome derived sequences using machine learning

Plasmids are important genetic elements that facilitate horizonal gene transfer between bacteria and contribute to the spread of virulence and antimicrobial resistance. Most bacterial genome sequences in the public archives exist in draft form with many contigs, making it difficult to determine if a contig is of chromosomal or plasmid origin. Using a training set of contigs comprising 10,584 chromosomes and 10,654 plasmids from the PATRIC database, we evaluated several machine learning models including random forest, logistic regression, XGBoost, and a neural network for their ability to classify chromosomal and plasmid sequences using nucleotide k-mers as features. Based on the methods tested, a neural network model that used nucleotide 6-mers as features that was trained on randomly selected chromosomal and plasmid subsequences 5kb in length achieved the best performance, outperforming existing out-of-the-box methods, with an average accuracy of 89.38% ± 2.16% over a 10-fold cross validation. The model accuracy can be improved to 92.08% by using a voting strategy when classifying holdout sequences. In both plasmids and chromosomes, subsequences encoding functions involved in horizontal gene transfer—including hypothetical proteins, transporters, phage, mobile elements, and CRISPR elements—were most likely to be misclassified by the model. This study provides a straightforward approach for identifying plasmid-encoding sequences in short read assemblies without the need for sequence alignment-based tools.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Comparison of linear regression, k-nearest neighbour and random forest methods in airborne laser-scanning-based prediction of growing stock

Abstract In this study, for five sites around the world, we look at the effects of different model types and variable selection approaches on forest yield modelling performances in an area-based approach (ABA). We compared ordinary least squares regression (OLS), k-nearest neighbours (kNN) and random forest (RF). Our objective was to test if there are systematic differences in accuracy between OLS, kNN and RF in ABA predictions of growing stock volume. The analyses are based on a 5-fold cross-validation at five study sites: an eucalyptus plantation, a temperate forest and three different boreal forests. Two completely independent validation datasets were also available for two of the boreal sites. For the kNN, we evaluated multiple measures of distance including Euclidean, Mahalanobis, most similar neighbour (MSN) and an RF-based distance metric. The variable selection approaches we examined included a heuristic approach (for OLS, kNN and RF), exhaustive search among all combinations (OLS only) and all variables together (RF only). Performances varied by model type and variable selection approaches among sites. OLS and RF had similar accuracies and were more efficient than any of the kNN variants. Variable selection did not affect RF performance. Heuristic and exhaustive variable selection performed similarly for OLS. kNN fared the poorest amongst model types, and kNN with RF distance was prone to overfitting when compared with a validation dataset. Additional caution is therefore required when building kNN models for volume prediction though ABA, being preferable instead to opt for models based on OLS with some variable selection, or RF with all variables together.

Cosenza, Diogo N.↗

DOE OSTI2021

Landsat 8 monitoring of multi-depth suspended sediment concentrations in Lake Erie’s Maumee River using machine learning

Satellite remote sensing has been widely used to map suspended sediment concentration (SSC) in waterbodies. However, due to the complexity of sediment-water interactions, it has been difficult to derive linear and non-linear regression equations to reliably predict SSC, especially when trying to estimate depth of integrated sediment. Herein, this study uses Landsat 8 OLI (Operational Land Imager) sensor to map SSC within the Maumee River in Ohio, USA, at multiple depth intervals (15, 61, 91, and 182 cm). Simple linear least squares regression (LLSR), and three common machine learning models: random forest (RF), support vector regression (SVR), and model averaged neural network (MANN) were used to estimate SSC at the depth intervals. All machine learning models significantly outperformed LLSR while RF performed the best. In both RF and MANN, R2 (coefficient of determination) increases with depth with a maximum R2 of 0.89 and 0.83, respectively, at a depth of 0–182 cm. The results show that machine learning models can implement nonlinear relationships that produce better predictions than traditional linear regression methods in estimating depth integrated SSC, especially when samples are limited.

47 OTHER INSTRUMENTATION↗