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At least 127 records · Page 7
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Application of Machine Learning Algorithms to Identify Problematic Nuclear Data

In this work we aim to show that Machine learning algorithms are promising tools for the identification of nuclear data that contribute to increased errors in transport simulations. We demonstrate this through an application of a machine learning algorithm (Random Forest) to the Whisper/MCNP6 criticality validation library to identify nuclear data that are associated with an increase of the bias (simulated - experimental $k_{eff}$) in the calculations. Specifically, the $k_{eff}$ sensitivity profiles (w.r.t. nuclear data) of 233 U solution benchmarks are used to predict the bias and Shapley Additive Explanations (SHAP) are used to explain how the sensitivities are related to the predicted bias. The SHAP values can be interpreted as sensitivity coefficients of the machine learning model to the $k_{eff}$ sensitivities which are used to make predictions of bias. Using the SHAP values we can identify specific subsets of nuclear data which have the highest probability of influencing bias. We demonstrate the utility of this method by showing how SHAP values were used to identify an inconsistency in the 19 F inelastic scattering nuclear data. The methodology presented here is not limited to transport problems and can be applied to other simulations if there are experimental measurements to compare against, simulations of those experimental measurements, and the ability to calculate sensitivities of the model output with respect to the data inputs.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Final report- UFL - RAPIDS2: A SciDAC Institute for Computer Science, Data, and Artificial Intelligence

The research initiatives supported by the U.S. Department of Energy (DOE) Grant DE-SC0022265 are fundamentally aimed at pioneering advanced machine learning (ML) techniques for scientific data compression within high-performance computing (HPC) environments. This comprehensive body of work addresses the critical challenge posed by the exponential growth of data generated by scientific simulations in domains such as fusion energy, climate modeling, and computational fluid dynamics (CFD). A core objective is to develop compression algorithms that achieve substantial data reduction—often by orders of magnitude—while rigorously ensuring the fidelity of both the primary data (PD) and scientifically crucial derived quantities of interest (QoI). The methodologies deployed under this grant integrate sophisticated deep learning architectures, prominently featuring autoencoders, advanced generative models like conditional diffusion, and hybrid learning techniques. Key innovations include the development of Guaranteed Autoencoders (GAE) and the Guaranteed Conditional Diffusion with Tensor Correction (GCDTC) framework, which provide explicit, instance-level error bounds on reconstructed data. Furthermore, specialized strategies such as nonlinear constraint satisfaction are employed to preserve the integrity of QoI, a vital requirement for the trustworthiness of downstream scientific analyses. This research also focuses on the design and implementation of scalable, GPU-accelerated software pipelines that seamlessly integrate into existing HPC workflows, ensuring both computational efficiency and practical applicability. The CAESAR framework, for example, unifies foundation and generative models to create an adaptive and efficient compression solution for spatio-temporal scientific data. Collectively, these efforts represent a significant advancement in mitigating the scientific data deluge, enabling more effective data management, accelerated scientific discovery, and optimized utilization of HPC resources.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Emerging anomaly detection techniques for electronic health records: A survey

Background Anomaly detection in electronic health records (EHRs) is a cornerstone of biomedical informatics, with direct implications for patient safety, clinical decision-making, and the prevention of healthcare fraud. Once guided primarily by simple rule-based methods, the field has advanced rapidly, driven by increased computing power, richer and more detailed health data, and the rise of machine learning and deep learning techniques. The objective of this paper is to provide a comprehensive overview of modern approaches to detecting anomalies in EHRs, outlining their strengths, limitations, and relevance to key healthcare challenges. We review traditional statistical methods alongside newer ML- and DL-based strategies and hybrid models, with particular attention to how these techniques support transparency and build clinical trust. Methods This paper presents a thorough and critical survey through systematic review (PRISMA-based) of the latest anomaly detection strategies in time-sequence data domains within electronic health record systems. Results We explore a broad spectrum of methodologies, including statistical models, supervised and unsupervised learning approaches, hybrid frameworks, and state-of-the-art ML-based techniques that collectively advance the precision and scalability of detecting anomalies in complex clinical datasets. In addition to mapping current capabilities, we address the enduring challenges that hinder widespread implementation and provide a forward-looking perspective on the future of anomaly detection in the data-rich landscape of modern healthcare. Summary The advancement in AI-based approaches is reported along with the basic principles of the individual approaches and their applicability. The increased availability of high-quality data, advancements in DL approaches, and enhanced computation power are leading to more frequent adaptation of DL-based approaches. Emerging DL-based approaches that have been adapted in other domains or recently applied in the EHR domain are also discussed in detail. Although DL-based approaches can improve model predictions by incorporating comorbidities, their application is limited in low-frequency data domains (e.g., when the total available data remains in the single digits). Therefore, the user must carefully consider the application based on data availability.

Anomaly detection↗
NASA NTRS1987

Application of Artificial Intelligence technology to the analysis and synthesis of reliable software systems

The development of a methodology for the production of highly reliable software is one of the greatest challenges facing the computer industry. Meeting this challenge will undoubtably involve the integration of many technologies. This paper describes the use of Artificial Intelligence technologies in the automated analysis of the formal algebraic specifications of abstract data types. These technologies include symbolic execution of specifications using techniques of automated deduction and machine learning through the use of examples. On-going research into the role of knowledge representation and problem solving in the process of developing software is also discussed.

Wild, Christian↗
NASA NTRS2023

EVA Task and 3D Pose Recognition from Video

Extravehicular Activity (EVA) has been known to involve potential risks of biomechanical stresses and injuries to crewmembers. Gathering of EVA motion patterns is necessary for risk analysis and mitigation. However, many existing techniques, such as motion capture systems, are not only cost-prohibitive but are impractical for retrospective analysis of past missions. In this work, a software tool was developed, which can estimate the 3D poses of a spacesuit from photographs or videos, without using special sensors or equipment. The tool is based on the state-of-the-art artificial intelligence and machine learning (AI/ML) system, which was trained by studying and capturing motion patterns of past and current spacesuit test data. The AI/ML tool was further enhanced using synthetically generated data, in which the suit postures, backgrounds, camera angles and illumination conditions were parametrically adjusted and rendered for training. The tool, incorporated the methodologies of Convolutional Neural Network (CNN), was trained, and tested in the cloud computing environment. The trained model was then applied on new imagery and video to extract estimated joint positions and suit outlines. The joint positions were further processed to capture activity (“digging”), pose labels (“bending”), and other useful downstream information. The model performance on new imagery and video was successfully assessed for accuracy and reliability. This AI/ML based posture recognition tool thus allows for the quantification of injury risk and task performance characterization for both current and past missions and training, which can immensely help to improve EVA task and suit design.

Kyung Han Kim↗
DOE OSTI2025

Dynamics and lipid membrane coupling of the RAS-RAF complex revealed via multiscale simulations

To gain molecular and mechanistic insights into initiation of the RAS-RAF signaling cascade, we developed and used a combination of multiscale simulation and experimental approaches. The influence and impact of the membrane on RAS and RAF proteins is a factor we are just beginning to understand and appreciate in more detail. Molecular simulation is an ideal methodology to further study this complicated relationship between the membrane and associated proteins. Our previous work using Multiscale Machine-learned Modeling Infrastructure investigated different lipid compositions solely around the KRAS4b protein and the interplay between protein behavior and these membrane environments. Multiscale Machine-learned Modeling Infrastructure uses machine learning to couple adjacent simulation scales and has been efficiently scaled across some of the world’s largest high-performance computers. Recently, we have expanded this multiresolution framework to include the all-atom simulation scale and to incorporate the RAF RBDCRD domains. Here, we present the overall analysis results from this new simulation campaign comprising a mixture of RAS and RAF RBDCRD proteins. Approximately 35,000 coarse-grained and 10,000 all-atom molecular dynamics simulations were completed, sampled from a variety of protein/lipid composition configurations that were generated from a micron-scale continuum simulation containing hundreds of copies of the proteins. Our studies suggest that orientations of the RAS-RBDCRD complex on the membrane occupy distinct configurational states, and the spatial patterns of lipid arrangements around these different protein states are unique to each state. The extent and size of lipid “fingerprints” imposed on the membrane by the RAS-RBDCRD protein complex are significantly larger than observed for just the RAS protein on its own. These protein complexes strongly associate, but we do not observe statistically significant preferred protein-protein orientations. These observations indicate that spatial colocalization of RAS-RBDCRD proteins in the same vicinity may be assisted by specific membrane environments, acting to increase the probability of signaling complex formation.

Carpenter, Timothy S. [Lawrence Livermore National↗
DOE OSTI2022

Automated System-wide Event Detection and Classification Using Machine Learning on Synchrophasor Data

As the number of phasor measurement units (PMUs) deployed in a power system increases, and their data volume streamed to the control canter intensifies, operators are facing challenges related to the analysis of such data, which need to be observed and responded to as the measurements are displayed in the Control Room. Humans are generally unable to process such large amount of data efficiently and rapidly. There is an apparent need for automated ways to analyze the data, extract actionable information about occurrence of specific events, and characterize the events quickly and cost effectively. This paper discusses the use of machine learning (ML) to facilitate such tasks by providing automated, highly computationally efficient, and cost-effective ways of extracting actionable information from synchrophasor big data in real-time. We developed Big Data Smart (BDSmart) ML-based prototype tool for the Control Room use that automatically analyses data properties from synchrophasor system measurements taken across the three grid Interconnections in the USA (Western, Eastern and ERCOT). The data collected from several hundreds of PMUs located across the Interconnections over a period of two years have been made available for our extensive study. As a result, we were able to identify a number of big data properties that influence how ML methodology is applied to select, develop, train and test the data models that can eventually be used for the tool implementation. The resulting set of candidate algorithms spans unsupervised, supervised, semi-supervised and transfer-learning approaches. Many ML techniques, such as decision trees, multinomial logistic regression, feed-forward neural networks, K-nearest neighbor, multiclass support vector machine, and single and multi-channel convolutional neural networks, are implemented, and their performance is examined. We offer the results from testing the data models. The novelty of our study is in the approaches for bad data detection and mitigation, selection of a simplified feature for event detection, and data label improvements. As a result, we came up with a list of recommendations for the utilities on how to improve the PMU recording practices to cater to the future ML applications aimed at automating the analysis of synchrophasor data.

Synchrophasors, Machine Learning, System-wide Even↗
DOE OSTI2025

Risk-informed Graded Approach for Reliability and Performance Assessment of Machine Learning and Artificial Intelligence for Advanced Condition Monitoring Techniques

With the shift away from time-based maintenance and toward condition-based maintenance, and to reduce overall maintenance costs, there has been an upsurge in the usage and development of advanced condition monitoring (ACM) techniques for real-time monitoring of nuclear power plant (NPP) components. ACM is particularly useful in the development of digital twins, which are designed to predict the failure or degradation of plant components. Successful implementation of ACM requires an assessment to inform the development of a risk-informed approach to evaluate the use of ACM to meet Nuclear Regulatory Committee (NRC) regulations for in-service testing (IST) programs. This includes the monitoring and diagnostics of reactor components and systems in current, new, and advanced reactors. A key component in ACM is the usage of machine learning (ML) and artificial intelligence (AI) algorithms that can employ real-time data from instrumentation and sensors to detect and predict reactor component degradations. Such predictive capabilities enable early detection of component degradation so as to help plant personnel plan and execute necessary maintenance. For successful implementation of ML/AI in ACM such that regulatory requirements are met, a risk-informed graded approach is needed to assess the reliability and performance of ML/AI for ACM. The American Society for Mechanical Engineers (ASME) developed their Operations and Maintenance (O&M) Code to provide guidance on safe, reliable O&M of NPPs. The IST section of the O&M Code specifically establishes requirements for IST and examination to gauge operational readiness of components in water-cooled NPPs. This paper presents a state-of-the-art review of how reliability and risk assessment can be integrated with ACM to assess component performance by non-nuclear industries. This is followed by different methodologies and approaches for conducting performance and reliability assessments so as to meet IST requirements for NPP components.

97 - MATHEMATICS AND COMPUTING↗
NASA NTRSDate not supplied

PM 2.5 Concentrations over Major Metropolitan Regions Inferred from Airborne High Spectral Resolution Lidar Measurements Using Machine Learning Regression

We use measurements of near-surface aerosol backscatter, extinction, and depolarization acquired by four NASA Langley Research Center airborne High Spectral Resolution Lidars (HSRLs) to develop a machine learning regression methodology to infer PM2.5 concentrations at the surface and aloft. These airborne HSRL measurements were acquired over major metropolitan regions in the United States and Asia during more than 170 flights since 2010. Hourly surface PM2.5 measurements from the EPA air quality system and similar networks in other countries acquired within 10 km and 15 minutes of these near-surface HSRL measurements are used to train models that compute PM2.5 concentrations from the HSRL measurements. We examine several regression methods and find that exponential Gaussian Process algorithms consistently give the best performance in terms of the lowest root-mean-square (RMS) errors and the highest correlations. Model performance varies significantly depending on various combinations of HSRL aerosol measurements (e.g., aerosol backscatter, extinction, depolarization, backscatter color ratios, lidar ratios, aerosol optical thickness) and retrievals (e.g., mixed layer height, aerosol type) used in the regressions. Models that use near-surface measurements of aerosol backscatter and aerosol intensive properties such as depolarization, backscatter color ratio, and lidar ratio typically give the best performance with RMS errors around 4 mg/m3 and correlation coefficients above 0.9. HSRL measurements were often acquired when the aircraft flew systematic “raster-scan” patterns for several hours over these cities. These flight patterns enabled measurements of the spatial, temporal, and vertical variabilities in the distributions of aerosol backscatter and aerosol intensive properties and allowed us to derive the corresponding variabilities in PM2.5 concentrations. We present examples of such variabilities over urban areas in the United States as well as Asia. We describe also how the distribution of surface PM2.5 varies with aerosol type and use these retrievals to examine model simulations of surface PM2.5 in these metropolitan regions. We also discuss how this methodology may be applied to measurements from satellite lidars such as CALIOP on CALIPSO and ATLID on EarthCARE.

lidar↗
NASA NTRS2003

Intelligent Machines in the 21st Century: Automating the Processes of Inference and Inquiry

The last century saw the application of Boolean algebra toward the construction of computing machines, which work by applying logical transformations to information contained in their memory. The development of information theory and the generalization of Boolean algebra to Bayesian inference have enabled these computing machines. in the last quarter of the twentieth century, to be endowed with the ability to learn by making inferences from data. This revolution is just beginning as new computational techniques continue to make difficult problems more accessible. However, modern intelligent machines work by inferring knowledge using only their pre-programmed prior knowledge and the data provided. They lack the ability to ask questions, or request data that would aid their inferences. Recent advances in understanding the foundations of probability theory have revealed implications for areas other than logic. Of relevance to intelligent machines, we identified the algebra of questions as the free distributive algebra, which now allows us to work with questions in a way analogous to that which Boolean algebra enables us to work with logical statements. In this paper we describe this logic of inference and inquiry using the mathematics of partially ordered sets and the scaffolding of lattice theory, discuss the far-reaching implications of the methodology, and demonstrate its application with current examples in machine learning. Automation of both inference and inquiry promises to allow robots to perform science in the far reaches of our solar system and in other star systems by enabling them to not only make inferences from data, but also decide which question to ask, experiment to perform, or measurement to take given what they have learned and what they are designed to understand.

Knuth, Kevin H.↗
DOE OSTI2024

Situational awareness-enhancing community-level load mapping with opportunistic machine learning

Motivated by present and forthcoming challenges in the adoption and integration of distributed renewable energy, we develop a machine learning (ML) approach that builds short-fuse mappings connecting the occasionally-unobservable true load in one target community with information-rich signals collected from relatively more instrumented reference communities. Our setting is inspired by and tailored to target communities with significant unobservable behind-the-meter solar generation, where true load (a relatively well-behaved quantity of interest to grid operators) is hard to discern during daytime due to insufficient instrumentation and/or privacy reasons, but that can be related to reference communities with low unobservable distributed variable generation or with sufficient instrumentation. The developed mapping, herein realized with Support Vector Machine regression, is built using nighttime data from all communities, when their distributed generation is low or zero. Our ML algorithm opportunistically learns to correlate signals of interest and then is operationally used the next day to shed light into target community load evolution. The mapping is subsequently rebuilt, rolling its short-fuse scope perpetually forward in time. Here, we demonstrate the efficacy of our approach on nine synthetically generated topologies and associated timeseries stemming from real-world data, on which we observe cumulative error performance that yields lower than 10% and 15% daily-averaged mean absolute percentage errors in target community load estimation on more than about 75% and 90% of days, respectively, in multiple yearly evaluations that shed light on long-term performance also under seasonal and one-off effects. The proposed ML-powered methodology can offer grid operators much-improved visibility into a previously obscure space and can also serve as an additional source of information in broader, multi-modal solar disaggregation solutions.

14 SOLAR ENERGY↗
DOE OSTI2024

Addressing bias in bagging and boosting regression models

As artificial intelligence (AI) becomes widespread, there is increasing attention on investigating bias in machine learning (ML) models. Previous research concentrated on classification problems, with little emphasis on regression models. This paper presents an easy-to-apply and effective methodology for mitigating bias in bagging and boosting regression models, that is also applicable to any model trained through minimizing a differentiable loss function. Our methodology measures bias rigorously and extends the ML model's loss function with a regularization term to penalize high correlations between model errors and protected attributes. We applied our approach to three popular tree-based ensemble models: a random forest model (RF), a gradient-boosted model (GBT), and an extreme gradient boosting model (XGBoost). We implemented our methodology on a case study for predicting road-level traffic volume, where RF, GBT, and XGBoost models were shown to have high accuracy. Despite high accuracy, the ML models were shown to perform poorly on roads in minority-populated areas. Our bias mitigation approach reduced minority-related bias by over 50%.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2022

Machine learning and shallow groundwater chemistry to identify geothermal prospects in the Great Basin, USA

This study discovers various geothermal prospects in the Great Basin, USA based on shallow groundwater chemical (geochemical) data. The geochemical data are expected to include hidden (latent) information that is a proxy for geothermal prospectivity. We processed the sparse geochemical data in the Great Basin at 14,341 locations including 18 attributes. Next, a non-negative matrix factorization with customized k-means clustering is applied to the geochemical data matrix that automatically finds three hidden geothermal signatures representing modestly, moderately, and highly confident geothermal prospects. The algorithm also evaluated the probability of occurrence of these types of resources through the studied region. There is a consistency between regional geothermal prospectivity as estimated by our ML methodology and the traditional play fairway analysis conducted over a portion of the study area. We also identify the dominant data attributes associated with each signature. Finally, our ML analyses allow us to reconstruct attributes from sparse into continuous over the study domain. The predicted continuous attributes can be used for future detailed geothermal explorations in the Great Basin.

15 GEOTHERMAL ENERGY↗
DOE OSTI2023

Machine Learning for Geothermal Resource Exploration in the Tularosa Basin, New Mexico

Geothermal energy is considered an essential renewable resource to generate flexible electricity. Geothermal resource assessments conducted by the U.S. Geological Survey showed that the southwestern basins in the U.S. have a significant geothermal potential for meeting domestic electricity demand. Within these southwestern basins, play fairway analysis (PFA), funded by the U.S. Department of Energy’s (DOE) Geothermal Technologies Office, identified that the Tularosa Basin in New Mexico has significant geothermal potential. This short communication paper presents a machine learning (ML) methodology for curating and analyzing the PFA data from the DOE’s geothermal data repository. The proposed approach to identify potential geothermal sites in the Tularosa Basin is based on an unsupervised ML method called non-negative matrix factorization with custom k-means clustering. This methodology is available in our open-source ML framework, GeoThermalCloud (GTC). Using this GTC framework, we discover prospective geothermal locations and find key parameters defining these prospects. Our ML analysis found that these prospects are consistent with the existing Tularosa Basin’s PFA studies. This instills confidence in our GTC framework to accelerate geothermal exploration and resource development, which is generally time-consuming.

15 GEOTHERMAL ENERGY↗
DOE OSTI2026

Multiscale modeling of packed-bed microwave reactors and estimation of intrinsic materials' permittivity

Modeling of packed-bed microwave reactors relies on an accurate representation of particle size, shape, and distribution within the bed, as well as the particles' dielectric properties. The measured permittivity of microwave susceptors (powders or structured materials) depends on the geometric features of the particles and the porosity of the bed, as well as the specific form factor of a structured material. These are effective properties and cannot be used to analyze other reactor configurations unless the geometric effects are removed. Therefore, we introduce a methodology for extracting the intrinsic particle permittivity from experimentally measured effective permittivity by combining cavity-based measurements with multiscale simulations and machine learning. Further, we develop the first multiscale model of packed-bed microwave reactors that incorporate particle effects (geometric features, random packing, and particle contact). This approach bridges macroscopic observables with mesoscopic physics, enabling analysis of local hotspots, arcing, and contact effects that control reactor performance. Using polymer-based spherical activated carbon (PBSAC) and silicon carbide (SiC) as examples, we demonstrate that the inferred particle permittivity is consistent with independent experimental heating profiles we collect from microwave reactors without adjustable parameters. Finally, this methodology establishes a foundation for predictive, multiscale design of microwave packed-bed reactors that explicitly accounts for particle-scale effects, enabling the estimation of intrinsic permittivity for the first time.

97 MATHEMATICS AND COMPUTING↗
NASA NTRSDate not supplied

Transcriptomics-based Machine Learning (ML) Analysis Predicts Space-Exposed Murine Livers

Limited sample sizes, high data dimensionality, and sensitivity to technical and biological variability of next generation sequencing (NGS), typically limits machine learning (ML) approaches in spaceflight studies that include radiation effects. However, pooling smaller studies while addressing intra- and inter-study variabilities allows for ML predictive modeling. Here, integration methods were applied to whole transcriptome shotgun sequencing (RNA-seq) data from six mouse liver GeneLab datasets (GLDS) (n ranging from 6 to 39 samples) from with a total of 81 spaceflight and ground-control samples to determine top features (i.e. genes) relevant to spaceflight including the effect of radiation exposure. RNASeq counts were normalized for each study, then merged and scaled across all datasets. Data dimensionality was reduced using a minimum redundancy maximum relevance (MRMR) methodology. Redundancy and relevance were computed using the Pearson correlation and F-statistic, respectively. The top 100 MRMR features were used to predict spaceflight vs. ground-control samples using Random Forest (RF), Support Vector Machine (SVM), and Linear Discriminant Analysis (LDA) classifiers with 5-fold cross validation (CV). Principal component analysis (PCA) on the complete feature set versus the MRMR features shows separation between spaceflight samples and ground controls (Figure 1A). The ML-based gene sets were compared against differential gene expression results obtained with DESeq2 from individual GLDS. Using all features or randomly sampled subsets at matching set sizes with MRMR, a maximum classifier accuracy of 69% on the test set over 5 folds. For all classifiers, CV training using at least the top 30 MRMR genes show minimum 89% accuracy and 0.95 AUC value on the test set over 5 folds (Figure 1B). Baseline set analysis on differentially expressed genes (DEGs) identified using padj ≤ 0.05 show 295 DEGs that overlap at least two studies and 13 DEGs that overlap three studies (Figure 1C). Set analysis between the top 100 MRMR features and the DEGs showed 47 genes that overlap at least one study and 24 genes that overlap two studies. Over-representation analysis showed overlapping biological processes related to fatty acid and lipid metabolism which may indicate these processes in the response to spaceflight stressors. MRMR feature selection for the selected ML methods improve performance relative to a classifier built on all features or randomly sampled subsets. Permutation feature importance within the decorrelated MRMR features showed concordance in feature ranking between ML methods. A challenge of applying ML methods across heterogeneous NGS data is accounting for signal:noise. Here, signal validation across studies was shown by intersecting sets between top MRMR genes and DEGs from DESeq2 analysis. Non-intersecting sets introduce opportunity to explore genes relevant to differentiating space flight exposed groups and implementing ML methods across existing NGS datasets may overcome sample size limitations.

Machine Learning↗
NASA NTRSDate not supplied

Transcriptomics-based Machine Learning Analysis Predicts Space-Exposed Murine Livers

Limited sample sizes, high data dimensionality, and sensitivity to technical and biological variability of next generation sequencing (NGS), typically limits machine learning (ML) approaches in spaceflight studies that include radiation effects. However, pooling smaller studies while addressing intra- and inter-study variabilities allows for ML predictive modeling. Here, integration methods were applied to whole transcriptome shotgun sequencing (RNA-seq) data from six mouse liver GeneLab datasets (GLDS) (n ranging from 6 to 39 samples) from with a total of 81 spaceflight and ground-control samples to determine top features (i.e. genes) relevant to spaceflight including the effect of radiation exposure. RNASeq counts were normalized for each study, then merged and scaled across all datasets. Data dimensionality was reduced using a minimum redundancy maximum relevance (MRMR) methodology. Redundancy and relevance were computed using the Pearson correlation and F-statistic, respectively. The top 100 MRMR features were used to predict spaceflight vs. ground-control samples using Random Forest (RF), Support Vector Machine (SVM), and Linear Discriminant Analysis (LDA) classifiers with 5-fold cross validation (CV). Principal component analysis (PCA) on the complete feature set versus the MRMR features shows separation between spaceflight samples and ground controls (Figure 1A). The ML-based gene sets were compared against differential gene expression results obtained with DESeq2 from individual GLDS. Using all features or randomly sampled subsets at matching set sizes with MRMR, a maximum classifier accuracy of 69% was shown on the test set over 5 folds. For all classifiers, CV training using at least the top 30 MRMR genes show minimum 89% accuracy and 0.95 AUC value on the test set over 5 folds (Figure 1B). Baseline set analysis on differentially expressed genes (DEGs) identified using padj ≤ 0.05 show 295 DEGs that overlap at least two studies and 13 DEGs that overlap three studies (Figure 1C). Set analysis between the top 100 MRMR features and the DEGs showed 47 genes that overlap at least one study and 24 genes that overlap two studies. Over-representation analysis showed overlapping biological processes related to fatty acid and lipid metabolism which may indicate these processes in the response to spaceflight stressors. MRMR feature selection for the selected ML methods improve performance relative to a classifier built on all features or randomly sampled subsets. Permutation feature importance within the decorrelated MRMR features showed concordance in feature ranking between ML methods. A challenge of applying ML methods across heterogeneous NGS data is accounting for signal:noise. Here, signal validation across studies was shown by intersecting sets between top MRMR genes and DEGs from DESeq2 analysis. Non-intersecting sets introduce opportunity to explore genes relevant to differentiating space flight exposed groups and implementing ML methods across existing NGS datasets may overcome sample size limitations.

Machine Learning↗
NASA NTRSDate not supplied

Transcriptomics-based Machine Learning Analysis Predicts Space-Exposed Murine Livers

Limited sample sizes, high data dimensionality, and sensitivity to technical and biological variability of next generation sequencing (NGS), typically limits machine learning (ML) approaches in spaceflight studies that include radiation effects. However, pooling smaller studies while addressing intra- and inter-study variabilities allows for ML predictive modeling. Here, integration methods were applied to whole transcriptome shotgun sequencing (RNA-seq) data from six mouse liver GeneLab datasets (GLDS) (n ranging from 6 to 39 samples) from with a total of 81 spaceflight and ground-control samples to determine top features (i.e. genes) relevant to spaceflight including the effect of radiation exposure. RNASeq counts were normalized for each study, then merged and scaled across all datasets. Data dimensionality was reduced using a minimum redundancy maximum relevance (MRMR) methodology. Redundancy and relevance were computed using the Pearson correlation and F-statistic, respectively. The top 100 MRMR features were used to predict spaceflight vs. ground-control samples using Random Forest (RF), Support Vector Machine (SVM), and Linear Discriminant Analysis (LDA) classifiers with 5-fold cross validation (CV). Principal component analysis (PCA) on the complete feature set versus the MRMR features shows separation between spaceflight samples and ground controls (Figure 1A). The ML-based gene sets were compared against differential gene expression results obtained with DESeq2 from individual GLDS. Using all features or randomly sampled subsets at matching set sizes with MRMR, a maximum classifier accuracy of 69% was shown on the test set over 5 folds. For all classifiers, CV training using at least the top 30 MRMR genes show minimum 89% accuracy and 0.95 AUC value on the test set over 5 folds (Figure 1B). Baseline set analysis on differentially expressed genes (DEGs) identified using padj ≤ 0.05 show 295 DEGs that overlap at least two studies and 13 DEGs that overlap three studies (Figure 1C). Set analysis between the top 100 MRMR features and the DEGs showed 47 genes that overlap at least one study and 24 genes that overlap two studies. Over-representation analysis showed overlapping biological processes related to fatty acid and lipid metabolism which may indicate these processes in the response to spaceflight stressors. MRMR feature selection for the selected ML methods improve performance relative to a classifier built on all features or randomly sampled subsets. Permutation feature importance within the decorrelated MRMR features showed concordance in feature ranking between ML methods. A challenge of applying ML methods across heterogeneous NGS data is accounting for signal:noise. Here, signal validation across studies was shown by intersecting sets between top MRMR genes and DEGs from DESeq2 analysis. Non-intersecting sets introduce opportunity to explore genes relevant to differentiating space flight exposed groups and implementing ML methods across existing NGS datasets may overcome sample size limitations.

Machine Learning↗