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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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At least 163 records · Page 9

An intercomparison of wall fluxes in a turbulent thermal convection chamber: Direct numerical simulations and wall-modeled large-eddy simulations enhanced by machine learning

Thermal convection in a closed chamber is driven by a warm bottom, a cold top, and side walls at various temperatures. Although wall fluxes are the source of convection energy, accurately modeling these fluxes (i.e., the wall model) is challenging. In large-eddy simulations (LESs), many wall models are traditionally derived from the canonical boundary layer, which may be unsuitable for thermal convection bounded by both horizontal and vertical walls. This study conducts a model intercomparison of dry convection in a cubic-meter chamber using three direct numerical simulations (DNSs) and four LESs with different wall models. The LESs employ traditional wall models, a new wall model employing physics-aware neural networks, and a refined grid near the walls. The experiment involves four cases with varying sidewall temperatures. Our results show that LESs capture the main flow features and the trends of mean fluxes. The physics-aware neural networks and refined wall grids can improve the temporally averaged local fluxes when the large-scale circulation has a preferred direction. Even without the local improvement of wall fluxes, the LES flow quantities (temperature and velocities) can still largely match those in DNSs, provided the mean flux largely matches the DNSs. Additionally, DNSs reveal that a variation in corner treatments has minimal impacts on the flow quantities away from corners. Finally, LESs underestimate the mean fluxes of the entire wall due to their inability to resolve corner regions, but their mean flux away from the corner can better match DNS.

54 ENVIRONMENTAL SCIENCES↗

Real-Time Anomaly Detection for Beyond Standard Model Searches in ProtoDUNE Horizontal Drift

This paper summarizes work conducted throughout a SULI internship at Fermi National Accelerator Laboratory focused on building an unsupervised machine learning model for real-time anomaly detection in ProtoDUNE Horizontal Drift. Using simulated data, we trained an autoencoder model on a pure cosmic dataset, and evaluated it on both cosmic and neutrino events---making the model an anomaly detector. The goal was to make a model which matches or exceeds the current ADC Simple Window trigger algorithm so that our model can perform at the same rate but provide sensitivity to potential beyond-the-Standard-Model (BSM) signatures. In the end, we were able to construct a model which slightly exceeds the capabilities of the ADC Simple Window while remaining completely unsupervised, achieving $31.9 \pm 0.2$\% ($26.6 \pm 0.2$\%) $\nu$ efficiency at 5 Hz (2 Hz), a 3.6 (3.2) percentage point increase. Additionally, $17.5 \pm 0.3$\% ($18.3 \pm 0.3$\%) of the events that passed the autoencoder at 5 Hz (2 Hz) were missed by the current trigger algorithm. Future work will investigate alternative normalization methods, including quantile transformation, and evaluate the model on ProtoDUNE-HD detector-glitch data if that data becomes available.

Wilson, Cameron C. [Cincinnati U., RWC]↗

Real-Time Anomaly Detection for Beyond Standard Model Searches in ProtoDUNE Horizontal Drift

This paper summarizes work conducted throughout a SULI internship at Fermi National Accelerator Laboratory focused on building an unsupervised machine learning model for real-time anomaly detection in ProtoDUNE Horizontal Drift. Using simulated data, we trained an autoencoder model on a pure cosmic dataset, and evaluated it on both cosmic and neutrino events---making the model an anomaly detector. The goal was to make a model which matches or exceeds the current ADC Simple Window trigger algorithm so that our model can perform at the same rate but provide sensitivity to potential beyond-the-Standard-Model (BSM) signatures. In the end, we were able to construct a model which slightly exceeds the capabilities of the ADC Simple Window while remaining completely unsupervised, achieving $31.9 \pm 0.2$\% ($26.6 \pm 0.2$\%) $\nu$ efficiency at 5 Hz (2 Hz), a 3.6 (3.2) percentage point increase. Additionally, $17.5 \pm 0.3$\% ($18.3 \pm 0.3$\%) of the events that passed the autoencoder at 5 Hz (2 Hz) were missed by the current trigger algorithm. Future work will investigate alternative normalization methods, including quantile transformation, and evaluate the model on ProtoDUNE-HD detector-glitch data if that data becomes available.

Wilson, Cameron C. [Cincinnati U., RWC]↗

Real-Time Anomaly Detection for Searches Beyond the Standard Model in the ProtoDUNE Horizontal Drift Detector

This paper summarizes work conducted throughout a SULI internship at Fermi National Accelerator Laboratory focused on building an unsupervised machine learning model for real-time anomaly detection in ProtoDUNE Horizontal Drift. Using simulated data, we trained an autoencoder model on a pure cosmic dataset, and evaluated it on both cosmic and neutrino events—making the model an anomaly detector. The goal was to make a model which matches or exceeds the current ADC Simple Window trigger algorithm so that our model can perform at the same rate but provide sensitivity to potential beyond-the-Standard-Model (BSM) signatures. In the end, we were able to construct a model which slightly exceeds the capabilities of the ADC Simple Window while remaining completely unsupervised, achieving 31.9 ± 0.2% (26.6 ± 0.2%) ν efficiency at 5 Hz (2 Hz), a 3.6 (3.2) percentage point increase. Additionally, 17.5 ± 0.3% (18.3 ± 0.3%) of the events that passed the autoencoder at 5 Hz (2 Hz) were missed by the current trigger algorithm. Future work will investigate alternative normalization methods, including quantile transformation, and evaluate the model on ProtoDUNE-HD detector-glitch data if that data becomes available.

Wilson, C. [Cincinnati U., RWC]↗

Advances in Molecular Beam Epitaxy Growth of Ultra-Wide Bandgap Ga2O3 Based Alloys

Gallium oxide (Ga2O3) is an emerging ultra-wide bandgap semiconductor material that has attracted attention for its potential to outperform existing SiC and GaN based devices operating at high breakdown voltages and high temperature. Isovalent alloying of In and Al in Ga2O3 provides the ability to engineer bandgap energy and strain of the material. Alloying with Al increases the bandgap energy and the theoretically achievable Baliga's figure of merit, a key measure of a material's ultimate performance limits for high power switching devices. Alloying with In introduces compressive strain and can be used to counteract the tensile strain of Al incorporation. The resulting (AlxGa1-x-yIny)2O3 alloy can be lattice-matched to commercially available Ga2O3 wafers and has a tunable bandgap energy greater than that of Ga2O3, 4.76 eV. Such lattice-matched material can be grown arbitrarily thick without the detrimental effects of elastic strain and relaxation, making it suitable for high voltage diodes and transistors. However, efforts to synthesize isovalent alloys are complicated by their tendency to phase separate into corundum Al2O3 or bixbyite In2O3. Literature reports of the quaternary (AlxGa1-x-yIny)2O3 are limited to <1% unintentional indium incorporation in In-catalyzed (AlxGa1-x)2O3. The primary limitation to quaternary growth is the limited incorporation of indium at elevated growth temperatures. This limited incorporation is due to both the volatility of indium oxide and Al and Ga cation exchange reactions which replace indium in In2O3. We report on the development of a novel high-throughput molecular beam epitaxy (MBE) technique to screen the growth conditions for the ternary alloy (InyGa1-y)2O3, and the application of these findings to the first successful synthesis of phase pure monoclinic (AlxGa1-x-yIny)2O3 by MBE. By leveraging the unique sub-oxide chemistry of Ga2O3 and in-situ monitoring of crystal properties by reflection high-energy electron diffraction (RHEED), a cyclical growth and etch-back method is developed and applied to rapidly characterize the (InyGa1-y)2O3 growth space. This cyclical method provides approximately 10x increase in experimental throughput and up to 46x improvement in Ga2O3 substrate utilization. Appropriate growth conditions for monoclinic (InyGa1- y)2O3 are identified by machine learning analysis of RHEED patterns and targeted growths are characterized ex-situ to confirm improved In incorporation. These growth conditions are then combined with established (AlxGa1-x)2O3 growth conditions to grow quaternary (AlxGa1-x-yIny)2O3 with Al mole fractions ranging from 1.4% - 24.4% and In mole fractions ranging from 3.1% to 15.5%. The chemical and optical properties of the alloys are investigated by XRD, XPS, and spectroscopic ellipsometry. A lattice-matched (AlxGa1-x-yIny)2O3 alloy is examined by 4D-STEM and the chemical and physical uniformity of Al and In incorporation are discussed.

alloy↗

Probe impedance measurements for millimeter-wave integrated horn antennas

In order to achieve an impedance-matched millimeter-wave integrated horn antenna mixer array, the characteristics of the antenna probes inside the horn must be known. This paper describes impedance measurements for various probes in low-frequency model horns of two different types: (1) a 3 x 3 array made of aluminum by electric discharge machining and (2) a half horn made of copper sheet placed on a big copper-clad circuit board that was used as an image plane. The results of measurements indicate that the presence of the horn increases the effective length of the probe element, in agreement with reports of Guo et al. (1991) and theoretical analysis of Eleftheriades et al. (1991). It was also found that the resonant frequencies can be controlled by changing the length of the probes or by loading the probes.

Guo, Yong↗

Distributed Antenna-Coupled TES for FIR Detectors Arrays

We describe a new architecture for a superconducting detector for the submillimeter and far-infrared. This detector uses a distributed hot-electron transition edge sensor (TES) to collect the power from a focal-plane-filling slot antenna array. The sensors lay directly across the slots of the antenna and match the antenna impedance of about 30 ohms. Each pixel contains many sensors that are wired in parallel as a single distributed TES, which results in a low impedance that readily matches to a multiplexed SQUID readout These detectors are inherently polarization sensitive, with very low cross-polarization response, but can also be configured to sum both polarizations. The dual-polarization design can have a bandwidth of 50The use of electron-phonon decoupling eliminates the need for micro-machining, making the focal plane much easier to fabricate than with absorber-coupled, mechanically isolated pixels. We discuss applications of these detectors and a hybridization scheme compatible with arrays of tens of thousands of pixels.

antenna↗

An information-matching approach to optimal experimental design and active learning

The efficacy of mathematical models heavily depends on the quality of the training data, yet collecting sufficient data is often expensive and challenging. Many modeling applications require inferring parameters only as a means to predict other quantities of interest (QoI). Because models often contain many unidentifiable (sloppy) parameters, QoIs often depend on a relatively small number of parameter combinations. Therefore, we introduce an information-matching criterion based on the Fisher information matrix to select the most informative training data from a candidate pool. This method ensures that the selected data contain sufficient information to learn only those parameters that are needed to constrain downstream QoIs. It is formulated as a convex optimization problem, making it scalable to large models and datasets. Here, we demonstrate the effectiveness of this approach across various modeling problems in diverse scientific fields, including power systems and underwater acoustics. Finally, we use information-matching as a query function within an active learning (AL) loop for materials science applications. In all these applications, we find that a relatively small set of optimal training data can provide the necessary information for achieving precise predictions. These results are encouraging for diverse future applications, particularly AL in large machine-learning models.

Materials science↗

Dypas: A dynamic payload scheduler for shuttle missions

Decision and analysis systems have had broad and very practical application areas in the human decision making process. These software systems range from the help sections in simple accounting packages, to the more complex computer configuration programs. Dypas is a decision and analysis system that aids prelaunch shutlle scheduling, and has added functionality to aid the rescheduling done in flight. Dypas is written in Common Lisp on a Symbolics Lisp machine. Dypas differs from other scheduling programs in that it can draw its knowledge from different rule bases and apply them to different rule interpretation schemes. The system has been coded with Flavors, an object oriented extension to Common Lisp on the Symbolics hardware. This allows implementation of objects (experiments) to better match the problem definition, and allows a more coherent solution space to be developed. Dypas was originally developed to test a programmer's aptitude toward Common Lisp and the Symbolics software environment. Since then the system has grown into a large software effort with several programmers and researchers thrown into the effort. Dypas is currently using two expert systems and three inferencing procedures to generate a many object schedule. The paper will review the abilities of Dypas and comment on its functionality.

Davis, Stephen↗

Machine-aided indexing for NASA STI

One of the major components of the NASA/STI processing system is machine-aided indexing (MAI). MAI is a computer process that generates a set of indexing terms selected from NASA's thesaurus, is used for indexing technical reports, is based on text, and is reviewed by indexers. This paper summarizes the MAI objectives and discusses the NASA Lexical Dictionary, subject switching, and phrase matching or natural languages. The benefits of using MAI are mentioned, and MAI production improvement and the future of MAI are briefly addressed.

Wilson, John↗

Remote Sensing and Fluxes Upscaling for Real-world Impact (Workshop Report)

The "Remote Sensing and Fluxes Upscaling for Real-world Impact" workshop, held on July 9-10, 2024, at Lawrence Berkeley National Lab, was a collaborative effort led by the AmeriFlux Management Project, NEON, and the Carbon Dew Community of Practice. The event brought together over 200 registrants and approximately 100 attendees each day, including leading experts, researchers, and practitioners. The primary focus was on bridging the gap between cutting-edge research and practical applications in environmental monitoring by integrating remote sensing and flux data. Key themes included the importance of site-level measurements for validating remote sensing products, providing nature-based climate solutions, and addressing challenges such as instrument costs and the need for standardized methods. At the regional scale, discussions centered on addressing spatial heterogeneity and using high-resolution remote sensing and machine learning methods to enhance data interpretation. Global scale challenges included data consistency, gap filling, and accurate emission source identification, with opportunities for international collaboration and standardized practices to improve global carbon budget assessments. The workshop emphasized the critical need for integrating data across local, regional, and global scales through explicit scale-matching and developed a workflow for scaling flux data using "straight shot" and "explicit nesting" approaches. The event highlighted the importance of connecting scientific research with real-world applications in carbon, energy, and water management, ensuring that advancements translate into tangible societal benefits. These insights will guide future research, technology transfer, and collaboration, maximizing the potential of environmental fluxes to address real-world challenges.

97 MATHEMATICS AND COMPUTING↗

A machine vision identification technique from range images

An orientation-independent identification technique from three-dimensional surface maps or range images is developed. Given the range image of an object, it is decomposed into orientation-independent patches using the sign of Gaussian curvature. A relational graph is then set up such that a node represents a patch and an edge represents the adjacency of two patches. The identification of the object is achieved by matching its graph representation to a number of model graphs. The matching is performed by employing the best-first search strategy. Examples of real range images show the merit of the technique.

Kehtarnavaz, N.↗

Incorporating Physical Priors into Weakly Supervised Anomaly Detection

We propose a new machine-learning-based anomaly detection strategy for comparing data with a background-only reference (a form of weak supervision). The sensitivity of previous strategies degrades significantly when the signal is too rare or there are many unhelpful features. Our prior-assisted weak supervision (PAWS) method incorporates information from a class of signal models to significantly enhance the search sensitivity of weakly supervised approaches. As long as the true signal is in the prespecified class, PAWS matches the sensitivity of a dedicated, fully supervised method without specifying the exact parameters ahead of time. On the benchmark LHC Olympics anomaly detection dataset, our mix of semisupervised and weakly supervised learning is able to extend the sensitivity over previous methods by a factor of 10 in cross section. Furthermore, if we add irrelevant (noise) dimensions to the inputs, classical methods degrade by another factor of 10 in cross section while PAWS remains insensitive to noise. This new approach could be applied in a number of scenarios and pushes the frontier of sensitivity between completely model-agnostic approaches and fully model-specific searches.

artificial neural networks↗

A Machine Learning Approach to Improve Air Traffic Management Initiatives

Collaborating closely with commercial air carriers and related organizations, the Federal Aviation Administration(FAA) regulates air traffic and ensures the safety and efficiency of air operations. Air traffic controllers make strategic decisions, such as delaying, rerouting, or canceling flights, partly based on guidance provided by the FAA’s Air TrafficControl System Command Center (ATCSCC). The guidance includes, among other things, control measures known asTraffic Management Initiatives (TMIs) designed to enhance safety and improve operational efficiency. TMIs play a crucial role in managing the demand and capacity within the U.S. National Airspace System (NAS). Two major TMIs that are routinely used (primarily to mitigate the adverse effects of bad weather) are Ground Delay Programs (GDPs) andGround Stops (GSs). In a GDP, flights destined for airports facing thunderstorm activity experience delays at their origin airports. This proactive approach minimizes the risk of routing aircraft through hazardous weather conditions and also replaces (fuel burning) airborne delays with ground delays. In a GS, a temporary restriction is imposed on the departure or arrival of aircraft at a specific airport or within a designated airspace. Although other TMIs (e.g., miles-in-trail) are also implemented as part of (air) traffic flow management in the NAS, the focus of this work is on GDPs and GSs. Since TMIs, by design, lead to flight delays or cancellations, it is crucial to put in place the right set of parameters(e.g., scope and duration of the GDP). For example, when the end time of a GDP extends beyond what is necessary, it imposes unnecessary delays on departing flights. This situation could occur as a result of inaccurate prediction of the(required) duration of the GDP based on the weather forecast. On the other hand, if a GDP ends prematurely before the underlying capacity constraints are resolved at the destination airport, it may result in airborne holding. The delicate balance lies in matching the termination of the GDP precisely with the resolution of capacity constraints, avoiding both the imposition of unnecessary ground delays and the need for airborne holding due to premature program termination.Failing to specify the right parameters for TMIs also leads to flight delays, creating a significant obstacle in managing the increasing traffic volumes causing increased work load for the controllers. To address this issue, we propose the integration of Machine Learning (ML) models in the traffic flow management(TFM) pipeline. In current operations, decisions are made by human experts based on extensive training, historical patterns, available traffic and weather data. Since we have an abundance of data from past events that tell us the likely impact of various TMIs, by ingesting historical data, properly trained ML models can offer valuable insights and aid human decision-making. With the FAA increasingly exploring advanced analytics, ML emerges as a focal point for enhancing TFM within the National Airspace System (NAS). As a first step, this study aims to provide traffic controllers with decision-making support for the issuance and adjustment of TMIs. Data analytics and machine learning have been previously employed to address some of the challenges associated with TMIs. Numerous studies have concentrated on various facets of TMI issuance, exploring factors influencing TMI parameters, including arrival rate, airport capacity, and delay prediction. For example, using weather forecasts, several statistical methods were used to produce probabilistic capacity profiles which in conjunction with deterministic models provided insights into the GDP planning process [1–4]. The downside of using deterministic models is that they rely on fixed inputs and predetermined rules, which lack the ability to account for the inherent uncertainty and variability present in real-world scenarios. In a separate series of studies, researchers aimed to predict the occurrences of GDPs and GSs. The majority of these studies utilized various supervised learning methods, including Decision Trees, Naive Bayes, Support VectorMachines, and Random Forests to analyze the influence of weather conditions and arrival demand on TMI incidents[5–8]. However, these studies primarily focused on predicting the incidence of TMIs without explicitly addressing the scope of TMIs, including their duration and their geographical coverage. Furthermore, the emphasis of these studies was largely on GDPs, given their higher frequency and longer duration when compared to GSs. A limited number of studies focused on predicting the parameters of TMIs, specifically addressing their duration and extent. In one such study focusing on optimizing the TMI parameters at San Francisco International Airport (SFO),the authors utilized a probabilistic forecast of fog [9]. They simulated various capacity scenarios based on the (fog)burn-off forecasts, selecting GDP parameters that minimized airborne and overall ground delays. However, this approach exclusively emphasizes stratus (fog) burn-off as the primary determinant of GDP and GS, neglecting other influential factors like severe weather events, runway closures, lower capacity than traffic demand, and other important variables. Given the complexity of predicting the TMI and determining its scope, we seek a more holistic approach. We aim to consider all significant factors that could impact TMIs and their parameters. What sets this research apart is the fusion of all data sources relevant to the issuance and adjustment of TMIs and it represents the first comprehensive attempt to optimize TMIs in this manner. Since this comprehensive solution involves various aspects, we break down the problem into smaller components and input all parameters into a unified model called the “TMI Adjuster”. Figure 1 shows the overall framework and the list of datasets used in each model. The objective of the TMI Adjuster module is to deliver reliable, consistent and expedited recommendations for the progression, adjustment, and termination of TMIs. The ML solution entails developing a pipeline capable of predicting the necessity of a TMI (e.g., GS or GDP) along with its various parameters. For example, in the case of a GS, this includes the scope of the GS either in terms of distance from the destination airport or based on pre-defined airspace sectors. Here, scope refers to those regions and departing airports that are subject to the GS. In this paper, we concentrate on the issuance of GSs in the three major airports in the New York area — LaGuardia(LGA), John F. Kennedy International (JFK), and Newark Liberty International (EWR). We fuse traffic, weather and other relevant aviation data from years 2017 to 2019 to train and validate the ML models. In particular, we use the following datasets: •Terminal Aerodrome Forecast (TAF): meteorological forecasts specific to each airport, issued four times a day, covering predefined time periods. •TMI data: includes all GSs and GDPs along with their respective parameters. •Aviation System Performance Metrics (ASPM): includes traffic related data such as aircraft delays, arrival, and departure rates. •Notices to Airmen (NOTAMs): utilized to extract runway closure data and manage interdependencies between terminals in close proximity. •Flight cancellation data •Airspace Flow Programs (AFP): includes information on flight airborne holdings caused by TMIs. The data preprocessing entails transforming ASPM, TMI, AFP, NOTAMs, and weather data into an hourly format and consolidating all datasets by merging them based on date and time as the primary key. The TMI Adjuster framework comprises two parallel models: one dedicated to GS and a second model focused on GDP. As previously mentioned, our specific focus is on the GS model as a multi-classification problem. In this framework, each data point of the GS model input summarizes ten hours of data. Specifically, the data loader for the GS model generates the input and output of the model as follows: at a given time step, the input includes the actual traffic, weather, and TMI data from the two-hour window before the time step, alongside the weather forecast and scheduled traffic for the next 8 hours starting from the time step. Based on this information, the output of the GS model for each time interval consists of three dimensions. The first dimension represents a binary decision on whether there should be a GS in place for the next hour or not. The second dimension is related to the scope of the GS in the United States, and the third dimension is related to the scope of the GS in Canada (i.e., to determine if the GS impacts airports in Canada).One of the challenges with TMI modeling is the sparsity of TMI events, particularly regarding its scope. To address this challenge in the scope of the GS model output, we implement grouping. The GS scope for the US region is defined based on a list of centers that should be included when the GS is in place. With 20 centers in the US, we utilized historical data to group them into 4 categories. In particular, we summarized our historical data in a graph format where nodes represent centers, and link weights are defined based on the co-occurrence of centers in the scope parameter ofTMIs. By identified strongly connected components in this graph, we were able to partition the centers into four groups. We consider two model structures for the GS Model. Firstly, a hierarchical classification model [10], where the human decision-making for a GS is of hierarchical nature. The decision-maker first decides whether there is a need fora GS, and if the answer is yes, determines the scope. A hierarchical classification model organizes the problem into a class hierarchy, typically a tree or a Directed Acyclic Graph (DAG) structure, and considers the dependency of the decision in the previous step to the next component [10]. Here, we employ the local classifier per level approach, which involves training one multi-class classifier for each level of the class hierarchy. The second structure is the independent structure. In this setting, as the name suggests, we do not consider the dependency of the decisions in the different dimensions of the output of the model. Instead, for each dimension, we train a multi-class classifier independently. Table 1 summarizes GS model statistics for training, validation and testing. The table documents the effect of limiting data to the time steps when there was actually a TMI in place or when a TMI had just terminated. This resulted in a more balanced distribution of the GS class(GS positive class)versus “No GS”(GS negative class), which might help the training process. While JFK and LGA follow very similar distributions, with 40% and 42% GS positive class respectively, EWR has proportionally fewer GS incidents at 28%. Our subsequent phase involves evaluating the performance of both hierarchical structure and independent structure using different state-of-the-art multi-class classifier models such as Random Forest, Decision Trees, K-nearest Neighbors, and Logistic Regression and forecast the duration and scope of the GSs.

Farzan Masrour Shalmani↗

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↗

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↗

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↗

Discovery of CWISE J052306.42-015355.4, an Extreme T Subdwarf Candidate

We present the discovery of CWISE J052306.42−015355.4, which was found as a faint, significant proper-motion object (0(\farcs)52 ± 0(\farcs)08 per yr) using machine-learning tools on the unWISE re-processing of time series images from the Wide-field Infrared Survey Explorer. Using the CatWISE2020 W1 and W2 magnitudes along with a J-band detection from the VISTA Hemisphere Survey, the location of CWISE J052306.42−015355.4 on the W1 − W2 versus J − W2 diagram best matches that of other known, or suspected, extreme T subdwarfs. As there is currently very little knowledge concerning extreme T subdwarfs we estimate a rough distance of ≤68 pc, which results in a tangential velocity of ≤167 km/s, both of which are tentative. A measured parallax is greatly needed to test these values. We also estimate a metallicity of −1.5 < [M/H] < −0.5 using theoretical predictions.

Hunter Brooks↗