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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 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization

Abstract Background Microbiome studies have uncovered associations between microbes and human, animal, and plant health outcomes. This has led to an interest in developing microbial interventions for treatment of disease and optimization of crop yields which requires identification of microbiome features that impact the outcome in the population of interest. That task is challenging because of the high dimensionality of microbiome data and the confounding that results from the complex and dynamic interactions among host, environment, and microbiome. In the presence of such confounding, variable selection and estimation procedures may have unsatisfactory performance in identifying microbial features with an effect on the outcome. Results In this manuscript, we aim to estimate population-level effects of individual microbiome features while controlling for confounding by a categorical variable. Due to the high dimensionality and confounding-induced correlation between features, we propose feature screening, selection, and estimation conditional on each stratum of the confounder followed by a standardization approach to estimation of population-level effects of individual features. Comprehensive simulation studies demonstrate the advantages of our approach in recovering relevant features. Utilizing a potential-outcomes framework, we outline assumptions required to ascribe causal, rather than associational, interpretations to the identified microbiome effects. We conducted an agricultural study of the rhizosphere microbiome of sorghum in which nitrogen fertilizer application is a confounding variable. In this study, the proposed approach identified microbial taxa that are consistent with biological understanding of potential plant-microbe interactions. Conclusions Standardization enables more accurate identification of individual microbiome features with an effect on the outcome of interest compared to other variable selection and estimation procedures when there is confounding by a categorical variable.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Causal Directions Matter: How Environmental Factors Drive Convective Cloud Detrainment Heights

This study investigates how environmental factors influence the level of maximum detrainment (LMD) in deep convective clouds. Through a novel application of the Linear Non‐Gaussian Acyclic Model (LiNGAM), we discover causal structures between environmental variables and LMD, observed at six tropical sites operated by the Atmospheric Radiation Measurement (ARM) user facility. LiNGAM effectively identifies causal directions among variables of interest, revealing robust relationships such as those among the lifting condensation level (LCL), level of free convection (LFC), and convective inhibition (CIN), aligning with prior knowledge. Relative humidity is shown to directly influence LMD; however, this relationship exhibits strong nonlinearity and becomes difficult to detect when the contrast between oceanic and continental environments is excluded from the analysis. This study highlights the importance of establishing causal relationships before performing statistical inference.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis

Counterfactual inference is a useful tool for comparing outcomes of interventions on complex systems. It requires us to represent the system in form of a structural causal model, complete with a causal diagram, probabilistic assumptions on exogenous variables, and functional assignments. Specifying such models can be extremely difficult in practice. The process requires substantial domain expertise, and does not scale easily to large systems, multiple systems, or novel system modifications. At the same time, many application domains, such as molecular biology, are rich in structured causal knowledge that is qualitative in nature. This manuscript proposes a general approach for querying a causal knowledge graph with a causal question and converting the qualitative result into a quantitative structural causal model that can learn from data to answer the question. Here, we demonstrate the feasibility, accuracy and versatility of this approach using two case studies in systems biology. The first demonstrates the appropriateness of the underlying assumptions and the accuracy of the results. The second demonstrates the versatility of the approach by querying a knowledge base for the molecular determinants of a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-induced cytokine storm and performing counterfactual inference to predict the causal effect of medical countermeasures for severely ill COVID-19 patients.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Space‐Time Causal Discovery in Earth System Science: A Local Stencil Learning Approach

Causal discovery tools enable scientists to infer meaningful relationships from observational data, spurring advances in fields as diverse as biology, economics, and climate science. Despite these successes, the application of causal discovery to space-time systems remains immensely challenging due to the high-dimensional nature of the data. For example, in climate sciences, modern observational temperature records over the past few decades regularly measure thousands of locations around the globe. To address these challenges, we introduce Causal Space-Time Stencil Learning (CaStLe), a novel meta-algorithm for discovering causal structures in complex space-time systems. CaStLe leverages regularities in local space-time dependencies to learn governing global dynamics. This local perspective eliminates spurious confounding and drastically reduces sample complexity, making space-time causal discovery practical and effective. For causal discovery, CaStLe flexibly accepts any appropriately adapted time series causal discovery algorithm to recover local causal structures. These advances enable causal discovery of geophysical phenomena that were previously unapproachable, including non-periodic, transient phenomena such as volcanic eruption plumes. Regularities in local space-time dependencies are transformed into informative spatial replicates, which actually improve CaStLe's performance when applied to ever-larger spatial grids. We successfully apply CaStLe to discover the atmospheric dynamics governing the climate response to the 1991 Mount Pinatubo volcanic eruption. We provide validation experiments to demonstrate the effectiveness of CaStLe over existing causal-discovery frameworks on a range of geophysics-inspired benchmarks while identifying the method's limitations and domains where its assumptions may not hold.

Nichol, J. Jake [Univ. of New Mexico, Albuquerque,↗
DOE OSTI2021

Classification and computation of extreme events in turbulent combustion

In the design of practical combustion systems, ensuring safety and reliability is an important requirement. For instance, reliably avoiding lean blowout, flame flashback or inlet unstart is critical for ensuring safe operation. Currently, the science of predicting such events is based on prior experience, limited modeling or diagnostic tools and purely statistical approaches. Even though computational and experimental tools for studying combustion devices have vastly advanced in the last three decades, the analysis of such failure events has not been pursued widely. While the use of data for model development and calibration is being widely accepted, the extension to failure events introduces numerous challenges. In particular, the focus here is on so-called data-poor problems, where the cost of generating data is extremely high and is not easily amenable to existing computational and experimental approaches. Data-poor problems are particularly relevant when related to extreme events (also called anomalous events) that can lead to catastrophic failure of the system. It is argued that transient events that describe such failure can have different causal mechanisms. To develop the scientific inference process, a classification of such problems is used to determine specific modeling paths as well as computational tools needed. Research opportunities in the emerging field of extreme event prediction are highlighted in order to identify critical and immediate needs.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2026

Overview of the Nephele Perturbed Parameter Ensemble for Aerosol‐Cloud Interactions in E3SMv3

Aerosol-cloud interactions (aci) are the leading source of uncertainty in inferring climate sensitivity from the historical record. Earth system models (ESMs) struggle to represent aci because the processes responsible for these phenomena occur at much finer time and space scales than can be resolved by any ESM. Observational constraints provide key benchmarks to test ESMs, but cannot be used alone to fully understand aci processes except in very specific cases where causality is controlled; some degree of modeling is required to infer aci and estimate radiative forcing. Here, we generate and characterize a perturbed parameter ensemble (PPE) in version 3 of the Energy Exascale ESM (E3SMv3). We perturb 25 parameters that govern aci processes over 250 members and integrate the model over present-day and preindustrial aerosol emissions. We find that the process representation in E3SMv3 is flexible and can generate global-mean effective radiative forcings due to aci (ERFaci) ranging from −3.0 to +0.9 W m −2 . The positive ERFaci values simulated by a portion of the PPE are implausible and result from parameter combinations that produce unrealistic top-of-atmosphere energy fluxes. While global-mean cloud droplet number concentration always increases in response to anthropogenic aerosol, cloud liquid water path can both increase and decrease, suggesting that precipitation suppression is not the only aerosol-cloud adjustment represented by E3SMv3. Analysis of which processes control liquid cloud adjustment in the PPE points toward stratiform precipitation processes and aerosol activation, which is consistent with many previous ESMs, as well as the new two-moment convective cloud microphysics in E3SMv3.

Nugent, Jacqueline M. [Univ. of Wyoming, Laramie, ↗
DOE OSTI2023

Causal interaction in high frequency turbulence at the biosphere–atmosphere interface: Structure–function coupling

At the biosphere–atmosphere interface, nonlinear interdependencies among components of an ecohydrological complex system can be inferred using multivariate high frequency time series observations. Information flow among these interacting variables allows us to represent the causal dependencies in the form of a directed acyclic graph (DAG). Here, we use high frequency multivariate data at 10 Hz from an eddy covariance instrument located at 25 m above agricultural land in the Midwestern US to quantify the evolutionary dynamics of this complex system using a sequence of DAGs by examining the structural dependency of information flow and the associated functional response. We investigate whether functional differences correspond to structural differences or if there are no functional variations despite the structural differences. We base our analysis on the hypothesis that causal dependencies are instigated through information flow, and the resulting interactions sustain the dynamics and its functionality. To test our hypothesis, we build upon causal structure analysis in the companion paper to characterize the information flow in similarly clustered DAGs from 3-min non-overlapping contiguous windows in the observational data. We characterize functionality as the nature of interactions as discerned through redundant, unique, and synergistic components of information flow. Through this analysis, we find that in turbulence at the biosphere–atmosphere interface, the variables that control the dynamic character of the atmosphere as well as the thermodynamics are driven by non-local conditions, while the scalar transport associated with CO and H 2 O is mainly driven by short-term local conditions.

58 GEOSCIENCES↗
DOE OSTI2021

Multisource Data Fusion Outage Location in Distribution Systems via Probabilistic Graphical Models

Efficient outage location is critical to enhancing the resilience of power distribution systems. However, accurate outage location requires combining massive evidence received from diverse data sources, including smart meter (SM) last gasp signals, customer trouble calls, social media messages, weather data, vegetation information, and physical parameters of the network. This is a computationally complex task due to the high dimensionality of data in distribution grids. In this paper, we propose a multi-source data fusion approach to locate outage events in partially observable distribution systems using Bayesian networks (BNs). A novel aspect of the proposed approach is that it takes multi-source evidence and the complex structure of distribution systems into account using a probabilistic graphical method. Our method can radically reduce the computational complexity of outage location inference in high-dimensional spaces. The graphical structure of the proposed BN is established based on the network’s topology and the causal relationship between random variables, such as the states of branches/customers and evidence. Utilizing this graphical model, accurate outage locations are obtained by leveraging a Gibbs sampling (GS) method, to infer the probabilities of de-energization for all branches. Compared with commonly-used exact inference methods that have exponential complexity in the size of the BN, GS quantifies the target conditional probability distributions in a timely manner. As a result, a case study of several real-world distribution systems is presented to validate the proposed method.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2021

System risk quantification and decision making support using functional modeling and dynamic Bayesian network

Risk-informed decision-making requires a probabilistic assessment of the likelihood of success of control action, given the system status. This paper presents a systematic state transition modeling approach integrating dynamic probabilistic risk assessment with a decision-making process using a dynamic Bayesian network (DBN) coupled with functional modeling. A functional model designed with multilevel flow modeling (MFM) technique was used to build a system state structure inferred by energy, mass, and information flow so that one can verify the developed model with respect to system functionality. The MFM model represents the causal relationship among the nodes, which captures the structure of process parameters and control units. Each node may have multiple possible states, and the DBN structured by the MFM model represents the time-domain transitions among the defined states. Furthermore, the MFM-DBN integrated state transition modeling is a white-box approach that allows one to draw the system's risk profile by updating the system states and supports the decisions probabilistically with physical inference. An example of a simple heating system has been used to illustrate this process, including decision-making support based on quantitative risk profile. For demonstrating its applicability to a complex system operational decision making, a case study of station blackout accident scenario leading to the seal loss of coolant accident in a nuclear power plant is presented. The proposed approach effectively provided the risk profile along time for each option so that the operators can make the best decision, which minimizes the plant risk.

42 ENGINEERING↗
DOE OSTI2021

Genetic program activity delineates risk, relapse, and therapy responsiveness in multiple myeloma

Despite recent advancements in the treatment of multiple myeloma (MM), nearly all patients ultimately relapse and many become refractory to multiple lines of therapies. Therefore, we not only need the ability to predict which patients are at high risk for disease progression but also a means to understand the mechanisms underlying their risk. Here, we report a transcriptional regulatory network (TRN) for MM inferred from cross-sectional multi-omics data from 881 patients that predicts how 124 chromosomal abnormalities and somatic mutations causally perturb 392 transcription regulators of 8549 genes to manifest in distinct clinical phenotypes and outcomes. We identified 141 genetic programs whose activity profiles stratify patients into 25 distinct transcriptional states and proved to be more predictive of outcomes than did mutations. The coherence of these programs and accuracy of our network-based risk prediction was validated in two independent datasets. We observed subtype-specific vulnerabilities to interventions with existing drugs and revealed plausible mechanisms for relapse, including the establishment of an immunosuppressive microenvironment. Investigation of the t(4;14) clinical subtype using the TRN revealed that 16% of these patients exhibit an extreme-risk combination of genetic programs (median progression-free survival of 5 months) that create a distinct phenotype with targetable genes and pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Effect of bars on evolution of SDSS spiral galaxies

ABSTRACT We explore the significance of bars in triggering central star formation (SF) and active galactic nucleus (AGN) activity for spiral galaxy evolution using a volume-limited sample with 0.020 < z < 0.055, Mr < −19.5, and σ > 70 km s−1 selected from Sloan Digital Sky Survey Data Release 7. On a central SF rate–σ plane, we measure the fraction of galaxies with strong bars in our sample and also the AGN fractions for barred and non-barred galaxies, respectively. The comparison between the bar and AGN fractions reveals a causal connection between the two phenomena of SF quenching and AGN activity. A massive black hole and abundant gas fuels are sufficient conditions to trigger AGNs. We infer that the AGNs triggered by satisfying the two conditions drive the strong AGN feedback, suddenly suppressing the central SF and leaving the SF sequence. We find that in galaxies where either of the two conditions is not sufficient, bars are a great help for the AGN triggering, accelerating the entire process of evolution, which is particularly evident in pseudo-bulge galaxies. All of our findings are obtained only when plotted in terms of their central velocity dispersion and central SFR (not galactic scale SFR), indicating that the AGN-driven SF quenching is confined in the central kpc region.

Kim, Minbae↗
DOE OSTI2024

Astrophysical Equation-of-State Constraints on the Color-Superconducting Gap

We demonstrate that astrophysical constraints on the dense-matter equation of state place an upper bound on the color-superconducting gap in dense matter above the transition from nuclear matter to quark matter. Pairing effects in the color-flavor locked quark matter phase increase the pressure at high density, and if this effect is sufficiently large then the requirements of causality and mechanical stability make it impossible to reach such a pressure in a way that is consistent with what is known at lower densities. The intermediate-density equation of state is inferred by considering extensions of chiral effective field theory to neutron star densities, and conditioning these using current astrophysical observations of neutron star radius, maximum mass, and tidal deformability (PSR J⁢0348+0432, PSR J1624-2230, PSR J⁢0740+6620, GW170817). At baryon number chemical potential μ = 2.6 GeV we find a 95% upper limit on the color-flavor locked pairing gap Δ of 457 MeV using overly conservative assumptions and 216 MeV with more reasonable assumptions. Furthermore, this constraint may be strengthened by future astrophysical measurements as well as by future advances in high-density QCD calculations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2023

Investigating signatures of phase transitions in neutron-star cores

Neutron stars explore matter at the highest densities in the universe such that their inner cores might undergo a phase transition from hadronic to exotic phases, e.g., quark matter. Such a transition could be associated with nontrivial structures in the density behavior of the speed of sound, such as jumps and sharp peaks. Here, in this work, we employ a physics-agnostic approach to model the density dependence of the speed of sound in neutron stars and study to what extent the existence of nontrivial structures can be inferred from existing astrophysical observations of neutron stars. For this, we exhaustively study different equations of state, including as well those with explicit first-order phase transitions. We obtain a large number of different equation of states which reproduce the same astrophysical observations and obey the same physical constraints, such as mechanical stability and causality. Among them, some have nontrivial structures in the sound speed whereas others do not. We conclude that astrophysical information to date do not require the existence of a phase transition to quark matter in the density range explored in the core of neutron stars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

Using discrete Bayesian networks for diagnosing and isolating cross-level faults in HVAC systems

Fault detection and diagnosis (FDD) technologies are critical to ensure satisfactory building performance, such as reducing energy wastes and negative impacts on occupant comfort and productivity. Existing FDD technologies mainly focus on component-level FDD solutions, which could lead to mis-diagnosis of cross-level faults in heating, ventilating, and air-conditioning (HVAC) systems. Cross-level faults are those faults that occur in one component or subsystem, but cause operational abnormalities in other components or subsystems, and result in a building level performance degradation. How to effectively diagnose the root cause of a cross-level fault is the focus of this study. Here, this paper presents a novel discrete Bayesian Network (DisBN)-based method for diagnosing cross-level faults in an HVAC system commonly used in commercial buildings. A two-level DisBN structure model is developed in this study. The parameters used in the DisBN model are obtained either from expert knowledge or through machine-learning strategies from normal system operation data. Meanwhile, the probability parameters are discretized to incorporate the uncertainties associated with typical expert knowledge. Thus, the developed DisBN method addresses the challenges many other BN based FDD methods face, i.e., the lack of fault data for BN parameter training. The developed DisBN represents causal relationships between a fault and its cross-level system impacts (i.e., fault symptoms or fault indicators) by considering how fault impacts propagate across different levels in an HVAC system. A weather and schedule information-based Pattern Matching (WPM) method is employed to automatically create WPM baseline data sets for each incoming real time snapshot data from the building systems. Consequently, BN inference and real-time diagnostics are achieved by comparing incoming snapshot data and the WPM baseline data set. The proposed method is evaluated using experimental fault data collected in a campus building. Fault diagnosis results demonstrate that the WPM-DisBN method is effective at locating the root causes of cross-level faults in an HVAC system.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Population structure limits the use of genomic data for predicting phenotypes and managing genetic resources in forest trees

There is overwhelming evidence that forest trees are locally adapted to climate. Thus, genecological models based on population phenotypes have been used to measure local adaptation, infer genetic maladaptation to climate, and guide assisted migration. However, instead of phenotypes, there is increasing interest in using genomic data for gene resource management. We used whole-genome resequencing and common-garden experiments to understand the genetic architecture of adaptive traits in black cottonwood. We studied the potential of using genome-wide association studies (GWAS) and genomic prediction to detect causal loci, identify climate-adapted phenotypes, and inform gene resource management. We analyzed population structure by partitioning phenotypic and genomic (single-nucleotide polymorphism) variation among 840 genotypes collected from 91 stands along 16 rivers. Most phenotypic variation (60 to 81%) occurred among populations and was strongly associated with climate. Population phenotypes were predicted well using genomic data (e.g., predictive abilityr> 0.9) but almost as well using climate or geography (r> 0.8). In contrast, genomic prediction within populations was poor (r< 0.2). We identified many GWAS associations among populations, but most appeared to be spurious based on pooled within-population analyses. Hierarchical partitioning of linkage disequilibrium and haplotype sharing suggested that within-population genomic prediction and GWAS were poor because allele frequencies of causal loci and linked markers differed among populations. Given the urgent need to conserve natural populations and ecosystems, our results suggest that climate variables alone can be used to predict population phenotypes, delineate seed zones and deployment zones, and guide assisted migration.

Science & Technology - Other Topics↗
DOE OSTI2026

Real-Time Detection of Charge Jumps in Superconducting Qubits with a Convolutional Neural Network

Ionizing radiation from cosmic rays and gammas can induce discontinuous jumps in the environmental charge of superconducting qubits (charge jumps), causing correlated errors that challenge fault-tolerant quantum computing while simultaneously providing a detection signature for quantum sensing applications. Current detection methods operate offline, introducing latency incompatible with in-the-loop qubit control. In this paper, an online detector of charge jumps for superconducting qubits, based on a dilated causal convolutional neural network (DCCNN) designed for in-the-loop deployment on the Quantum Instrumentation Control Kit (QICK) platform, is presented. The network is trained on synthetic Ramsey tomography scans generated from qubit templates measured at the Northwestern Experimental Underground Site (NEXUS) at Fermilab, and translated to FPGA firmware via hls4ml with ap_fixed$\langle 16,6 \rangle$ quantization, reaching a per-inference latency of $6.19 μ$s on the Zynq UltraScale+ RFSoC ZCU216. At this operating point the DCCNN matches the detection efficiency of the established offline $χ^2$ algorithm ($0.843 \pm 0.022$ vs. $0.866 \pm 0.020$ on $|Δq| \in [0.1, 0.5] e$ at matched false-positive rate), while requiring no per-qubit hyperparameter tuning. This shifts charge-jump detection from a post-hoc diagnostic to a control-loop primitive, enabling adaptive protocols that respond to radiation-induced events in situ, with applications to quantum-computing error mitigation and to the use of superconducting qubits as particle detectors.

Gaytan-Villarreal, Daniel [Carnegie Mellon U.]↗