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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2024

Application of advanced causal analyses to identify processes governing secondary organic aerosols

Abstract Understanding how different physical and chemical atmospheric processes affect the formation of fine particles has been a persistent challenge. Inferring causal relations between the various measured features affecting the formation of secondary organic aerosol (SOA) particles is complicated since correlations between variables do not necessarily imply causality. Here, we apply a state-of-the-art information transfer measure coupled with the Koopman operator framework to infer causal relations between isoprene epoxydiol SOA (IEPOX-SOA) and different chemistry and meteorological variables derived from detailed regional model predictions over the Amazon rainforest. IEPOX-SOA represents one of the most complex SOA formation pathways and is formed by the interactions between natural biogenic isoprene emissions and anthropogenic emissions affecting sulfate, acidity and particle water. Since the regional model captures the known relations of IEPOX-SOA with different chemistry and meteorological features, their simulated time series implicitly include their causal relations. We show that our causal model successfully infers the known major causal relations between total particle phase 2-methyl tetrols (the dominant component of IEPOX-SOA over the Amazon) and input features. We provide the first proof of concept that the application of our causal model better identifies causal relations compared to correlation and random forest analyses performed over the same dataset. Our work has tremendous implications, as our methodology of causal discovery could be used to identify unknown processes and features affecting fine particles and atmospheric chemistry in the Earth’s atmosphere.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Decomposing causality into its synergistic, unique, and redundant components

Causality lies at the heart of scientific inquiry, serving as the fundamental basis for understanding interactions among variables in physical systems. Despite its central role, current methods for causal inference face significant challenges due to nonlinear dependencies, stochastic interactions, self-causation, collider effects, and influences from exogenous factors, among others. While existing methods can effectively address some of these challenges, no single approach has successfully integrated all these aspects. Here, we address these challenges with SURD: Synergistic-Unique-Redundant Decomposition of causality. SURD quantifies causality as the increments of redundant, unique, and synergistic information gained about future events from past observations. The formulation is non-intrusive and applicable to both computational and experimental investigations, even when samples are scarce. We benchmark SURD in scenarios that pose significant challenges for causal inference and demonstrate that it offers a more reliable quantification of causality compared to previous methods.

applied mathematics↗
NASA NTRSDate not supplied

Using Federated Learning to Overcome Data Gravity in Space

Humans intend to take longer missions to outer space. Understanding the impact that space has on human health is paramount to the success of these missions. Controlled experiments with model organisms are run to infer the impact of space conditions on human health, but the data these experiments generate are too large to transfer to Earth for building models. The same is true for space-relevant data generated on Earth. Ideally, these datasets should be combined to improve statistical power and model accuracy without having to transfer data. Federated learning is such a method which trains an algorithm across decentralized computing systems, each of which has their own local copy of training and testing data. In this research, made possible by NASA@Work, the AI for Life in Space group at NASA demonstrates the use of federated learning to train an ensemble of causality inference models on a combination of data residing on the International Space Station (ISS) and in the cloud. Our work leverages CRISP, a causal inference platform developed during the 2020 Frontier Development Lab’s “Astronaut Health Challenge.” We also leverage the OpenFL federated learning library which was collaboratively developed at Intel and UPenn. We used publicly available data from the NASA Ames Life Sciences Data Archive to identify features in ionizing radiation experiments as causal of changes in cardiac blood velocity. This research demonstrates, for the first time, the possibility of running machine learning algorithms on datasets separated by astronomical distances. In this experiment, all the data were generated in terra, half of which were transferred to the ISS and analyzed on the Spaceborne Computer. In the future, our research will leverage federated learning on data generated in situ on the ISS with data generated terrestrially to predict the impact of spaceflight on mammalian female reproductive capacity.

James Casaletto↗
DOE OSTI2025

Assessing the cumulative effects of nearshore habitat restoration actions for multiple populations of juvenile salmon in Whidbey Basin, Washington: foundation and approach for synthesis and evaluation

Ecosystem restoration is a common tool for re-establishing ecosystem processes, structures, and functions to improve biodiversity and services in coastal and estuarine ecosystems. In the Salish Sea, salmon habitats have been fragmented, reduced in size, and diminished in quality, and the ecosystem processes that form and sustain these habitats have been degraded and disrupted as well. This loss is especially prevalent in estuaries, where up to 90% of former salmon habitat has been lost or compromised. Salmon species are integral to the identities and cultures of people in the Pacific Northwest, yet salmon abundances remain at historic lows, especially in urbanized areas. Recent investments in restoration are creating rearing habitat and repairing lost ecosystem function. However, restoration efforts in this region have largely proceeded at the site scale, with less attention to big-picture thinking regarding how restoration will effectively recover degraded or lost habitats for target species. As a result, no landscape-scale evaluation program exists, and the cumulative benefits of multiple interventions are unknown. We describe innovative methods for science synthesis related to the evaluation of cumulative effects of ecosystem restoration for Pacific salmon, using years of existing, but disparate data. Building from previous work on cumulative effects evaluation and incorporating a hierarchy of hypotheses approach, we propose using causal inference across numerous hypotheses in a framework to assess the cumulative benefits to Pacific salmon from multiple estuarine restoration projects. We present the framework as a method that can be used to address many complex questions and provide examples from the Salish Sea where the approach is being implemented. The framework draws on science synthesis from numerous fields and uses a hierarchy of hypotheses, causal analysis at multiple scales, and a new hierarchy of synthesis for assessing multiple lines of evidence documenting restoration effects on Pacific salmon. We propose causal inference to synthesize dissimilar data streams, in our case, to identify various manifestations of cumulative effects of restoration and benefits to salmon, and to further inform restoration and recovery planning. A unifying framework would allow for the detection of thresholds at which restoration provides measurable improvement and would greatly advance understanding of the effects of restoration on ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Deep Koopman operators for causal discovery

Causal discovery aims to identify cause-effect mechanisms for better scientific understanding, explainable decision-making, and more accurate modeling. Standard statistical frameworks, such as Granger causality, lack the ability to quantify causal relationships in nonlinear dynamics due to the presence of complex feedback mechanisms, timescale mixing, and nonstationarity. Thus, applying these methods to study causal dynamics in real-world systems, such as the Earth, is a major challenge. Addressing this shortcoming, we leverage deep learning and a Koopman operator-theoretic formalism to present a class of causal discovery algorithms. Kausal uses deep Koopman operator methods to approximate nonlinear dynamics in a linearized vector space in which traditional causal inference methods such as Granger causality can be more easily applied. Our idealized experiments demonstrate Kausal’s superior ability in discovering and characterizing causal signals compared to existing deep learning and non-deep learning state-of-the-art approaches. Finally, the successful identification of major El Niño and La Niña events in observations showcases Kausal’s skill to handle real-world applications.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Opportunistic experiments to constrain aerosol effective radiative forcing

Aerosol–cloud interactions (ACIs) are considered to be the most uncertain driver of present-day radiative forcing due to human activities. The nonlinearity of cloud-state changes to aerosol perturbations make it challenging to attribute causality in observed relationships of aerosol radiative forcing. Using correlations to infer causality can be challenging when meteorological variability also drives both aerosol and cloud changes independently. Natural and anthropogenic aerosol perturbations from well-defined sources provide “opportunistic experiments” (also known as natural experiments) to investigate ACI in cases where causality may be more confidently inferred. These perturbations cover a wide range of locations and spatiotemporal scales, including point sources such as volcanic eruptions or industrial sources, plumes from biomass burning or forest fires, and tracks from individual ships or shipping corridors. We review the different experimental conditions and conduct a synthesis of the available satellite datasets and field campaigns to place these opportunistic experiments on a common footing, facilitating new insights and a clearer understanding of key uncertainties in aerosol radiative forcing. Cloud albedo perturbations are strongly sensitive to background meteorological conditions. Strong liquid water path increases due to aerosol perturbations are largely ruled out by averaging across experiments. Opportunistic experiments have significantly improved process-level understanding of ACI, but it remains unclear how reliably the relationships found can be scaled to the global level, thus demonstrating a need for deeper investigation in order to improve assessments of aerosol radiative forcing and climate change.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
NASA NTRS2022

Opportunistic Experiments to Constrain Aerosol Effective Radiative Forcing

Aerosol-cloud interactions (ACI) are considered to be the most uncertain driver of present-day radiative forcing due to human activities. The non-linearity of cloud-state changes to aerosol perturbations make it challenging to attribute causality in observed relationships of aerosol radiative forcing. Using correlations to infer causality can be challenging when meteorological variability also drives both aerosol and cloud changes independently. Natural and anthropogenic aerosol perturbations from well defined sources provide ‘opportunistic experiments’ (also known as natural experiments) to investigate ACI in cases where causality may be more confidently inferred. These perturbations cover a wide range of locations and spatio-temporal scales, including point sources such as volcanic eruptions or industrial sources, plumes from biomass burning or forest fires, and tracks from individual ships or shipping corridors.We review the different experimental conditions and conduct a synthesis of the available satellite data sets and field campaigns to place these opportunistic experiments on a common footing, facilitating new insights and a clearer understanding of key uncertainties in aerosol radiative forcing. Cloud albedo perturbations are strongly sensitive to background meteorological conditions. Strong liquid water path increases due to aerosol perturbations are largely ruled out by averaging across experiments. Opportunistic experiments have significantly improved process-level understanding of ACI, but it remains unclear how reliably the relationships found can be scaled to the global level, thus demonstrating a need for deeper investigation in order to improve assessments of aerosol radiative forcing and climate change.

Matthew W Christensen↗
DOE OSTI2022

Discovering causal structure with reproducing-kernel Hilbert space ε -machines

We merge computational mechanics’ definition of causal states (predictively equivalent histories) with reproducing-kernel Hilbert space (RKHS) representation inference. The result is a widely applicable method that infers causal structure directly from observations of a system’s behaviors whether they are over discrete or continuous events or time. A structural representation—a finite- or infinite-state kernel ϵ-machine—is extracted by a reduced-dimension transform that gives an efficient representation of causal states and their topology. In this way, the system dynamics are represented by a stochastic (ordinary or partial) differential equation that acts on causal states. We introduce an algorithm to estimate the associated evolution operator. Paralleling the Fokker–Planck equation, it efficiently evolves causal-state distributions and makes predictions in the original data space via an RKHS functional mapping. We demonstrate these techniques, together with their predictive abilities, on discrete-time, discrete-value infinite Markov-order processes generated by finite-state hidden Markov models with (i) finite or (ii) uncountably infinite causal states and (iii) continuous-time, continuous-value processes generated by thermally driven chaotic flows. The method robustly estimates causal structure in the presence of varying external and measurement noise levels and for very high-dimensional data.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2024

A Generation-Storage Coordination Dispatch Strategy for Power System Based on Causal Reinforcement Learning

In the backdrop of global energy transformation, power systems integrating high proportions of renewable energy sources are facing unprecedented challenges in operational stability and dispatch efficiency. To address these challenges, this study introduces a generation-storage coordination real-time dispatch strategy based on Causal Power System Dynamic Reinforcement Learning (CPSDRL). Diverging from traditional reinforcement learning approaches, CPSDRL innovatively incorporates causal inference within the state prediction model - the crux of model-based reinforcement learning - thereby establishing the Power Causal Dynamic Model (PCDM). Assisted by the prior knowledge of power systems, the model significantly enhances prediction accuracy and reliability through a two-stage training process. Utilizing PCDM, this study further applies a direct policy search algorithm to optimize the real-time dispatch strategy. Experimental results indicate that the proposed method improves the stability of generation-storage coordination real-time dispatch and exhibits competitive advantages in sample efficiency and computational speed, compared to traditional model-based and model-free reinforcement learning algorithms. This method is expected to enhance the practicality and adaptability of causal reinforcement learning techniques in power system scheduling and control.

causal reinforcement learning↗
DOE OSTI2022

Do-calculus enables estimation of causal effects in partially observed biomolecular pathways

Abstract Motivation Estimating causal queries, such as changes in protein abundance in response to a perturbation, is a fundamental task in the analysis of biomolecular pathways. The estimation requires experimental measurements on the pathway components. However, in practice many pathway components are left unobserved (latent) because they are either unknown, or difficult to measure. Latent variable models (LVMs) are well-suited for such estimation. Unfortunately, LVM-based estimation of causal queries can be inaccurate when parameters of the latent variables are not uniquely identified, or when the number of latent variables is misspecified. This has limited the use of LVMs for causal inference in biomolecular pathways. Results In this article, we propose a general and practical approach for LVM-based estimation of causal queries. We prove that, despite the challenges above, LVM-based estimators of causal queries are accurate if the queries are identifiable according to Pearl’s do-calculus and describe an algorithm for its estimation. We illustrate the breadth and the practical utility of this approach for estimating causal queries in four synthetic and two experimental case studies, where structures of biomolecular pathways challenge the existing methods for causal query estimation. Availability and implementation The code and the data documenting all the case studies are available at https://github.com/srtaheri/LVMwithDoCalculus. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

What can simulation test beds teach us about social science? Results of the ground truth program

The ground truth program used simulations as test beds for social science research methods. The simulations had known ground truth and were capable of producing large amounts of data. This allowed research teams to run experiments and ask questions of these simulations similar to social scientists studying real-world systems, and enabled robust evaluation of their causal inference, prediction, and prescription capabilities. We tested three hypotheses about research effectiveness using data from the ground truth program, specifically looking at the influence of complexity, causal understanding, and data collection on performance. We found some evidence that system complexity and causal understanding influenced research performance, but no evidence that data availability contributed. The ground truth program may be the first robust coupling of simulation test beds with an experimental framework capable of teasing out factors that determine the success of social science research.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

Cellular, molecular, and therapeutic characterization of pilocarpine-induced temporal lobe epilepsy

Animal models have expanded our understanding of temporal lobe epilepsy (TLE). However, translating these to cell-specific druggable hypotheses is not explored. Herein, we conducted an integrative insilico-analysis of an available transcriptomics dataset obtained from animals with pilocarpine-induced-TLE. A set of 119 genes with subtle-to-moderate impact predicted most forms of epilepsy with ~ 97% accuracy and characteristically mapped to upregulated homeostatic and downregulated synaptic pathways. The deconvolution of cellular proportions revealed opposing changes in diverse cell types. The proportion of nonneuronal cells increased whereas that of interneurons, except for those expressing vasoactive intestinal peptide (Vip), decreased, and pyramidal neurons of the cornu-ammonis (CA) subfields showed the highest variation in proportion. A probabilistic Bayesian-network demonstrated an aberrant and oscillating physiological interaction between nonneuronal cells involved in the blood–brain-barrier and Vip interneurons in driving seizures, and their role was evaluated insilico using transcriptomic changes induced by valproic-acid, which showed opposing effects in the two cell-types. Additionally, we revealed novel epileptic and antiepileptic mechanisms and predicted drugs using causal inference, outperforming the present drug repurposing approaches. These well-powered findings not only expand the understanding of TLE and seizure oscillation, but also provide predictive biomarkers of epilepsy, cellular and causal micro-circuitry changes associated with it, and a drug-discovery method focusing on these events.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt

Snowmelt dynamics are a significant determinant of microbial metabolism in soil and regulate global biogeochemical cycles of carbon and nutrients by creating seasonal variations in soil redox and nutrient pools. With an increasing concern that climate change accelerates both snowmelt timing and rate, obtaining an accurate characterization of microbial response to snowmelt is important for understanding biogeochemical cycles intertwined with soil. However, observing microbial metabolism and its dynamics non-destructively remains a major challenge for systems such as soil. Microbial volatile compounds (mVCs) emitted from soil represent information-dense signatures and when assayed non-destructively using state-of-the-art instrumentation such as Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-TOF-MS) provide time resolved insights into the metabolism of active microbiomes. In this study, we used PTR-TOF-MS to investigate the metabolic trajectory of microbiomes from a subalpine forest soil, and their response to a simulated wet-up event akin to snowmelt. Using an information theory approach based on the partitioning of mutual information, we identified mVC metabolite pairs with robust interactions, including those that were non-linear and with time lags. The biological context for these mVC interactions was evaluated by projecting the connections onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) network of known metabolic pathways. Simulated snowmelt resulted in a rapid increase in the production of trimethylamine (TMA) suggesting that anaerobic degradation of quaternary amine osmo/cryoprotectants, such as glycine betaine, may be important contributors to this resource pulse. Unique and synergistic connections between intermediates of methylotrophic pathways such as dimethylamine, formaldehyde and methanol were observed upon wet-up and indicate that the initial pulse of TMA was likely transformed into these intermediates by methylotrophs. Increases in ammonia oxidation signatures (transformation of hydroxylamine to nitrite) were observed in parallel, and while the relative role of nitrifiers or methylotrophs cannot be confirmed, the inferred connection to TMA oxidation suggests either a direct or indirect coupling between these processes. Overall, it appears that such mVC time-series from PTR-TOF-MS combined with causal inference represents an attractive approach to non-destructively observe soil microbial metabolism and its response to environmental perturbation.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Evaluation of Methods for Causal Discovery in Hydrometeorological Systems

Understanding causal relations is of utmost importance in hydrology and climate research for systems identification, prediction, and understanding systems behavior in a changing climate. Traditionally, researchers in hydrometeorology attempted to study causal questions by conducting controlled experiments using numerical models. This approach, however, in most cases of interest provides uncertain results because the models are approximate representation of the natural system. An alternative approach that has recently drawn significant attention in several fields is to infer causal relations from purely observational data. It possesses several traits to its utility particularly in hydrometeorology due to the rapid accumulation of in situ and remotely sensed data records. The first objective of this study is to present a brief description of four causal discovery methods (Granger causality, Transfer Entropy, graph-based algorithms, and Convergent Cross Mapping) with special emphasis on the assumptions on which they are built. Second, using synthetic data generated from a hydrological model, we assess their performance in retrieving causal information taking into account sensitivity to sample size and presence of noise. Last, we use causal analysis to examine and formulate hypotheses on causal drivers of evapotranspiration in a shrubland region during summer and winter seasons. An interpretation of the hypotheses based on canopy seasonal dynamics and evapotranspiration processes is presented. It is hoped that the results presented here can be useful in guiding researchers studying hydrometeorological systems as to which causal method is most appropriate to the characteristics of the system under study.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The Ground Truth Program: Simulations as Test Beds for Social Science Research Methods.

Social systems are uniquely complex and difficult to study, but understanding them is vital to solving the world’s problems. The Ground Truth program developed a new way of testing the research methods that attempt to understand and leverage the Human Domain and its associated complexities. The program developed simulations of social systems as virtual world test beds. Not only were these simulations able to produce data on future states of the system under various circumstances and scenarios, but their causal ground truth was also explicitly known. Research teams studied these virtual worlds, facilitating deep validation of causal inference, prediction, and prescription methods. The Ground Truth program model provides a way to test and validate research methods to an extent previously impossible, and to study the intricacies and interactions of different components of research.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2020

Integration of ecosystem science into radioecology: A consensus perspective

In the Fall of 2016 a workshop was held which brought together over 50 scientists from the ecological and radiological fields to discuss feasibility and challenges of reintegrating ecosystem science into radioecology. There is a growing desire to incorporate attributes of ecosystem science into radiological risk assessment and radioecological research more generally, fueled by recent advances in quantification of emergent ecosystem attributes and the desire to accurately reflect impacts of radiological stressors upon ecosystem function. This work is a synthesis of the discussions and consensus of the workshop participant's responses to three primary questions, which were: 1) How can ecosystem science support radiological risk assessment? 2) What ecosystem level endpoints potentially could be used for radiological risk assessment? and 3) What inference strategies and associated methods would be most appropriate to assess the effects of radionuclides on ecosystem structure and function? The consensus of the participants was that ecosystem science can and should support radiological risk assessment through the incorporation of quantitative metrics that reflect ecosystem functions which are sensitive to radiological contaminants. The participants also agreed that many such endpoints exit or are thought to exit and while many are used in ecological risk assessment currently, additional data need to be collected that link the causal mechanisms of radiological exposure to these endpoints. Finally, the participants agreed that radiological risk assessments must be designed and informed by rigorous statistical frameworks capable of revealing the causal inference tying radiological exposure to the endpoints selected for measurement.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Further adoption of conservation tillage can increase maize yields in the western US Corn Belt

Conservation tillage can reduce soil erosion, increase soil health, and decrease labor and fuel input costs. Despite these benefits, potential yield impacts remain an important concern for farmers considering adoption. Previous research suggests that conservation tillage is likely to have the largest yield benefits in more arid conditions, but a lack of field-level analyses across climatic, management and soil conditions limits confidence in such predictions. Satellite imagery provides the opportunity to monitor agricultural lands at sub-field resolution across large spatial scales and wide environmental gradients. Here we investigate the maize yield impacts of conservation tillage in the semi-arid western US Corn Belt, using sub-field resolution datasets on tillage practices and crop yields derived from satellite data spanning four states (Nebraska, Kansas, South Dakota, and North Dakota) between 2008 and 2020. On these datasets, we estimate heterogenous yield outcomes for several thousand maize fields across gradients in climate, soil quality and irrigation status by using a causal forests analysis, an adaptation of the random forests machine-learning algorithm for causal inference on observational data. We find that long-term adoption of conservation tillage increased rainfed maize yields by an average of 9.9% in the region. Impacts on irrigated yields were small and not statistically significant. These results, along with an analysis of variables related to greater than average yield benefits, indicate that improved water infiltration and retention are the primary reasons for conservation tillage benefits. Despite yield benefits, many fields estimated to see increased yields under long term low till have not adopted the practice. Therefore, we identify specific counties likely to benefit most from increased levels of adoption. Our results strengthen the understanding of the impacts of conservation agriculture on crop yields and help define environments and counties most likely to benefit from conservation tillage.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Anthropogenic Contributions to the 2021 Pacific Northwest Heatwave

Abstract Daily maximum temperatures during the 2021 heatwave in the Pacific Northwest United States and Canada shattered century old records. Multiple causal factors, including anthropogenic climate change, contributed to these high temperatures, challenging traditional methods of attributing human influence. We demonstrate that the observed 2021 daily maximum temperatures are far above the bounds of Generalized Extreme Value distributions fitted from historical data. Hence, confidence in Granger causal inference statements about the human influence on this heatwave is low. Alternatively, we present a more conditional hindcast attribution study using two regional models. We performed ensembles of simulations of the heatwave to investigate how the event would have changed if it had occurred without anthropogenic climate change and with future warming. We found that global warming caused a ∼0.8°C–1°C increase in heatwave temperatures. Future warming would lead to a ∼5°C increase in heatwave temperature by the end of the 21st century.

54 ENVIRONMENTAL SCIENCES↗