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At least 55 records · Page 3

MINE: a new way to design genetics experiments for discovery

Abstract The Maximally Informative Next Experiment or MINE is a new experimental design approach for experiments, such as those in omics, in which the number of effects or parameters p greatly exceeds the number of samples n (p > n). Classical experimental design presumes n > p for inference about parameters and its application to p > n can lead to over-fitting. To overcome p > n, MINE is an ensemble method, which makes predictions about future experiments from an existing ensemble of models consistent with available data in order to select the most informative next experiment. Its advantages are in exploration of the data for new relationships with n < p and being able to integrate smaller and more tractable experiments to replace adaptively one large classic experiment as discoveries are made. Thus, using MINE is model-guided and adaptive over time in a large omics study. Here, MINE is illustrated in two distinct multiyear experiments, one involving genetic networks in Neurospora crassa and a second one involving a genome-wide association study in Sorghum bicolor as a comparison to classic experimental design in an agricultural setting.

Biochemistry & Molecular Biology↗

Exploring uncertainties in global crop yield projections in a large ensemble of crop models and CMIP5 and CMIP6 climate scenarios

Concerns over climate change are motivated in large part because of their impact on human society. Assessing the effect of that uncertainty on specific potential impacts is demanding, since it requires a systematic survey over both climate and impacts models. We provide a comprehensive evaluation of uncertainty in projected crop yields for maize, spring and winter wheat, rice, and soybean, using a suite of nine crop models and up to 45 CMIP5 and 34 CMIP6 climate projections for three different forcing scenarios. To make this task computationally tractable, we use a new set of statistical crop model emulators. We find that climate and crop models contribute about equally to overall uncertainty. While the ranges of yield uncertainties under CMIP5 and CMIP6 projections are similar, median impact in aggregate total caloric production is typically more negative for the CMIP6 projections (+1% to −19%) than for CMIP5 (+5% to −13%). In the first half of the 21st century and for individual crops is the spread across crop models typically wider than that across climate models, but we find distinct differences between crops: globally, wheat and maize uncertainties are dominated by the crop models, but soybean and rice are more sensitive to the climate projections. Climate models with very similar global mean warming can lead to very different aggregate impacts so that climate model uncertainties remain a significant contributor to agricultural impacts uncertainty. These results show the utility of large-ensemble methods that allow comprehensively evaluating factors affecting crop yields or other impacts under climate change. The crop model ensemble used here is unbalanced and pulls the assumption that all projections are equally plausible into question. Better methods for consistent model testing, also at the level of individual processes, will have to be developed and applied by the crop modeling community.

crop yield projections↗

An out-of-distribution-aware autoencoder model for reduced chemical kinetics

While detailed chemical kinetic models have been successful in representing rates of chemical reactions in continuum scale computational fluid dynamics (CFD) simulations, applying the models in simulations for engineering device conditions is computationally prohibitive. To reduce the cost, data-driven methods, e.g., autoencoders, have been used to construct reduced chemical kinetic models for CFD simulations. Despite their success, data-driven methods rely heavily on training data sets and can be unreliable when used in out-of-distribution (OOD) regions (i.e., when extrapolating outside of the training set). In this paper, we present an enhanced autoencoder model for combustion chemical kinetics with uncertainty quantification to enable the detection of model usage in OOD regions, and thereby creating an OOD-aware autoencoder model that contributes to more robust CFD simulations of reacting flows.Here, we first demonstrate the effectiveness of the method in OOD detection in two well-known datasets, MNIST and Fashion-MNIST, in comparison with the deep ensemble method, and then present the OOD-aware autoencoder for reduced chemistry model in syngas combustion.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Exploring Data Set Bias and Decision Support with Predictive Uncertainty Through Bayesian Approximations and Convolutional Neural Networks

Individual seismic catalogs can contain multiscale observations from fault level to global scales and associated waveforms from discrete events reflect crustal structure across many different scales and locations. Seismic network aperture, geographic location, and observation distance may not provide informative guidance or intuition on how different catalogs will behave across models trained under different conditions. We rely on uncertainty to provide guardrails for when to trust model decisions, but understanding when our uncertainty is trustworthy is an open challenge. Here, in this work, we explore Bayesian approximation methods for assigning predictive uncertainty in seismic event classification problems. We find that computationally expensive Bayesian approximations do not outperform simple ensemble methods. We also find that when exploiting multiple seismic event catalogs, joint training with data from all the catalogs combined with Bayesian approximations and supervised training for classification can obscure bias and result in less robust uncertainty while also not providing substantial performance benefits compared to training individual models for each catalog.

58 GEOSCIENCES↗

Statistical properties of ideal three-dimensional magnetohydrodynamics

Classical Gibbs ensemble methods are used to study the spectral structure of three-dimensional ideal MHD in periodic geometry. In this paper the equilibrium ensemble incorporates constraints of total energy, magnetic helicity, and cross helicity. Several new results are proven for ensemble averages, including the constraint that magnetic energy equal or exceed kinetic energy, and that cross helicity represents a constant fraction of magnetic energy across the spectral domain, for arbitrary size systems. Two zero-temperature limits are considered in detail, emphasizing the role of complete and partial condensaiton of spectral quantities to the longest wavelength states. The ensemble predictions are compared to direct numerical solution using a low-order truncation Galerkin spectral code. Implications for spectral transfer of nonequilibrium, dissipative turbulent MHD systems are discussed.

Stribling, T.↗

Improving Climate Projections Using "Intelligent" Ensembles

Recent changes in the climate system have led to growing concern, especially in communities which are highly vulnerable to resource shortages and weather extremes. There is an urgent need for better climate information to develop solutions and strategies for adapting to a changing climate. Climate models provide excellent tools for studying the current state of climate and making future projections. However, these models are subject to biases created by structural uncertainties. Performance metrics-or the systematic determination of model biases-succinctly quantify aspects of climate model behavior. Efforts to standardize climate model experiments and collect simulation data-such as the Coupled Model Intercomparison Project (CMIP)-provide the means to directly compare and assess model performance. Performance metrics have been used to show that some models reproduce present-day climate better than others. Simulation data from multiple models are often used to add value to projections by creating a consensus projection from the model ensemble, in which each model is given an equal weight. It has been shown that the ensemble mean generally outperforms any single model. It is possible to use unequal weights to produce ensemble means, in which models are weighted based on performance (called "intelligent" ensembles). Can performance metrics be used to improve climate projections? Previous work introduced a framework for comparing the utility of model performance metrics, showing that the best metrics are related to the variance of top-of-atmosphere outgoing longwave radiation. These metrics improve present-day climate simulations of Earth's energy budget using the "intelligent" ensemble method. The current project identifies several approaches for testing whether performance metrics can be applied to future simulations to create "intelligent" ensemble-mean climate projections. It is shown that certain performance metrics test key climate processes in the models, and that these metrics can be used to evaluate model quality in both current and future climate states. This information will be used to produce new consensus projections and provide communities with improved climate projections for urgent decision-making.

Baker, Noel C.↗

Improving Climate Projections Using "Intelligent" Ensembles

Recent changes in the climate system have led to growing concern, especially in communities which are highly vulnerable to resource shortages and weather extremes. There is an urgent need for better climate information to develop solutions and strategies for adapting to a changing climate. Climate models provide excellent tools for studying the current state of climate and making future projections. However, these models are subject to biases created by structural uncertainties. Performance metrics-or the systematic determination of model biases-succinctly quantify aspects of climate model behavior. Efforts to standardize climate model experiments and collect simulation data-such as the Coupled Model Intercomparison Project (CMIP)-provide the means to directly compare and assess model performance. Performance metrics have been used to show that some models reproduce present-day climate better than others. Simulation data from multiple models are often used to add value to projections by creating a consensus projection from the model ensemble, in which each model is given an equal weight. It has been shown that the ensemble mean generally outperforms any single model. It is possible to use unequal weights to produce ensemble means, in which models are weighted based on performance (called "intelligent" ensembles). Can performance metrics be used to improve climate projections? Previous work introduced a framework for comparing the utility of model performance metrics, showing that the best metrics are related to the variance of top-of-atmosphere outgoing longwave radiation. These metrics improve present-day climate simulations of Earth's energy budget using the "intelligent" ensemble method. The current project identifies several approaches for testing whether performance metrics can be applied to future simulations to create "intelligent" ensemble-mean climate projections. It is shown that certain performance metrics test key climate processes in the models, and that these metrics can be used to evaluate model quality in both current and future climate states. This information will be used to produce new consensus projections and provide communities with improved climate projections for urgent decision-making.

Baker, Noel C.↗

Application-specific optimal model weighting of global climate models: A red tide example

Global climate models (GCMs) and Earth system models (ESMs) provide many climate services with environmental relevance. The High Resolution Model Inter-comparison Project (HighResMIP) of the Coupled Model Intercomparison Project Phase 6 (CMIP6) provides model runs of GCMs and ESMs to address regional phenomena. Developing a parsimonious ensemble of CMIP6 requires multiple ensemble methods such as independent-model subset selection, prescreening-based subset selection, and model weighting. The work presented here focuses on application-specific optimal model weighting, with prescreening-based subset selection. As such, independent ensemble members are categorized, selected, and weighted based on their ability to reproduce physically-interpretable features of interest that are problem-specific. We discuss the strengths and caveats of optimal model weighting using a case study of red tide prediction in the Gulf of Mexico along the West Florida Shelf. Red tide is a common name of specific harmful algal blooms that occur worldwide, causing adverse socioeconomic and environmental impacts. Our results indicate the importance of prescreening-based subset selection as optimal model weighting can underplay robust ensemble members by optimizing error cancellation. Prescreening-based subset selection also provides insights about the validity of the model weights. By illustrating the caveats of using non-representative models when optimal model weighting is used, the findings and discussion of this study are pertinent to many other climate services.

54 ENVIRONMENTAL SCIENCES↗

Large Ensemble Exploration of Global Energy Transitions Under National Emissions Pledges

Global climate goals require a transition to a deeply decarbonized energy system. Meeting the objectives of the Paris Agreement through countries' nationally determined contributions and long-term strategies represents a complex problem with consequences across multiple systems shrouded by deep uncertainty. Robust, large-ensemble methods and analyses mapping a wide range of possible future states of the world are needed to help policymakers design effective strategies to meet emissions reduction goals. This study contributes a scenario discovery analysis applied to a large ensemble of 5,760 model realizations generated using the Global Change Analysis Model. Eleven energy-related uncertainties are systematically varied, representing national mitigation pledges, institutional factors, and techno-economic parameters, among others. The resulting ensemble maps how uncertainties impact common energy system metrics used to characterize national and global pathways toward deep decarbonization. Results show globally consistent but regionally variable energy transitions as measured by multiple metrics, including electricity costs and stranded assets. Larger economies and developing regions experience more severe economic outcomes across a broad sampling of uncertainty. The scale of CO 2 removal globally determines how much the energy system can continue to emit, but the relative role of different CO 2 removal options in meeting decarbonization goals varies across regions. Previous studies characterizing uncertainty have typically focused on a few scenarios, and other large-ensemble work has not (to our knowledge) combined this framework with national emissions pledges or institutional factors. Our results underscore the value of large-ensemble scenario discovery for decision support as countries begin to design strategies to meet their goals.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗

Rock Physics-Based Data Assimilation of Integrated Continuous Active-Source Seismic and Pressure Monitoring Data during Geological Carbon Storage

Summary There has been substantial controversy concerning the role of geological carbon storage (GCS) in sequestering anthropogenic carbon emissions to mitigate climate change and global warming. Arguments center on the inability to monitor a geological storage site precisely and continuously, especially highlighting the associated costs and spatiotemporal trade-offs when using conventional subsurface monitoring techniques (well logs, core samples, chemical tracers, and 4D seismics). Active surveillance of GCS sites is essential for managing and mitigating potential leaks but is also required by regulation. With the goal of enhancing the monitoring capability at GCS sites, we present a rock physics-based joint data assimilation model to study a popular GCS site at Cranfield, Mississippi, USA. Synthetic continuous active-source seismic monitoring (CASSM) data (in the form of Vp and Qp measurements) and wellbore pressure monitoring data are assimilated with an ensemble of reservoir realizations to monitor gas saturation and reservoir pressure changes over a period of 100 years. Synthetic seismic attributes are generated using rock physics models (RPMs) and wellbore pressure monitoring data are extracted from the ground truth. Two assimilation methods, ensemble Kalman filter (EnKF) and ensemble Kalman smoother (EnKS), are tested in an observation system simulation experiment (OSSE) environment to assess the prediction accuracy of the individual and composite observation systems. The joint monitoring system achieves more accurate estimates of gas saturation and pressure, across the time span from start of injection to end of forecast, as compared to a single type of monitoring tool and irrespective of data assimilation algorithm choice. These results indicate that jointly assimilated data from two types of sensors (in this case, crosswell seismic and downhole pressure) may lead to a more risk-reducing monitoring design. One would expect that more data, vis-à-vis inclusion of a new sensor type, will improve the accuracy of any GCS monitoring system. However, from a practical standpoint, one important question is whether such a gain in accuracy is worth the additional cost associated with the new sensor. This paper focuses on quantifying the gain in accuracy, such that a practitioner can answer this question.

Engineering↗

Deep neural network uncertainty quantification for LArTPC reconstruction

We evaluate uncertainty quantification (UQ) methods for deep learning applied to liquid argon time projection chamber (LArTPC) physics analysis tasks. As deep learning applications enter widespread usage among physics data analysis, neural networks with reliable estimates of prediction uncertainty and robust performance against overconfidence and out-of-distribution (OOD) samples are critical for their full deployment in analyzing experimental data. While numerous UQ methods have been tested on simple datasets, performance evaluations for more complex tasks and datasets are scarce. Here we assess the application of selected deep learning UQ methods on the task of particle classification using the PiLArNet monte carlo 3D LArTPC point cloud dataset. We observe that UQ methods not only allow for better rejection of prediction mistakes and OOD detection, but also generally achieve higher overall accuracy across different task settings. We assess the precision of uncertainty quantification using different evaluation metrics, such as distributional separation of prediction entropy across correctly and incorrectly identified samples, receiver operating characteristic curves (ROCs), and expected calibration error from observed empirical accuracy. We conclude that ensembling methods can obtain well calibrated classification probabilities and generally perform better than other existing methods in deep learning UQ literature.

47 OTHER INSTRUMENTATION↗

CholecTriplet2021: A benchmark challenge for surgical action triplet recognition

Context-aware decision support in the operating room can foster surgical safety and efficiency by leveraging real-time feedback from surgical workflow analysis. Most existing works recognize surgical activities at a coarse-grained level, such as phases, steps or events, leaving out fine-grained interaction details about the surgical activity; yet those are needed for more helpful AI assistance in the operating room. Recognizing surgical actions as triplets of ‹ instrument, verb, target › combination delivers more comprehensive details about the activities taking place in surgical videos. This paper presents CholecTriplet2021: an endoscopic vision challenge organized at MICCAI 2021 for the recognition of surgical action triplets in laparoscopic videos. Here, the challenge granted private access to the large-scale CholecT50 dataset, which is annotated with action triplet information. In this paper, we present the challenge setup and the assessment of the state-of-the-art deep learning methods proposed by the participants during the challenge. Here, a total of 4 baseline methods from the challenge organizers and 19 new deep learning algorithms from the competing teams are presented to recognize surgical action triplets directly from surgical videos, achieving mean average precision (mAP) ranging from 4.2% to 38.1%. This study also analyzes the significance of the results obtained by the presented approaches, performs a thorough methodological comparison between them, in-depth result analysis, and proposes a novel ensemble method for enhanced recognition. Our analysis shows that surgical workflow analysis is not yet solved, and also highlights interesting directions for future research on fine-grained surgical activity recognition which is of utmost importance for the development of AI in surgery.

60 APPLIED LIFE SCIENCES↗

Efficient Ensemble-Based Stochastic Gradient Methods for Optimization Under Geological Uncertainty

Ensemble-based stochastic gradient methods, such as the ensemble optimization (EnOpt) method, the simplex gradient (SG) method, and the stochastic simplex approximate gradient (StoSAG) method, approximate the gradient of an objective function using an ensemble of perturbed control vectors. These methods are increasingly used in solving reservoir optimization problems because they are not only easy to parallelize and couple with any simulator but also computationally more efficient than the conventional finite-difference method for gradient calculations. In this work, we show that EnOpt may fail to achieve sufficient improvement of the objective function when the differences between the objective function values of perturbed control variables and their ensemble mean are large. On the basis of the comparison of EnOpt and SG, we propose a hybrid gradient of EnOpt and SG to save on the computational cost of SG. We also suggest practical ways to reduce the computational cost of EnOpt and StoSAG by approximating the objective function values of unperturbed control variables using the values of perturbed ones. We first demonstrate the performance of our improved ensemble schemes using a benchmark problem. Results show that the proposed gradients saved about 30–50% of the computational cost of the same optimization by using EnOpt, SG, and StoSAG. As a real application, we consider pressure management in carbon storage reservoirs, for which brine extraction wells need to be optimally placed to reduce reservoir pressure buildup while maximizing the net present value. Results show that our improved schemes reduce the computational cost significantly.

58 GEOSCIENCES↗

Analysis of Narrow Bipolar Events Using Mode Decomposition Methods

Multi-resolution analysis methods can reveal the underlying physical dynamics of nonstationary signals, such as those from lightning. In this paper we demonstrate the application of two multi-resolution analysis methods: Ensemble Empirical Mode Decomposition (EEMD) and Variational Mode Decomposition (VMD) in a comparative way in the analysis of electric field change waveforms from lightning. EEMD and VMD decompose signals into a set of Intrinsic Mode Functions (IMFs). The IMFs can be combined using distance and divergence metrics to obtain noise reduction or to obtain new waveforms that isolate the physical processes of interest while removing irrelevant components of the original signal. We apply the EEMD and VMD methods to the observations of three close Narrow Bipolar Events (NBEs) that were reported by Rison et al. The ΔE observations reveal the occurrence of complex oscillatory processes after the main NBE sferic. We show that both EEMD and VMD are able to isolate the oscillations from the main NBE, with VMD being more effective of the two methods since it requires the least user supervision. The oscillations are found to begin at the end of the NBEs' downward fast positive breakdown and appear to be produced by a half-wavelength standing wave within a weakly-conducting resonant ionization cavity left behind in the wake of the streamer-based NBE event. In conclusion, additional analysis shows that one of the NBEs was likely initiated by an energetic cosmic ray shower, and also corrects a misinterpretation in the literature that fast breakdown is an artifact of NBE-like events in interferometer observations.

54 ENVIRONMENTAL SCIENCES↗

Comparison of machine learning techniques to optimize the analysis of plutonium surrogate material via a portable LIBS device

The utilization of machine learning techniques has become commonplace in the analysis of optical emission spectra. These methods are often limited to variants of principal components analysis (PCA), partial-least squares (PLS), and artificial neural networks (ANNs). A plethora of other techniques exist and are well established in the world of data science, yet are seldom investigated for their use in spectroscopic problems. In this study, machine learning techniques were used to analyze optical emission spectra of laser-induced plasma from ceria pellets doped with silicon in order to predict silicon content. Additionally, a boosted regression ensemble model was created, and its predictive accuracy was compared to that of traditional PCA, PLS, and ANN regression models. Boosted regression tree ensembles yielded fits with R-squared (R2) values as high as 0.964 and mean-squared errors of prediction (MSEPs) as low as 0.074, providing the most accurate predictive model. Neural networks performed with slightly lower R2 values and higher MSEPs compared to the ensemble methods, thus indicating susceptibility to overfitting.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Artificial Neural Network Modeling for Airline Disruption Management

Since the 1970s, most airlines have incorporated computerized support for managing disruptions during flight schedule execution. However, existing platforms for airline disruption management (ADM) employ monolithic system design methods that rely on the creation of specific rules and requirements through explicit optimization routines, before a system that meets the specifications is designed. Thus, current platforms for ADM are unable to readily accommodate additional system complexities resulting from the introduction of new capabilities, such as the introduction of unmanned aerial systems (UAS), operations and infrastructure, to the system. To this end, we use historical data on airline scheduling and operations recovery to develop a system of artificial neural networks (ANNs), which describe a predictive transfer function model (PTFM) for promptly estimating the recovery impact of disruption resolutions at separate phases of flight schedule execution during ADM. Furthermore, we provide a modular approach for assessing and executing the PTFM by employing a parallel ensemble method to develop generative routines that amalgamate the system of ANNs. Our modular approach ensures that current industry standards for tardiness in flight schedule execution during ADM are satisfied, while accurately estimating appropriate time-based performance metrics for the separate phases of flight schedule execution.

Kolawole Ogunsina↗

Prediction of DIII-D Pedestal Structure from Externally Controllable Parameters

The sharp increase of pressure at the edge of a high confinement mode (H-mode) plasma, the pedestal, strongly impacts overall plasma performance. Predicting the pedestal is a necessity to control and optimize tokamak operations. An experimental data-driven machine learning (ML) approach is presented that predicts the pedestal heights and widths of electron density (ne) and electron temperature (Te) profiles as well as the separatrix ne from externally controllable parameters such as the plasma shape, heating method and power, and gas puff rate and integrated gas puff. The OMFIT framework was used with DIII-D data to efficiently, robustly, and automatically build a database of pedestal parameters to train machine learning models. Database creation was enabled by the search engine tool for DIII-D data, TokSearch, which parallelizes data fetching, enabling fast searches through basic signals of thousands of DIII-D shots and selection of relevant time intervals. Principal Component Analysis (PCA) separated the database into three clusters that represent classes of plasma shapes that are regularly used in DIII-D. The most important parameters for setting the pedestal structure were plasma current (Ip), toroidal magnetic field (Bφ), neutral beam heating power (PNBI) and shaping quantities. The Deep Jointly Informed Neural Networks (DJINN) algorithm was applied to identify suitable neural network (NN) architectures that appropriately capture the features of the pedestal database. Separate NNs were implemented for each pedestal parameter, and ensembling methods were used to improve the prediction accuracy and allowed estimation of the prediction uncertainty. The pedestal predictions of the test dataset lie within the measurement uncertainties of the pedestal parameters. The NN outperformed simple Linear Regression (LR) analysis, indicating non-linear dependencies in the pedestal structure. The presented achievements illustrate a promising path for future research, using feature extraction to infer experimental trends and thereby improve pedestal models as well as deploying NN for a fast pedestal prediction in DIII-D scenario development.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Prediction of DIII-D Pedestal Structure From Externally Controllable Parameters

The sharp increase of pressure at the edge of a high confinement mode (H-mode) plasma, the pedestal, strongly impacts overall plasma performance. Predicting the pedestal is a necessity to control and optimize tokamak operations. Here, an experimental data-driven machine learning (ML) approach is presented that predicts the pedestal heights and widths of electron density (n e ) and electron temperature (T e ) profiles as well as the separatrix ne from externally controllable parameters such as the plasma shape, heating method and power, and gas puff rate and integrated gas puff. The OMFIT framework was used with DIII-D data to efficiently, robustly, and automatically build a database of pedestal parameters to train machine learning models. Database creation was enabled by the search engine tool for DIII-D data, TokSearch, which parallelizes data fetching, enabling fast searches through basic signals of thousands of DIII-D shots and selection of relevant time intervals. Principal Component Analysis (PCA) separated the database into three clusters that represent classes of plasma shapes that are regularly used in DIII-D. The most important parameters for setting the pedestal structure were plasma current (I p ), toroidal magnetic field (B Φ ), neutral beam heating power (P NBI ) and shaping quantities. The Deep Jointly Informed Neural Networks (DJINN) algorithm was applied to identify suitable neural network (NN) architectures that appropriately capture the features of the pedestal database. Separate NNs were implemented for each pedestal parameter, and ensembling methods were used to improve the prediction accuracy and allowed estimation of the prediction uncertainty. The pedestal predictions of the test dataset lie within the measurement uncertainties of the pedestal parameters. The NN outperformed simple Linear Regression (LR) analysis, indicating non-linear dependencies in the pedestal structure. The presented achievements illustrate a promising path for future research, using feature extraction to infer experimental trends and thereby improve pedestal models as well as deploying NN for a fast pedestal prediction in DIII-D scenario development.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗