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At least 37 records · Page 2

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↗

Evaluating offshore legacy wells for geologic carbon storage: A case study from the Galveston and Brazos areas in the Gulf of Mexico

In this article, federal offshore waters in the Gulf of Mexico are of interest for large-scale geologic carbon storage (GCS). However, more than 80,000 offshore oil and gas wells exist in the region, which could impact the integrity of sealing intervals. In this study, we propose a screening methodology for ranking offshore legacy wells based on the challenge they may present to GCS. The methodology relies on the review of well regulatory records to 1) identify leakage pathways and assess the potential hazards that wells pose to planned GCS operations, 2) evaluate well features that impact the accessibility of wells to determine the feasibility of potential corrective actions, and 3) rank wells based on the overall challenge they may pose for GCS. We demonstrate our framework by evaluating the construction and abandonment of 156 wells across eight areas of interest (AOIs) in shallow federal waters along the Texas Gulf Coast. The majority (99.3 %) of wells considered were constructed and plugged in a manner that did not isolate prospective GCS targets in the Upper and Lower Miocene formations and may potentially require a challenging or uncertain corrective action prior to GCS. Dataset trends suggest that the observed well construction and plugging designs may be common in shallow offshore federal waters along the Texas Gulf Coast. Consequently, operators pursuing offshore GCS projects in the region may consider selecting areas that avoid challenging wells or performing robust evaluations of legacy well leakage risks to plan corrective action prior to CO 2 injection.

58 GEOSCIENCES↗

Improving deep learning performance for predicting large-scale geological ${{CO}_{2}}$ sequestration modeling through feature coarsening

Physics-based reservoir simulation for fluid flow in porous media is a numerical simulation method to predict the temporal-spatial patterns of state variables (e.g. pressure p) in porous media, and usually requires prohibitively high computational expense due to its non-linearity and the large number of degrees of freedom (DoF). This work describes a deep learning (DL) workflow to predict the pressure evolution as fluid flows in large-scale 3-dimensional(3D) heterogeneous porous media. In particular, we develop an efficient feature coarsening technique to extract the most representative information and perform the training and prediction of DL at the coarse scale, and further recover the resolution at the fine scale by spatial interpolation. We validate the DL approach to predict pressure field against physics-based simulation data for a field-scale 3D geologic CO 2 sequestration reservoir model. We evaluate the impact of feature coarsening on DL performance, and observe that the feature coarsening not only decreases the training time by >74% and reduces the memory consumption by >75%, but also maintains temporal error 0.63% on average. Besides, the DL workflow provides predictive efficiency with 1406 times speedup compared to physics-based numerical simulation. The key findings from this research significantly improve the training and prediction efficiency of deep learning model to deal with large-scale heterogeneous reservoir models, and thus it can also be further applied to accelerate workflows of history matching and reservoir optimization for close-loop reservoir management.

58 GEOSCIENCES↗

A meshing framework for digital twins for extrusion based additive manufacturing

Additive manufacturing (AM) allows for manufacturing of complex three-dimensional geometries not typically realizable with standard manufacturing practices. The internal microstructure of AM components has a significant impact on mechanical, vibrational, and shock properties and permits richer design space when this is controllable. Due to complex interactions of internal geometry of an extrusion-based AM component, it is common practice to assume homogeneous behavior or to perform characterization testing on specific toolpath configurations. To avoid testing or material waste, it is necessary to develop a consistently accurate numerical simulation framework with relevant boundary value problems that can handle the complicated geometry of internal material microstructure present in AM components. Herein, a framework is proposed to directly create computational meshes suitable for finite element analysis (FEA) of the fine-scale features generated from extrusion-based AM tool paths to maintain a strong process–structure–property-performance linkage. This mesh can be manually or automatically analyzed using standard FEA simulations such as quasi-static preloading or modal analysis. The framework allows an in-silico assessment of a target AM geometry where fine-scale features greatly impact quantities of design interest such as in soft elastomeric lattices where toolpath infill can greatly influence the self-contact of a structure in compression, which we use as a motivating exemplar. This approach greatly reduces both time and resource waste present in traditional build and test design cycles for non-intuitive design spaces, and acts as a tool for use in the production of a key component of a digital twin, a mesh suitable for finite element analysis. In conclusion, it also further allows for the exploration of toolpath infill to optimize component properties beyond simple linear properties such as density and stiffness.

Additive manufacturing↗

The benefits of CMB delensing

The effects of gravitational lensing of the cosmic microwave background (CMB) have been measured at high significance with existing data and will be measured even more precisely in future surveys. Reversing the effects of lensing on the observed CMB temperature and polarization maps provides a variety of benefits. Delensed CMB spectra have sharper acoustic peaks and more prominent damping tails, allowing for improved inferences of cosmological parameters that impact those features. Delensing reduces B-mode power, aiding the search for primordial gravitational waves and allowing for lower variance reconstruction of lensing and other sources of secondary CMB anisotropies. Lensing-induced power spectrum covariances are reduced by delensing, simplifying analyses and improving constraints on primordial non-Gaussianities. Biases that result from incorrectly modeling nonlinear and baryonic feedback effects on the lensing power spectrum are mitigated by delensing. All of these benefits are possible without any changes to experimental or survey design. Here, we develop a self-consistent, iterative, all-orders treatment of CMB delensing on the curved sky and demonstrate the impact that delensing will have with future surveys.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Data efficiency assessment of generative adversarial networks in energy applications

This study investigates the data requirements of generative artificial intelligence (AI), particularly generative adversarial networks (GANs), for reliable data augmentation in energy applications. Generative AI, though seen as a solution to data limitations, requires substantial data to learn meaningful distributions—a challenge often overlooked. This study addresses the challenge through synthetic data generation for critical heat flux (CHF) and power grid demand, focusing on renewable and nuclear energy. Two variants of GAN employed are conditional GAN (cGAN) and Wasserstein GAN (wGAN). Our findings include the strong dependency of GAN on data size, with performance declining on smaller datasets and varying performance when generalizing to unseen experiments. Mass flux and heated length significantly influence CHF predictions. wGAN is more robust to feature exclusion, making it suitable for constrained synthetic data generation. In energy demand forecasting, wGAN performed well for solar, wind, and load predictions. Longer lookback hours and larger datasets improved predictions, especially for load power. Seasonal variations posed challenges, with wGAN achieving a relatively high error of Root Mean Squared Error (RMSE) of 0.32 for load power prediction, compared to RMSE of 0.07 under same-season conditions. Feature exclusions impacted cGAN the most, while wGAN showed greater robustness. This study concludes that, while generative AI is effective for data augmentation, it requires substantial data and careful training to generate realistic synthetic data and generalize to new experiments in engineering applications.

22 - GENERAL STUDIES OF NUCLEAR REACTORS↗

Multimodal Nanoscale Mapping of Local Structure and CO 2 Adsorption in Metal–Organic Frameworks

Diamine functionalization of the metal−organic framework Mg 2 (dobpdc) (dobpdc 4− = 4,4′-dioxidobiphenyl-3,3′-dicarboxylate) significantly enhances its selectivity for CO 2 capture from flue gases and air. The structure and CO 2 capacity of such materials are typically assessed using bulk techniques that rely on averaging signal over large ensembles of unit cells, obscuring local heterogeneities, such as variations in CO 2 occupancy across individual nanocrystals. To resolve this limitation, we demonstrate a multimodal, nanoscale characterization of Mg 2 (dobpdc) appended with 1,3-diaminopropane. By employing recently developed characterization techniques at progressively smaller length scales, we uncover insights from correspondingly smaller populations of unit cells. First, we use parallel-beam 3D electron diffraction (3D ED) to identify a prominent expansion in lattice parameters upon desorption of CO 2 , as observed at the level of single nanocrystals. Second, we use convergent-probe 4D scanning transmission electron microscopy (4D-STEM) to quantify associated differences in lattice strain as a function of gas loading and diamine appending. These measurements sample small subvolumes within individual nanocrystals. Finally, we apply infrared scattering scanning near-field optical microscopy (IR s- SNOM) to confirm variable CO 2 chemisorption across adsorption sites at the surface of single nanocrystals. This multimodal, multiscale approach allows us to map heterogeneity within individual nanocrystals. Collectively, these findings emphasize the importance of local, nanoscale characterization of metal−organic frameworks in revealing previously unresolvable features that impact their performance.

Karstens, Sarah L. [University of California, Berk↗

Genome dependent Cas9/gRNA search time underlies sequence dependent gRNA activity

Abstract CRISPR-Cas9 is a powerful DNA editing tool. A gRNA directs Cas9 to cleave any DNA sequence with a PAM. However, some gRNA sequences mediate cleavage at higher efficiencies than others. To understand this, numerous studies have screened large gRNA libraries and developed algorithms to predict gRNA sequence dependent activity. These algorithms do not predict other datasets as well as their training dataset and do not predict well between species. Here, to better understand these discrepancies, we retrospectively examine sequence features that impact gRNA activity in 44 published data sets. We find strong evidence that gRNA sequence dependent activity is largely influenced by the ability of the Cas9/gRNA complex to find the target site rather than activity at the target site and that this drives sequence dependent differences in gRNA activity between different species. This understanding will help guide future work to understand Cas9 activity as well as efforts to identify optimal gRNAs and improve Cas9 variants.

59 BASIC BIOLOGICAL SCIENCES↗

Ultrafast Bragg coherent diffraction imaging of epitaxial thin films using deep complex-valued neural networks

Abstract Domain wall structures form spontaneously due to epitaxial misfit during thin film growth. Imaging the dynamics of domains and domain walls at ultrafast timescales can provide fundamental clues to features that impact electrical transport in electronic devices. Recently, deep learning based methods showed promising phase retrieval (PR) performance, allowing intensity-only measurements to be transformed into snapshot real space images. While the Fourier imaging model involves complex-valued quantities, most existing deep learning based methods solve the PR problem with real-valued based models, where the connection between amplitude and phase is ignored. To this end, we involve complex numbers operation in the neural network to preserve the amplitude and phase connection. Therefore, we employ the complex-valued neural network for solving the PR problem and evaluate it on Bragg coherent diffraction data streams collected from an epitaxial La 2-x Sr x CuO 4 (LSCO) thin film using an X-ray Free Electron Laser (XFEL). Our proposed complex-valued neural network based approach outperforms the traditional real-valued neural network methods in both supervised and unsupervised learning manner. Phase domains are also observed from the LSCO thin film at an ultrafast timescale using the complex-valued neural network.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Automating neutron resonances classification with Machine Learning [Slides]

Team reported the following accomplishments: the development of a Machine-Learning method to properly assign spins to neutron resonances (automated, general, reproducible); full integration with evaluated resonances in the Atlas (automation of new editions); training and optimization in synthetic data; validation and deployment to real experimental resonances. Future perspectives include exploration of other classifiers and hyper-parameter combinations, further validation with well-known nucleus (e.g. 235 U), and publication pipeline.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Using Geophysical Information to Investigate Subsurface Structure within the High-Hydraulic Conductivity Analysis Zone

Within the 200 East Area of the Central Plateau and southeastward toward the Columbia River, a high-hydraulic conductivity zone (HCZ) has been interpreted to extend through the 200-PO-1 and 200-BP-5 operable units on the Hanford Site. The HCZ is a controlling hydraulic feature that impacts groundwater flow out of the 200 East Area and the fate of eastwardly migrating plumes from the 200 West Area. The lateral extent of the HCZ is highly uncertain, and despite strong evidence for the existence of the HCZ based on water-level data and contaminant plume tracking, there is still a limited understanding of how to define its boundaries. To provide additional information on the nature and extent of the HCZ, three surface geophysical methods – electrical resistivity tomography (ERT), time-domain electromagnetics (TEM), and seismic methods – were used to collect data south of 200 East. In addition, existing data from 200 East, consisting of surface seismic data, a borehole check shot survey in 699-37-47A, and borehole stratigraphic interpretations, were used to aid interpretations of newly collected seismic data south of 200 East. This work presumed that the contrast in subsurface geophysical properties would be a first-order aid identifying a transmissive zone(s) within the HCZ analysis area by imaging contrasts and/or anomalies in geophysical properties. While seismic, ERT, and TEM methods have sensitivity to overlapping physical properties (porosity, moisture content, lithology), the resolution and physics used to acquire each of these datasets are different, and therefore the information can also be different. Figure S.1 shows the locations of the geophysical data considered in this report.

58 GEOSCIENCES↗

Processes in Salt Repositories for Radioactive Waste Disposal

This document summarizes the key processes (thermal, hydrological, mechanical, and chemical; THMC) impacting the features of a deep geological repository for radioactive waste in salt. Some processes are natural and on-going whether the repository is there or not, and other processes are driven by the perturbation associated with the repository. The features considered here include both engineered and natural components of the repository system. The engineered barrier system (EBS) in a salt repository is quite different from those implemented for a repository in clay or crystalline rocks, because it is comprised mostly of granular salt and salt-compatible cements, rather than bentonite. When compared to other rocks (i.e., silicates), salt has unique properties that make it an excellent potential host rock. Openings and fractures in salt creep closed readily. Salt has high thermal conductivity, which can reduce peak temperatures. Additionally, far away from the excavations the porosity of salt is unconnected, which leads to essentially zero advective or diffusive transport. The small amount of hypersaline brine occurring in salt minimizes microbial activity, reduces colloid-assisted transport, and eliminates in-package criticality (i.e., chloride is a neutron poison). At the end of the report, we present a brief outline for a potential salt repository, including considerations avoided in previous repository disposal concepts. We propose considering higher-temperature processes in future disposal concepts, rather than trying to minimize the thermal perturbation of the repository. Since hot salt is drier, a dry repository would limit corrosion, gas generation, and solute transport. Openings and fractures creep shut faster in hot salt. Therefore, higher temperatures could be seen as beneficial, rather than something to minimize, through increased spacing between waste packages (increasing repository costs).

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

High-temperature thermal imaging to inform the arc-melt synthesis of nuclear materials

The advancement of nuclear energy technology necessitates the development of novel materials and synthesis methods to produce materials which enable new fuel cycles. Alongside the maturation of R&D scale technologies to produce these materials, there is an ongoing effort to develop in situ monitoring capabilities to reduce the time to the discovery and development of these fuels. Monitoring data can be leveraged in artificial intelligence platforms to detect phenomena which lead to varied macro- and microstructural features which impact the application and performance of samples synthesized. The present study presents early-stage findings of the implementation of high-temperature, high-frame-rate infrared thermal imaging to monitor the arc-melt synthesis of novel fuels and compounds relevant to advanced nuclear reactors. The study illustrates both the challenges and opportunities of this methodology, highlighting the importance of internal standards while determining emissivity and transmission values as well as visualizing volatilization during melt synthesis.

Stone, Jordan↗

Performance evaluation of automated data-driven feature extraction and selection methods for practical and scalable building energy consumption prediction models

Here, this study quantifies the impact of automated feature engineering methods (feature extraction and selection) on the quality and accuracy of machine learning models that predict building energy consumption. The case study compares model performance for three main scenarios: baseline (no feature extraction and selection), feature extraction only, and feature extraction combined with feature selection (filter and/or wrapper methods) for fully trained machine learning models for 200 metered/sub-metered energy measurements across 118 real buildings. For consistency, the same machine learning model architecture (a black box deep learning neural network with probabilistic forecast output) was used for all scenarios. Based on results, all feature engineering methods provided noticeable prediction accuracy improvements (e.g., 29%-68% median prediction improvement) compared to baseline scenarios. However, in this application, feature selection methods provide little practical value due to their limited performance gains and high computational cost. Smarter algorithm development supported by better computational environments will be needed before feature selection methods can reliably and efficiently improve predictive model performance.

97 MATHEMATICS AND COMPUTING↗

Feature Selection Techniques for a Machine Learning Model to Detect Autonomic Dysreflexia

Feature selection plays a crucial role in the development of machine learning algorithms. Understanding the impact of the features on a model, and their physiological relevance can improve the performance. This is particularly helpful in the healthcare domain wherein disease states need to be identified with relatively small quantities of data. Autonomic Dysreflexia (AD) is one such example, wherein mismanagement of this neurological condition could lead to severe consequences for individuals with spinal cord injuries. We explore different methods of feature selection needed to improve the performance of a machine learning model in the detection of the onset of AD. We present different techniques used as well as the ideal metrics using a dataset of thirty-six features extracted from electrocardiograms, skin nerve activity, blood pressure and temperature. The best performing algorithm was a 5-layer neural network with five relevant features, which resulted in 93.4% accuracy in the detection of AD. The techniques in this paper can be applied to a myriad of healthcare datasets allowing forays into deeper exploration and improved machine learning model development. Through critical feature selection, it is possible to design better machine learning algorithms for detection of niche disease states using smaller datasets.

electrocardiography↗

Design optimization of integrated cooling inserts in modular Fischer-Tropsch reactors

Sustainable production of liquid fuels and feedstocks from atmospheric CO 2 through carbon recycling technologies is necessary to broaden decarbonization efforts and further reduce global emissions. Fischer–Tropsch (FT) reactors can address this challenge by providing storable, high-value liquid hydrocarbon fuels and feedstocks from syngas generated through reductive CO 2 utilization. FT technology, however, is most cost effective at large-scale, fixed-site plants and does not effectively address the smaller, globally distributed CO 2 point sources. Alternatively, smaller, modular reactors can be composed together to the specific scale of the emission source, yielding a flexible solution that enables more widespread deployment. In these modular reactors, thermal management using a finned cooling insert embedded within the catalyst matrix is critical to maintaining the performance and viability. Thus, in this work, topology optimization is used to determine the cooling insert geometry that maximizes reactor productivity while preventing auto-thermal runaway. Optimal designs are generated for varying number of constituent fins and over a range of maximum operating temperatures. Constraints including minimum feature length-scales and prescribed cooling insert material are imposed on the designs to enhance manufacturability. The impact of design features such as insert tapering and increased length scale hierarchy is automatically revealed by the systematic design framework employed. Here, this approach thus generates novel optimal geometries while automating, accelerating, and enhancing the design process compared to traditional heuristic approaches for cooling insert design in modular FT reactors.

30 DIRECT ENERGY CONVERSION↗

Signatures of large-scale cold fronts in the optically-selected merging cluster HSC J085024+001536

Abstract We represent a joint X-ray, weak-lensing, and optical analysis of the optically-selected merging cluster, HSC J085024+001536, from the Subaru HSC-SSP survey. Both the member galaxy density and the weak-lensing mass map show that the cluster is composed of south-east and north-west components. The two-dimensional weak-lensing analysis shows that the south-east component is the main cluster, and the sub-cluster and main cluster mass ratio is $0.32^{+0.75}_{-0.23}$. The north-west sub-cluster is offset by ∼700 kpc from the main cluster center, and their relative line-of-sight velocity is ∼1300 km s−1 from spectroscopic redshifts of member galaxies. The X-ray emission is concentrated around the main cluster, while the gas mass fraction within a sphere of 1′ radius of the sub-cluster is only $f_{\mathrm{gas}}=4.0^{+2.3}_{-3.3}\%$, indicating that the sub-cluster gas was stripped by ram pressure. An X-ray residual image shows three arc-like excess patterns, of which two are symmetrically located at ∼550 kpc from the X-ray morphological center, and the other is close to the X-ray core. The excess close to the sub-cluster has a cold-front feature where dense-cold gas and thin-hot gas contact. The two outer excesses are tangentially elongated about ∼450–650 kpc, suggesting that the cluster is merged with a non-zero impact parameter. Overall features revealed by the multi-wavelength datasets indicate that the cluster is at the second impact or later. Since the optically-defined merger catalog is unbiased for merger boost of the intracluster medium, X-ray follow-up observations will pave the way to understand merger physics at various phases.

Tanaka, Keigo↗