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At least 199 records · Page 11

Comparison of Machine Learning-Based Predictive Models of the Nutrient Loads Delivered from the Mississippi/Atchafalaya River Basin to the Gulf of Mexico

Predicting nutrient loads is essential to understanding and managing one of the environmental issues faced by the northern Gulf of Mexico hypoxic zone, which poses a severe threat to the Gulf’s healthy ecosystem and economy. The development of hypoxia in the Gulf of Mexico is strongly associated with the eutrophication process initiated by excessive nutrient loads. Due to the complexities in the excessive nutrient loads to the Gulf of Mexico, it is challenging to understand and predict the underlying temporal variation of nutrient loads. The study was aimed at identifying an optimal predictive machine learning model to capture and predict nonlinear behavior of the nutrient loads delivered from the Mississippi/Atchafalaya River Basin (MARB) to the Gulf of Mexico. For this purpose, monthly nutrient loads (N and P) in tons were collected from US Geological Survey (USGS) monitoring station 07373420 from 1980 to 2020. Machine learning models—including autoregressive integrated moving average (ARIMA), gaussian process regression (GPR), single-layer multilayer perceptron (MLP), and a long short-term memory (LSTM) with the single hidden layer—were developed to predict the monthly nutrient loads, and model performances were evaluated by standard assessment metrics—Root Mean Square Error (RMSE) and Correlation Coefficient (R). The residuals of predictive models were examined by the Durbin–Watson statistic. The results showed that MLP and LSTM persistently achieved better accuracy in predicting monthly TN and TP loads compared to GPR and ARIMA. In addition, GPR models achieved slightly better test RMSE score than ARIMA models while their correlation coefficients are much lower than ARIMA models. Moreover, MLP performed slightly better than LSTM in predicting monthly TP loads while LSTM slightly outperformed for TN loads. Furthermore, it was found that the optimizer and number of inputs didn’t show effects on the LSTM performance while they exhibited impacts on MLP outcomes. This study explores the capability of machine learning models to accurately predict nonlinearly fluctuating nutrient loads delivered to the Gulf of Mexico. Further efforts focus on improving the accuracy of forecasting using hybrid models which combine several machine learning models with superior predictive performance for nutrient fluxes throughout the MARB.

54 ENVIRONMENTAL SCIENCES↗

Super-resolution and segmentation deep learning for breast cancer histopathology image analysis

Traditionally, a high-performance microscope with a large numerical aperture is required to acquire high-resolution images. However, the images’ size is typically tremendous. Therefore, they are not conveniently managed and transferred across a computer network or stored in a limited computer storage system. As a result, image compression is commonly used to reduce image size resulting in poor image resolution. Here, we demonstrate custom convolution neural networks (CNNs) for both super-resolution image enhancement from low-resolution images and characterization of both cells and nuclei from hematoxylin and eosin (H&E) stained breast cancer histopathological images by using a combination of generator and discriminator networks so-called super-resolution generative adversarial network-based on aggregated residual transformation (SRGAN-ResNeXt) to facilitate cancer diagnosis in low resource settings. The results provide high enhancement in image quality where the peak signal-to-noise ratio and structural similarity of our network results are over 30 dB and 0.93, respectively. The derived performance is superior to the results obtained from both the bicubic interpolation and the well-known SRGAN deep-learning methods. In addition, another custom CNN is used to perform image segmentation from the generated high-resolution breast cancer images derived with our model with an average Intersection over Union of 0.869 and an average dice similarity coefficient of 0.893 for the H&E image segmentation results. Finally, we propose the jointly trained SRGAN-ResNeXt and Inception U-net Models, which applied the weights from the individually trained SRGAN-ResNeXt and inception U-net models as the pre-trained weights for transfer learning. The jointly trained model’s results are progressively improved and promising. We anticipate these custom CNNs can help resolve the inaccessibility of advanced microscopes or whole slide imaging (WSI) systems to acquire high-resolution images from low-performance microscopes located in remote-constraint settings.

60 APPLIED LIFE SCIENCES↗

Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization

The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy microbial communities to produce specific products from the different agroindustrial residues. To address this, we fed anaerobic bioreactors one of several agroindustrial residues (carbohydrate-rich lignocellulosic fermentation conversion residue, xylose, dairy manure hydrolysate, ultra-filtered milk permeate, and thin stillage from a starch bioethanol plant) and inoculated them with a microbial community from an acid-phase digester operated at the wastewater treatment plant in Madison, WI, United States. The bioreactors were monitored over a period of months and sampled to assess microbial community composition and extracellular fermentation products. We obtained metagenome assembled genomes (MAGs) from the microbial communities in each bioreactor and performed comparative genomic analyses to identify common microorganisms, as well as any community members that were unique to each reactor. Collectively, we obtained a dataset of 217 non-redundant MAGs from these bioreactors. This metagenome assembled genome dataset was used to evaluate whether a specific microbial ecology model in which medium chain fatty acids (MCFAs) are simultaneously produced from intermediate products (e.g., lactic acid) and carbohydrates could be applicable to all fermentation systems, regardless of the feedstock. MAGs were classified using a multiclass classification machine learning algorithm into three groups, organisms fermenting the carbohydrates to intermediate products, organisms utilizing the intermediate products to produce MCFAs, and organisms producing MCFAs directly from carbohydrates. This analysis revealed common biological functions among the microbial communities in different bioreactors, and although different microorganisms were enriched depending on the agroindustrial residue tested, the results supported the conclusion that the microbial ecology model tested was appropriate to explain the MCFA production potential from all agricultural residues.

60 APPLIED LIFE SCIENCES↗

Conotoxin Prediction: New Features to Increase Prediction Accuracy

Conotoxins are toxic, disulfide-bond-rich peptides from cone snail venom that target a wide range of receptors and ion channels with multiple pathophysiological effects. Conotoxins have extraordinary potential for medical therapeutics that include cancer, microbial infections, epilepsy, autoimmune diseases, neurological conditions, and cardiovascular disorders. Despite the potential for these compounds in novel therapeutic treatment development, the process of identifying and characterizing the toxicities of conotoxins is difficult, costly, and time-consuming. This challenge requires a series of diverse, complex, and labor-intensive biological, toxicological, and analytical techniques for effective characterization. While recent attempts, using machine learning based solely on primary amino acid sequences to predict biological toxins (e.g., conotoxins and animal venoms), have improved toxin identification, these methods are limited due to peptide conformational flexibility and the high frequency of cysteines present in toxin sequences. This results in an enumerable set of disulfide-bridged foldamers with different conformations of the same primary amino acid sequence that affect function and toxicity levels. Consequently, a given peptide may be toxic when its cysteine residues form a particular disulfide-bond pattern, while alternative bonding patterns (isoforms) or its reduced form (free cysteines with no disulfide bridges) may have little or no toxicological effects. Similarly, the same disulfide-bond pattern may be possible for other peptide sequences and result in different conformations that all exhibit varying toxicities to the same receptor or to different receptors. We present here new features, when combined with primary sequence features to train machine learning algorithms to predict conotoxins, that significantly increase prediction accuracy.

collisional cross section↗

Discovery of Self-Assembling π-Conjugated Peptides by Active Learning-Directed Coarse-Grained Molecular Simulation

Electronically active organic molecules have demonstrated great promise as novel soft materials for energy harvesting and transport. Self-assembled nanoaggregates formed from π-conjugated oligopeptides composed of an aromatic core flanked by oligopeptide wings offer emergent optoelectronic properties within a water-soluble and biocompatible substrate. Nanoaggregate properties can be controlled by tuning core chemistry and peptide composition, but the sequence–structure–function relations remain poorly characterized. Here, we employ coarse-grained molecular dynamics simulations within an active learning protocol employing deep representational learning and Bayesian optimization to efficiently identify molecules capable of assembling pseudo-1D nanoaggregates with good stacking of the electronically active π-cores. We consider the DXXX-OPV3-XXXD oligopeptide family, where D is an Asp residue and OPV3 is an oligophenylenevinylene oligomer (1,4-distyrylbenzene), to identify the top performing XXX tripeptides within all 20 3 = 8000 possible sequences. By direct simulation of only 2.3% of this space, we identify molecules predicted to exhibit superior assembly relative to those reported in prior work. Spectral clustering of the top candidates reveals new design rules governing assembly. This work establishes new understanding of DXXX-OPV3-XXXD assembly, identifies promising new candidates for experimental testing, and presents a computational design platform that can be generically extended to other peptide-based and peptide-like systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Patch-Based Convolutional Neural Networks for Multiple Microstructural Features Detection in FIB-SEM Micrographs of Irradiated Nuclear Fuel

Focused ion beam scanning electron microscopy (FIB-SEM) tomography has increasingly been utilized for acquiring three-dimensional (3D) microstructure features at the sub-micron scale in irradiated nuclear materials. This technique involves sequential ion beam slicing followed by electron beam imaging and compositional mapping using energy dispersive spectroscopy (EDS). Despite its growing use, several challenges persist. These include the time-intensive nature of data collection of EDS data, difficulties in distinguishing between various microstructures, and issues with image alignment. These challenges currently limit the broader application of FIB-SEM tomography in the field. To overcome these limitations, we propose using convolutional neural networks (CNNs) to automate microstructure identification in SEM images. Our study introduces a new framework for identifying microstructures in irradiated U-10Zr (wt. %) metallic fuel with limited annotated data. The framework includes the creation of a reliable annotated dataset with paired SEM and ground truth data from EDS maps, the applications of CNNs for microstructure identification, and the validation of model performance. Specifically, we employed the Segment Anything Model (SAM) to align SEM images with corresponding EDS maps and focused ion beam (FIB) tomography SEM data. We evaluate several models, including Patch-based U-Net, Attention U-Net, and Residual U-Net, finding that patch-based U-Net exhibits superior segmentation performance and consistency. This approach reduces reliance on EDS detectors and aids in accelerating nuclear material analysis process, highlighting the potential of advanced deep learning techniques to improve microstructural understanding in nuclear material. This is the first framework to integrate SAM and Patch-based CNN models for semantic segmentation of irradiated nuclear materials, with potential applicability to other tomography datasets.

36 - MATERIALS SCIENCE↗

NASA Composite Materials Development: Lessons Learned and Future Challenges

Composite materials have emerged as the materials of choice for increasing the performance and reducing the weight and cost of military, general aviation, and transport aircraft and space launch vehicles. Major advancements have been made in the ability to design, fabricate, and analyze large complex aerospace structures. The recent efforts by Boeing and Airbus to incorporate composite into primary load carrying structures of large commercial transports and to certify the airworthiness of these structures is evidence of the significant advancements made in understanding and use of these materials in real world aircraft. NASA has been engaged in research on composites since the late 1960 s and has worked to address many development issues with these materials in an effort to ensure safety, improve performance, and improve affordability of air travel for the public good. This research has ranged from synthesis of advanced resin chemistries to development of mathematical analyses tools to reliably predict the response of built-up structures under combined load conditions. The lessons learned from this research are highlighted with specific examples to illustrate the problems encountered and solutions to these problems. Examples include specific technologies related to environmental effects, processing science, fabrication technologies, nondestructive inspection, damage tolerance, micromechanics, structural mechanics, and residual life prediction. The current state of the technology is reviewed and key issues requiring additional research identified. Also, grand challenges to be solved for expanded use of composites in aero structures are identified.

Tenney, Darrel R.↗

The Spaceport Command and Control System Security Assessor Project

This Summer, I worked as a National Aeronautics and Space Administration (NASA) Internships and Fellowships (NIF) intern under my mentor, Jill Giles within the Software Engineering Branch. Within this project, I worked alongside the Cyber Security branch to identify a list of Commercial Off the Shelf (COTS) software to analyze, research, and gain insight about potential vulnerabilities within the software that could become a threat of attack. After identifying the list of COTS software, my team and I used Microsoft Excel to create a worksheet to easily organize and design a questionnaire about the software. Security reports weregiven to us to identify the software used on the machines in the firing rooms. With these reports, we created a script that would populate the database with the software information to identify potential security weaknesses of COTS software.The goal of the project was to produce a final report, summarizing the most vulnerable launch control system servers and configurations and document vulnerabilities, residual risk, likelihood, and consequence. This project is important for the Cyber Security and Information Technology branches because it will identify security weaknesses and help to mitigate risk. From the Spaceport Command and Control System Security Assessor Project, I learned how to properly identify weaknesses and vulnerabilities within software and how to mitigate the risks within the software. This project also taught me how to create databases using scripts and input files.

Destani Satora Van Arsdalen↗

A Nonergodic Ground-Motion Model for the San Francisco Bay Area for Small-Magnitude Earthquakes

ABSTRACT Recently, generative models have become a computationally efficient alternative to physics-based numerical simulations of ground motions. Neural networks can learn from existing ground-motion data to generate unobserved ground-motion data at new source and site locations. A key challenge with generative models is ensuring that predicted ground motions remain within a physically realistic range. For this purpose, we developed an empirical, nonergodic ground-motion model (GMM) for small-magnitude earthquakes in the San Francisco Bay area based on about 5000 recordings per component for Mw ≤ 4 earthquakes. The nonergodic GMM predicts spatially varying median source, site, and path effects for both the Fourier amplitude spectrum (FAS) and the Fourier phase derivative (a proxy for duration), as well as the corresponding epistemic uncertainty for each term. For FAS, our model shows above-average source and site effects in the western part of the region and below-average effects in the eastern part, with regional effects exhibiting larger spatial correlation lengths with increasing frequency. For duration, the source term is negligible for small-magnitude earthquakes, and the site term leads to site-specific variations up to 5 s. Path effects for FAS and duration depend on the source–site pair and are extrapolated spatially using recent methods for path-effect modeling. The aleatory variability of the within-site within-path residuals is similar to the variability found in previous studies for other regions. The nonergodic model provides two key contributions: first, median adjustment terms that are transferable to larger magnitude earthquakes, further reducing aleatory variability in probabilistic seismic hazard analysis; second, region-specific criteria for validating machine learning-based ground-motion generators to evaluate whether synthetic ground motions exhibit physically realistic source, site, and path effects.

Lacour, Maxime↗

The geometry of signal space: a case study of direct mapping between seismic signals and event distribution

SUMMARY Under favourable circumstances, seismic waveforms corresponding to an ensemble of events related by a common, spatially distributed process collectively exhibit a regular, signal-space geometry. When events in the ensemble have a common, or nearly common, source mechanism, this geometry is a distorted image of the distribution of events in the source region. The signal-space image can be visualized using a relatively simple waveform alignment and projection operation. Ensemble waveform correlation measurements can be inverted to estimate the distribution of the events in the source region, up to an arbitrary rotation, reflection and scaling, with residual distortion. We demonstrate these concepts with synthetic waveforms and with observations of long-wall mining induced seismicity for which substantial ground truth information is available. Our experience with these data has implications for location, correlation detection and machine learning and possible application to studies of repeating events in induced, volcanic and glacial seismicity. Our results place limits on the widely held assumption that waveform correlation is a useful measure of event separation. We suggest that the constraints on event separation need to be evaluated in the context of a population of related events, whose waveforms sample the signal space image of the source region. A better indicator of event separation is the length of the shortest path in signal space along the image.

58 GEOSCIENCES↗

Deep-learning-based image registration for nano-resolution tomographic reconstruction

Nano-resolution full-field transmission X-ray microscopy has been successfully applied to a wide range of research fields thanks to its capability of non-destructively reconstructing the 3D structure with high resolution. Due to constraints in the practical implementations, the nano-tomography data is often associated with a random image jitter, resulting from imperfections in the hardware setup. Without a proper image registration process prior to the reconstruction, the quality of the result will be compromised. Here a deep-learning-based image jitter correction method is presented, which registers the projective images with high efficiency and accuracy, facilitating a high-quality tomographic reconstruction. This development is demonstrated and validated using synthetic and experimental datasets. We report the method is effective and readily applicable to a broad range of applications. Together with this paper, the source code is published and adoptions and improvements from our colleagues in this field are welcomed.

deep learning↗

Forecast of Wildfire Potential Across California USA Using a Transformer

Wildfires are a major issue facing the United States, a matter further exacerbated by an ever-changing climate. In California alone, wildfires are responsible for billions of dollars in damages and take lives each year. Accurately predicting fire danger conditions allows preparation awareness before wildfires start. Transformers are a class of deep learning models designed to identify patterns in sequential datasets. In recent years, transformers have gained popularity through their impressive performance in natural language processing and other applications of signal recognition. This analysis demonstrates the ability of a transformer with a residual connection to forecast fire danger potential over the state of California. Wildland fire potential index (WFPI) maps collected from the US Geological Survey database from January 1st 2020 to December 31st 2023 were used to tune, train and evaluate the transformer. Meteorological inputs (provided by Daymet daily weather and climatological summaries), the normalized difference vegetation index (NDVI) (calculated from the Moderate Resolution Imaging Spectroradiometer (MODIS)), and outputs from the Scott and Burgman fire behavior fuel models (to characterize maps of fuel types), were used as inputs. Our results show that a transformer can effectively emulate the US Forest Service modeled WFPI maps of California USA for four week long forecasts over the month of July, 2023, with correlations ranging from 0.85 – 0.98.

Limber, Russell [ORNL]↗

LL18-Signal Analysis-NDD2Ad (Final Report)

Under favorable circumstances, seismic waveforms corresponding to an ensemble of events related by a common, spatially-distributed process collectively exhibit a regular, signal-space geometry. When events in the ensemble have a common, or nearly common, source mechanism, this geometry is a distorted image of the distribution of events in the source region. The signal space image can be visualized using a relatively simple waveform alignment and projection operation. Ensemble waveform correlation measurements can be inverted to estimate the distribution of the events in the source region, up to an arbitrary rotation, reflection, and scaling with residual distortion. We demonstrate these concepts with synthetic waveforms and with observations of long-wall mining induced seismicity for which substantial ground truth information is available. Our experience with these data has implications for location, correlation detection and machine learning, and possible application to studies of repeating events in induced, volcanic, and glacial seismicity. Our results place limits on the widely-held assumption that waveform correlation is a useful measure of event separation. We suggest that the constraints on event separation need to be evaluated in the context of a population of related events, whose waveforms sample the signal space image of the source region. A better indicator of event separation is the length of the shortest path in signal space along the image.

58 GEOSCIENCES↗

Scaling Resolution of Gigapixel Whole Slide Images Using Spatial Decomposition on Convolutional Neural Networks

Gigapixel images are prevalent in scientific domains ranging from remote sensing, and satellite imagery to microscopy, etc. However, training a deep learning model at the natural resolution of those images has been a challenge in terms of both, overcoming the resource limit (e.g. HBM memory constraints), as well as scaling up to a large number of GPUs. In this paper, we trained Residual neural Networks (ResNet) on 22,528 x 22,528-pixel size images using a distributed spatial decomposition method on 2,304 GPUs on the Summit Supercomputer. We applied our method on a Whole Slide Imaging (WSI) dataset from The Cancer Genome Atlas (TCGA) database. WSI images can be in the size of 100,000 x 100,000 pixels or even larger, and in this work we studied the effect of image resolution on a classification task, while achieving state-of-the-art AUC scores. Moreover, our approach doesn't need pixel-level labels, since we're avoiding patching from the WSI images completely, while adding the capability of training arbitrary large-size images. This is achieved through a distributed spatial decomposition method, by leveraging the non-block fat-tree interconnect network of the Summit architecture, which enabled GPU-to-GPU direct communication. Finally, detailed performance analysis results are shown, as well as a comparison with a data-parallel approach when possible.

Tsaris, Aristeidis (aris)↗

Fast-RF-Shimming: Accelerate RF shimming in 7T MRI using deep learning

Ultrahigh field (UHF) Magnetic Resonance Imaging (MRI) offers an elevated signal-to-noise ratio (SNR), enabling exceptionally high spatial resolution that benefits both clinical diagnostics and advanced research. However, the jump to higher fields introduces complications, particularly transmit radiofrequency (RF) field ($B^{+}_{1}$) inhomogeneities, manifesting as uneven flip angles and image intensity irregularities. These artifacts can degrade image quality and impede broader clinical adoption. Traditional RF shimming methods, such as Magnitude Least Squares (MLS) optimization, effectively mitigate $B^{+}_{1}$ inhomogeneity, but remain time-consuming. Recent machine learning approaches, including RF Shim Prediction by Iteratively Projected Ridge Regression and other deep learning architectures, suggest alternative pathways. Although these approaches show promise, challenges such as extensive training periods, limited network complexity, and practical data requirements persist. In this paper, we introduce a holistic learning-based framework called Fast-RF-Shimming, which achieves a 5000 ​× ​speed-up compared to the traditional MLS method. In the initial phase, we employ random-initialized Adaptive Moment Estimation (Adam) to derive the desired reference shimming weights from multi-channel $B^{+}_{1}$ fields. Next, we train a Residual Network (ResNet) to map $B^{+}_{1}$ fields directly to the ultimate RF shimming outputs, incorporating the confidence parameter into its loss function. Finally, we design Non-uniformity Field Detector (NFD), an optional post-processing step, to ensure the extreme non-uniform outcomes are identified. Comparative evaluations with standard MLS optimization underscore notable gains in both processing speed and predictive accuracy, which indicates that our technique shows a promising solution for addressing persistent inhomogeneity challenges.

Deep learning↗

Improved naive Bayesian probability classifier in predictions of nuclear mass

Recently, novel statistical methods such as neural networks and Bayesian learning methods are implemented to describe the nuclear masses. Based on previous studies, an improved naive Bayesian probability (iNBP) classifier is proposed to study the nuclear masses by refining the results of sophisticated nuclear models. In the iNBP method, the prediction for nuclear masses is treated as a classification problem. The residuals are classified into several groups to generate prior and conditional probabilities, and the posterior probabilities are further determined by the Bayesian formula. We choose the expectation with maximum probability as the final prediction. Reliability of the iNBP method is assessed by analyzing the global optimizations and the extrapolating capabilities. Here, the iNBP method exhibits impressive improvements on global descriptions for different mass models. Moreover, the method shows robust extrapolating capabilities. Results demonstrate the iNBP method can be applied to predict the nuclear masses of unknown regions. Considering the local mass relations, the iNBP method can offer considerable fine-tuning of the mass descriptions from nuclear models. The methodology proposed in this paper can also be applied to other model-based extrapolations of nuclear observables.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Oxygen Compatibility and Challenge Testing of the PLSS Variable Oxygen Regulator (VOR) for the Advanced EMU

The Variable Oxygen Regulator (VOR), a stepper actuated two-stage mechanical regulator, is being developed for the purpose of serving as the Primary Oxygen Regulator (POR) and Secondary Oxygen Regulator (SOR) within the Advanced EMU PLSS, now referred to as the xEMU and xPLSS. Three prototype designs have been fabricated and tested as part of this development. Building upon the lessons learned from the 35 years of Shuttle/ISS EMU Program operation including the fleet-wide EMU Secondary Oxygen Pack (SOP) contamination failure that occurred in 2000, the VOR is being analyzed, designed, and tested for oxygen compatibility with controlled Non-Volatile Residue (NVR) and a representative worst-case hydro-carbon system contamination event (>100mg/sq ft dodecane). This paper discusses the steps taken in testing of VOR 2.0 with for oxygen compatibility and then discusses follow-on design changes implemented in the VOR 3.0 (3rd prototype) as a result.

Campbell, Colin↗

Lessons Learned—Lithium Silicide Hydration Fire

Alkali metals, such as lithium, sodium, potassium, etc., are highly reactive elements. While researchers generally handle these metals with caution, less caution is taken when these elements have been “reacted”. In this work, a recent incident is examined in which a pair of researchers ignited a lithium silicide alloy sample that was assumed to be fully hydrated to lithium hydroxide and, thereby, no longer water-reactive. However, variations in the original chemical composition of the lithium compounds examined resulted in select mixtures failing to hydrate and react completely to lithium hydroxide in the time frame allowed. This gave rise to residual unreacted, water-sensitive lithium silicide which resulted in a violent exothermic reaction with water and autoignition of the produced hydrogen gas. This Article describes this incident and improvements that can be implemented to prevent similar incidents from occurring.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗