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At least 289 records · Page 16

Efficiency of parallel direct optimization

Tremendous progress has been made at the level of sequential computation in phylogenetics. However, little attention has been paid to parallel computation. Parallel computing is particularly suited to phylogenetics because of the many ways large computational problems can be broken into parts that can be analyzed concurrently. In this paper, we investigate the scaling factors and efficiency of random addition and tree refinement strategies using the direct optimization software, POY, on a small (10 slave processors) and a large (256 slave processors) cluster of networked PCs running LINUX. These algorithms were tested on several data sets composed of DNA and morphology ranging from 40 to 500 taxa. Various algorithms in POY show fundamentally different properties within and between clusters. All algorithms are efficient on the small cluster for the 40-taxon data set. On the large cluster, multibuilding exhibits excellent parallel efficiency, whereas parallel building is inefficient. These results are independent of data set size. Branch swapping in parallel shows excellent speed-up for 16 slave processors on the large cluster. However, there is no appreciable speed-up for branch swapping with the further addition of slave processors (>16). This result is independent of data set size. Ratcheting in parallel is efficient with the addition of up to 32 processors in the large cluster. This result is independent of data set size. c2001 The Willi Hennig Society.

NASA Discipline Evolutionary Biology↗

An Automated Detection Methodology for Dry Well-Mixed Layers

The intense surface heating over arid land surfaces produces dry well-mixed layers (WML) via dry convection. These layers are characterized by nearly constant potential temperature and low, nearly constant water vapor mixing ratio. To further the study of dry WMLs, we created a detection methodology and supporting software to automate the identification and characterization of dry WMLs from multiple data sources including rawinsondes, remote sensing platforms, and model products. The software is a modular code written in Python, an open source language. Radiosondes from a network of synoptic stations in North Africa were used to develop and test the WML detection process. The detection involves an iterative decision tree that ingests a vertical profile from an input data file, performs a quality check for sufficient data density, and then searches upward through the column for successive points where the simultaneous changes in water vapor mixing ratio and potential temperature are less than the specified maxima. If points in the vertical profile meet the dry WML identification criteria, statistics are generated detailing the characteristics of each layer in the profile. At the end of the vertical profile analysis, there is an option to plot analyzed profiles in a variety of file formats. Initial results show that the detection methodology can be successfully applied across a wide variety of input data and North African environments and for all seasons. It is sensitive enough to identify dry WMLs from other types of isentropic phenomena such as subsidence layers and distinguish the current day’s dry WML from previous days.

Stephen D. Nicholls↗

Scalable filesystem enumeration and metadata operations

Systems, apparatus, and methods are disclosed for performing scalable operations in a file system, including POSIX-like file systems. Metadata entries in a namespace or directory tree are sharded across multiple file metadata servers. An enumeration operation, such as listing a directory, is parallelized across the multiple file metadata servers, while retaining standard functionality transparently to clients. Other enumeration operations include no-output operations such as changing file attributes or deleting a file, and cumulative operations such as counting total disk space usage. The parallelization is compatible with tree-level parallelization and storage-level parallelization. Disclosed technologies can be applied to other fields requiring scalable enumeration, such as database and network applications.

Grider, Gary A.↗

Scalable augmented enumeration and metadata operations for large filesystems

Systems, apparatus, and methods are disclosed for performing scalable operations in a file system. Metadata entries in a namespace or directory tree are sharded across multiple file metadata servers. An augmented enumeration operation, such as listing a directory, is parallelized across the multiple file metadata servers, transparently to clients. Exemplary augmentation features can include filtering and sorting. Augmentation features can be executed concurrently with enumeration, prior to enumeration, after enumeration, or as a combination of these, and can utilize pre-built index structures or holding structures for intermediate results. Augmented enumeration operations can also include no-output operations such as changing file attributes or deleting a file, and cumulative operations such as counting total disk space usage. The parallelization is compatible with tree-level parallelization and storage-level parallelization. Disclosed technologies can be applied to other fields requiring scalable enumeration, such as database and network applications.

Grider, Gary A.↗

Cyber risk assessment and investment optimization using game theory and ML-based anomaly detection and mitigation for wide-area control in smart grids

The electric power grid is increasingly becoming susceptible to cyber attacks that exploit vulnerabilities in the smart grid control, information, and physical layers. Successful cyber attacks can have catastrophic impacts on the social and economic well-being of any nation all over the globe. It has, thus, become imperative to secure the smart grid against such adversarial actions to ensure stable, secure, and reliable operation of the grid. The existing research and industry practices prove to be inadequate in terms of providing pragmatic and effective defense methodologies and measures for long-term cybersecurity planning and real-time cybersecurity for grid operation. For example, existing works lack models that incorporate uncertain behavior of cyber-attackers and pragmatic defense measures for cyber risk assessment and cybersecurity investment optimization which often provide unreliable and strictly qualitative solutions to these problems. At the same time, with the growing number of cyber incidents in the grid, there still exists a need to develop attack-resilient algorithms for wide-area monitoring, protection, and control (WAMPAC) applications like the wide-area voltage control systems (WAVCS) for Flexible AC Transmissions Systems (FACTS) that lack in scalable and feasible solutions from the cybersecurity perspective. This dissertation proposes novel models and methodologies for: (1) Cybersecurity planning, and (2) Cybersecurity for system operation. The cybersecurity planning is achieved through cyber risk assessment and cybersecurity resource investment optimization for long-term cybersecurity of the grid using game theory and attack-defense trees. Cybersecurity for system operation consists of development of cyber anomaly detection and mitigation algorithms for flexible AC transmission system (FACTS) controller-based wide-area voltage control systems (WAVCS) using machine learning (ML), and software defined networking-based moving target defense network routing for achieving real-time cyber-physical security for grid operations. This is followed by hardware-in-the-loop (HIL) implementation and evaluation of these attack prevention, detection, and mitigation algorithms and methodologies showcasing their feasibility in a close to real-world environment. For cybersecurity planning, a novel approach involving a combination of game theory and attack defense trees (ADT) for optimal cybersecurity resource allocation in the smart grid is proposed. This methodology involves modeling of the cyber-physical smart grid substations as ADTs, defining attacker costs, defense costs, and attack probabilities for attack access points. Using game theoretical formulation, optimal defense strategies for the defender of the system to invest cybersecurity resources in the grid are obtained. Additionally, a game-theoretic framework is developed for quantitative cyber-physical risk assessment of the grid under a dynamically changing cyber threat space and uncertain behavior of cyber attackers which is further used to optimize investments in the smart grid's cybersecurity resources. The attacker, defender, and the smart grid system are modeled while incorporating attacker-stochasticity and federal guidelines for smart grid cybersecurity. This allows quantification of threat, vulnerabilities, and attack impact of the grid for quantitative risk assessment. The defender's budget to invest in the security resources in the grid is optimized based on the strategies leading to minimum system risk. The evaluation of the proposed solutions highlight the feasibility for practical implementation of these methodologies and algorithms in the smart grid, while taking the federal requirements and guidelines for smart grid security into consideration. For achieving cybersecurity for system operation, attack prevention, detection, and mitigation algorithms and methodologies are developed specifically for FACTS-based WAVCS. Anomaly detection and mitigation in the WAVCS are achieved using algorithms based on machine learning which involves offline training and testing of ML models with CPS datasets incorporating physics-based features that allow accurate distinction between system faults and cyber attacks. For attack prevention, a methodology based on software defined network (SDN)-based moving target defense (MTD) network routing is proposed that enables prevention of Denial of Service (DoS) type attacks on the smart grid communication system. Subsequently, these methodologies and algorithms are implemented and evaluated on an HIL testbed that allows for real-time attack prevention, detection, and mitigation of emulated cyber attacks on the WAVCS in a close to real-world environment. The results show highly accurate and efficient performance of the implemented algorithms and methodologies with the smart grid system operating within the NERC's system operation limits even in the presence of DoS and data integrity cyber attacks. This work opens up future research opportunities in other directions such as (1) Expanding cybersecurity planning methodologies to real-time cyber contingency analysis with different game formulations; and (2) Applying the cybersecurity for system operation algorithms to broader categories of wide-area control applications.

24 POWER TRANSMISSION AND DISTRIBUTION↗

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↗

Python Codebase and Jupyter Notebooks - Applications of Machine Learning Techniques to Geothermal Play Fairway Analysis in the Great Basin Region, Nevada

Git archive containing Python modules and resources used to generate machine-learning models used in the "Applications of Machine Learning Techniques to Geothermal Play Fairway Analysis in the Great Basin Region, Nevada" project. This software is licensed as free to use, modify, and distribute with attribution. Full license details are included within the archive. See "documentation.zip" for setup instructions and file trees annotated with module descriptions.

Brown, Stephen↗

AmeriFlux US-NYh NYSM - Owego

This is the AmeriFlux version of the carbon flux data for the site US-NYh NYSM - Owego. Site Description - Located in a grassy field setting. It is surrounded by a flat, open field with some trees and a pond to the north. Obstructions within 100m include small trees, small pond, pavement. The soil type is Volusia channery silt loam. This site is a part of the New York State Mesonet Flux Network, one of multiple subnetworks (e.g. Profiler, Snow) operated by the New York State Mesonet. It also operates as a Profiler and Standard meteorological site.

Miller, Scott [University at Albany]↗

Climate, soil mineralogy and mycorrhizal fungi influence soil organic matter fractions in eastern US temperate forests

Identifying the primary controls of particulate (POM) and mineral-associated organic matter (MAOM) content in soils is critical for determining future stocks of soil carbon (C) and nitrogen (N) across the globe. However, drivers of these soil organic matter fractions are likely to vary among ecosystems in response to climate, soil type and the composition of local biological communities. We tested how soil factors, climate and plant–fungal associations influenced the distribution and concentrations of C and N in MAOM and POM in seven temperate forests in the National Ecological Observatory Network (NEON) across the eastern United States. Samples of upper mineral horizon soil within each forest were collected in plots representing a gradient of dominant tree–mycorrhizal association, allowing us to test how plant and microbial communities influenced POM and MAOM across sites differing in climate and soil conditions. We found that concentrations of C and N in soil organic matter were primarily driven by soil mineralogy, but the relative abundance of MAOM versus POM C was strongly linked to plot-level mycorrhizal dominance. Furthermore, the effect of dominant tree mycorrhizal type on the distribution of N among POM and MAOM fractions was sensitive to local climate: in cooler sites, an increasing proportion of ectomycorrhizal-associated trees was associated with lower proportions of N in MAOM, but in warmer sites, we found the reverse. As an indicator of soil carbon age, we measured radiocarbon in the MAOM fraction but found that within and across sites, Δ 14 C was unrelated to mycorrhizal dominance, climate, or soil factors, suggesting that additional site-specific factors may be primary determinants of long-term SOM persistence. Our results indicate that while soil mineralogy primarily controls SOM C and N concentrations, the distribution of SOM among density fractions depends on the composition of vegetation and microbial communities, with these effects varying across sites with distinct climates. Here we also suggest that within biomes, the age of mineral-associated soil carbon is not clearly linked to the factors that control concentrations of MAOM C and N.

54 ENVIRONMENTAL SCIENCES↗

Hierarchical Poly Tree computer architectures defined by computational multidisciplinary mechanics

This paper will develop an alternative computer architecture called the Poly Tree. Based on the requirements of computational mechanics and the concept of hierarchical substructuring, the paper will explore the development of problem-dependent parallel networks of processors which will enable significant, often superlinear, speed enhancements; provide a logical/efficient framework for linear/nonlinear and transient structural mechanics problems; and provide a logical framework from which to apply model reduction procedures. In addition, the paper will explore optimal processor arrangements which define the overall system granularity. Consideration will also be given to system I/O requirements.

Padovan, Joe↗

Initialization and Restart in Stochastic Local Search: Computing a Most Probable Explanation in Bayesian Networks

For hard computational problems, stochastic local search has proven to be a competitive approach to finding optimal or approximately optimal problem solutions. Two key research questions for stochastic local search algorithms are: Which algorithms are effective for initialization? When should the search process be restarted? In the present work we investigate these research questions in the context of approximate computation of most probable explanations (MPEs) in Bayesian networks (BNs). We introduce a novel approach, based on the Viterbi algorithm, to explanation initialization in BNs. While the Viterbi algorithm works on sequences and trees, our approach works on BNs with arbitrary topologies. We also give a novel formalization of stochastic local search, with focus on initialization and restart, using probability theory and mixture models. Experimentally, we apply our methods to the problem of MPE computation, using a stochastic local search algorithm known as Stochastic Greedy Search. By carefully optimizing both initialization and restart, we reduce the MPE search time for application BNs by several orders of magnitude compared to using uniform at random initialization without restart. On several BNs from applications, the performance of Stochastic Greedy Search is competitive with clique tree clustering, a state-of-the-art exact algorithm used for MPE computation in BNs.

Mengshoel, Ole J.↗

Global Landslide Hazard Assessment for Situational Awareness (LHASA) Version 2: New Activities and Future Plans

A remote sensing-based system has been developed to characterize the potential for rainfall-triggered landslides across the globe in near real-time. The Landslide Hazard Assessment for Situational Awareness (LHASA) model uses a decision tree framework to combine a static susceptibility map derived from information on slope, rock characteristics, forest loss, distance to fault zones and distance to road networks with satellite precipitation estimates from the Global Precipitation Measurement (GPM) mission. Since 2016, the LHASA model has been providing near real-time and retrospective estimates of potential landslide activity. Results of this work are available at https://landslides.nasa.gov. In order to advance LHASA’s capabilities to characterize landslide hazards and impacts dynamically, we have implemented a new approach that leverages machine learning, new parameters, and new inventories. LHASA 2.0 uses the XGBoost machine learning model to bring in dynamic variables as well as additional static variables to better represent landslide hazard globally. Global rainfall forecasts are also being evaluated to provide a 1-3 day forecast of potential landslide activity. Additional factors such as recent seismicity and burned areas are also being considered to represent the preconditioning or changing interactions with subsequent rainfall over affected areas. A series of parameters are being tested within this structure using NASA’s Global Landslide Catalog as well as many other event-based and multi-temporal inventories mapped by the project team or provided by project partners. In addition to estimates of landslide hazard, LHASA Version 2 will incorporate dynamic estimates of exposure including population, roads and infrastructure to highlight the potential impacts that rainfall-triggered landslides. The ultimate goal of LHASA Version 2.0 is to approximate the relative probabilities of landslide hazard and exposure across different space and time scales to inform hazard assessment retrospectively over the past 20 years, in near real-time, and in the future. In addition to the hazard. This presentation will outline the new activities for LHASA Version 2.0 and present some next steps for this system.

Dalia Kirschbaum↗

DeepSAT: A Deep Learning Approach to Tree-Cover Delineation in 1-m NAIP Imagery for the Continental United States

High resolution tree cover classification maps are needed to increase the accuracy of current land ecosystem and climate model outputs. Limited studies are in place that demonstrates the state-of-the-art in deriving very high resolution (VHR) tree cover products. In addition, most methods heavily rely on commercial softwares that are difficult to scale given the region of study (e.g. continents to globe). Complexities in present approaches relate to (a) scalability of the algorithm, (b) large image data processing (compute and memory intensive), (c) computational cost, (d) massively parallel architecture, and (e) machine learning automation. In addition, VHR satellite datasets are of the order of terabytes and features extracted from these datasets are of the order of petabytes. In our present study, we have acquired the National Agriculture Imagery Program (NAIP) dataset for the Continental United States at a spatial resolution of 1-m. This data comes as image tiles (a total of quarter million image scenes with ~60 million pixels) and has a total size of ~65 terabytes for a single acquisition. Features extracted from the entire dataset would amount to ~8-10 petabytes. In our proposed approach, we have implemented a novel semi-automated machine learning algorithm rooted on the principles of "deep learning" to delineate the percentage of tree cover. Using the NASA Earth Exchange (NEX) initiative, we have developed an end-to-end architecture by integrating a segmentation module based on Statistical Region Merging, a classification algorithm using Deep Belief Network and a structured prediction algorithm using Conditional Random Fields to integrate the results from the segmentation and classification modules to create per-pixel class labels. The training process is scaled up using the power of GPUs and the prediction is scaled to quarter million NAIP tiles spanning the whole of Continental United States using the NEX HPC supercomputing cluster. An initial pilot over the state of California spanning a total of 11,095 NAIP tiles covering a total geographical area of 163,696 sq. miles has produced true positive rates of around 88 percent for fragmented forests and 74 percent for urban tree cover areas, with false positive rates lower than 2 percent for both landscapes.

Imagery↗

MDLoader: A Hybrid Model-Driven Data Loader for Distributed Graph Neural Network Training

Scalable data management is essential for processing large scientific dataset on HPC platforms for distributed deep learning. In-memory distributed storage is preferred for its speed, enabling rapid, random, and frequent data access required by stochastic optimizers. Processes use one-sided or collective communication to fetch remote data, with optimal performance depending on (i) dataset characteristics, (ii) training scale, and (iii) interconnection network. Empirical analysis shows collective communication excels with larger mini-batch sizes and/or fewer processes, whereas one-sided communication outperforms at larger scales. We propose MDLoader, a hybrid in-memory data loader for distributed graph neural network training. MDLoader features a model-driven performance estimator that dynamically selects between one-sided and collective communication at the beginning of training using Tree of Parzen Estimators (TPE). Evaluations on NERSC Perlmutter and OLCF Summit show MDLoader outperforms single-backend loaders by up to 2.83 × and predicts the suitable communication method with 96.3% (Perlmutter) and 94.3% (Summit) success rate.

Bae, Jonghyun↗

AmeriFlux US-NYm NYSM - Belleville

This is the AmeriFlux version of the carbon flux data for the site US-NYm NYSM - Belleville. Site Description - Located in a grass/crop field setting. It is a in a flat, open field with high vegetation to the northeast, paved road to the east, and a small treeline to the north. Obstructions within 100m include trees, paved road, high crops. The soil type is Collamer silt loam, bedrock substratum. This site is a part of the New York State Mesonet Flux Network, one of multiple subnetworks (e.g. Profiler, Snow) operated by the New York State Mesonet. It also operates as a Profiler and Standard meteorological site.

Miller, Scott [University at Albany]↗

Airborne LiDAR to Improve Canopy Fuels Mapping for Wildfire Modeling

Increasing conflict between wildfire and the built environment has increased the need for more up-to-date and finer resolution canopy fuels data to improve wildfire modeling and associated risk forecasts. The US Forest Service and US Department of the Interior’s LANDFIRE product, which provides 30-m resolution canopy fuels data for the entire US, is one of the most widely used sources of fuels data. However, the last complete mapping effort for LANDFIRE is based on 2016 conditions, and subsequent updates reflect disturbances 1-2 years behind the release year. Airborne systems equipped with Light Detection and Ranging (LiDAR) sensors can be deployed to actively sense canopy structure and estimate canopy fuels data (cover, height, base height, bulk density) at finer resolutions. Canopy base height (CBH) and canopy bulk density (CBD) are difficult to measure both in the field and in LiDAR point clouds. Still, they are important for accurately modeling crown fires, which are often intense and difficult to contain. Additionally, point cloud datasets are large, and calculations require efficient utilization of computational resources. To address these challenges, we are working on an approach that uses openly available National Ecological Observatory Network (NEON) airborne LiDAR data, with calculations processed in the R programming language and parallelized through the lidR package. CBH and CBD are often derived from tree height, diameter at breast height, and species-specific allometries using the Fire and Fuels Extension of the Forest Vegetation Simulator (FFE-FVS). We aim to test if airborne LiDAR can estimate CBH and CBD without the use of empirical equations. Reliable estimates of canopy fuels data directly from airborne LiDAR could streamline quick, fine-resolution updates for use in wildfire behavior models.

54 ENVIRONMENTAL SCIENCES↗

STARBASE: Database software for the automated plate scanner

The Automated Plate Scanner (APS) of the University of Minnesota, a unique high speed 'flying spot' laser scanner, is currently being used to scan and digitize the 936 O and E plate pairs of the first epoch Palomar Sky Survey. The resultant database will be used to produce a catalog of approximately a billion stars and several million galaxies. The authors describe the ongoing development of a dedicated APS database management system which will be made available to the astronomical community via INTERNET. A specialized DBMS called STARBASE has been written to provide fast access to the hundreds of millions of images collected by the APS. This system provides an initial reduction mode for parameterizing APS images and classifying image types using a novel set of neural network image classifiers. A second analysis mode, which will be that commonly used by the general user, provides for searches of the database which may be constrained by any combination of physical and positional parameters. Through the use of pointer hash trees, the system has been optimized for extremely fast positional searches using either right ascension and declination on the sky or linear X and Y positions on the POSS field. In addition to fast data retrieval, the system provides a graphical interface for displaying scatter plots or histograms of the collected data. In addition, a specialized image display system is being developed to allow the user to view densitometric data for all objects classified as extended by the neural network system. Finally, STARBASE has a flexible programmable interface which allows other programs to access information in the database. This allows users to write applications suited to their particular needs to process APS data.

Odewahn, S. C.↗

Physics-guided machine learning approaches to predict the ideal stability properties of fusion plasmas

One of the biggest challenges to achieve the goal of producing fusion energy in tokamak devices is the necessity of avoiding disruptions of the plasma current due to instabilities. The disruption event characterization and forecasting (DECAF) framework has been developed in this purpose, integrating physics models of many causal events that can lead to a disruption. Two different machine learning approaches are proposed to improve the ideal magnetohydrodynamic (MHD) no-wall limit component of the kinetic stability model included in DECAF. First, a random forest regressor (RFR), was adopted to reproduce the DCON computed change in plasma potential energy without wall effects for a large database of equilibria from the national spherical torus experiment (NSTX). This tree-based method provides an analysis of the importance of each input feature, giving an insight into the underlying physics phenomena. Secondly, a fully-connected neural network has been trained on sets of calculations with the DCON code, to get an improved closed form equation of the no-wall β limit as a function of the relevant plasma parameters indicated by the RFR. The neural network has been guided by physics theory of ideal MHD in its extension outside the domain of the NSTX experimental data. The estimated value has been incorporated into the DECAF kinetic stability model and tested against a set of experimentally stable and unstable discharges. Moreover, the neural network results were used to simulate a real-time stability assessment using only quantities available in real-time. Finally, the portability of the model was investigated, showing encouraging results by testing the NSTX-trained algorithm on the mega ampere spherical tokamak (MAST).

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗