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At least 55 records · Page 3

GPM Plans for Radiometer Intercalibration

The international Global Precipitation Measurement (GPM) mission led by NASA and JAXA is planned as a multi-radiometer constellation mission. A key mission component is the ability to intercalibrate the Tb from the partner constellation radiometers and create inter-calibrated, mission consistent Tc. One of the enabling strategies for this approach is the launching of a joint NASA/JAXA core satellite which contains a JAXA/NICT provided dual precipitation radar and a NASA provided Microwave Imaging passive radiometer. The observations from these instruments on the core satellite provide the opportunity to develop a transfer reference standard that can then be applied across the partner provided constellation radiometers that enables the creation of mission consistent brightness temperatures. The other aspect of the strategy is the development of a community consensus intercalibration algorithm that will be applied to the Tb observations from partner radiometers and create the best calibrated Tc. Also described is the development of the framework in which the inter-calibration is included in the final algorithm. A part of the latter effort has been the development of a generic, logical structure which can be applied across radiometer types and which guarantees the user community that key information for using Tc properly is recorded. Key

Stocker, Erich Franz↗

Solving the Grid Optimization Competition Challenge 3 Problem

The Grid Optimization Competition Challenge 3 Problem posed a multiperiod security-constrained unit commitment problem with base-case AC power flow. The problem formulation includes binary unit commitment decisions, nonlinear AC power flow and balance, dispatchable loads, and linearized contingency real power flow, among other features. This talk will present a modified consensus ADMM algorithm, which splits the problem into mixed-integer linear and nonlinear components, as a heuristic solution method for this large-scale mixed integer nonlinear program. We will present some computational results from the competition for our implementation and reflect on the challenges of participating the grid optimization competition.

AC power flow↗

SeaWiFS Technical Report Series: Satellite Primary Productivity Data and Algorithm Development: A Science Plan for Mission to Planet Earth - Volume 42

Two issues regarding primary productivity, as it pertains to the Sea-viewing Wide Field-of-view Sensor (SeaWiFS) Program and the National Aeronautics and Space Administration (NASA) Mission to Planet Earth (MTPE) are presented in this volume. Chapter 1 describes the development of a science plan for deriving primary production for the world ocean using satellite measurements, by the Ocean Primary Productivity Working Group (OPPWG). Chapter 2 presents discussions by the same group, of algorithm classification, algorithm parameterization and data availability, algorithm testing and validation, and the benefits of a consensus primary productivity algorithm.

Falkowski, Paul G.↗

Fast Tuning-Free Distributed Algorithm for Solving the Network-Constrained Economic Dispatch

With the increasing penetration of distributed energy resources (DERs) and their participation in the electricity market, it becomes more desirable to apply distributed algorithms for resource allocation in order to address the resulting computational and communicational challenges. Most of the existing distributed algorithms for solving the network-constrained economic dispatch (NCED) problem require the tuning of certain auxiliary parameters. As a result, the robustness of these algorithms against the varieties in DERs is greatly undermined. In this paper, a new distributed algorithm, optimality condition consensus (OCC), is proposed to solve the NCED problem by using distributed power flow (DPF) and ratio consensus as fundamental tools. It inherits the advantages of existing distributed algorithms for the NCED problem but removes the need for parameter tuning to improve performance in practice. In conclusion, the effectiveness of the proposed distributed algorithm in terms of efficiency, scalability, and robustness is demonstrated through detailed case studies.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Distributed Optimal Power Management for Battery Energy Storage Systems: A Novel Accelerated Tracking ADMM Approach

Optimal power management (OPM) is critical for large-scale battery energy storage systems. Today’s methods often require formidable computational effort due to the design based on centralized numerical optimization. Thus, this paper investigates computationally distributed OPM where the agents based on the cells communicate over a network to cooperatively solve the OPM problem. We propose an accelerated tracking alternating direction method of multipliers (ADMM) algorithm to solve the distributed OPM. The proposed algorithm embeds dynamic average consensus and Nesterov’s acceleration technique in the ADMM algorithm. Not only is the proposed algorithm fully distributed without a need for fusion or aggregating nodes, but it also accelerates convergence. The paper formulates the OPM in a model predictive control framework where it seeks to regulate the charging/discharging power of each battery cell to minimize the total power losses and promote balanced use of the constituent cells while complying with the safety constraints. The paper provides ample simulation results to demonstrate the effectiveness and advantages of the proposed distributed OPM in terms of computation and convergence.

Farakhor, Amir↗

Parallel String Graph Construction and Transitive Reduction for De Novo Genome Assembly

One of the most computationally intensive tasks in computational biology is de novo genome assembly, the decoding of the sequence of an unknown genome from redundant and erroneous short sequences. A common assembly paradigm identifies overlapping sequences, simplifies their layout, and creates consensus. Despite many algorithms developed in the literature, the efficient assembly of large genomes is still an open problem. In this work, we introduce new distributed-memory parallel algorithms for overlap detection and layout simplification steps of de novo genome assembly, and implement them in the diBELLA 2D pipeline. Our distributed memory algorithms for both overlap detection and layout simplification are based on linear-algebra operations over semirings using 2D distributed sparse matrices. Our layout step consists of performing a transitive reduction from the overlap graph to a string graph. We provide a detailed communication analysis of the main stages of our new algorithms. diBELLA 2D achieves near linear scaling with over 80% parallel efficiency for the human genome, reducing the runtime for overlap detection by 1.2-1.3× for the human genome and 1.5-1.9× for C.elegans compared to the state-of-the-art. Our transitive reduction algorithm outperforms an existing distributed-memory implementation by 10.5-13.3× for the human genome and 18-29× for the C. elegans. Our work paves the way for efficient de novo assembly of large genomes using long reads in distributed memory.

59 BASIC BIOLOGICAL SCIENCES↗

Novel CHI3L1 ‐Associated Angiogenic Phenotypes Define Glioma Microenvironments: Insights From Multi‐Omics Integration

ABSTRACT The CHI3L1 signaling pathway significantly influences glioma angiogenesis, but its role in the tumor microenvironment (TME) remains elusive. We propose a novelCHI3L1‐associated vascular phenotype classification for glioma through integrative analyses of multiple datasets with bulk and single‐cell transcriptome, genomics, digital pathology, and clinical data. We investigated the biological characteristics, genomic alterations, therapeutic vulnerabilities, and immune profiles within these phenotypes through a comprehensive multi‐omics approach. We constructed the vascular‐related risk (VR) score based onCHI3L1‐associated vascular signatures (CAVS) identified by machine learning algorithms. Utilizing unsupervised consensus clustering, gliomas were stratified into three distinct vascular phenotypes: Cluster A, marked by high vascularization and stromal activation with a relatively low levels of tumor‐infiltrating lymphocytes (TILs); Cluster B, characterized by moderate vascularization and stromal activity, coupled with a high density of TILs; and Cluster C, defined by low vascularization and sparse immune cell infiltration. We observed that the CAVS effectively indicated glioma‐associated angiogenesis and immune suppression by single‐cell RNA‐seq analysis. Moreover, the high‐VR‐score group exhibited enhanced angiogenic activity, reduced immune response, resistance to immunotherapy, and poorer clinical outcomes. The VR score independently predicted glioma prognosis and, combined with a nomogram, provided a robust clinical decision‐making tool. Potential drug prediction based on transcription factors for high‐risk patients was also performed. Our study reveals thatCHI3L1‐associated vascular phenotypes shape distinct immune landscapes in gliomas, offering insights for optimizing therapeutic strategies to improve patient outcomes.

Oncology↗

Metrics and Methods for Radiation Detection Algorithm Characterization for Nuclear/Radiological Source Search

This report presents a series of recommendations for data to train and evaluate radiation detection algorithms and performance metrics to evaluate these algorithms. These recommendations were formed through a community consensus approach through the Detection Radiation Algorithms Group (DRAG), a multi-institution collaboration spanning eight Department of Energy laboratories and John Hopkins Applied Physics Laboratory. This report includes recommendations on background data variability, and metrics to quantify variability, sources and shielding configurations to include in data collection campaigns and detector response variability. In addition, this report describes several anomaly detection and identification algorithms and recommends metrics to report their performance. Finally, this report ends with a discussion on machine learning algorithms.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Equitable Transactive Market Design to Coordinate Networked Microgrids with Mixed Ownership

This paper presents an inter-microgrid peer-topeer (P2P) transactive market mechanism to support the coordination of multiple microgrids in a mixed-ownership environment, while enabling prosumers to actively participate in the market to get their own benefits. An equitable P2P transactive energy market is designed, in which the energy burden to customers within microgrids is fairly distributed by leveraging a peer-to-peer communication network among MG owners and the distribution system operator (DSO). To reach the market settlement, a consensus-based distributed optimization algorithm is introduced to enable each MG owner and the DSO to distributedly determine the cleared price which is compensated by a household-income-based discount factor to encourage the energy-burden equity among customers in networked microgrids service territory. Numerical results on the modified 123 node test feeder including 6 microgrids are used to demonstrate the operation of the introduced equitable transactive energy market.

Vu, Thanh Long↗

Survivable algorithms and redundancy management in NASA's distributed computing systems

The design of survivable algorithms requires a solid foundation for executing them. While hardware techniques for fault-tolerant computing are relatively well understood, fault-tolerant operating systems, as well as fault-tolerant applications (survivable algorithms), are, by contrast, little understood, and much more work in this field is required. We outline some of our work that contributes to the foundation of ultrareliable operating systems and fault-tolerant algorithm design. We introduce our consensus-based framework for fault-tolerant system design. This is followed by a description of a hierarchical partitioning method for efficient consensus. A scheduler for redundancy management is introduced, and application-specific fault tolerance is described. We give an overview of our hybrid algorithm technique, which is an alternative to the formal approach given.

Malek, Miroslaw↗

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in many neuroscience laboratories interested in neuron tracing. Here, we report generated gold standard manual annotations for a subset of the available imaging datasets and quantified tracing quality for 35 automatic tracing algorithms. The goal of generating such a hand-curated diverse dataset is to advance the development of tracing algorithms and enable generalizable benchmarking. Together with image quality features, we pooled the data in an interactive web application that enables users and developers to perform principal component analysis, t-distributed stochastic neighbor embedding, correlation and clustering, visualization of imaging and tracing data, and benchmarking of automatic tracing algorithms in user-defined data subsets. The image quality metrics explain most of the variance in the data, followed by neuromorphological features related to neuron size. Furthermore, we observed that diverse algorithms can provide complementary information to obtain accurate results and developed a method to iteratively combine methods and generate consensus reconstructions. The consensus trees obtained provide estimates of the neuron structure ground truth that typically outperform single algorithms in noisy datasets. However, specific algorithms may outperform the consensus tree strategy in specific imaging conditions. Finally, to aid users in predicting the most accurate automatic tracing results without manual annotations for comparison, we used support vector machine regression to predict reconstruction quality given an image volume and a set of automatic tracings.

97 MATHEMATICS AND COMPUTING↗

FY21 Progress Report: SRNL Analysis of ICCWR LCM and WAMS data for Corrosion and Cracking

The development of algorithms for machine learning and data analysis for the 3013 Surveillance Program is a collaborative effort by the Savannah River National Laboratory (SRNL) and the University of South Carolina (USC). For corrosion detection, Laser Confocal Microscope (LCM) or Wide Area 3D Measurement System (WAMS) data is extracted from large binary files, with software written to convert the data to physical attributes (e.g., height, color and grayscale values; all as functions of a location in a plane projection). A user-friendly Matlab Graphical User Interface (GUI) that reads data from either LCM or WAMS files was developed to integrate input data with software developed for processing and evaluation. The GUI can selectively download binary data, interrogate data attributes, label data, flag significant features, execute Machine Learning (ML) algorithms, output parameters for trained ML algorithms, report ML model accuracy with respect to labeled data, and generate graphical representations for various analyses. Features can be called out by user-specified thresholds, manual labeling or machine learning algorithms when they have been completed. The ability to rapidly label data is important because of the volume of data required for training machine learning algorithms. The GUI has the flexibility to allow addition of improved ML algorithms, methods for data visualization, and statistical computations. Statistical analyses via the GUI include areas of pits within a defined range of pit depths, correlations between Red-Green-Blue (RGB) or grayscale intensity and relative surface height, covariances between values associated with features, and feature histograms. The development of supervised machine learning algorithms, however, has been hindered by a lack of training data. The machine learning algorithms for crack identification are being refined but require improvements to the true positive rate for crack detection. This shortcoming is an artifact of the limited training data currently available, perhaps more so than the structure of the neural networks. At present, the best results are had from a consensus over an ensemble of randomly generated Deep Neural Network (DNN) or Convolutional Neural Network (CNN) algorithms. Although the consensus accuracy method has yielded optimum true positive and true negative rates in excess of 80%, additional validation testing is necessary. In addition to the suite of LCM data that was initially used, and which represents the majority of the work presented in this report, WAMS image data was also reviewed at a preliminary level. The review included a comparison between image resolution and dynamic range for each method. WAMS (ZON file) image data was found to have a pixel pitch of 3.69μm compared to 1 μm for the LCM (vk4 file) data, which implies a lower resolution for the WAMS images. Conversely, the ratio of dynamic range of the WAMS data to the LCM data was approximately 41:20 for height data, suggesting that information from WAMS should more accurately determine the depth of pits. At present, the significance of the greater dynamic range of the WAMS data relative to the LCM data has not yet been evaluated.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

An Updated TRMM Composite Climatology of Tropical Rainfall and Its Validation

An updated 15-yr Tropical Rainfall Measuring Mission (TRMM) composite climatology (TCC) is presented and evaluated. This climatology is based on a combination of individual rainfall estimates made with data from the primaryTRMMinstruments: theTRMM Microwave Imager (TMI) and the precipitation radar (PR). This combination climatology of passive microwave retrievals, radar-based retrievals, and an algorithm using both instruments simultaneously provides a consensus TRMM-based estimate of mean precipitation. The dispersion of the three estimates, as indicated by the standard deviation sigma among the estimates, is presented as a measure of confidence in the final estimate and as an estimate of the uncertainty thereof. The procedures utilized by the compositing technique, including adjustments and quality-control measures, are described. The results give a mean value of the TCC of 4.3mm day(exp -1) for the deep tropical ocean beltbetween 10 deg N and 10 deg S, with lower values outside that band. In general, the TCC values confirm ocean estimates from the Global Precipitation Climatology Project (GPCP) analysis, which is based on passive microwave results adjusted for sampling by infrared-based estimates. The pattern of uncertainty estimates shown by sigma is seen to be useful to indicate variations in confidence. Examples include differences between the eastern and western portions of the Pacific Ocean and high values in coastal and mountainous areas. Comparison of the TCC values (and the input products) to gauge analyses over land indicates the value of the radar-based estimates (small biases) and the limitations of the passive microwave algorithm (relatively large biases). Comparison with surface gauge information from western Pacific Ocean atolls shows a negative bias (~16%) for all the TRMM products, although the representativeness of the atoll gauges of open-ocean rainfall is still in question.

(GPCP) Global Precipitation Project analysis↗

CONSTAX2: improved taxonomic classification of environmental DNA markers

Abstract Summary CONSTAX—the CONSensus TAXonomy classifier—was developed for accurate and reproducible taxonomic annotation of fungal rDNA amplicon sequences and is based upon a consensus approach of RDP, SINTAX and UTAX algorithms. CONSTAX2 extends these features to classify prokaryotes as well as eukaryotes and incorporates BLAST-based classifiers to reduce classification errors. Additionally, CONSTAX2 implements a conda-installable command-line tool with improved classification metrics, faster training, multithreading support, capacity to incorporate external taxonomic databases and new isolate matching and high-level taxonomy tools, replete with documentation and example tutorials. Availability and implementation CONSTAX2 is available at https://github.com/liberjul/CONSTAXv2, and is packaged for Linux and MacOS from Bioconda with use under the MIT License. A tutorial and documentation are available at https://constax.readthedocs.io/en/latest/. Data and scripts associated with the manuscript are available at https://github.com/liberjul/CONSTAXv2_ms_code. Supplementary information Supplementary data are available at Bioinformatics online.

59 BASIC BIOLOGICAL SCIENCES↗

Network Analysis of Rodent Transcriptomes in Spaceflight

Network analysis methods leverage prior knowledge of cellular systems and the statistical and conceptual relationships between analyte measurements to determine gene connectivity. Correlation and conditional metrics are used to infer a network topology and provide a systems-level context for cellular responses. Integration across multiple experimental conditions and omics domains can reveal the regulatory mechanisms that underlie gene expression. GeneLab has assembled rich multi-omic (transcriptomics, proteomics, epigenomics, and epitranscriptomics) datasets for multiple murine tissues from the Rodent Research 1 (RR-1) experiment. RR-1 assesses the impact of 37 days of spaceflight on gene expression across a variety of tissue types, such as adrenal glands, quadriceps, gastrocnemius, tibalius anterior, extensor digitorum longus, soleus, eye, and kidney. Network analysis is particularly useful for RR-1 -omics datasets because it reinforces subtle relationships that may be overlooked in isolated analyses and subdues confounding factors. Our objective is to use network analysis to determine potential target nodes for therapeutic intervention and identify similarities with existing disease models. Multiple network algorithms are used for a higher confidence consensus.

genomics↗

cWINNOWER algorithm for finding fuzzy dna motifs

The cWINNOWER algorithm detects fuzzy motifs in DNA sequences rich in protein-binding signals. A signal is defined as any short nucleotide pattern having up to d mutations differing from a motif of length l. The algorithm finds such motifs if a clique consisting of a sufficiently large number of mutated copies of the motif (i.e., the signals) is present in the DNA sequence. The cWINNOWER algorithm substantially improves the sensitivity of the winnower method of Pevzner and Sze by imposing a consensus constraint, enabling it to detect much weaker signals. We studied the minimum detectable clique size qc as a function of sequence length N for random sequences. We found that qc increases linearly with N for a fast version of the algorithm based on counting three-member sub-cliques. Imposing consensus constraints reduces qc by a factor of three in this case, which makes the algorithm dramatically more sensitive. Our most sensitive algorithm, which counts four-member sub-cliques, needs a minimum of only 13 signals to detect motifs in a sequence of length N = 12,000 for (l, d) = (15, 4). Copyright Imperial College Press.

Evaluation Studies↗

cWINNOWER Algorithm for Finding Fuzzy DNA Motifs

The cWINNOWER algorithm detects fuzzy motifs in DNA sequences rich in protein-binding signals. A signal is defined as any short nucleotide pattern having up to d mutations differing from a motif of length l. The algorithm finds such motifs if multiple mutated copies of the motif (i.e., the signals) are present in the DNA sequence in sufficient abundance. The cWINNOWER algorithm substantially improves the sensitivity of the winnower method of Pevzner and Sze by imposing a consensus constraint, enabling it to detect much weaker signals. We studied the minimum number of detectable motifs qc as a function of sequence length N for random sequences. We found that qc increases linearly with N for a fast version of the algorithm based on counting three-member sub-cliques. Imposing consensus constraints reduces qc, by a factor of three in this case, which makes the algorithm dramatically more sensitive. Our most sensitive algorithm, which counts four-member sub-cliques, needs a minimum of only 13 signals to detect motifs in a sequence of length N = 12000 for (l,d) = (15,4).

Liang, Shoudan↗

Autonomous Formations of Multi-Agent Systems

Autonomous formation control of multi-agent dynamic systems has a number of applications that include ground-based and aerial robots and satellite formations. For air vehicles, formation flight ("flocking") has the potential to significantly increase airspace utilization as well as fuel efficiency. This presentation addresses two main problems in multi-agent formations: optimal role assignment to minimize the total cost (e.g., combined distance traveled by all agents); and maintaining formation geometry during flock motion. The Kuhn-Munkres ("Hungarian") algorithm is used for optimal assignment, and consensus-based leader-follower type control architecture is used to maintain formation shape despite the leader s independent movements. The methods are demonstrated by animated simulations.

Dhali, Sanjana↗