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Open Source Lessons Learned with Open MCT

Open source enables flexible use, and reduces or eliminates the proprietary nature of software that can impede collaboration. While still in the early stages, we have built a community of users and contributors, with participation inside and outside of the space community. The model for collaboration is to empower missions by enabling them to adopt the software as their own, make modifications and contributions, and see those contributions used in a larger space community. All missions benefit from the larger user base enabled by open source, as each critical eye on the software results in improvements. The Open MCT user base ranges from missions, to industry outside the space industry, to research and student projects.

Trimble, Jay↗

Prediction of Distributed River Sediment Respiration Rates Using Community-Generated Data and Machine Learning

River sediment microbial respiration is a key indicator of ecosystem functioning and the biogeochemical fluxes across this critical zone link surface and subsurface waters. As such, there is tremendous interest in measuring and mapping these respiration rates. Respiration observations are expensive and labor intensive; there is limited data available to the community. An open science, collaborative initiative is collecting samples for respiration rate analysis and multi-scale metadata; this evolving data set is being used for making machine learning (ML) predictions at unsampled sites to help inform continued community engagement. However, it is a challenge to find an optimum configuration for ML models to work with this feature-rich (i.e., 100+ possible input variables) data set. Here, we present results from a two-tiered approach to managing the analysis of this complex data set: (a) a stacked ensemble of models that automatically optimizes hyperparameters and manages the training of many models and (b) feature permutation importance to detect the most important features in the models. The major elements of this workflow are modular, portable, open, and cloud-based thus making this implementation a potential template for other applications. The models developed here predict that sediment organic matter chemistry is one of the most important features for predicting sediment respiration rate. Other larger-scale, important features fall into the categories of climatic, ecological, geological, and fluvial settings. Leveraging these larger-scale features to generate data-driven estimates of river sediment respiration rates reveals spatially consistent but heterogeneous patterns across the river network of the Columbia River Basin.

54 ENVIRONMENTAL SCIENCES↗

Electronic Visualization Laboratory's 50th Anniversary Retrospective: Look to the Future, Build on the Past

September 2023 marks the 50th anniversary of the Electronic Visualization Laboratory (EVL) at University of Illinois Chicago (UIC). EVL's introduction of the CAVE Automatic Virtual Environment in 1992, the first widely replicated, projection-based, walk-in, virtual-reality (VR) system in the world, put EVL at the forefront of collaborative, immersive data exploration and analytics. However, the journey did not begin then. Since its founding in 1973, EVL has been developing tools and techniques for real-time, interactive visualizations—pillars of VR. But EVL's culture is also relevant to its successes, as it has always been an interdisciplinary lab that fosters teamwork, where each person's expertise contributes to the development of the necessary tools, hardware, system software, applications, and human interface models to solve problems. Over the years, as multidisciplinary collaborations evolved and advanced scientific instruments and data resources were distributed globally, the need to access and share data and visualizations while working with colleagues, local and remote, synchronous and asynchronous, also became important fields of study. This paper is a retrospective of EVL's past 50 years that surveys the many networked, immersive, collaborative visualization and VR systems and applications it developed and deployed, as well as lessons learned and future plans.

Johnson, Andrew E.↗

Navier: Dataflow Architecture for Computation Chemistry

Navier’s objectives were two evaluate the use of emerging technologies, especially dataflow accelerators, for high-performance computing (HPC) applications, specifically in the domain of chemistry, and to develop a prototype software stack to support such applications. Navier builds on capabilities previously developed by synergistic projects, such as PNNL Data Model Convergence (DMC) LDRD Hardware Advanced Workflows (HAW) and DuOMO, as well as DOE ARIAA. Throughout its 18 months, the Navier team developed new capabilities and artifacts at all levels of the HW/SW stack, provided a seamless way to integrate novel computing architectures (Sambanova SN10 and Xilinx Versal AI) into an existing software stack, developed chemistry workflows, data analytics tools, and HPC molecular dynamics workflows that leverage the developed stack and PNNL institutional investments in emerging architectures. Navier also explored the use of active learning to accelerate a computational chemistry workflow for organic molecules on PNNL Junction cluster (in collaboration with AMD/Xilinx). Navier developed tools, methodologies, and studies for hardware software co-design and (sparse) dataflow accelerators that are composable and can be used together or separately. These methodologies are now used in other projects, such as DOE AMAIS and HPDA. This report describes Navier’s achievement, the developed tools and methodologies, and the research findings and conclusions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

GeneLab: Current and Future Omics Data Integration Between Space Biology and HRP

For the past five years, the Biological and Physical Sciences Division has pioneered Open Science in Space Biology by funding the NASA GeneLab project. Along with the Ames Life Sciences Data Archive, GeneLab has quickly become the world leader in archiving and scientifically curating spaceflight and spaceflight relevant multi-omics data. Specifically, the GeneLab Data System has become a full enterprise solution providing advanced mining capabilities, several application programming interfaces for data federation and machine learning approaches, and delivering to the world an analytical and visualization platform which has enabled collaboration within the scientific community. Over the past three years, large meta-analysis and modeling studies have been published by the GeneLab Analysis Working Groups (AWGs), which are comprised of ~200 volunteer scientists. One natural extension of GeneLab data reuse has recently turned towards linking animal data with human data, which is the next necessary step to further validate animal models for inferring biological risks to humans conducting LEO, lunar or Martian missions. As such, data from the Human Research Program are an essential component of GeneLab and ALSDA. At the moment, simulated space radiation experiments conducted at Brookhaven National Laboratory make the most of HRP GeneLab data, and the scientific community has been eager to also link their animal spaceflight results to actual Astronaut data and human analog data. We will discuss further the current status of knowledge and future approaches to accelerate our basics understanding of the impact of space stressors on humans using latest omics technology.

omics↗

Accelerating Engineered Microbe Optimization through Machine Learning and Multi-Omics Datasets [Abstract]

The Agile Biofoundry (ABF) is a multi-national lab consortium funded by the DOE Bioenergy Technologies Office that has developed a biofoundry enabling the rapid deployment of bioproducts into the market. The ABF is a flexible platform that can adjust to the needs of numerous government, academic and industrial partners, thus enabling them to rapidly develop and optimize the production of a wide range of bioproducts. To demonstrate this capability, three ABF labs (NTESS, LBNL, and PNNL) have collaborated with the biomanufacturer Lygos, Inc. to use the ABF to demonstrate a high-throughput Design-Build-Test-Learn (DBTL) engineering cycle incorporating multi-omics analysis and machine learning with best in industry cycle times.

60 APPLIED LIFE SCIENCES↗

On the specificity between mapping of initial and final states of the magneto Rayleigh-Taylor instability

In this LDRD we investigated the application of machine learning methods to understand dimensionality reduction and evolution of the Rayleigh-Taylor instability (RTI). As part of the project, we undertook a significant literature review to understand current analytical theory and machine learning based methods to treat evolution of this instability. We note that we chose to refocus on assessing the hydrodynamic RTI as opposed to the magneto-Rayleigh-Taylor instability originally proposed. This choice enabled utilizing a wealth of analytic test cases and working with relatively fast running open-source simulations of single-mode RTI. This greatly facilitated external collaboration with URA summer fellowship student, Theodore Broeren. In this project we studied the application of methods from dynamical systems learning and traditional regression methods to recover behavior of RTI ranging from the fully nonlinear to weakly nonlinear (wNL) regimes. Here we report on two of the tested methods SINDy and a more traditional regression-based approach inspired by analytic wNL theory with which we had the most success. We conclude with a discussion of potential future extensions to this work that may improve our understanding from both theoretical and phenomenological perspectives.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

FY23 Progress Report: SRNL Analysis of ICCWR LCM and WAMS data for Corrosion and Cracking

Algorithms for Machine Learning (ML) and data analysis for the 3013 Surveillance Program have been developed in an ongoing collaborative effort by the Savannah River National Laboratory (SRNL) and the University of South Carolina (USC). The objective of the algorithms is to automate the identification of corrosion and crack formation in the Inner Container Closure Weld Region (ICCWR) of the canister system used to store Pu-bearing material. Data for corrosion and cracking is collected from large binary files generated by a Laser Confocal Microscope (LCM), the Wide Area 3D Measurement System (WAMS), and in a recent proposal, by a Scanning Electron Microscope (SEM). The ML software uses the physical attributes in the data files (e.g., one or all of: height, color, and grayscale values as functions of position in a plane projection) to detect the presence of surface corrosion and cracking after being trained on similar data with the features to be detected labeled.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

SMALE: Enhancing Scalability of Machine Learning Algorithms on Extreme-Scale Computing Platforms

Deployment and execution of machine learning tasks on extreme-scale computing platforms face several significant technical challenges: 1) High computing cost incurred by dense networks – The computing workload of deep networks with densely-connected topology increases rapidly with the network size, imposing a non-scalable computing model of extreme-scale computing platforms; 2) Non-optimized workload distribution – Many advanced deep learning algorithms, e.g., sparsification and irregular net-work topology, produce very unbalanced workload distribution on extreme-scale computing platforms. The computation efficiency is greatly hindered by the incurred data and computation redundancies as well as long tails of the node with extensive workload; 3) Constraints in data movement and I/O bottle-neck – Inter-node data movement in extreme-scale computing platforms are associated with high energy and latency costs, and subject to the constraints of I/O bandwidth; and 4) Generalization of algorithm realization and acceleration on computing platforms – The large varieties of machine learning algorithms and structures of extreme-scale computing platforms make the derivation of a generalized algorithm realization and acceleration method very challenging, which, however, is the requirement by domain scientists and interested users. We call the above challenges Smale’s Problems in Machine Learning and Understanding for High-Performance Computing Scientific Discovery. The objective of our three-year research project is to develop a holistic innovation set at structure, assembly, and acceleration layers of machine learning algorithms to address the above challenges in algorithm deployment and execution. Three tasks are particularly performed, including: At the algorithm structure level, we investigate the techniques that can structurally sparsify on the topology of deep networks for computing workload reduction. We also study clustering and pruning techniques that can optimize the workload distributions over the extreme-scale computing platforms; At the algorithm assembly level, we derive a unified learning framework for unsupervised transfer learning and dynamic growing capabilities. Novel training methods are also exploited to enhance the training efficiency of the proposed framework; At the algorithm acceleration level, we will develop a series of techniques that can accelerate the computation of sparse matrix operations, which are one of the core executions in deep learning and optimize memory access of the concerned platforms. Our proposed techniques attack the fundamental problems in machine learning algorithms running on extreme-scale computing platforms by vertically integrating the solutions at three closely entangled layers, paving the long-term scaling path of machine learning applications under DOE context. Three tasks corresponding to the above respective research orientations are performed during the three-year project period with our collaborators at ORNL. The outcome of the proposed project is anticipated to form a holistic solution set of novel algorithms and network topologies, efficient training techniques, and fast acceleration methods to promote the computing scalability of the machine learning applications of particular interest to DOE.

97 MATHEMATICS AND COMPUTING↗

Multi-omics Characterization of the Host Response to COVID-19

This project is a multi-disciplinary collaboration between investigators at PNNL with expertise in mass spectrometry (MS)-based omics technology development, omics measurement methods development and application, statistics, machine learning and integration of disparate datasets for a systems-level understanding, and expertise in pathogenic coronaviruses, and investigators at the University of Wisconsin-Madison (UW-Madison) with expertise in pathogenic respiratory viruses (e.g. influenza). The goal of this project is to obtain a comprehensive picture of the human host factors critical for the outcome of SARS-CoV-2 infection. We will generate broad untargeted multi-omics profiles using both state-of-the-art and novel instrumentation and approaches to enable the identification of the molecular mechanisms and host response pathways that impact human COVID-19 outcomes. We anticipate these results will lead to the generation of biomarker panels that are predictive of disease outcomes and mechanistic hypotheses that can be further interrogated in future studies and will provide the basis for vaccine or therapeutic development. To do so, we are obtaining and analyzing blood samples from COVID-19 patients with a range of disease outcomes that were treated at the Center Hospital of the National Center for Global Health and Medicine in Tokyo, Japan and other collaborating hospitals in our network. Specifically, this project will fund proteomics and metabolomics analyses of clinical COVID samples, machine learning-based integration of the data, and pathway-based interpretation of the data. This project was funded in June 2020. In the time span of June to September 2020, the project team developed an analytically and statistically robust analysis plan and made various preparations to facilitate sample receipt from our UW-Madison collaborators. This included blocking and randomization of sample prep orders, ordering of reagents and reference materials, and shipping of materials needed for preparation of the samples under BSL3 conditions to our collaborators at UW-Madison. As of FY21, this project has been picked up via a sponsor, the Naval Medical Research Center, which will cover the remainder of the proposed scope of work.

60 APPLIED LIFE SCIENCES↗

Accuracy of real-time multi-model ensemble forecasts for seasonal influenza in the U.S.

Seasonal influenza results in substantial annual morbidity and mortality in the United States and worldwide. Accurate forecasts of key features of influenza epidemics, such as the timing and severity of the peak incidence in a given season, can inform public health response to outbreaks. As part of ongoing efforts to incorporate data and advanced analytical methods into public health decision-making, the United States Centers for Disease Control and Prevention (CDC) has organized seasonal influenza forecasting challenges since the 2013/2014 season. In the 2017/2018 season, 22 teams participated. A subset of four teams created a research consortium called the FluSight Network in early 2017. During the 2017/2018 season they worked together to produce a collaborative multi-model ensemble that combined 21 separate component models into a single model using a machine learning technique called stacking. This approach creates a weighted average of predictive densities where the weight for each component is determined by maximizing overall ensemble accuracy over past seasons. In the 2017/2018 influenza season, one of the largest seasonal outbreaks in the last 15 years, this multi-model ensemble performed better on average than all individual component models and placed second overall in the CDC challenge. It also outperformed the baseline multi-model ensemble created by the CDC that took a simple average of all models submitted to the forecasting challenge. This project shows that collaborative efforts between research teams to develop ensemble forecasting approaches can bring measurable improvements in forecast accuracy and important reductions in the variability of performance from year to year. Efforts such as this, that emphasize real-time testing and evaluation of forecasting models and facilitate the close collaboration between public health officials and modeling researchers, are essential to improving our understanding of how best to use forecasts to improve public health response to seasonal and emerging epidemic threats.

59 BASIC BIOLOGICAL SCIENCES↗

Solar Energy Research Institute for India and the United States (SERIIUS): Lessons and Results from a Binational Consortium

This book describes the development, functioning, and results of a successful binational program to promote significant scientific advances in Earth-abundant photovoltaics (PV) and concentrated solar power (CSP), advanced process/manufacturing technologies, multiscale modeling and reliability testing, and analysis of integrated solar energy systems. SERIIUS is a consortium between India and the United States dedicated to developing new solar technologies and assessing their potential impact in the two countries. The consortium consists of nearly 50 institutions including academia, national laboratories, and industry, with the goal of developing significant new technologies in all areas of solar deployment. In addition, the program focused on workforce development through graduate students, post-doctoral students, and an international exchange program. Particular emphasis was placed on the following efforts: creating disruptive technologies in PV and CSP through high-impact fundamental and applied research and development (R&D); identifying and quantifying the critical technical, economic, and policy issues for solar energy development and deployment in India; overcoming barriers to technology transfer by teaming research institutions and industry in an effective project structure; building a new platform for binational collaboration using a formalized R&D project structure, along with effective management, coordination, and decision processes; creating a sustainable network and workforce development program from which to build large collaborations and fostering a collaborative culture and outreach programs. This includes using existing and new methodologies for collaboration based on advanced electronic and web-based communication to facilitate functional international teams. The book summarizes the general lessons learned from these experiences.

14 SOLAR ENERGY↗

Technology Development, Implementation, and Assessment: K-16 Pre-Service, In-Service, and Distance Learning Initiatives

This summer 22 kindergarten through 8th grade teachers attended a 3-week Teacher Enhancement Institute (TEI) at NASA Langley Research Center. TEI is funded by NASA Education Division and is a collaborative effort between NASA Langley's Office of Education and Christopher Newport University. Selected teacher teams were drawn from Langley's 5-state precollege service region, which includes Kentucky, North Carolina, South Carolina, Virginia, and West Virginia. The goal of TEI was for teachers to learn aeronautics and the broad application of science and technology through a problem-based learning (PBL) strategy. PBL is an instructional method using a real world problem, also known as an ill-structured problem, as the context for an in-depth investigation. Most real life problems are ill-structured, as are all the really important social, political and scientific problems. The teachers were immediately immersed in an ill-structured problem to design a communication strategy for the White House Commission on Aviation Safety and Security to educate and disseminate aviation information to the general public. Specifically, the communication strategy was to focus on aeronautics principles, technology and design associated with US general aviation revitalization and aviation safety programs. The presented problem addressed NASA's strategic outcome to widely communicate the content, relevancy and excitement of its missions and discoveries to the general population. Further, the PBL scenario addressed the technological challenges being taken up by NASA to revolutionize air travel and the way in which aircraft are designed, built, and operated. It also addressed getting people and freight safely and efficiently to any location in the world at a reasonable cost. With a "real" need-to-know problem facing them, the teachers set out to gather information and to better understand the problem using inquiry-based and scientific methods. The learning in this aeronautics scenario was driven by the direction taken by participants. With the support of the TEI faculty, the teachers quickly identified NASA Langley researchers that served as consultants to help solve the problem. To achieve their goal, the teacher teams developed lesson plans for elementary and middle school students, wrote a newspaper, published a brochure to educate the general public, constructed games for children of all ages, and produced a video. As a second problem, the TEI participants will design their own aeronautic lesson plan and immerse their 1997-98 school year students in the problem. The problem is for the students "to create a traveling hands-on, minds-on aeronautics museum exhibit created for children by children." As a culminating activity, the Virginia Air and Space Center in Hampton, VA, will set up a special display of the exhibits in the Summer 1998. The TEI faculty will visit each TEI teacher's classroom during the academic school year to observe the implementation of the unit. In addition to the classroom observations, electronic follow-up sessions will be conducted during the school year to support the teachers' efforts in developing their PBL units to integrate technology in math and science instruction. These sessions eill be conducted using the Internet. Teachers will be connected through a chat-line to share ideas, ask questions, and generate solutions.

Petersen, Richard↗

ImageLabler: Labeling and Managing Image Data for Machine Learning in the Earth Sciences

While machine learning techniques for image classification have been around for a long time, storing and managing the vast number of images required as training data is still a problem for scientists. This is especially true for the field of Earth science, where only recently have experts begun using machine learning techniques for image-based phenomena classification. Image Labeler, a fast and scalable cloud-based tagging platform for Earth science images, seeks to improve upon existing methods of managing images and associated metadata, such as maintaining categorized folders of images on a local machine, a process that can be cumbersome and difficult to scale. The platform facilitates rapid development of image-based Earth science phenomena training datasets by allowing scientists to upload their existing imagery as well as extract new samples from open satellite imagery services made available through NASA’s Global Imagery Browse Service (GIBS). Image Labeler also supports GeoTIFF data, with capabilities such as displaying GeoTIFFs on an interactive map, drawing shapefiles over them, and tagging them with additional metadata. This allows scientists to perform spatiotemporal subsetting with geographic information and develop training data more quickly. Built using modern web technologies, Image Labeler includes additional capabilities such as team collaboration for large-scale image tagging projects. Users can download their data in a machine-learning-ready format, allowing scientists to spend time on experimentation rather than on the collection of training data. In this presentation, we demonstrate how Image Labeler seeks to become a one-stop image data management solution for machine learning applications in Earth science.

Ashish Acharya↗

Recent Progress of JT-60SA Project toward Plasma Operation

Superconducting tokamak JT-60SA plays an essential role in fusion research and development by supporting and complementing ITER project, providing directions to the DEMO design activity and fostering next generation scientists and engineers. Since the incident of the Equilibrium Field coil #1 during the Integrated Commissioning (IC) in March 2021, both EU and JA Implementing agencies (IAs) have examined how to ensure safety operation of JT-60SA by mitigating the risk of possible discharge occurrence inside the cryostat. Based on the experience of the Global Paschen tests, the IAs have established a strategy of risk mitigation measures, which is a combination of (i) reinforcement of insulation, (ii) avoiding unnecessary voltage application to the coil systems and (iii) immediate de-energization of the coils when deteriorated vacuum condition is detected. Thanks to the considerable efforts of the Integrated Project Team (IPT) members, the IC restarted in May 2023. After the confirmation of superconducting state of coil systems (TF, EF and CS), the coil energization test and the plasma operation (OP-1) starts. The first plasma was successfully achieved on 23 October 2023 with a limited value of applied voltage and current to the coils. The plasma configuration control will be also confirmed with low plasma current and low auxiliary heating power conditions. Based on the IO-F4E-QST collaboration, activities of JT-60SA have been shared with the IO and provided an important lesson learned for ITER assembly and commissioning, and will provide an outstanding contribution to fusion research at large. After OP-1, Maintenance & Enhancement phase 1 (M/E-1) starts from January 2024, in which in-vessel components are installed, and heating system and diagnostic system are extensively upgraded to allow high power heating experiment planned in OP-2. In order to make the best use of JT-60SA, newly organized JT-60SA experiment team will refine the research plan in the future high heating power operation phase.

Broader Approach activities↗

FY25 Progress Report: SRNL Analysis of ICCWR LCM and WAMS data for Corrosion and Cracking

Algorithms for Machine Learning (ML) and image analysis for the 3013 Surveillance Program have been developed in an ongoing collaborative effort by the Savannah River National Laboratory (SRNL) and the University of South Carolina (USC). The objective of the algorithms is to automate the identification of corrosion and cracks in the Inner Container Closure Weld Region (ICCWR) of the canister system used to store Pu-bearing material. Data for corrosion and cracking is collected from large binary files generated by a Laser Confocal Microscope (LCM), the Wide Area 3D Measurement System (WAMS), or, in a recent proposal, by a Scanning Electron Microscope (SEM). The ML software uses the physical attributes in the data files (e.g., one or more of: height, color, and 16-bit grayscale values as functions of position in a plane projection) to detect signs of surface corrosion and cracking after being trained on similar data with the features to be detected. Although the initial scope included screening for broader indicators of corrosion, e.g., pitting, the identification of potential cracks was prioritized for the past several years at the request of program leadership.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

A Tale of Two Chambers: Iterative Approaches and Lessons Learned from Life Support Systems Testing in Altitude Chambers

With a brand new fire set ablaze by a serendipitous convergence of events ranging from a science fiction novel and movie ("The Martian"), to ground-breaking recent discoveries of flowing water on its surface, the drive for the journey to Mars seems to be in a higher gear than ever before. We are developing new spacecraft and support systems to take humans to the Red Planet, while scientists on Earth continue using the International Space Station as a laboratory to evaluate the effects of long duration space flight on the human body. Written from the perspective of a facility test director rather than a researcher, and using past and current life support systems tests as examples, this paper seeks to provide an overview on how facility teams approach testing, the kind of information they need to ensure efficient collaborations and successful tests, and how, together with researchers and principal investigators, we can collectively apply what we learn to execute future tests.

Callini, Gianluca↗

A Global Land Cover Training Dataset From 1984 to 2020

State-of-the-art cloud computing platforms such as Google Earth Engine (GEE) enable regional-to-global land cover and land cover change mapping with machine learning algorithms. However, collection of high-quality training data, which is necessary for accurate land cover mapping, remains costly and labor-intensive. To address this need, we created a global database of nearly 2 million training units spanning the period from 1984 to 2020 for seven primary and nine secondary land cover classes. Our training data collection approach leveraged GEE and machine learning algorithms to ensure data quality and biogeographic representation. We sampled the spectral-temporal feature space from Landsat imagery to efficiently allocate training data across global ecoregions and incorporated publicly available and collaborator-provided datasets to our database. To reflect the underlying regional class distribution and post-disturbance landscapes, we strategically augmented the database. We used a machine learning-based cross-validation procedure to remove potentially mis-labeled training units. Our training database is relevant for a wide array of studies such as land cover change, agriculture, forestry, hydrology, urban development, among many others.

Radost Stanimirova↗