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At least 343 records · Page 19

Artificial Intelligence and Machine Learning for Bioenergy Research: Opportunities and Challenges

The integration of artificial intelligence and machine learning (AI/ML) with automated experimentation, genomics, biosystems design, and bioprocessing technologies is poised to revolutionize scientific investigation and, particularly, bioenergy research. To identify the opportunities and challenges in this emerging research area, the U.S. Department of Energy’s (DOE) Biological and Environmental Research program (BER) and Bioenergy Technologies Office (BETO) held a joint virtual workshop on AI/ML for Bioenergy Research (AMBER) on August 23–25, 2022. These interests have since been amplified in a September 2022 Executive Order, “Advancing Biotechnology and Biomanufacturing Innovation for a Sustainable, Safe, and Secure U.S. Bioeconomy,” to promote a whole-of government approach to biotechnology development (White House 2022). Approximately 50 scientists with various backgrounds and expertise from academia, industry, and DOE national laboratories met to discuss the opportunities and challenges of AI/ML for bioenergy research. Workshop participants were tasked with assessing the potential for AI/ML and laboratory automation to advance biological understanding and engineering in general. They particularly examined how integrating AI/ML tools with laboratory automation could accelerate biosystems design and optimize biomanufacturing. Discussions included the data and computational infrastructure needed to augment biosystems design applications and the expertise and workforce development efforts urgently required to shift integrated systems toward bioenergy research more broadly. Participants discussed many existing and future applications of AI/ML for biosystems design ranging from enzymes to plants and microbes, microbiomes, and bioprocess development. They also identified three key categories of scientific and technical opportunities and challenges: high-quality data, AI/ML algorithms, and laboratory automation. Several main takeaways emerged from the workshop: 1. Numerous AI/ML and automated experimentation applications exist for a variety of DOE mission needs in energy and the environment; 2. Exemplary research grand challenges for which AI/ML could provide solutions include: building microbes and microbial communities to specifications, developing closed-loop autonomous design and control for biosystems design, and advancing scale-up and automation; 3. Lack of sufficient high-quality, annotated data hinders the development of AI/ML applications; 4. New and improved AI/ML tools are needed, particularly those meeting the specific needs of the BER and BETO research communities; 5. Trade-offs in performance, cost, and reliability exist between deploying commercially available versus building custom-developed instrumentation and software for automated or autonomous experimentation; translation of manual to automated or autonomous methods is often a nontrivial endeavor; 6. Training a new generation of young scientists who can develop and apply AI/ML tools is needed to solve long-standing scientific challenges in bioenergy research. The integration of AI/ML tools and automated experimentation represents a new data-driven research paradigm complementary to the traditional hypothesis-driven research paradigm. This paradigm accelerates design and optimization of biological systems and processes for a variety of DOE mission needs in energy and the environment. The AMBER workshop broadly explored the potential of this new paradigm for bioenergy research, of particular interest to BER and BETO, and identified key challenges and opportunities that DOE can address in the coming years by leveraging its unique capabilities and resources.

59 BASIC BIOLOGICAL SCIENCES↗

Pre-exascale accelerated application development: The ORNL Summit experience

High-performance computing (HPC) increasingly relies on heterogeneous architectures to achieve higher performance. In the Oak Ridge Leadership Facility (OLCF), Oak Ridge, TN, USA, this trend continues as its latest supercomputer, Summit, entered production in early 2019. The combination of IBM POWER9 CPU and NVIDIA V100 GPU, along with a fast NVLink2 interconnect and other latest technologies, pushes system performance to a new height and breaks the exascale barrier by certain measures. Due to Summit's powerful GPUs and much higher GPU–CPU ratio, offloading to accelerators becomes a requirement for any application, which intends to effectively use the system. To facilitate navigating a complex landscape of competing heterogeneous architectures, a collection of applications from a wide spectrum of scientific domains is selected for early adoption on Summit. In this article, the experience and lessons learned are summarized, in the hope of providing useful guidance to address new programming challenges, such as scalability, performance portability, and software maintainability, for future application development efforts on heterogeneous HPC systems.

97 MATHEMATICS AND COMPUTING↗

Ground data systems resource allocation process

The Ground Data Systems Resource Allocation Process at the Jet Propulsion Laboratory provides medium- and long-range planning for the use of Deep Space Network and Mission Control and Computing Center resources in support of NASA's deep space missions and Earth-based science. Resources consist of radio antenna complexes and associated data processing and control computer networks. A semi-automated system was developed that allows operations personnel to interactively generate, edit, and revise allocation plans spanning periods of up to ten years (as opposed to only two or three weeks under the manual system) based on the relative merit of mission events. It also enhances scientific data return. A software system known as the Resource Allocation and Planning Helper (RALPH) merges the conventional methods of operations research, rule-based knowledge engineering, and advanced data base structures. RALPH employs a generic, highly modular architecture capable of solving a wide variety of scheduling and resource sequencing problems. The rule-based RALPH system has saved significant labor in resource allocation. Its successful use affirms the importance of establishing and applying event priorities based on scientific merit, and the benefit of continuity in planning provided by knowledge-based engineering. The RALPH system exhibits a strong potential for minimizing development cycles of resource and payload planning systems throughout NASA and the private sector.

Berner, Carol A.↗

Small Spacecraft for Planetary Atmospheric, Surface, and Interior Structure Using Radio Links

Scientific studies using spacecraft radio links have been conducted on almost every Solar System exploration mission in the past five decades and have led to numerous discoveries. Radio Science experiments have elucidated the thermal history of the Moon from high resolution gravitational field measurements, unveiled the interiors of Titan, Enceladus, Mercury, Phobos, Vesta and Ceres providing key evidence for identifying subsurface oceans on icy moons; sounded Titan, Saturn, and Pluto’s atmospheres, and refined models for the atmospheres, surfaces, and interior structure of Mars and Venus. A Juno experiment is in progress measuring the gravitational field of Jupiter to reveal its interior structures, as did a similar recent Cassini experiment with Saturn. Experiments at Mercury, the Jovian system, and other targets, are in development or planning phases. Over the next 30 years, significant advances in radio and laser link-science technologies, including nearly one order of magnitude improvement achievable in range-rate and range accuracy, could enable many new scientific breakthroughs. Future exploration concepts in many cases focus on applications of small spacecraft and can include spacecraft constellations for studies of atmospheric dynamics, interior structures, and surface properties. A set of science-enabling radio link technologies specific to small spacecraft instrumentation on future solar system missions are under study and development. Examples include field tests of radio scattering to determine soil properties, smallsat constellations for dense geographic and temporal atmospheric probing, small science-quality software-defined transponders, miniature ultra-stable oscillators, and advanced radio-metric calibrations at the Deep Space Network. This paper describes many of these technologies and their scientific applications.

Elliott, Harvey↗

Advanced flight experiment automation development

NASA's space science program suffers under operational constraints that severely limit scientific reactivity. We describe a possible extension to an existing system that enables space science to be conducted in a more reactive manner through advanced automation techniques that have recently been used in the Space Transportation System (STS)-based Spacelab. This automation allows sophisticated autonomous control of the experiment by monitoring and dynamically controlling the progress of the experiment protocol. This new approach permits intelligent conduct of experimental research investigations whether or not the crew is available or contact with the ground is possible. We describe an intelligent software assistant that can manage the conduct of the experiment autonomously, by providing responsive telepresence science, or by assisting the astronaut operator with scientific advice. The crew could be unavailable for short periods when the experiment has low priority, or for longer periods on partially tended Space Station. We suggest this system could be developed as a ground prototype using commercial hardware, versions of which have been flight qualified, in order to provide a natural transition path towards flight use. In order to make this demonstration most valuable, we propose not to select a particular Life Sciences experiment, but to include an experiment simulator representative of major scientific domains.

Groleau, Nicolas↗

Standards, dissemination, and best practices in systems biology

In this study, the reproducibility of scientific research is crucial to the success of the scientific method. Here, we review the current best practices when publishing mechanistic models in systems biology. We recommend, where possible, to use software engineering strategies such as testing, verification, validation, documentation, versioning, iterative development, and continuous integration. In addition, adhering to the Findable, Accessible, Interoperable, and Reusable modeling principles allows other scientists to collaborate and build off of each other’s work. Existing standards such as Systems Biology Markup Language, CellML, or Simulation Experiment Description Markup Language can greatly improve the likelihood that a published model is reproducible, especially if such models are deposited in well-established model repositories. Where models are published in executable programming languages, the source code and their data should be published as open-source in public code repositories together with any documentation and testing code. For complex models, we recommend container-based solutions where any software dependencies and the run-time context can be easily replicated.

59 BASIC BIOLOGICAL SCIENCES↗

Software Defined Architectures for Portability and Performance

The Software Defined Architectures for Portability and Performance (SODAPOP) project developed a co-design framework to partition and map converged applications on specialized heterogeneous architectures. We started from key domain applications that combine scientific simulation with data analytics and machine learning as drivers to integrate our framework. The framework includes high-level compilers that interfaces with high-level programming frameworks, domain-specific optimization passes, and hardware-oriented optimizations. The framework leverages hardware generators to enable specialization and facilitate exploration of custom system designs.

97 MATHEMATICS AND COMPUTING↗

Data processing for a cosmic ray experiment onboard the solar probes Helios 1 and 2: Experiment 6

The data processing system for the Helios experiment 6, measuring energetic charged particles of solar, planetary and galactic origin in the inner solar system, is described. The aim of this experiment is to extend knowledge on origin and propagation of cosmic rays. The different programs for data reduction, analysis, presentation, and scientific evaluation are described as well as hardware and software of the data processing equipment. A chronological presentation of the data processing operation is given. Procedures and methods for data analysis which were developed can be used with minor modifications for analysis of other space research experiments.

Mueller-Mellin, R.↗

FAST: A multi-processed environment for visualization of computational fluid

Three dimensional, unsteady, multizoned fluid dynamics simulations over full scale aircraft is typical of problems being computed at NASA-Ames on CRAY2 and CRAY-YMP supercomputers. With multiple processor workstations available in the 10 to 30 Mflop range, it is felt that these new developments in scientific computing warrant a new approach to the design and implementation of analysis tools. These large, more complex problems create a need for new visualization techniques not possible with the existing software or systems available as of this time. These visualization techniques will change as the supercomputing environment, and hence the scientific methods used, evolve ever further. Visualization of computational aerodynamics require flexible, extensible, and adaptable software tools for performing analysis tasks. FAST (Flow Analysis Software Toolkit), an implementation of a software system for fluid mechanics analysis that is based on this approach is discussed.

Bancroft, Gordon V.↗

FAST: A multi-processed environment for visualization of computational fluid dynamics

Three-dimensional, unsteady, multi-zoned fluid dynamics simulations over full scale aircraft are typical of the problems being investigated at NASA Ames' Numerical Aerodynamic Simulation (NAS) facility on CRAY2 and CRAY-YMP supercomputers. With multiple processor workstations available in the 10-30 Mflop range, we feel that these new developments in scientific computing warrant a new approach to the design and implementation of analysis tools. These larger, more complex problems create a need for new visualization techniques not possible with the existing software or systems available as of this writing. The visualization techniques will change as the supercomputing environment, and hence the scientific methods employed, evolves even further. The Flow Analysis Software Toolkit (FAST), an implementation of a software system for fluid mechanics analysis, is discussed.

Bancroft, Gordon V.↗

Bridging the time scale in exascale computing of chemical systems (Final Technical Report)

This report summarizes the work carried out with support of the United States Department of Energy under Award DE-SC0019441. The theme of this project was to develop and apply methods that allowed for the acceleration of atomistic calculations, particularly in challenging areas such as multiphase systems, electrified interfaces, uncertainty estimation, and applications requiring chemical accuracy, which tend to be applications where simulation time is severely bottlenecked by the computational time requirements. Much of the focus was on the application of emerging machine-learning methodologies, although a wide range of methodologies were employed. This report has two major sections. The first focuses on the methodological advances themselves. Within this part, we report a number of major advances, a few examples of which are described here. We report the first machine-learning scheme for the acceleration of electronically grand-canonical calculations (that is, those applicable to electrochemistry). We report new methods of performing transfer learning, in which physics-based priors can be used to provide predictions, often with uncertainty estimates, of images well outside of training sets; we also offer ways to fine-tune these transfer-learning models. We provide a new systematic means to generate and apply minimal training data sets to very large (10,000’s of atoms) systems, with only small training sets appropriate for electronic structure. We developed new methodologies to integrate surface vibrations into surface adsorption calculations. We made advances to the applicability of diffusion Monte Carlo methods to allow (learned) force prediction, finite-size error correction, and force-free means of searching for transition states. We integrated machine-learned atomistic predictions into mechanism generation codes. Additionally, we released new software including AmpTorch, a modernized version of our original atomistic machine-learning code Amp. The second part of this report focuses on the scientific applications that accompanied, and were often enabled by, the methodological advances described earlier. A few examples follow, but full details are in the individual chapters of the report. For example, we developed a general theory of phonon-induced friction on molecular adsorbates. We showed fundamentally how solvent influences the adsorption and desorption process and how it differs from the processes typically involved at the solid–gas interface, making aqueous-phase and electrocatalysis different from traditional thermocatalysis. We examined how metal–insulator and magnetic transitions can be probed, and accelerated exciton dynamics via Frenkel Hamiltonian parameters. We showed that the nearsighted force-training approach, developed within this project, can predict both the stability and reactivity of large nanoparticles, and can also lead to insights on catalyst coverage on binding energies and entropies. These applied studies, which generally integrated with our method development, allowed us to push forward the theoretical understanding of several reaction classes.

08 HYDROGEN↗

Multi-Task with Procter and Gamble (CRADA No. NFE-10-02672)

The purpose of this Cooperative Research and Development Agreement (CRADA) between UT-Battelle, LLC (the “Contractor) and Procter & Gamble Company (the “Participant”) is the development of a research partnership to create new tools, tests and analytical methods to improve the performance, safety and/or environmental quality of chemicals, advanced materials, food products and manufacturing processes. The Participant operates in three global business units: Beauty, Health and Well-Being and Household Care. Some of its worldwide products include Head and Shoulders®, Pantene®, Gillette® razors and personal care products, Crest®, Dawn®, Tide®, Bounty®, Duracell® batteries; and Iams® pet food among others. At its core, however, the Participant is a science driven company. It supports one of the most robust industrial research and development (R&D) programs in the world. The Participant uses this rich foundation of science to drive innovation across all of its product lines. But the innovation process is not confined in-house The Participant pursues an “open innovation” policy, seeking partnerships with scientists and researchers in universities and national laboratories where it can contribute its extensive knowledge assets and collaborate to advance scientific understanding. The research under this multi-task CRADA was directed under the following general task areas and, throughout the duration of this CRADA the work statement was modified to match the needs of the Parties and the direction of the research. (1) Software modeling, simulation and development; (2) Manufacturing Technologies; (3) Supply Chain Optimization, (4) Advanced Materials.

36 MATERIALS SCIENCE↗

A NASA initiative: Software engineering for reliable complex systems

The objective is the development of methods, technology, and skills that will enable NASA to cost-effectively specify, build, and manage reliable software which can evolve and be maintained over an extended period. The need for such software is rooted in the increasing integration of software and computing components into NASA systems. Current NASA Software Engineering expertise was applied toward some of the largest reliable systems including: shuttle launch; ground support; shuttle simulation; minor control; satellite tracking; and scientific data systems. Unfortunately, no theory exists for reliable complex software systems. NASA is seeking to fill this theoretical gap through a number of approaches. One such approach is to conduct research on theoretical foundations for managing complex software systems. It includes: communication models, new and modified paradigms, and life-cycle models. Another approach is research in the theoretical foundations for reliable software development and validation. It focuses upon formal specifications, programming languages, software engineering systems, software reuse, formal verification, and software safety. Further approaches involve benchmarking a NASA software environment, experimentation within the NASA context, evolution of present NASA methodology, and transfer of technology to the space station software support environment.

Holcomb, Lee B.↗

Software Deployment Process at NERSC: Deploying the Extreme-scale Scientific Software Stack (E4S) Using Spack at the National Energy Research Scientific Computing Center (NERSC)

One of the many benefits of using a high-performance computing (HPC) system at a Department of Energy (DOE) Office of Science (SC) HPC facility is the large number of software products, built and optimized for the system. The HPC center staff and HPC vendors provide optimized software such as libraries and even full scientific applications, ready to be used by users as building blocks to accelerate scientific discovery. Behind each provided packaged software module are a large number of decisions - which compiler, optimizations, variants/options - to build the software on the target system. And, even before the software gets deployed, the software must be developed, tested, and maintained, including deprecating old versions and ensuring compatibility across versions. The software lifecycle is complex and is further convoluted by a web of interdependencies on other software.

97 MATHEMATICS AND COMPUTING↗

Triton: Environmental Monitoring Technology Development, Collision Risk Data Collection (Final Report)

In this project, we assembled a sensor suite that combines a scientific echosounder (sonar) system with video and acoustic cameras (secondary sensors). The sensor suite generates data that is amenable to automated target detection algorithms and can provide inputs to animal encounter models. We developed software (archiving software) to collect data simultaneously from all sensors in the suite, analyze the sonar data automatically in near real-time to identify time periods when targets of interest were present, and automatically archive data from the secondary sensors for these time periods. The product of the archiving software is a data set for the secondary sensors, containing data only for the times when targets of interest were determined to be present by the sonar. We performed controlled field testing to verify the operation of the sensor suite and the archiving software.

47 OTHER INSTRUMENTATION↗

A ranking algorithm for spacelab crew and experiment scheduling

The problem of obtaining an optimal or near optimal schedule for scientific experiments to be performed on Spacelab missions is addressed. The current capabilities in this regard are examined and a method of ranking experiments in order of difficulty is developed to support the existing software. Experimental data is obtained from applying this method to the sets of experiments corresponding to Spacelab mission 1, 2, and 3. Finally, suggestions are made concerning desirable modifications and features of second generation software being developed for this problem.

Grone, R. D.↗

The CCD/Transit Instrument (CTI) data-analysis system

The automated software system for archiving, analyzing, and interrogating data from the CCD/Transit Instrument (CTI) is described. The CTI collects up to 450 Mbytes of image-data each clear night in the form of a narrow strip of sky observed in two colors. The large data-volumes and the scientific aims of the project make it imperative that the data are analyzed within the 24-hour period following the observations. To this end a fully automatic and self evaluating software system has been developed. The data are collected from the telescope in real-time and then transported to Tucson for analysis. Verification is performed by visual inspection of random subsets of the data and obvious cosmic rays are detected and removed before permanent archival is made to the optical disc. The analysis phase is performed by a pair of linked algorithms, one operating on the absolute pixel-values and the other on the spatial derivative of the data. In this way both isolated and merged images are reliably detected in a single pass. In order to isolate the latter algorithm from the effects of noise spikes a 3x3 Hanning filter is applied to the raw data before the analysis is run. The algorithms reduce the input pixel-data to a database of measured parameters for each image which has been found. A contrast filter is applied in order to assign a detection-probability to each image and then x-y calibration and intensity calibration are performed using known reference stars in the strip. These are added to as necessary by secondary standards boot-strapped from the CTI data itself. The final stages involve merging the new data into the CTI Master-list and History-list and the automatic comparison of each new detection with a set of pre-defined templates in parameter-space to find interesting objects such as supernovae, quasars and variable stars. Each stage of the processing from verification to interesting image selection is performed under a data-logging system which both controls the pipe-lining of data through the system and records key performance monitor parameters which are built into the software. Furthermore, the data from each stage are stored in databases to facilitate evaluation, and all stages offer the facility to enter keyword-indexed free-format text into the data-logging system. In this way a large measure of certification is built into the system to provide the necessary confidence in the end results.

Cawson, M. G. M.↗

Development of a High Accuracy Angular Measurement System for Langley Research Center Hypersonic Wind Tunnel Facilities

Modern experimental and test activities demand innovative and adaptable procedures to maximize data content and quality while working within severely constrained budgetary and facility resource environments. This report describes development of a high accuracy angular measurement capability for NASA Langley Research Center hypersonic wind tunnel facilities to overcome these deficiencies. Specifically, utilization of micro-electro-mechanical sensors including accelerometers and gyros, coupled with software driven data acquisition hardware, integrated within a prototype measurement system, is considered. Development methodology addresses basic design requirements formulated from wind tunnel facility constraints and current operating procedures, as well as engineering and scientific test objectives. Description of the analytical framework governing relationships between time dependent multi-axis acceleration and angular rate sensor data and the desired three dimensional Eulerian angular state of the test model is given. Calibration procedures for identifying and estimating critical parameters in the sensor hardware is also addressed.

Newman, Brett↗