SBIR Phase II Final Report for Rhizomatic - Next Generation Image Processing for In Situ Fine Root Measurement
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54 ENVIRONMENTAL SCIENCES↗
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I/O in Machine Learning Applications on HPC Systems: A 360-degree Survey
Growing interest in Artificial Intelligence (AI) has resulted in a surge in demand for faster methods of Machine Learning (ML) model training and inference. This demand for speed has prompted the use of high performance computing (HPC) systems that excel in managing distributed workloads. Because data is the main fuel for AI applications, the performance of the storage and I/O subsystem of HPC systems is critical. In the past, HPC applications accessed large portions of data written by simulations or experiments or ingested data for visualizations or analysis tasks. ML workloads perform small reads spread across a large number of random files. This shift of I/O access patterns poses several challenges to modern parallel storage systems. In this paper, we survey I/O in ML applications on HPC systems, and target literature within a 6-year time window from 2019 to 2024. We define the scope of the survey, provide an overview of the common phases of ML, review available profilers and benchmarks, examine the I/O patterns encountered during offline data preparation, training, and inference, and explore I/O optimizations utilized in modern ML frameworks and proposed in recent literature. Lastly, we seek to expose research gaps that could spawn further R&D.
97 MATHEMATICS AND COMPUTING↗
Early Information Parameter-Set Analysis for Satellite Close Approaches using Machine Learning
Understanding orbital mechanics is essential in space flight and navigation applications, and leveraging modern force models for flight path projection remains an important aspect in space mission design and operation. However, force models do not capture all the dynamics or perturbations in the space environment and thus are subject to errors in predicting the state vectors. The further out the predicted miss distance between spacecraft is from the time of closest approach (TCA), the larger the propagated errors in the predicted miss distance at TCA is. The dependency on these force models for spacecraft flight state prediction calls for a more reliable method that can quantify, or even reduce, these propagated errors. With recent advances in the field artificial intelligence, specifically in machine and deep learning algorithms, a model that implements these approaches can improve on the modern force model approach. The goal for this work is to provide an early-information decision-making threshold, in order to prioritize risk assessment implementation, given the ongoing increase of space objects. In analyzing the relationship of several parameters from conjunction data messages(CDMs) and solar information, early information becomes viable in miss distance prediction with unsupervised learning techniques, which learn the parameters that are linked together with miss distance and probability of collision (Pc) variables. Another approach implemented for identifying relationships within CDMs is supervised learning, in which a shallow neural network binary classifier learns to distinguish events with Pc values¡108. These parameters detected in the unsupervised process are then applied to a regression neural network, which predicts the miss distance at TCA for a specific event within a given uncertainty bound. For the regression neural network, a Long Short Term Memory (LSTM) neural network is implemented, which yields memory about each time step in an event. Using an LSTM network, the model learns to predict miss distance within 0.2km of the value measured at TCA. Although there is a limited amount of "close miss" data to train a network, the network learns to associate parameters, like large energy dissipation rates with the secondary object, with an elevated Pc
Brianna I. Robertson↗
A Machine-Learning Approach to Assess Aircraft Engine System Performance
Artificial intelligence (AI)/machine learning, and big data are transforming the global business environment. They have become the most disruptive technologies for organizations to improve workplace efficiency and productivity. This work explored the application of machine learning-based predictive analytics that would enable aircraft engine designers to estimate engine system performance quickly during the conceptual design stage. Supervised machine-learning algorithm was employed to study patterns in an existing database of production and research turbofan engines, and built predictive analytics for use in predicting system performance of new turbofan designs. Specifically, the author developed deep-learning analytics to predict turbofan system weight, using turbofan design parameters as the input. The predictive analytics were trained and deployed in Keras, an open-source neural networks API (application program interface) written in Python, with TensorFlow (an open-source artificial AI library developed by Google) serving as the backend engine. The current engine-weight prediction results, together with those for the TSFC (thrust specific fuel consumption) and core-size predictions that were studied previously by the author, show that machine learning-based predictive analytics can be an effective, time-saving tool for aircraft engine design-space exploration during the conceptual design stage. It would enable expeditious identification of the best engine design amongst several candidates.
Michael T Tong↗
Research and Technology Challenges for Human Data Analysts in Future Safety Management Systems
Enabling new and novel concepts of operations for Advanced Air Mobility poses an important need to evolve current safety management systems (SMS) and is posited to be realized through advances in Machine Learning (ML) Data Sciences and Artificial Intelligence. The “In-time Aviation Safety Management System” (IASMS) concept of operations supports the need to evolve today’s SMS to become more tailorable, scalable, and interoperable in response to forecasted changes expected for the future airspace system. Key to IASMS is integration of proactive and predictive ML algorithms trained to provide “in time” detection and mitigation of hazards and emergent risks through new methods and novel data types. IASMS research and technology development includes human factors design considerations for these systems to include human-system teaming, innovations in human interfaces and management of complex digital data information, human-system interaction/model-based system engineering, and verification and validation for data assurance and trust.
Chad L Stephens↗
Integrating Machine-learning-assisted Computer Vision with RICH System
Developments in artificial intelligence have vastly expanded the capabilities of robots. Currently, the Spallation Neutron Source (SNS) beamlines at Oak Ridge National Lab (ORNL) have robotic sample loaders to increase the efficiency of running experiments. However, they require retraining if anything about the situation changes, e.g., where the samples are, and cannot notice if errors occur. So, the viability of using computer vision and machine learning to enhance these sample loaders’ functionality was investigated. In this project, the RICH system with a Dobot CR3 6-axis robot present at the VULCAN beamline assisted by an Intel Realsense D435i camera, a unique camera that enables convenient translation of 2D pixel coordinates to 3D world points, was programmed to load ceramic crucibles into a thermogravimetric analyzer (TGA) furnace. An algorithm was constructed in Python with three major phases planned: (1) obtaining a sample, (2) moving it to the target location, and then (3) bringing the sample back to its original location once the experiment finished. In the first phase, the algorithm would dynamically detect sample locations using ArUco markers to recognize the samples’ general location and a custom-trained yolov5 object detection model to locate the crucibles’ centers. Afterward, the robot would be directed to pick up samples based on the crucibles’ calculated positions. In the second phase, the robot would move the sample to a secondary point, reorient its grip, and place the sample at the target location. In the final phase, the robot would determine whether the sample was intact and would bring it back to its original place if it was or raise an alarm. Using this algorithm, the robot was able to pick up different types of crucibles at varying positions. These results indicate that integrating machine-learning-assisted computer vision with robotic sample loaders can result in effective autonomous detection of samples.
97 MATHEMATICS AND COMPUTING↗
Design of a Low-Cost, Submersible, Digital Holographic Microscope for in Situ Microbial Imaging
The methodologies for studying marine microbiology typically consist of utilizing instrumentation within a laboratory. This typically requires extracting a sample from its place of origin prior to examination, which may be days after collection. Oftentimes, the solution is to bring the lab to the ocean, which may be costly and provide further limitations for a sterile and stable laboratory environment. Here we present a low-cost, submersible, digital holographic microscope (DHM) designed to image marine microorganisms (such as bacteria and plankton) in their natural underwater environment. Our instrument eliminates the need to transport samples and allows for instantaneous data collection of microbes in-situ. The DHM achieves sub-micron spatial resolution and is paired with artificial intelligence for the detection and tracking of specimens to reduce the overall collected data. This instrument also aims to reduce the cost of manufacturing and field expenses relative to marine microbiological research. “Off the shelf” components were selected in the design process of this instrument which allows us to achieve precise results without sacrificing data quality. The DHM itself costs under one thousand dollars and features a low-cost high-resolution camera, the Arducam MT9J001. Included in the design were five main subsystems: optical, mechanical, electrical, power, and machine learning. Our on board computer and artificial intelligence consist of a Raspberry Pi 4 (8 Gb) and Google Coral USB Tensorflow accelerator. Instrument testing has successfully proven our abilities of data acquisition for at least two hours in depths of at least forty meters below sea level. Additionally, our artificial intelligence system is currently capable of tracking up to ten areas of interest in a fraction of a second with over ninety percent confidence via the neural net driven by the tensor cores on the Google Coral. Furthermore, we have demonstrated the versatility of our instrument by mounting it on an ocean-going ROV, the BlueRov2 by BlueRobotics. Our tests on the BlueRov2 exemplified the cost-effective nature of a submersible and reusable instrument that can be implemented in moderate environments and on most vessels.
Wallace, James Kent↗
Survey of learning control systems for space vehicle applications.
On-line and off-line self-organizing control systems for space vehicle application
CONTROL SYSTEM↗
Data-driven gradient optimization for field emission management in a superconducting radio-frequency linac
Field emission can cause significant problems in superconducting radio-frequency linear accelerators (linacs). When cavity gradients are pushed higher, radiation levels within the linacs may rise exponentially, causing degradation of many nearby systems. This research aims to utilize machine learning with uncertainty quantification to predict radiation levels at multiple locations throughout the linacs and ultimately optimize cavity gradients to reduce field emission-induced radiation while maintaining the total linac energy gain necessary for the experimental physics program. The optimized solutions show over 40% reductions for both neutron and gamma radiation from the standard operational settings. Published by the American Physical Society 2025
43 PARTICLE ACCELERATORS↗
MLtool: Universal Supervised Machine Learning Tool to Model Tabulated Data
Machine Learning (ML) is a subfield of Artificial Intelligence that gives computers the ability to learn from past data without being explicitly programmed. The predictive capabilities of ML models have already been used to facilitate several scientific breakthroughs. However, the practical application of ML is often limited due to the gaps in technical knowledge of its users. The common issue faced by many scientific researchers is the inability to choose the appropriate ML pipelines that are needed to treat real-world data, which is often sparse and noisy. To solve this problem, we have developed an automated Machine Learning tool (MLtool) that includes a set of ML algorithms and approaches to aid scientific researchers. The current version of MLtool is implemented as an object-oriented Python code that is easily extensible. It includes 44 different regression algorithms used to model data. MLtool helps users select the best model for their data, based on the scoring metrics used. Besides regression algorithms, MLtool also includes a suite of pre- and post-processing techniques such as missing value imputation, categorical variable encoding, input feature normalization, uncertainty quantification, exploratory data analysis (EDA), etc. MLtool was tested on several publicly available multi-dimensional data sets and was found capable of making accurate predictions.
Machine learning↗
Enhanced Detection of Primary Biological Aerosol Particles Using Machine Learning and Single-Particle Measurement
Accurately identifying primary biological aerosol particles (PBAPs) using analytical techniques poses inherent challenges due to their resemblance to other atmospheric carbonaceous particles. Here, we present a study of an enhanced method for detecting PBAPs by combining single-particle measurement with advanced supervised machine learning (SML) techniques. We analyzed ambient particles from a variety of environments and lab-generated standards, focusing on chemical composition for traditional rule-based and clustering approaches and incorporating morphological features into the SML approaches, neural networks and XGBoost, for improved accuracy. This study demonstrates that SML methods outperform traditional methods in quantifying PBAPs, achieving significant improvements in precision, recall, F1-score, and accuracy, leading to an increased number of detected PBAPs by at least 19%. The adaptability of the proposed XGBoost-based SML model is showcased in comparison to traditional methods in categorizing PBAPs for blind data sets from different geographical locations. Two field case studies were investigated, over agricultural land and Amazonia rain forest, representing relatively low and high concentrations of PBAPs, respectively, where XGBoost consistently detected up to 3.5 times more PBAPs than traditional methods. Precise detection of PBAPs in the atmosphere could significantly improve the prediction of climatic impacts by them.
42 ENGINEERING↗
Fundamental limit of jet tagging
Identifying the origin of high-energy hadronic jets (jet tagging) has been a critical benchmark problem for machine learning in particle physics. Jets are ubiquitous at colliders and are complex objects that serve as prototypical examples of collections of particles to be categorized. Over the last decade, machine learning-based classifiers have replaced classical observables as the state of the art in jet tagging. Increasingly complex machine learning models are leading to increasingly more effective tagger performance. Our goal is to address the question of convergence—are we getting close to the fundamental limit on jet tagging or is there still potential for computational, statistical, and physical insights for further improvements? We address this question using state-of-the-art generative models to create a realistic, synthetic dataset with a known jet tagging optimum. Various state-of-the-art taggers are deployed on this dataset, showing that there is a significant gap between their performance and the optimum. Our dataset and software are made public to provide a benchmark task for future developments in jet tagging and other areas of particle physics.
Artificial intelligence↗
Machine learning approaches for intentional materials engineering
In this article, the development of nanoporous metals and metallic composites through dealloying processes presents significant opportunities in materials engineering. However, designing multicomponent precursor alloys and establishing corresponding processing methods that yield predictable compositions and nanostructures remain a complex challenge. This article explores how machine learning (ML)-augmented computational and experimental methodologies can tackle these challenges by predicting precursor alloy compositions, final nanoporous structures, and mechanical properties, while integrating ML-enabled autonomous experimentation for material design and quantification. We highlight recent advancements in applying ML to nanostructured materials design via dealloying and discuss how techniques from other nanomaterial designs can be adapted for improved control over morphological and compositional outcomes in nanoporous and nanocomposite materials. Furthermore, we explore the role of ML in autonomous synchrotron x-ray experimentation, enabling real-time feedback between modeling and experimental setups. ML-driven approaches to microstructure characterization and mechanical property prediction are also examined, with a focus on modeling and advanced imaging techniques such as three-dimensional nanotomography. Finally, this article outlines future directions for ML-enhanced materials science, emphasizing the exploration of high-dimensional parameter spaces and the incorporation of materials kinetics into processing and property evaluation, ultimately advancing the design of nanoporous structures and materials science.
36 MATERIALS SCIENCE↗
A versatile machine learning workflow for high-throughput analysis of supported metal catalyst particles
Accurate and efficient characterization of nanoparticles (NPs), particularly regarding particle size distribution, is essential for advancing our understanding of their structure-property relationship and facilitating their design for various applications. In this study, we introduce a novel two-stage artificial intelligence (AI)-driven workflow for NP analysis that leverages prompt engineering techniques from state-of-the-art single-stage object detection and large-scale vision transformer (ViT) architectures. This methodology is applied to transmission electron microscopy (TEM) and scanning TEM (STEM) images of heterogeneous catalysts, enabling high-resolution, high-throughput analysis of particle size distributions for supported metal catalyst NPs. The model's performance in detecting and segmenting NPs is validated across diverse heterogeneous catalyst systems, including various metals (Ru, Cu, PtCo, and Pt), supports (silica (SiO 2 ), γ-alumina (γ-Al 2 O 3 ), and carbon black), and particle diameter size distributions with mean and standard deviations ranging from 1.6 ± 0.2 nm to 9.7 ± 4.6 nm. The proposed machine learning (ML) methodology achieved an average F1 overlap score of 0.91 ± 0.01 and demonstrated the ability to disentangle overlapping NPs anchored on catalytic support materials. The segmentation accuracy is further validated using the Hausdorff distance and robust Hausdorff distance metrics, with the 90th percent of the robust Hausdorff distance showing errors within 0.4 ± 0.1 nm to 1.4 ± 0.6 nm. In conclusion, our AI-assisted NP analysis workflow demonstrates robust generalization across diverse datasets and can be readily applied to similar NP segmentation tasks without requiring costly model retraining.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Real-time charged track reconstruction for CLAS12
Abstract This paper presents the results of charged particle track reconstruction in CLAS12 using artificial intelligence. In our approach, we use machine learning algorithms to reconstruct tracks, including their momentum and direction, with high accuracy from raw hits of the CLAS12 drift chambers. The reconstruction is performed in real-time, with the rate of data acquisition, and allows for the identification of event topologies in real-time. This approach revolutionizes the Nuclear Physics experiments' data processing, allowing us to identify and categorize the experimental data on the fly, and will lead to a significant reduction in experiment data processing. It can also be used in streaming readout applications leading to more efficient data acquisition and post-processing.
Instruments & Instrumentation↗
Editorial: Visualizing offline and live data with AI (VOLDA) workshop first edition Princeton 11-13th June 2024
The first edition of the Visualizing Offline and Live Data with AI’ (VOLDA) Workshop took place at the Princeton University Campus, Mader Hall from 11 to 13 June 2024. This annual workshop held for the first time aims at bringing together the fusion community to discuss the challenges brought by Artificial Intelligence (AI) and visualizing large datasets in fusion experiment and simulation.
artificial intelligence↗
Artificial Intelligence Transforming Post-Translational Modification Research
Post-Translational Modifications (PTMs) are covalent changes to amino acids that occur after protein synthesis, including covalent modifications on side chains and peptide backbones. Many PTMs profoundly impact cellular and molecular functions and structures, and their significance extends to evolutionary studies as well. In light of these implications, we have explored how artificial intelligence (AI) can be utilized in researching PTMs. Initially, rationales for adopting AI and its advantages in understanding the functions of PTMs are discussed. Then, various deep learning architectures and programs, including recent applications of language models, for predicting PTM sites on proteins and the regulatory functions of these PTMs are compared. Finally, our high-throughput PTM-data-generation pipeline, which formats data suitably for AI training and predictions is described. We hope this review illuminates areas where future AI models on PTMs can be improved, thereby contributing to the field of PTM bioengineering.
59 BASIC BIOLOGICAL SCIENCES↗
Parametric Mechanism Design Through Numerical Optimization and Physics Simulation
Design-Build-Test approaches for developing spaceflight hardware are prohibitively time and cost intensive and often lead to suboptimal mechanism designs. Approaches that couple machine learning and high-fidelity physics simulation could eliminate the need for hardware prototyping and dramatically accelerate the engineering design cycle, ultimately reducing cost. This work presents a modular NASA-developed toolchain to optimize hardware mechanisms in a virtual environment using numerical optimization and multi-body physics simulation. The toolchain enables multi-objective optimization, generates parametric CAD files that can be further post-processed by an end user, and can be expanded to optimize full systems and non-mechanical parameters such as feedback control variables. We demonstrate the toolchain through an independently verifiable design problem that optimizes wheel radius to achieve a desired linear velocity in a rigid-body physics environment when the wheel rotates at a constant angular speed, and then post-process the parametric CAD file of the optimal design generated by the tool before ultimately manufacturing it via 3D printing. We end with a discussion of how the toolchain can incorporate other analysis tools, including finite element analysis, computational fluid dynamics, and granular media simulations.
Optimization↗