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At least 1,369 records · Page 76

Machine learning-enabled computer vision for plant phenotyping: a primer on AI/ML and a case study on stomatal patterning

Abstract Artificial intelligence and machine learning (AI/ML) can be used to automatically analyze large image datasets. One valuable application of this approach is estimation of plant trait data contained within images. Here we review 39 papers that describe the development and/or application of such models for estimation of stomatal traits from epidermal micrographs. In doing so, we hope to provide plant biologists with a foundational understanding of AI/ML and summarize the current capabilities and limitations of published tools. While most models show human-level performance for stomatal density (SD) quantification at superhuman speed, they are often likely to be limited in how broadly they can be applied across phenotypic diversity associated with genetic, environmental, or developmental variation. Other models can make predictions across greater phenotypic diversity and/or additional stomatal/epidermal traits, but require significantly greater time investment to generate ground-truth data. We discuss the challenges and opportunities presented by AI/ML-enabled computer vision analysis, and make recommendations for future work to advance accelerated stomatal phenotyping.

Plant Sciences↗

HD-Bind: Encoding of Molecular Structure with Low Precision, Hyperdimensional Binary Representations

Publicly available collections of drug-like molecules have grown to comprise tens of billions of compounds due to advances in combinatorial chemistry. Traditional methods for identifying "hit" molecules from a large collection of potential drug-like candidates have relied on biophysical theory to compute approximations to the Gibbs free energy of the binding interaction between the drug and its protein target. These approaches have the major drawback that they require exceptional computing capabilities for even relatively small collections of molecules. Hyperdimensional Computing (HDC) is a recently-proposed learning paradigm that represents data with high-dimension binary vectors; this allows the use of low-precision binary vector arithmetic to create models of the data that can be learned without the need for the gradient-based optimization required in many conventional machine learning and deep learning methods. This algorithmic simplicity allows for acceleration in hardware that has been previously demonstrated in a range of application areas. We consider existing HDC approaches for molecular property classification and introduce two novel encodings of a commonly-used molecular representation, the extended connectivity fingerprint (ECFP). We show that HDC-based inference methods are as much as 91 times more efficient than traditional machine learning methods, and achieve an acceleration of nearly nine orders of magnitude compared to molecular docking. Our results show that HDC accelerated methods retain competitive accuracy on a number of well-studied tasks such as molecular property predictions using the MoleculeNet dataset, and bind/no-bind activity classification using the DUD-E and LIT-PCBA datasets. Our work thus motivates further investigation into molecular representation learning to develop ultraefficient pre-screening tools.

Jones, William↗

Curifactory: A research experiment manager

Curifactory is a command line tool and framework for organizing Python experiment code, configuration parameters, and results. It is an opinionated and lightweight approach to workflow management infrastructure and is primarily intended to support researchers conducting experiments on one machine. This software was developed to support the reproducibility of results for several data science projects in the Nuclear Nonproliferation Division at Oak Ridge National Laboratory. Curifactory is intended to be a general framework and is not specific to machine learning or data science. It can aid in any field in which experiments are primarily computation-based studies and can be implemented in Python (e.g., high-energy physics, astronomy, computational chemistry). Here, the design emphasizes the automated caching of intermediate data analysis artifacts to speed up development involving computationally intensive tasks. It also allows for data provenance and experiment reproduction. Individual experiment runs are tracked through logs and their output reports, and entire copies of a run with all cached data and metadata can be exported for others to run using Curifactory on another machine. Curifactory experiments can either be integrated into a project from the beginning or can be written on top of an existing codebase without needing significant modification. A few important views of the Curifactory library can be seen in Figure 1.

97 MATHEMATICS AND COMPUTING↗

Strong Correlation DMRG and DFT

This project developed new ways to improve computer simulations of materials where electrons interact strongly with each other, a challenge for today’s most widely used method, density functional theory (DFT). We used an exact numerical method, the density matrix renormalization group (DMRG), to create highly accurate reference results for simple model systems, and used these to test DFT, prove when it will converge, and even train machine-learned functionals. We also invented new kinds of localized basis functions (“gausslets” and “multi-sliced gausslets”) and a “sliced-basis” approach that make high-accuracy simulations faster and more practical. These methods were applied to extended hydrogen systems, enabling the direct derivation of accurate low-energy models from first-principles calculations. We also introduced a new formalism, Conditional-Probability DFT, which could bypass traditional approximations. The tools and results from this work, including open-source software releases, will help scientists design and understand complex quantum materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Biocene 2018

This 'minds-on' workshop will explore emerging cross-discipline tools and techniques for moving Bio-Inspired Design (BID) into “standard practice” in systems engineering and engineering design. Discussion will center on state-of-the-art in BID tools, emerging toolkits for engineering innovation, and industry best practices. The aerospace industry is at a point where components are reaching design maturity and performance improvements are incremental. Aggressive goals for fuel burn reduction and the threat of climate change necessitate a new paradigm. An artificial intelligence (AI) approach that enables revolutionary changes in system architecture, mission analysis and performance metrics is needed. The growing interest and development in the field of machine learning presents an opportunity to speed up by 10 times or more the discovery, analysis and development of aerospace systems using artificial intelligence and natural systems.

Shyam, Vikram↗

Describing Point Defect Topology in 2D Energy Materials Through Computer Vision

Point defects such as vacancies and impurity atoms strongly impact the performance of 2D materials. Traditional efforts often rely on manual detection, a process that is time-intensive, prone to human error, and challenging to scale. Here we leverage machine learning (ML) methods to identify and quantify vacancies within 2D transition metal carbides (Ti3C2, MXenes), aiming to expedite detection while improving accuracy. MXenes exhibit valuable defect-defined electrochemical properties, but we currently lack statistical understanding of defect topology needed to fully harness these materials. Here we employ a convolutional neural network for semantic segmentation of experimental MXene images, opening an opportunity to conduct a rigorous statistical study on defect hierarchy while investigating local relaxation in the lattice. We show how the integration of ML can yield fundamental insight into point defects, providing a powerful tool that will play an increasingly crucial role in the future of materials science. ML is often not just a matter of straightforward application, and pretrained models proved ineffective in this case. Instead, we trained our own neural network (NN) and applied data augmentation techniques and fine-tuning to the training dataset. Since labeled microscopy data is often scarce, we developed training data from a previously published wide-frame MXene image, using customized Gaussian fitting to locate atomic positions. Our trained model was then applied to a large dataset of experimental images, enabling a statistical study of defect configurations across three samples prepared with different HF etchant concentrations (5%, 9.1%, and 12.5%), as shown in Fig. 1. This also allowed us to investigate local strain around vacancies, though we find that we are limited by the precision of measurements using high-angle annular dark field (HAADF) images, as shown in Fig. 2. This study demonstrates how ML enables large-scale, quantitative analysis of atomic defects - an otherwise infeasible task with traditional methods. While our NN was specialized for Ti3C2 MXenes, the pipeline we developed provides a foundation for future ML models tailored to other materials. Ultimately, we envision embedding the NN onto the microscope to give real-time feedback to the user. To make this a reality, continued work is necessary to fully understand the NN's capabilities and limitations. This study gets one step closer to our goals of automated experimentation moving away from traditional methods of manual labeling. As ML capabilities advance, we hope to continue adapting and applying these techniques in microscopy.

2D materials↗

Inverse design of photonic surfaces via multi fidelity ensemble framework and femtosecond laser processing

We demonstrate a multi-fidelity (MF) machine learning ensemble framework for the inverse design of photonic surfaces, trained on a dataset of 11,759 samples that we fabricate using high throughput femtosecond laser processing. The MF ensemble combines an initial low fidelity model for generating design solutions, with a high fidelity model that refines these solutions through local optimization. The combined MF ensemble can generate multiple disparate sets of laser-processing parameters that can each produce the same target input spectral emissivity with high accuracy (root mean squared errors < 2%). SHapley Additive exPlanations analysis shows transparent model interpretability of the complex relationship between laser parameters and spectral emissivity. Finally, the MF ensemble is experimentally validated by fabricating and evaluating photonic surface designs that it generates for improved efficiency energy harvesting devices. Our approach provides a powerful tool for advancing the inverse design of photonic surfaces in energy harvesting applications.

97 MATHEMATICS AND COMPUTING↗

Interactive automated Bragg peak identification with 3D neutron scattering data

Neutron scattering experiments have undergone significant technological development through large area detectors with concurrent enhancements in neutron transport and electronic functionality. Data collected for neutron events include detector pixel location in 3D, time and associated metadata, such as, sample orientation, neutron wavelength, and environmental conditions. RadiaSoft and Oak Ridge National Laboratory personnel are considering single-crystal diffraction data from the TOPAZ instrument. We are leveraging a new method for rapid, interactive analysis of neutron data using NVIDIA’s IndeX 3D volumetric visualization framework. We have implemented machine learning techniques to automatically identify Bragg peaks and separate them from diffuse backgrounds and analyze the crystalline lattice parameters for further analysis. The implementation of automatic peak identification into IndeX allows scientists to visualize and analyze data in real-time. Our methods include a robust comparison with current analysis techniques which show improvement in a variety of aspects. These improvements will be incorporated into IndeX for visualization to allow scientists an interactive tool for crystal analysis.

Kilpatrick, Matthew↗

Open data sets for assessing photovoltaic system reliability

Photovoltaic (PV) systems have become a cornerstone of renewable energy strategies, particularly due to the significant reduction in solar power costs over the past decade. However, the long-term reliability of PV installations presents a persistent challenge, requiring the development of advanced monitoring and predictive maintenance strategies. A wide range of data types is used to evaluate the health of PV systems, including environmental conditions, electrical performance, and inspection imagery. These data enable methodologies such as machine learning (ML) models for lifetime prediction and computer vision techniques for defect detection. However, the acquisition of high-quality and comprehensive data is difficult, particularly in terms of long-term consistency and data variety. Publicly available data sets serve as valuable resources for addressing these challenges, but they often suffer from fragmentation and are difficult to access. This paper presents a comprehensive review of existing open-source data sets related to PV degradation, analyzing their features, functionalities, and potential applications. We categorize these data sets based on the specific aspects of PV system information they cover, such as environmental conditions, operational monitoring, image inspection and module materials, and propose relevant tools and ML models for processing them. In addition, we propose practices for future data collection and usage, while also discussing potential directions in data-driven research. Our aim is to enhance data utilization and publication among researchers and industry professionals, promoting a deeper understanding of the role of data in enhancing the performance and durability of PV systems.

14 SOLAR ENERGY↗

Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440

ABSTRACT There is growing interest in engineering Pseudomonas putida KT2440 as a microbial chassis for the conversion of renewable and waste-based feedstocks, and metabolic engineering of P. putida relies on the understanding of the functional relationships between genes. In this work, independent component analysis (ICA) was applied to a compendium of existing fitness data from randomly barcoded transposon insertion sequencing (RB-TnSeq) of P. putida KT2440 grown in 179 unique experimental conditions. ICA identified 84 independent groups of genes, which we call fModules (“functional modules”), where gene members displayed shared functional influence in a specific cellular process. This machine learning-based approach both successfully recapitulated previously characterized functional relationships and established hitherto unknown associations between genes. Selected gene members from fModules for hydroxycinnamate metabolism and stress resistance, acetyl coenzyme A assimilation, and nitrogen metabolism were validated with engineered mutants of P. putida . Additionally, functional gene clusters from ICA of RB-TnSeq data sets were compared with regulatory gene clusters from prior ICA of RNAseq data sets to draw connections between gene regulation and function. Because ICA profiles the functional role of several distinct gene networks simultaneously, it can reduce the time required to annotate gene function relative to manual curation of RB-TnSeq data sets. IMPORTANCE This study demonstrates a rapid, automated approach for elucidating functional modules within complex genetic networks. While Pseudomonas putida randomly barcoded transposon insertion sequencing data were used as a proof of concept, this approach is applicable to any organism with existing functional genomics data sets and may serve as a useful tool for many valuable applications, such as guiding metabolic engineering efforts in other microbes or understanding functional relationships between virulence-associated genes in pathogenic microbes. Furthermore, this work demonstrates that comparison of data obtained from independent component analysis of transcriptomics and gene fitness datasets can elucidate regulatory-functional relationships between genes, which may have utility in a variety of applications, such as metabolic modeling, strain engineering, or identification of antimicrobial drug targets.

09 BIOMASS FUELS↗

RxnRover/amlro

AMLRO (Active Machine Learning Reaction Optimizer) is an open-source framework designed to accelerate chemical reaction optimization using active learning with classical machine learning regression models. AMLRO integrates space-filling sampling strategies (e.g., Sobol and Latin Hypercube sampling) with iterative model training, prediction, and experiment selection to efficiently navigate complex reaction spaces. The platform supports multiple regression models, flexible multi-objective definitions, and user-defined parameter bounds, enabling data-efficient optimization from small initial datasets. AMLRO is designed for ease of use by experimentalists and can operate as a standalone decision-support tool or be integrated into closed-loop automated experimentation workflows.

Kulathunga, Dulitha Prasanna [Iowa State Universit↗

Overcoming the Challenges to Enhancing Experimental Plant Biology With Computational Modeling

The study of complex biological systems necessitates computational modeling approaches that are currently underutilized in plant biology. Many plant biologists have trouble identifying or adopting modeling methods to their research, particularly mechanistic mathematical modeling. Here we address challenges that limit the use of computational modeling methods, particularly mechanistic mathematical modeling. We divide computational modeling techniques into either pattern models (e.g., bioinformatics, machine learning, or morphology) or mechanistic mathematical models (e.g., biochemical reactions, biophysics, or population models), which both contribute to plant biology research at different scales to answer different research questions. We present arguments and recommendations for the increased adoption of modeling by plant biologists interested in incorporating more modeling into their research programs. As some researchers find math and quantitative methods to be an obstacle to modeling, we provide suggestions for easy-to-use tools for non-specialists and for collaboration with specialists. This may especially be the case for mechanistic mathematical modeling, and we spend some extra time discussing this. Through a more thorough appreciation and awareness of the power of different kinds of modeling in plant biology, we hope to facilitate interdisciplinary, transformative research.

58 GEOSCIENCES↗

Cluster Analysis of Spectroscopic Line Profiles and EUV Emission in RMHD Simulations and Observations of the Solar Atmosphere

Spatially-resolved observations from the IRIS, SDO/AIA, and other space mission and ground-based telescopes, coupled with realistic 3D RMHD simulations, are a powerful tool for analysis of processes in the solar atmosphere. To better understand the dynamical and thermodynamic properties in the simulation data and their connection to observations, it is essential to determine similarities in the behaviors of the synthesized and observed emission. However, the complexity of observational data and physical processes makes comparison of observations and modeling results difficult. In this work, we show the initial results of application of K-Means clustering (unsupervised machine learning) algorithm to two different problems: 1) recognition of the typical spectroscopic line profiles observed by IRIS during solar flares and their typical dynamic behavior; 2) recognition of shocks and heating events in synthetic AIA emission data obtained from StellarBox quiet-Sun simulations. The average silhouette width technique for the KMeans algorithm is utilized in different ways to obtain optimal numbers of clusters. We discuss application of the emission clustering to visualizations of the computational volume, understanding its evolutionary trends and behavior patterns, and inversion (reconstruction) of physical properties of the solar atmosphere from synthesizes emission data.

Sadykov, Viacheslav↗

Development of an Airspace Simulation and Modeling Tool for Enhanced Spectrum Management

The emergence of new aerial vehicles into the National Airspace System creates an increased demand for aeronautical communications to support aviation operations. However, the issue of spectrum scarcity remains an ever-present concern, and the growing demand cannot be supported using existing spectrum allocation strategies. As a result, a new spectrum management approach is required, and the National Aeronautics and Space Administration (NASA) is investigating advanced concepts to modernize the management and use of aviation spectrum by leveraging the latest advancements in wireless communications, big data and machine learning. This research proposes an autonomous spectrum allocation concept, which allocates communications resources, such as spectrum and power, based on the predicted communications and air traffic demands throughout the airspace, as opposed to the use of fixed allocations as is done today. This approach will result in improved spectrum utilization efficiency and enhanced airspace capacity. The autonomous spectrum allocation concept decomposes into three research areas: demand prediction, resource allocation, and use case evaluation. As part of the use case evaluation effort, a modeling and simulation capability is currently under development. This simulation capability includes the implementation of various features, including visualization of both live or virtually-generated airspace traffic, simulation scenario development, simulation management with data collection, and flight plan creation with corresponding trajectory generation. This modeling and simulation capability will continue to evolve as new and advanced airspace applications are introduced into existing and emerging operational environments.

Eric J. Knoblock↗

Agent-Based, Bottom-Up Medium- and Heavy-duty Electric Vehicle Economics, Operation, Charging and Adoption (Research Performance Final Report)

This is the research performance final report for the project entitled: Agent-Based, Bottom-Up Medium- and Heavy-duty Electric Vehicle Economics, Operation, Charging and Adoption This project was able to achieve the DOE’s goals of developing new modeling tools to understand MDHD vehicle operation and adoption. The first modeling tool is a fleet-level techno-economic analysis model capable of estimating energy use and associated environmental and cost impacts for electrified and conventional vehicles of any MDHD vocation, using real-world cost and operations data, including approaches to optimizing schedules for charging and/or vehicle dispatch. The second modeling tool is a system-level, bottom-up, agent-based adoption model capable of generating geographically-resolved estimates of market projections for MDHD vehicles and charging infrastructure. These tools will be developed and published to serve dual purposes as analysis tools for researchers, and decision-support tools for decision makers within the MDHD system.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

GeoThermalCloud for EGS – An Open-source, User-friendly, Scalable AI Workflow for Modeling Enhanced Geothermal Systems

Enhanced Geothermal Systems (EGS) offer a vast potential to expand the use of geothermal energy. Heat is extracted from this engineered system by injecting relatively cold water into subsurface fractures, which are in contact with hot dry rock, and brought back to surface through production wells. Creating EGS requires improving the natural permeability of hot crystalline rocks. In this short conference paper, we present a reproducible workflow for modeling EGS. Our workflow called the GeoThermalCloud (GTC) for EGS, leverages recent advances in machine learning, deep learning, and high-performance computing. This GTC framework is currently being made open-source, user-friendly, and reproducible through python scripts as well as Google Colab/Jupyter Notebooks. This GTC for EGS modeling scripts are made available at https://github.com/SmartTensors/GeoThermalCloud.jl/tree/master/EGS and will constantly be updated to cater for geothermal community. Current GTC framework provides scripts to train deep learning (DL) models for techno-economics and data worth analysis. The Geothermal Design Tool (https://github.com/GeoDesignTool/GeoDT.git), a fast and simplified multi-physics solver, is used to develop a database for training DL models. This short paper provides details on the scripts to curate, process, and train DL models. The scripts can easily be modified to train on databases generated by other popular open-source simulators such as PFLOTRAN, STOMP, TOUGH, and GEOSX or commercial software such as ResFrac and COMSOL.

15 GEOTHERMAL ENERGY↗

Future North Atlantic tropical cyclone intensities in thermodynamically modified historical environments

Tropical cyclones (TCs) have ranked as the deadliest and most financially crippling natural disasters in the United States. It is imperative to assess potential shifts in TC intensity within the paradigm of an evolving climate. In this study we apply a fixed-constraint storyline approach that holds storm tracks and initial conditions constant to probe future TC intensity in the North Atlantic Basin. First, we simulate 618 historical TC events using the Risk Analysis Framework for Tropical Cyclones (RAFT)'s deep-learning intensity model. Next, we apply warming signals derived from eight CMIP6 climate scenarios and rerun each event to explore how intensities respond across scenarios. Finally, we develop an interactive dashboard that allows users to explore individual storm simulations and the scenario-modified environmental drivers. Together, this dataset and tool provide a clear, illustrative way to investigate how TC intensity responds to changes in air-sea state.

Climate Change↗

BASIN-3D: A brokering framework to integrate diverse environmental data

Diverse observational and simulation datasets are needed to understand and predict complex ecosystem behavior over seasonal to decadal and century time-scales. Integration of these datasets poses a major barrier towards advancing environmental science, particularly due to differences in the structure and formats of data provided by various sources. Here, we describe BASIN-3D (Broker for Assimilation, Synthesis and Integration of eNvironmental Diverse, Distributed Datasets), a data integration framework designed to dynamically retrieve and transform heterogeneous data from different sources into a common format to provide an integrated view. BASIN-3D enables users to adopt a standardized approach for data retrieval and avoid customizations for the data type or source. We demonstrate the value of BASIN-3D with two use cases that require integration of data from regional to watershed spatial scales. The first application uses the BASIN-3D Python library to integrate time-series hydrological and meteorological data to provide standardized inputs to analytical and machine learning codes in order to predict the impacts of hydrological disturbances on large river corridors of the United States. The second application uses the BASIN-3D Django framework to integrate diverse time-series data in a mountainous watershed in East River, Colorado, United States to enable scientific researchers to explore and download data through an interactive web portal. Thus, BASIN-3D can be used to support data integration for both web-based tools, as well as data analytics using Python scripting and extensions like Jupyter notebooks. The framework is expected to be transferable to and useful for many other field and modeling studies.

Varadharajan, C↗