A data fusion approach to optimize compositional stability of halide perovskites
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Sun, Shijing↗
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Results for “machine learning and data science”
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Feedforward-feedback ammonia control at a water resource recovery facility based on a digital twin with hybrid model
Ammonia-based aeration control (ABAC) at full-scale Water Resource Recovery Facilities (WRRFs) can be challenged by diurnal loading and transport delays. This work addressed these challenges using a hybrid feedforward–feedback controller built on Activated Sludge Model 1 (ASM1), marking the first full-scale deployment to pair a mechanistic feedforward core with data-driven corrections. The objectives were to improve ammonia setpoint tracking, assess performance of the mechanistic model when enhanced with data-driven corrections, and document full-scale operation. The hybrid model incorporates two data-driven components: (1) a Mechanistic Error Forecasting Engine (MEFE), consisting of a multivariate linear regressor and a long short-term memory (LSTM) ensemble. Defying expectations, low-parameter models outperformed more complex alternatives, reducing the mechanistic error by 71%. (2) A Residual Oscillation Forecasting Engine (ROFE), based on Fast Fourier Transform, reduced the remaining error by another 35%. Two proportional–integral (PI) feedback loops further (i) trim the feedforward output and (ii) eliminate residual controller error in the final aerobic zone. In full-scale operation, the controller reduced mean-squared error (MSE) by 94% over the baseline and produced more stable dissolved oxygen (DO) setpoints. Overall, it was proven that layering multi-timescale data-driven models on a mechanistic core can yield reliable ABAC performance at WRRFs.
54 ENVIRONMENTAL SCIENCES↗
Deep learning for Alzheimer's disease: Mapping large-scale histological tau protein for neuroimaging biomarker validation
Abnormal tau inclusions are hallmarks of Alzheimer's disease and predictors of clinical decline. Several tau PET tracers are available for neurodegenerative disease research, opening avenues for molecular diagnosis in vivo. However, few have been approved for clinical use. Understanding the neurobiological basis of PET signal validation remains problematic because it requires a large-scale, voxel-to-voxel correlation between PET and (immuno) histological signals. Large dimensionality of whole human brains, tissue deformation impacting co-registration, and computing requirements to process terabytes of information preclude proper validation. We developed a computational pipeline to identify and segment particles of interest in billion-pixel digital pathology images to generate quantitative, 3D density maps. The proposed convolutional neural network for immunohistochemistry samples, IHCNet, is at the pipeline's core. We have successfully processed and immunostained over 500 slides from two whole human brains with three phospho-tau antibodies (AT100, AT8, and MC1), spanning several terabytes of images. Our artificial neural network estimated tau inclusion from brain images, which performs with ROC AUC of 0.87, 0.85, and 0.91 for AT100, AT8, and MC1, respectively. Introspection studies further assessed the ability of our trained model to learn tau-related features. We present an end-to-end pipeline to create terabytes-large 3D tau inclusion density maps co-registered to MRI as a means to facilitate validation of PET tracers.
60 APPLIED LIFE SCIENCES↗
End-to-end jet classification of quarks and gluons with the CMS Open Data
Not Available
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Cooperative Research and Development Agreement With Georgetown University Report: National Institutes of Health, National Center for Advancing Translational Sciences Clinical and Translational Science Award
Oak Ridge National Laboratory (ORNL) is participating with Georgetown University (GU) as a subrecipient in response to the National Institutes of Health (NIH), National Center for Advancing Translational Sciences (NCATS) Clinical and Translational Science Award (CTSA) (U54 Clinical Trial Optional) funding opportunity announcement. This Cooperative Research and Development Agreement is put in to place to facilitate the development and implementation of clinical interventions that demonstrably improve human health is currently a complex, recursive, and inefficient process that leads to delays of years or decades before discoveries in biomedical research result in health benefits for patients and communities. NCATS conducts and supports research in the science of translation, to discover the mechanistic and operational principles of the intervention development and dissemination process, thereby providing the scientific foundation for improvements in translational efficiency that will accelerate the realization of interventions that improve human health. Under NCATS’ leadership, the CTSA Program supports a national network of medical research institutions called hubs. GU is the lead institution in one of the NIH hubs that was created as a result of a previous NIH CTSA. The missions of the GU have historically included the advancement of health through research in the clinical and biomedical sciences, the education of future leaders in medical and nursing practice and academia, and the provision of compassionate and scientifically competent patient care and service to the Washington, DC community and the nation. GU is the lead institution for the Georgetown-Howard Universities Center for Clinical and Translational Science (GHUCCTS), a multi-institutional partnership of medical research institutions forged from a desire to promote clinical research and translational science. Through multiple collaborations among these institutions, GHUCCTS is transforming clinical research and translational science in order to bring new scientific advances to health care. Oak Ridge National Laboratory is the Department of Energy's (DOE) largest science and energy laboratory. Managed since April 2000 by a partnership of the University of Tennessee and Battelle, ORNL was established in 1943 as a part of the secret Manhattan Project to pioneer a method for producing and separating plutonium. During the 1950s and 1960s, ORNL became an international center for the study of nuclear energy and related research in the physical and life sciences. With the creation of DOE in the 1970s, ORNL's mission broadened to include a variety of energy technologies and strategies. Today the laboratory supports the nation with a peacetime science and technology mission that is just as important as, but very different from, its role during the Manhattan Project. ORNL is home to the world's premier center for high performance supercomputing to enable scientific discovery. ORNL has extensive expertise in various areas of computer science that are uniquely situated to support GU. Additionally, ORNL’s leading computational user facilities present a unique opportunity to leverage the largest scale machines for open science in support of the stated mission of the NCATS CTSA. ORNL's partnership with GU will offer unparalleled opportunity in data analytics, deep-learning, artificial intelligence, and urban dynamics.
59 BASIC BIOLOGICAL SCIENCES↗
Large Scale MD to Predict Epitope Regions in HIV Env [Slides]
Highly dense carbohydrates located on the surface of the HIV Env protein play a key role in immune evasion. Such evolutionary adaptation hampers any attempt to obtain a full mechanistic understanding of the role played by the glycans in protecting the virus against an effective immune response. Moreover, and due to their chemical variability, an accurate molecular understanding of the so called “glycan shield” is still limited by the lack of effective resolution of state-of-the-art experimental technics. Here, we have used extensive computational modelling in order to fill this gap, addressing the presence of a large glycan variability as observed experimentally. Based on an automated pipeline, we were able to assemble, set-up and simulate via Molecular dynamics hundreds of different glycosylated Env variants at nearly atomic resolution, recapitulating the glycosylation distributions observed experimentally. Results from these simulations were subjected to machine learning and very accurate prediction of simulation derived glycan shielding areas of each glycan as a function of static sequence features. Such predictive models of per-glycan shielding, incorporating both glycan dynamics and heterogeneity, were used to develop a novel sequence-based glycan shield mapping strategy. Parallel to these studies, we also developed an accurate machine learning approach to predict glycan heterogeneity data using sequence features and found good prediction accuracy.
59 BASIC BIOLOGICAL SCIENCES↗
Denoising diffusion models with geometry adaptation for high fidelity calorimeter simulation
Simulation is crucial for all aspects of collider data analysis, but the available computing budget in the High Luminosity LHC era will be severely constrained. Generative machine learning models may act as surrogates to replace physics-based full simulation of particle detectors, and diffusion models have recently emerged as the state of the art for other generative tasks. Here, we introduce CaloDiffusion, a denoising diffusion model trained on the public CaloChallenge datasets to generate calorimeter showers. Our algorithm employs 3D cylindrical convolutions, which take advantage of symmetries of the underlying data representation. To handle irregular detector geometries, we augment the diffusion model with a new geometry latent mapping (GLaM) layer to learn forward and reverse transformations to a regular geometry that is suitable for cylindrical convolutions. The showers generated by our approach are nearly indistinguishable from the full simulation, as measured by several different metrics.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Audacity of huge: overcoming challenges of data scarcity and data quality for machine learning in computational materials discovery
Machine learning (ML)-accelerated discovery requires large amounts of high-fidelity data to reveal predictive structure–property relationships. For many properties of interest in materials discovery, the challenging nature and high cost of data generation has resulted in a data landscape that is both scarcely populated and of dubious quality. Data-driven techniques starting to overcome these limitations include the use of consensus across functionals in density functional theory, the development of new functionals or accelerated electronic structure theories, and the detection of where computationally demanding methods are most necessary. When properties cannot be reliably simulated, large experimental data sets can be used to train ML models. In the absence of manual curation, increasingly sophisticated natural language processing and automated image analysis are making it possible to learn structure–property relationships from the literature. Finally, models trained on these data sets will improve as they incorporate community feedback.
36 MATERIALS SCIENCE↗
OPEN-Augmented Reality GUI for Bioenergy Crop Phenotyping and Precision Agriculture (Donald Danforth Plant Science Center Final Scientific Technical Report)
The project led by the Donald Danforth Plant Science Center, in collaboration with Arizona State University, George Washington University, and Saint Louis University, has made significant strides in advancing the phenotypic analysis of bioenergy crops through the development of an innovative AI processing pipeline. This initiative was primarily funded by ARPA-E, with additional cost-sharing provided by the participating institutions. The project successfully utilized a variety of sensors—3D scanners, thermal, RGB, and hyperspectral—to refine algorithms for data-driven trait signature identification and improve the classification and visualization of plant traits. The developed AI processing pipeline is capable of handling the complex, multidimensional data characteristic of dynamic agricultural environments. 1) Contributions to understanding: The research has advanced the field of plant phenomics by showcasing the synergistic use of various sensor data to enhance the precision of trait analysis in bioenergy crops. Through the integration of 3D scanners, thermal, RGB, and hyperspectral sensors, the project has developed robust data-driven trait signature algorithms and visualization techniques. These innovations have facilitated detailed monitoring and management of plant traits, providing vital insights into plant growth dynamics and stress responses. Further, the project has broadened our understanding of how machine learning can be effectively applied in multi-sensor environments to refine trait analysis. By leveraging diverse datasets, the research has not only improved the accuracy of phenotypic assessments but also established a versatile methodological framework that can be extended beyond agriculture to other fields requiring detailed phenotypic analysis. 2) Technical effectiveness and economic feasibility: The AI processing pipeline developed in this project demonstrated significant technical effectiveness, achieving high throughput analysis of extensive phenotypic data and meeting targeted accuracies. This system exemplified the capability of advanced machine learning technologies to efficiently manage and analyze large, complex datasets. Economically, the implementation of the project-developed pipelines may offer substantial cost savings across multiple sectors. It enhances data analysis processes and significantly reduces the need for manual data interpretation, thereby decreasing both the time and resources required. 3) Public benefit: The project has significantly broadened the scope of agricultural methodologies to enhance phenotypic analysis, with potential applications in various sectors beyond agriculture. Additionally, the initiative fostered an enriching educational and collaborative environment, significantly enhancing the technical skills of participants. It also made substantial contributions to the scientific community by providing open-access data sets and tools, encouraging ongoing research and development across various disciplines. Overall, the project not only met its scientific goals but also showcased the extensive utility of integrating advanced machine learning and sensor data analysis technologies. These advancements have proven instrumental in driving forward both theoretical research and practical applications, setting a strong foundation for future explorations and innovations in data-driven science.
60 APPLIED LIFE SCIENCES↗
An Update on the Geothermal Data Repository's Data Standards and Pipelines: Geospatial Data and Distributed Acoustic Sensing Data
The Department of Energy's (DOE) Geothermal Data Repository (GDR) team has implemented data standards and automated data pipelines for the following data types: 1) drilling data, 2) geospatial datasets, and 3) DAS data. An additional data pipeline is proposed for stimulation data. These data standards and pipelines are intended to improve the real-world applicability of geothermal machine learning outputs through improving the quality of data. More specifically, through standardizing high-value datasets, the GDR is reducing project-specific data curation requirements, allowing more time to be spent on actual research. By automating this process, the burden of standardization is taken off of the user, overall increasing the availability of standardized data. This paper provides an update on the GDR's transition toward data standardization through automated data pipelines and calls for feedback from the community on how we can improve this process.
cloud-optimized↗
Reflections on one million compounds in the open quantum materials database (OQMD)
Abstract Density functional theory (DFT) has been widely applied in modern materials discovery and many materials databases, including the open quantum materials database (OQMD), contain large collections of calculated DFT properties of experimentally known crystal structures and hypothetical predicted compounds. Since the beginning of the OQMD in late 2010, over one million compounds have now been calculated and stored in the database, which is constantly used by worldwide researchers in advancing materials studies. The growth of the OQMD depends on project-based high-throughput DFT calculations, including structure-based projects, property-based projects, and most recently, machine-learning-based projects. Another major goal of the OQMD is to ensure the openness of its materials data to the public and the OQMD developers are constantly working with other materials databases to reach a universal querying protocol in support of the FAIR data principles.
08 HYDROGEN↗
Predicting oxidation damage in ultra high-temperature borides: A machine learning approach
Ultra-high temperature (UHT) borides are ceramics materials with melting points above 3000 °C for structural applications in extreme environments. However, at temperatures exceeding 1600 °C and under oxidizing conditions, the material suffers from detrimental degradation. Optimized design and performance of diboride materials under such extreme conditions requires filling the missing composition-microstructure-oxidation gap. This study proposes a computational data-driven framework to connect the processing and microstructure of Ultra-high temperature borides with the oxidation damage. Random Forest Regressor (RFR) model is adopted to forecast the oxide scale thickness developed after oxidation testing based on processing variables and microstructural features. The model trained on a dataset consisting of 107 samples of experimental data extracted from the literature aims to predict oxidation damage. With proper data manipulation and fine model tuning, the predictor could forecast the oxide scale thickness of UHT diborides with a Mean Absolute Error of 37.45 μm and an R-square of 0.83. This model could be used as a high-throughput scheme to design and test new UHT diborides materials computationally. Furthermore, a model with larger composition capabilities could also be developed in the future as more experimental data become available.
36 MATERIALS SCIENCE↗
Towards Lightweight Data Integration Using Multi-Workflow Provenance and Data Observability
Modern large-scale scientific discovery requires multidisciplinary collaboration across diverse computing facilities, including High Performance Computing (HPC) machines and the Edge-to-Cloud continuum. Integrated data analysis plays a crucial role in scientific discovery, especially in the current AI era, by enabling Responsible AI development, FAIR, Reproducibility, and User Steering. However, the heterogeneous nature of science poses challenges such as dealing with multiple supporting tools, cross-facility environments, and efficient HPC execution. Building on data observability, adapter system design, and provenance, we propose MIDA: an approach for lightweight runtime Multi-workflow Integrated Data Analysis. MIDA defines data observability strategies and adaptability methods for various parallel systems and machine learning tools. With observability, it intercepts the dataflows in the background without requiring instrumentation while integrating domain, provenance, and telemetry data at runtime into a unified database ready for user steering queries. We conduct experiments showing end-to-end multi-workflow analysis integrating data from Dask and MLFlow in a real distributed deep learning use case for materials science that runs on multiple environments with up to 276 GPUs in parallel. We show near-zero overhead running up to 100,000 tasks on 1,680 CPU cores on the Summit supercomputer.
Santos Souza, Renan↗
Data Fusion and Feature Extraction of Explosions Recorded on Smartphones
The prompt detection of explosions is a key element of the nuclear non-proliferation mission. With traditional sensors being limited in number and scale, smartphones as compact and economical multi-modal sensors are gaining traction and are being deployed. To address the flood of heterogeneous smartphone data, our team proposes a feature extraction using standardized constant-Q frequency bands across acoustic, barometric, and accelerometer data. The work presented in this poster utilizes three explosions collected on smartphones with Idaho National Lab. More explosions are planned in the near future at INL and NNSS. These extracted features will be used in machine learning methods in future iterations.
46 - INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AN↗
End-to-End Differentiable Modeling and Management of the Environment
Focal Area: (2) Data acquisition and assimilation enabled by machine learning, AI, and advanced methods including experimental/network design/optimization. We emphasize the importance of leveraging optimization techniques from AI/machine learning (ML) to solve challenging problems in Earth system modeling. Science Challenge: Automatic differentiation has had a transformative effect on ML by allowing the calculation of gradients of arbitrary functions in an incredibly large class of models. We can potentially realize similar improvements in parameter estimation and control for Earth system models (ESMs) by reimplementing them in computational frameworks from ML. Practitioners working with large (>10 7 parameters) models in ML and AI can obtain good predictive performance in a range of spatiotemporal tasks by making use of optimization via stochastic gradient descent and incorporating prior knowledge at multiple levels. We propose writing ESMs in open-source computational frameworks such as Torch, Tensorflow, and JAX to greatly expand the scope of environmental forecasting and management challenges, which can be addressed by leveraging automatic differentiation and gradient descent-like algorithms. We do not call for a wholesale replacement of physical models with data-driven surrogates, but rather advocate for interleaving physical and empirical equations in a manner that is most faithful to the extent of our scientific knowledge and observational data. Central to this topic is the merging of differentiable physical simulations with differentiable optimization layers, which are now both beginning to come to the forefront.
54 ENVIRONMENTAL SCIENCES↗
Materials genome innovation for computational software (magics) center
Functional layered material (LM) architectures will dominate nanomaterials science in this century. We have developed theory, modeling, simulation, and software and data tools that enhance understanding and AI guide synthesis, enable characterization of complex structures, and improve capabilities in the predictive design and growth of LMs. Research at the Center has focused on: Computational synthesis and characterization: AI guided synthesis and experimental synthesis of stacked LMs with tailored properties via optimized chemical vapor deposition (CVD) growth and liquid-phase exfoliation; study defects, edges, grain boundaries, wrinkling of atomic layers and their effects on chemical, mechanical, electrical, and optical properties. Far-from-equilibrium processes: Joint experimental and simulation based probe of electronic processes with NAQMD and ultrafast X-ray free-electron laser (XFEL) and ultrafast electron diffraction (UED) facilities at Stanford. Experimentally validate NAQMD by ultrafast electron diffraction and X-ray spectroscopy studies of structural and excited state dynamics, shape fluctuations, and phonon dynamics. Scalable software: Simulation engines for desktop-to-exascale platforms using low-overhead, linear-scaling QMD algorithms; divide-conquer-recombine NAQMD with electronic excitations; extended-Lagrangian reactive molecular dynamics (RMD), machine learning (ML) based neural-network quantum molecular dynamics (NNQMD), and super-state accelerated molecular dynamics (AMD) and kinetic Monte Carlo codes; thermal and electrical transport software; and design 3D architectures of LMs with desired functionality using scalable software. Distribution of software and data, and training: Software and simulation-experimental data generated within the Center are distributed to the materials science community via Berkeley Materials Project (MP) framework. We have also organized three workshops for software distribution and training at USC (Nov. 2017, Mar. 2018) and Gaithersburg, MD (Nov. 2018) to train researchers, with the last one in focused on underrepresented groups, in collaboration with Howard University which is one of the largest HBCUs. The Center supported a total of 46 personnel and 6 undergraduate students. These include 14 faculty, 11 postdoctoral research associates, 20 graduate research assistants, and mentored 6 undergraduate students. This resulted in the publications of 63 research papers that include 46 publications on Reactive and Quantum Dynamics Simulations, 13 publications on Machine Learning for Quantum Materials, and 4 publications on Quantum Computing.
2D Materials↗
Concrete Structure Health Monitoring Using Vibro-acoustic Testing and Machine Learning
Assessment and management of aging concrete structures in nuclear power plants require a more systematic approach than simple reliance on margins of safety in existing codes. Research is required to deploy online monitoring capability to assess the health of concrete structures in nuclear power plants and perform predictive analytics based on heterogeneous measurements, in order to reduce the operation and maintenance costs. The research effort described in this report focuses on the health monitoring of concrete slabs containing reactive aggregates using the vibro-acoustic modulation (VAM) technique and predictive modeling. The research is developing an approach to enable detection, localization, and estimation of the extent of degradation in concrete slabs due to alkali-silica reaction (ASR). The project outcomes are generic and extendable to other degradation modes in concrete. A concrete slab without reinforcements was cast at Vanderbilt University and cured in aggressive conditions to accelerate ASR degradation. In this report, we develop a methodology for the automation of VAM testing, and the construction of machine learning models to facilitate damage localization in concrete structures. We investigate how machine learning models based on physics simulation data can be effectively utilized for damage localization (damage location and depth) and estimation in a concrete slab specimen. Our study indicates that these models could potentially support damage localization and estimation for NPP structures.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
Machine learning approaches for influenza A virus risk assessment identifies predictive correlates using ferret model in vivo data
In vivo assessments of influenza A virus (IAV) pathogenicity and transmissibility in ferrets represent a crucial component of many pandemic risk assessment rubrics, but few systematic efforts to identify which data from in vivo experimentation are most useful for predicting pathogenesis and transmission outcomes have been conducted. To this aim, we aggregated viral and molecular data from 125 contemporary IAV (H1, H2, H3, H5, H7, and H9 subtypes) evaluated in ferrets under a consistent protocol. Three overarching predictive classification outcomes (lethality, morbidity, transmissibility) were constructed using machine learning (ML) techniques, employing datasets emphasizing virological and clinical parameters from inoculated ferrets, limited to viral sequence-based information, or combining both data types. Among 11 different ML algorithms tested and assessed, gradient boosting machines and random forest algorithms yielded the highest performance, with models for lethality and transmission consistently better performing than models predicting morbidity. Comparisons of feature selection among models was performed, and highest performing models were validated with results from external risk assessment studies. Our findings show that ML algorithms can be used to summarize complex in vivo experimental work into succinct summaries that inform and enhance risk assessment criteria for pandemic preparedness that take in vivo data into account.
59 BASIC BIOLOGICAL SCIENCES↗