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Recent advances and applications of deep learning methods in materials science

Deep learning (DL) is one of the fastest-growing topics in materials data science, with rapidly emerging applications spanning atomistic, image-based, spectral, and textual data modalities. DL allows analysis of unstructured data and automated identification of features. The recent development of large materials databases has fueled the application of DL methods in atomistic prediction in particular. In contrast, advances in image and spectral data have largely leveraged synthetic data enabled by high-quality forward models as well as by generative unsupervised DL methods. In this article, we present a high-level overview of deep learning methods followed by a detailed discussion of recent developments of deep learning in atomistic simulation, materials imaging, spectral analysis, and natural language processing. For each modality we discuss applications involving both theoretical and experimental data, typical modeling approaches with their strengths and limitations, and relevant publicly available software and datasets. We conclude the review with a discussion of recent cross-cutting work related to uncertainty quantification in this field and a brief perspective on limitations, challenges, and potential growth areas for DL methods in materials science.

36 MATERIALS SCIENCE↗

Querying Semi-Structured Data

The amount of data of all kinds available electronically has increased dramatically in recent years. The data resides in different forms, ranging from unstructured data in the systems to highly structured in relational database systems. Data is accessible through a variety of interfaces including Web browsers, database query languages, application-specic interfaces, or data exchange formats. Some of this data is raw data, e.g., images or sound. Some of it has structure even if the structure is often implicit, and not as rigid or regular as that found in standard database systems. Sometimes the structure exists but has to be extracted from the data. Sometimes also it exists but we prefer to ignore it for certain purposes such as browsing. We call here semi-structured data this data that is (from a particular viewpoint) neither raw data nor strictly typed, i.e., not table-oriented as in a relational model or sorted-graph as in object databases. As will seen later when the notion of semi-structured data is more precisely de ned, the need for semi-structured data arises naturally in the context of data integration, even when the data sources are themselves well-structured. Although data integration is an old topic, the need to integrate a wider variety of data- formats (e.g., SGML or ASN.1 data) and data found on the Web has brought the topic of semi-structured data to the forefront of research. The main purpose of the paper is to isolate the essential aspects of semi- structured data. We also survey some proposals of models and query languages for semi-structured data. In particular, we consider recent works at Stanford U. and U. Penn on semi-structured data. In both cases, the motivation is found in the integration of heterogeneous data.

DATA MANAGEMENT↗

Haar-Like Wavelets on Hierarchical Trees

Here, discrete wavelet methods, originally formulated in the setting of regularly sampled signals, can be adapted to data defined on a point cloud if some multiresolution structure is imposed on the cloud. A wide variety of hierarchical clustering algorithms can be used for this purpose, and the multiresolution structure obtained can be encoded by a hierarchical tree of subsets of the cloud. Prior work introduced the use of Haar-like bases defined with respect to such trees for approximation and learning tasks on unstructured data. This paper builds on that work in two directions. First, we present an algorithm for constructing Haar-like bases on general discrete hierarchical trees. Second, with an eye towards data compression, we present thresholding techniques for data defined on a point cloud with error controlled in the $L$ $\infty$ norm and in a Hölder-type norm. In a concluding trio of numerical examples, we apply our methods to compress a point cloud dataset, study the tightness of the $L$ $\infty$ error bound, and use thresholding to identify MNIST classifiers with good generalizability.

97 MATHEMATICS AND COMPUTING↗

MFA-DVR: direct volume rendering of MFA models

3D volume rendering is widely used to reveal insightful intrinsic patterns of volumetric datasets across many domains. However, the complex structures and varying scales of volumetric data can make efficiently generating high-quality volume rendering results a challenging task. Multivariate functional approximation (MFA) is a new data model that addresses some of the critical challenges: high-order evaluation of both value and derivative anywhere in the spatial domain, compact representation for large-scale volumetric data, and uniform representation of both structured and unstructured data. Here, in this paper, we present MFA-DVR, the first direct volume rendering pipeline utilizing the MFA model, for both structured and unstructured volumetric datasets. We demonstrate improved rendering quality using MFA-DVR on both synthetic and real datasets through a comparative study. We show that MFA-DVR not only generates more faithful volume rendering than using local filters but also performs faster on high-order interpolations on structured and unstructured datasets. MFA-DVR is implemented in the existing volume rendering pipeline of the Visualization Toolkit (VTK) to be accessible by the scientific visualization community.

97 MATHEMATICS AND COMPUTING↗

AI Curation Methods for NASA Scientific Data

The NASA Open Science Data Repository (OSDR) serves as a central hub for sharing and accessing NASA's vast collection of scientific data, supporting researchers across diverse fields. To enhance the efficiency, accuracy, and accessibility of this data, we are leveraging advanced artificial intelligence (AI) techniques as part of the AI for Curation project. By integrating large language models (LLMs) into our data curation workflow, we aim to streamline the entire process—from data submission to user interaction. This initiative focuses on improving key areas, including data ingestion, curation, and user engagement with curated datasets, impacting multiple domains and a wide user base. First, we are developing tools that can automatically parse data in various formats, using LLMs to convert unstructured data into structured, standardized formats. This reduces the manual effort required for curation, allowing curators to focus on more critical scientific analyses. Additionally, AI and machine learning (ML) models are being implemented to automate data validation and verification, ensuring the highest standards of data quality and reliability. Finally, we are creating a conversational AI agent to interact with the curated scientific studies in OSDR, helping users easily navigate the repository and access relevant data. By enhancing data discoverability and accessibility, these advancements will foster new research opportunities and promote the principles of open science.

Walter Alvarado↗

Natural Language Processing-Enhanced Nuclear Industry Operating Experience Data Analysis: Aggregation and Interpretation of Multi-Report Analysis Results

Industry-wide operating experience is a critical source of raw data for reliability and risk model parameter estimations for nuclear power plants. A large portion of operating experience data are failure events stored as reports that contain unstructured data, such as narratives. In current practice, a failure report is usually reviewed and manually coded by analysts. The coding is based on extracting several event characteristics such as system name, component type, sub-part type, failure mode, and failure cause. Event narratives are mostly used to help understand events and extract their characteristics. In this line of research, we aim to maximize the usage of event narratives by leveraging natural language processing (NLP) methods to automatically convert an event narrative to a causal graph. This research has promise to improve physical understanding of failure initiation and propagation and to facilitate use of non-failure data (e.g., near-misses and degradations) to complement the limited data pool of failures. In our previous work, we developed an NLP tool and applied it to analyze a number of licensee event reports submitted by U.S. nuclear power plants to the Nuclear Regulatory Commission. In this paper, we will report our recent research progress in aggregating the results of multiple reports, developing network model(s), and drawing statistical insights.

99 GENERAL AND MISCELLANEOUS↗

Natural Language Processing for Extracting Rich Disease Data Aligned To Satellite Meteorological Data

Global climate change is redefining our understanding of how diseases spread. In Sri Lanka, vector-borne diseases such as dengue fever, encephalitis, and leptospirosis historically surged during the monsoon seasons when temperatures were high enough for mosquito eggs to hatch. Unfortunately, due to rising temperatures and more erratic rainfall patterns, mosquito eggs can now hatch year-round and are increasingly unpredictable, leading to an alarmingly increasing number of hospitalizations and deaths. More data is needed to adapt our response to these diseases in an increasingly warmer world. In the contemporary landscape, a wealth of disease information is available, yet accessibility remains limited due to unstructured data formats such as PDFs. Therefore, converting unstructured disease reports into structured formats is necessary for effectively leveraging data. This paper introduces a comprehensive framework for collecting unstructured disease reports and transforming them into analyzable formats. By creating separate models tailored to each data format, we can ensure accuracy compared to general models. These straightforward models enhance accessibility and empower other researchers to use our tools. The returned structured data can then be harnessed for analysis, statistical purposes, and informing evidence-based public health interventions, thus facilitating more informed decision-making in healthcare. We deploy this framework to produce geospatial data for Sri Lanka and Brazil for many different conditions and align these data with satellite environmental data, providing for the first time a structured, aligned powerful dataset for disease modeling.

Open Source Open Science↗

Connecting Minds: AI Use Cases to Bridge Power Systems and Large Language Models for Practical Applications

Recent advances in artificial intelligence (AI) and development of large language models (LLMs) present the opportunity to develop a new generation of power systems applications. In contrast with early power system AI applications based on structured numerical data, LLMs offer unique capabilities to perform logical reasoning using text documents, unstructured data, and application programming interface (API) calls to computational software. This paper seeks to bridge the knowledge gap between power systems engineers and LLM developers through a crosscutting explanation of use cases, characteristics, requirements, practical considerations from the perspectives of both LLM capabilities and industry needs. Specific focus is given to applications that can be realistically deployed by electric utilities. After introducing the architecture of LLMs and unique challenges of the power systems domain, this paper proposes twenty representative LLM applications grouped into categories of 1) power system operations, 2) asset management, 3) system planning and analytics, and 4) energy management and protection systems. Five use cases are presented within each category with descriptions of the motivation, objectives, approaches, example inputs / outputs, and benefits of each use case.

24 POWER TRANSMISSION AND DISTRIBUTION↗

Open Data and Deep Semantic Segmentation for Automated Extraction of Building Footprints

Advances in machine learning and computer vision, combined with increased access to unstructured data (e.g., images and text), have created an opportunity for automated extraction of building characteristics, cost-effectively, and at scale. These characteristics are relevant to a variety of urban and energy applications, yet are time consuming and costly to acquire with today’s manual methods. Several recent research studies have shown that in comparison to more traditional methods that are based on features engineering approach, an end-to-end learning approach based on deep learning algorithms significantly improved the accuracy of automatic building footprint extraction from remote sensing images. However, these studies used limited benchmark datasets that have been carefully curated and labeled. How the accuracy of these deep learning-based approach holds when using less curated training data has not received enough attention. The aim of this work is to leverage the openly available data to automatically generate a larger training dataset with more variability in term of regions and type of cities, which can be used to build more accurate deep learning models. In contrast to most benchmark datasets, the gathered data have not been manually curated. Thus, the training dataset is not perfectly clean in terms of remote sensing images exactly matching the ground truth building’s foot-print. A workflow that includes data pre-processing, deep learning semantic segmentation modeling, and results post-processing is introduced and applied to a dataset that include remote sensing images from 15 cities and five counties from various region of the USA, which include 8,607,677 buildings. The accuracy of the proposed approach was measured on an out of sample testing dataset corresponding to 364,000 buildings from three USA cities. The results favorably compared to those obtained from Microsoft’s recently released US building footprint dataset.

97 MATHEMATICS AND COMPUTING↗

Question-answering system extracts information on injection drug use from clinical notes

Background. Injection drug use (IDU) can increase mortality and morbidity. Therefore, identifying IDU early and initiating harm reduction interventions can benefit individuals at risk. However, extracting IDU behaviors from patients’ electronic health records (EHR) is difficult because there is no other structured data available, such as International Classification of Disease (ICD) codes, and IDU is most often documented in unstructured free-text clinical notes. Although natural language processing can efficiently extract this information from unstructured data, there are no validated tools. Methods. Here, to address this gap in clinical information, we design a question-answering (QA) framework to extract information on IDU from clinical notes for use in clinical operations. Our framework involves two main steps: (1) generating a gold-standard QA dataset and (2) developing and testing the QA model. We use 2323 clinical notes of 1145 patients curated from the US Department of Veterans Affairs (VA) Corporate Data Warehouse to construct the gold-standard dataset for developing and evaluating the QA model. We also demonstrate the QA model’s ability to extract IDU-related information from temporally out-of-distribution data. Results. Here, we show that for a strict match between gold-standard and predicted answers, the QA model achieves a 51.65% F1 score. For a relaxed match between the gold-standard and predicted answers, the QA model obtains a 78.03% F1 score, along with 85.38% Precision and 79.02% Recall scores. Moreover, the QA model demonstrates consistent performance when subjected to temporally out-of-distribution data. Conclusions. Our study introduces a QA framework designed to extract IDU information from clinical notes, aiming to enhance the accurate and efficient detection of people who inject drugs, extract relevant information, and ultimately facilitate informed patient care.

60 APPLIED LIFE SCIENCES↗

Machine Learning for Automated Extraction of Building Geometry

As data science comes to buildings, the promise of using machine learning and novel sources of data has received much attention. Advances in machine learning and computer vision algorithms, combined with increased access to unstructured data (e.g., images and text), have created an opportunity for automated extraction of building characteristics – cost-effectively, and at scale. Acquisition of features such as footprint are time consuming and costly to acquire with today’s manual methods, but can be streamlined through intelligent software-based solutions applied to satellite images. When combined with aerial RGB and thermal images, full 3D geometries and thermal maps can be constructed to determine additional characteristics such as window to wall ratio, height, number of stories and envelope thermal characteristics. In this paper we present three contributions to accelerate these high potential opportunities: (1) a methodical analysis of how these features can be integrated into today’s simulation and data driven software tools to enhance efficiency measure identification and owner/operator decision making; (2) development and accuracy testing of open source deep neural network methods to extract building footprints from satellite imagery, including the curation and application of openly available GIS datasets for training and continued development by others; and (3) an open framework for drone-based image capture and creation of 3D building geometries. This work represents an important bridge between high-level studies that span diverse application areas and those that detail point solutions yet cannot be easily replicated or extended.

Touzani, Samir↗

Toward Drilling the Perfect Geothermal Well: An International Research Coordination Network for Geothermal Drilling Optimization Supported by Deep Machine Learning and Cloud Based Data Aggregation

The EDGE project, supported by the U.S. Department of Energy Geothermal Technologies Office under award DE-EE0008793, established a data-driven framework for improving the efficiency, cost-effectiveness, and reliability of geothermal well drilling. The project focused on developing scalable data infrastructure, advanced machine learning and probabilistic models, and integrated analytics tools to support continuous drilling optimization. A central objective was to reduce geothermal drilling costs by up to seventy percent while minimizing the risk of well failure through predictive diagnostics and adaptive planning. Over the project period, a comprehensive data repository was designed and deployed, incorporating records from over one hundred geothermal wells across varied geological settings. This repository supported both structured and unstructured data and adhered to FAIR data principles, enabling provenance tracking, quality control, and standardized metadata. The project introduced automated ingestion pipelines and a cloud-hosted platform that facilitated access to raw, processed, and derived datasets. This infrastructure served as the foundation for model development and analysis. Machine learning workflows were developed to predict key drilling metrics including rate of penetration, non-productive time, and total drilling costs. Self-organizing maps and dimensionality reduction methods were used to uncover operational patterns and outliers, while supervised learning algorithms such as random forests and deep neural networks were applied to forecast performance outcomes. The models were validated on heterogeneous datasets from both U.S. and Icelandic fields, demonstrating variable but significant predictive accuracy. The results indicated that finer temporal resolution, inclusion of lithological data, and consistency in operational annotations could substantially improve model performance. The project also implemented process mining techniques to reconstruct state-transition models from drilling event logs. These models enabled the identification of deviations from optimal workflows and provided insights into recurring failure modes. Analysis of non-productive time highlighted the impact of equipment failures, geological challenges, and human factors, offering opportunities for targeted mitigation strategies. The EDGE Dashboard was developed as a web-based expert system integrating data visualization, model outputs, and user-driven queries. It provided an accessible interface for operators to explore historical data, evaluate predicted outcomes, and compare drilling scenarios. Initial feedback from project partners suggested that the dashboard could serve as a foundation for more advanced advisory and optimization tools. Overall, the EDGE project demonstrated the feasibility and value of applying modern data science techniques to geothermal drilling. It delivered a set of interoperable tools and models that can support more efficient, lower-risk well development. The findings point toward a viable path for transitioning from advisory analytics to semi-autonomous drilling systems, contingent on continued collaboration, expanded datasets, and field validation. The project results have immediate relevance for drilling operations, data management practices, and future geothermal R&D efforts aimed at achieving reliable, cost-competitive geothermal energy at scale.

15 GEOTHERMAL ENERGY↗

Scalable edge clustering of dynamic graphs via weighted line graphs

Timestamped relational datasets consisting of records (or connections) between pairs of entities are ubiquitous in network science. For applications like peer-to-peer communication, email, various social network interactions, and computer network security, it is useful to organize these records into groups based on how and when they are occurring. Weighted line graphs offer a natural way to model how records are related in such datasets but for large real-world graph topologies, building and utilizing the line graph is prohibitively expensive. Here, we present the framework to cluster the edges of a dynamic graph via the associated line graph that contains two major contributions. The first is a method to work with the line graph implicitly and the second is a distributed scale implementation of an agglomerative hierarchical graph clustering algorithm. We outline a novel hierarchical dynamic graph edge clustering approach that efficiently breaks massive relational datasets into small sets of edges containing events at various timescales. This is in stark contrast to traditional graph clustering algorithms that prioritize highly connected (clique-like) community structures. Our approach relies on constructing a sufficient subgraph of a weighted line graph and applying a hierarchical agglomerative clustering. This approach is related to scalable techniques from spatial clustering, nonlinear-dimension reduction, topological data analysis, and draws particular inspiration from HDBSCAN. As an edge clustering, this method yields an overlapping node clustering. Our algorithm is parallelizable and we demonstrate efficient clustering of a billion-scale, real-world dynamic graph into small edge sets that correlate in topology and time. The entire clustering process for a graph with tens of billions of edges takes just a few minutes of run time on 256 nodes of a distributed compute environment. We argue how the output of the edge clustering is useful for a multitude of data visualization and powerful machine learning tasks, both involving the original massive dynamic graph data and metadata associated with the nodes and edges. Finally, we describe how this approach can be extended to dynamic hypergraphs and dynamic graphs/hypergraphs with unstructured data living on vertices and edges.

Data Analysis↗

Application of Modified Meshgraphnets for Subsurface Prediction during CO2 Sequestration

In the face of the increasingly dire consequences of anthropogenic climate change, capturing and storing carbon dioxide is paramount. However, several impediments exist to the safe and effective subsurface storage of CO2, such as cost of transport, identification of suitable sites for subsurface storage, and assessment of long-term risk from storage in subsurface aquifers. Accurate subsurface modeling is necessary to ensure that CO2 storage is both safe and effective. Still, such modeling has traditionally required either substantial time and computational power (numerical simulation) or a substantial amount of pre-existing data for training (machine learning models). Additionally, these models lack flexibility in dealing with both changes in discretization of the input data and generalizability beyond the data on which they are trained. In order to address these issues, this research applies graph neural networks (GNNs) to predict subsurface saturation and pressure during CO₂ injection in a model of the Illinois Basin-Decatur Project (IBDP). GNNs provide a flexible, intuitive method for representing and manipulating complex unstructured data, which is often found in many practical domain problems such as fluid flow and subsurface characterization. These unstructured grids are easily represented in GNNs by representing spatially-localized features such as permeability, porosity, saturation, and pressure as nodes in a graph and relationships between these properties as edges connecting these nodes. This research applies a specific GNN model called MeshGraphNets (MGN) to model the change in CO2 saturation and pressure over a 50-month time period (36 months of injection, 14 months post-injection). The MGN model leverages a message passing process that allows the network to learn both the spatial and temporal dynamics of this system simultaneously. Additionally, training on a limited dataset (64 realizations, 20 time points each) resulted in a high degree of accuracy in saturation prediction both within the same timeframe as the training (20 months, 0.039 average RMSE) and when projecting out to the end of injection (36 months, 0.053 average RMSE). Temporal predictions such as those generated by MGNs and other similar models are prone to accumulated error over time; in order to address this, a multi-step rollout (MSR) training process was applied to calculate training loss. This method mimics the forward prediction during inference by “rolling out” multiple time points in a single training step using the previous prediction as input to the MGN model. By calculating the loss several time steps forward from the current prediction, the model is forced to find a more stable state over time. Application of MSR to the MGN model resulted in an average 15% reduction in inference error over time during forward prediction. This study showcases the immense potential of GNNs as a game-changing methodology for predicting pressure and saturation evolution in CCS projects, ultimately paving the way for more sustainable and effective carbon storage solutions. Presentation prepared for the 2024 AiChE Annual Meeting, October 27 to November 1 2024, San Diego, CA.

Holcomb, Paul↗

Computational tools and data integration to accelerate vaccine development: challenges, opportunities, and future directions

The development of effective vaccines is crucial for combating current and emerging pathogens. Despite significant advances in the field of vaccine development there remain numerous challenges including the lack of standardized data reporting and curation practices, making it difficult to determine correlates of protection from experimental and clinical studies. Significant gaps in data and knowledge integration can hinder vaccine development which relies on a comprehensive understanding of the interplay between pathogens and the host immune system. In this review, we explore the current landscape of vaccine development, highlighting the computational challenges, limitations, and opportunities associated with integrating diverse data types for leveraging artificial intelligence (AI) and machine learning (ML) techniques in vaccine design. We discuss the role of natural language processing, semantic integration, and causal inference in extracting valuable insights from published literature and unstructured data sources, as well as the computational modeling of immune responses. Furthermore, we highlight specific challenges associated with uncertainty quantification in vaccine development and emphasize the importance of establishing standardized data formats and ontologies to facilitate the integration and analysis of heterogeneous data. Through data harmonization and integration, the development of safe and effective vaccines can be accelerated to improve public health outcomes. Looking to the future, we highlight the need for collaborative efforts among researchers, data scientists, and public health experts to realize the full potential of AI-assisted vaccine design and streamline the vaccine development process.

60 APPLIED LIFE SCIENCES↗

VISILIENCE: An Interactive Visualization Framework for Resilience Analysis using Control-Flow Graph

Soft errors have become one of the major concerns for the error resilience of HPC applications, as those errors can cause HPC applications to generate serious outcomes such as Silent Data Corruptions (SDCs). A large body of approaches has been proposed to analyze the resilience of HPC applications. However, existing studies rarely address the challenges of the analysis result perception. Specifically, resilience analysis techniques often produce a massive volume of unstructured data, making it difficult for programmers to conduct the resilience analysis due to non-intuitive raw data. Furthermore, different analysis models produce diverse results with multiple levels of details, which may create hurdles to compare and explore the resilience of HPC program execution. To this end, we present VISILIENCE, an interactive VISual resILIENCE analysis framework to allow programmers to facilitate the resilience analysis of HPC applications. In particular, VISILIENCE leverages an effective visualization approach Control Flow Graph (CFG) to present a function execution. In addition, three widely-used models for resilience analysis (i.e., Y-Branch, IPAS, and TRIDENT) are seamlessly embedded into the framework for resilience analysis and result comparison. Multiple case studies have been conducted to demonstrate the effectiveness of our proposed framework VISILIENCE.

Jiang, Hailong↗

System-Level Integration of Modular Language Models for Real-Time Risk Assessment in Third-Party Risk Management Systems

Large enterprises typically rely on dedicated teams to govern and implement security measures throughout their supply chains, ensuring compliance with enterprise security procedures. There is a significant reliance on Third-Party Risk Management (TPRM) platforms, which often require complete, highly structured information from potential vendors. The review and compliance assurance processes are time- and labor intensive, often requiring several rounds of review between the supply chain security risk management teams, business users, and potential vendors, leading to delays in the supply chain processing and consumer experience. Significant challenges in the risk management paradigm include handling unstructured data in various formats and providing real-time feedback to users to reduce the required review time. This paper presents a novel solution to these challenges. A modular multi-step system architecture is proposed using advances in language processing, specifically for unstructured responses and provides real-time feedback (i.e., 3 seconds) so that users can improve their responses before the TPSRM team review. This novel system architecture will increase information accuracy and significantly reduce time and labor during the review process.

99 - GENERAL AND MISCELLANEOUS↗

Advanced Astrophysics Discovery Technology in the Era of Data Driven Astronomy

Astrophysics is at the threshold of a new epoch in which increasinglycomplex, heterogeneous datasets will challenge our existing information infrastructure and traditional approaches to analysis. The rapid advancement of graphics processing units, compact field programmable gate arrays and dedicated artificial intelligence accelerator chips is now permitting the use of scientific methods, processes and algorithms to extract knowledge and insights from structured and unstructured data in ways never before seen. Miniaturization of spacecraft architectures and supporting infrastructure is opening new observing strategies and new discovery spaces for science. The community is just beginning to awaken to these imminent challenges as evidenced by their relative lack of emphasis in the New Worlds, New Horizons ASTRO2010 decadal survey, in the ExoPAG Science Analysis Group 11 report andin the formulation of the WFIRST Data Challenge. We suggest that the Astrophysics Science Division (ASD), which has clearly recognized this new epoch of rapidly evolving information technology, could be more affirmative in its approach. We offer a modest structural solution.

Barry, Richard K.↗