High-throughput 16S informatics (HTP16S) v1.0
Command-line application to do the informatics to support a high-throughout 16S sequencing run using LBL robotics and sequencing technology.
McCauley, Joshua [Lawrence Berkeley National Labor↗
SEARCH · Search NASA
Results for “informatics”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Analysis of Bis(trifluoromethylsulfonyl)imide Interactions with Metal Cations Through a Chemical Informatics Approach
Nominally weakly coordinating anions are useful for modulating the solubility and chemical properties of metal complexes, but identification and analysis of the systematics of the interactions of anions with cationic metal complexes has not received the attention it deserves. Here, a chemical informatics approach is demonstrated for identifying and quantitatively analyzing the ways that the bis(trifluoromethylsulfonyl)imide anion (TFSI) can interact with metal-containing species. An open access computer program (PyCIFTer) was developed to facilitate large-scale structural analysis of TFSI-containing species by utilization of experimental atomic coordinate data from single-crystal X-ray diffraction (XRD) studies obtained from the Cambridge Structural Database (CSD). PyCIFTer establishes a three-dimensional vector space from the raw atomic coordinates, generating acyclic, undirected graphs that are used to rapidly analyze the structural properties (bond lengths and angles) of TFSI in individual structures in sequential/batch fashion. The structures are sorted by PyCIFTer into groups based on pre-set and chemically sensible criteria, affording a comprehensive and systematic view of TFSI structural chemistry. This approach avoids tedious one-at-a-time interrogation of structures, a prospect unreasonable in this case, and many others of contemporary chemical relevance; there were over 1500 structures in the CSD containing TFSI as of November 2024. The results demonstrate that TFSI only rarely binds to cations in the solid state, favoring the formation of species in which TFSI is found in cations’ outer coordination spheres. The prospect of applying PyCIFTer to other moieties is also discussed. PyCIFTer is also schematically compared to the commercial CSD Python application programming interface (API). Taken together, this work demonstrates the usefulness of modular workflows for sequential/batch analysis of structural data from XRD, an approach that appears poised to accelerate the translation of legacy structural results into new chemical insights and hypotheses.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Integrating Intelligent Hydro-informatics into an effective Early Warning System for risk-informed urban flood management
The urban drainage system constantly facing flooding issues in coastal and urban areas. Robust and accurate urban flood management, particularly considering fast-moving compound floods, is crucial to minimize the impact of flood disasters in coastal cities. Till now, Ho Chi Minh City (HCMC) lacks an effective means of urban flood management because of flood risk communication among residents. Existing flood risk communication tools rely on post-disaster flood model outcomes and data. Therefore, this research proposes a real-time Early Urban Flooding Warning System (EUFWS) integrated with a user-friendly web and app interface. The backbone of this system consists of flood models developed using machine learning (ML) algorithms, combined with big data and Web-GIS visualization, with ML serving as the core for constructing the EUFWS. EUFWS offer several key advantages: they are available at all times, accessible from anywhere, and provide a real-time, multi-user working platform. Additionally, the system is flexible, allowing for the easy addition of components and services and scalable, adjusting to workload demands. EUFWS have been successfully deployed in Thu Duc City, Vietnam, as a case study and are operating effectively. EUFWS have been successfully deployed in Thu Duc City, Vietnam, as a case study and are operating effectively. Research results indicate that EUFWS supported decision-makers to be effectively risk informed and make intelligent decisions during urban flood emergencies. Finally, this underscores the significant potential of integrating ML and information technology to enhance the management of smart urban drainage systems in flood-prone cities worldwide.
54 ENVIRONMENTAL SCIENCES↗
How to Feed AI: Creating a Cu-Ag Alloy Nanocrystalline Thin Films Library for Materials Informatics
Explore the source record for details and available documents.
Dorman, Kyle Rhys↗
Heterogeneous Multi-Domain Dataset Synthesis to Facilitate Privacy and Risk Assessments in Smart City IoT
The emergence of the Smart Cities paradigm and the rapid expansion and integration of Internet of Things (IoT) technologies within this context have created unprecedented opportunities for high-resolution behavioral analytics, urban optimization, and context-aware services. However, this same proliferation intensifies privacy risks, particularly those arising from cross-modal data linkage across heterogeneous sensing platforms. To address these challenges, this paper introduces a comprehensive, statistically grounded framework for generating synthetic, multimodal IoT datasets tailored to Smart City research. The framework produces behaviorally plausible synthetic data suitable for preliminary privacy risk assessment and as a benchmark for future re-identification studies, as well as for evaluating algorithms in mobility modeling, urban informatics, and privacy-enhancing technologies. As part of our approach, we formalize probabilistic methods for synthesizing three heterogeneous and operationally relevant data streams—cellular mobility traces, payment terminal transaction logs, and Smart Retail nutrition records—capturing the behaviors of a large number of synthetically generated urban residents over a 12-week period. The framework integrates spatially explicit merchant selection using K-Dimensional (KD)-tree nearest-neighbor algorithms, temporally correlated anchor-based mobility simulation reflective of daily urban rhythms, and dietary-constraint filtering to preserve ecological validity in consumption patterns. In total, the system generates approximately 116 million mobility pings, 5.4 million transactions, and 1.9 million itemized purchases, yielding a reproducible benchmark for evaluating multimodal analytics, privacy-preserving computation, and secure IoT data-sharing protocols. To show the validity of this dataset, the underlying distributions of these residents were successfully validated against reported distributions in published research. We present preliminary uniqueness and cross-modal linkage indicators; comprehensive re-identification benchmarking against specific attack algorithms is planned as future work. This framework can be easily adapted to various scenarios of interest in Smart Cities and other IoT applications. By aligning methodological rigor with the operational needs of Smart City ecosystems, this work fills critical gaps in synthetic data generation for privacy-sensitive domains, including intelligent transportation systems, urban health informatics, and next-generation digital commerce infrastructures.
IoT↗
Combining computational modeling and experimental library screening to affinity-mature VEEV-neutralizing antibody F5
Engineered monoclonal antibodies have proven to be highly effective therapeutics in recent viral outbreaks. However, despite technical advancements, an ability to rapidly adapt or increase antibody affinity and by extension, therapeutic efficacy, has yet to be fully realized. We endeavored to stand-up such a pipeline using molecular modeling combined with experimental library screening to increase the affinity of F5, a monoclonal antibody with potent neutralizing activity against Venezuelan Equine Encephalitis Virus (VEEV), to recombinant VEEV (IAB) E1E2 antigen. We modeled the F5/E1E2 binding interface and generated predictions for mutations to improve binding using a Rosetta-based approach and dTERMen, an informatics approach. The modeling was complicated by the fact that a high-resolution structure of F5 is not available and the H3 loop of F5 exceeds the length for which current modeling approaches can determine a unique structure. A subset of the predicted mutations from both methods were incorporated into a phage display library of scFvs. This library and a library generated by error-prone PCR were screened for binding affinity to the recombinant antigen. Results from the screens identified favorable mutations which were incorporated into 12 human-IgG1 variants. The best variant, containing eight mutations, improved KD from 0.63 nM (parental) to 0.01 nM. While this did not improve neutralization or therapeutic potency of F5 against IAB, it did increase cross-reactivity to other closely related VEEV epizootic and enzootic strains, demonstrating the potential of this method to rapidly adapt existing therapeutics to emerging viral strains.
affinity-maturation↗
FREDA: A Web Application for the Processing, Analysis, and Visualization of Fourier‐Transform Mass Spectrometry Data
The high-resolution measurement capability of Fourier-transform mass spectrometry (FT-MS) has made it a necessity for exploring the molecular composition of complex organic mixtures, like soil, plant, aquatic, and petroleum samples. This demand has driven a need for informatics tools to explore and analyze FT-MS data in a robust and reproducible manner. FREDA is an interactive web application developed to enable spectrometrists to format, process, and explore their FT-MS data without the need for statistical programming expertise. FREDA was built to explore outputs from a molecular identification tool, like CoreMS, and provide a suite of methods to filter data, compute chemical properties of peaks, statistically compare samples and groups of samples, conduct exploratory data analysis, and download the results with a report detailing all steps conducted. To demonstrate the utility of FREDA, an example analysis was conducted using FT-MS data from a soil microbiology study of samples collected in two different soil depths at the Sphagnum bog forest north of Grand Rapids, Minnesota. Differences between the two depths are observed using Kendrick, Gibbs free energy, and van Krevelen plots. G-tests are used to quantify a significant difference between the groups. All analyses and plotting are conducted using only the FREDA application. FREDA is an open-source and readily available web application that allows users to explore and make statistically valid conclusions about their FT-MS data. The application is available online (https://map.emsl.pnnl.gov/app/freda) with a tutorial web series (https://youtu.be/k5HLE2kNSBY?si=yB6sGoyvzxrFf5MP) and freely accessible code on Github (https://github.com/EMSL-Computing/FREDA).
47 OTHER INSTRUMENTATION↗
Emerging anomaly detection techniques for electronic health records: A survey
Background Anomaly detection in electronic health records (EHRs) is a cornerstone of biomedical informatics, with direct implications for patient safety, clinical decision-making, and the prevention of healthcare fraud. Once guided primarily by simple rule-based methods, the field has advanced rapidly, driven by increased computing power, richer and more detailed health data, and the rise of machine learning and deep learning techniques. The objective of this paper is to provide a comprehensive overview of modern approaches to detecting anomalies in EHRs, outlining their strengths, limitations, and relevance to key healthcare challenges. We review traditional statistical methods alongside newer ML- and DL-based strategies and hybrid models, with particular attention to how these techniques support transparency and build clinical trust. Methods This paper presents a thorough and critical survey through systematic review (PRISMA-based) of the latest anomaly detection strategies in time-sequence data domains within electronic health record systems. Results We explore a broad spectrum of methodologies, including statistical models, supervised and unsupervised learning approaches, hybrid frameworks, and state-of-the-art ML-based techniques that collectively advance the precision and scalability of detecting anomalies in complex clinical datasets. In addition to mapping current capabilities, we address the enduring challenges that hinder widespread implementation and provide a forward-looking perspective on the future of anomaly detection in the data-rich landscape of modern healthcare. Summary The advancement in AI-based approaches is reported along with the basic principles of the individual approaches and their applicability. The increased availability of high-quality data, advancements in DL approaches, and enhanced computation power are leading to more frequent adaptation of DL-based approaches. Emerging DL-based approaches that have been adapted in other domains or recently applied in the EHR domain are also discussed in detail. Although DL-based approaches can improve model predictions by incorporating comorbidities, their application is limited in low-frequency data domains (e.g., when the total available data remains in the single digits). Therefore, the user must carefully consider the application based on data availability.
Anomaly detection↗
A machine learning approach to quantify degradation of nuclear fuels and the effects of fission products
Nuclear fuel performance is critically dependent on understanding the evolution of fuel properties under operational conditions, a complex challenge driven by chemical changes and substantial radiation damage during fission. Traditionally, property evolution has been determined via empirical data collected following irradiation. However, these empirical correlations are limited in their applicability beyond the specific conditions in which they were obtained. This study explores a novel approach to address this challenge by applying materials informatics to develop a machine learning random forest (ML-RF) model that captures the effects of fission products on fuel compounds. The model predicts formation enthalpy (ΔH f ) by leveraging extensive quantum materials property data and correlating it with material descriptors such as composition, atomic and site features, and crystal lattice properties. This ML-RF model enables rapid interpolation across the compositional and structural spaces covered by the training data, thus supporting high-throughput screening and energetic ranking of candidate phases. The model demonstrates the ability to predict ΔH f with a mean absolute error (MAE) of approximately 0.1 to 0.2 eV/atom across a wide range of compounds, including key nuclear fuel systems (U-O, U-N, U-C, U-Si, and U-Mo). For example, it was used to assess shifts in stoichiometry for UO 2 (O/M) and UN (N/M) fuels, revealing their distinct tendencies in chemical potential variation and enabling preliminary convex hull analyses. Furthermore, the model provides insights into how individual fission products affect fuel properties. Results indicate that larger fission products (e.g., Nd, Pu, Ce) have a more pronounced impact on UO 2 , while lighter ones (e.g., Zr) strongly influence UN. Here, the model developed in this work can be used to support the Accelerated Fuel Qualification approach by facilitating preliminary evaluations prior to extensive materials modeling and experimentation. To this end, the trained model has been made available to the fuel community to support ongoing fuel development efforts.
Accelerated fuel qualification↗
A model to assess Zircaloy’s mechanical property changes following a transient beyond critical heat flux
Maintaining the integrity of nuclear fuel rods is essential for ensuring public health and safety in nuclear power generation. During reactor operation, this integrity is confirmed by demonstrating compliance with established regulatory acceptance criteria. For moderate-frequency events, such as limiting transients and anticipated operational occurrences (AOOs), the current fuel integrity criterion is based on preventing boiling transition. This criterion assumes that prevention of boiling transition will prevent excessive cladding heating and, thus, fuel failure during normal operations. While conservative, this approach places significant constraints on core design, fuel cycle economics, and a plant’s ability to perform major power uprates, leading to suboptimal fuel utilization and inefficient carbon-free energy production. A more efficient approach could be achieved by revising the failure criterion to a material-specific limit rather than strictly preventing the boiling transition, since boiling transition per se is not a cause of fuel cladding failure. Here, as a result, a new licensing framework based on material properties, termed time-at-temperature (t@T), is needed. This approach would allow for brief periods of post–critical heat flux operation during an AOO without compromising safety. Implementing the t@T licensing strategy requires a robust technical foundation in material properties, which must be established through comprehensive data collection on both unirradiated and irradiated fuel and cladding materials. This foundation would enable the development of a safety basis that ensures safe operation while providing greater flexibility and efficiency for reactor operation. This paper documents a thorough review of the available data to establish a baseline knowledge that can inform the development of cladding mechanical models, as well as identify experimental data gaps that need to be addressed in future research. Machine learning and data informatics were utilized to extract the importance of parameters on the t@T parameter. Industry tools were used to perform baseline analyses to define the relevant transient conditions for data analysis. The subsequent review successfully identified applicable experimental data, as well as sufficient data to evaluate changes in cladding mechanical properties following an AOO transient. Rather than developing new models, this work coupled existing irradiation annealing and recrystallization models to calculate changes in hardness, yield stress, and ultimate tensile stress following an AOO event. The findings from this review were summarized to highlight the experimental data needs required to fill remaining gaps and support the development of future t@T licensing methodologies.
Cladding performance↗
Autonomous Synthesis and Inverse Design of Electrochromic Polymers with High Efficiency and Accuracy
Here, the design and synthesis of functional polymers, aimed at targeted properties through specific structures, have long been challenged by their complex and often nonlinear structure–property relationships. Key processes, including knowledge accumulation for predictive design and experimental refinement and validation, are traditionally labor-insensitive and time-consuming, making it difficult to balance accuracy and efficiency. Here, we introduce an accelerated, autonomous system for the on-demand synthesis of electronic polymers that achieves the desired electrochromic functionality with high accuracy and efficiency. Our approach leverages large language model-assisted data mining, a physics-informed copolymer machine learning model, and an AI-driven autonomous robotic workflow in the Polybot lab. Within 72 h, Polybot autonomously synthesized electrochromic polymers (ECPs) with targeted, previously-unreported color values, including green polymers with specific absorption profiles, precisely fine-tuning copolymer structures with a 5% step size in comonomer composition within a three-monomer system. A publicly accessible ECP informatics database has also been created to foster knowledge exchange.
AI-driven Robotic Lab↗
Modeling the impact of structure and coverage on the reactivity of realistic heterogeneous catalysts
Adsorbates often cover the surfaces of catalysts densely as they carry out reactions, dynamically altering their structure and reactivity. Understanding adsorbate-induced phenomena and harnessing them in our broader quest for improved catalysts is a substantial challenge that is only beginning to be addressed. Here, in this work, we chart a path toward a deeper understanding of such phenomena by focusing on emerging in silico modeling methodologies, which will increasingly incorporate machine learning techniques. We first examine how adsorption on catalyst surfaces can lead to local and even global structural changes spanning entire nanoparticles, and how this affects their reactivity. We then evaluate current efforts and the remaining challenges in developing robust and predictive simulations for modeling such behavior. Last, we provide our perspectives in four critical areas—integration of artificial intelligence, building robust catalysis informatics infrastructure, synergism with experimental characterization, and adaptive modeling frameworks—that we believe can help surmount the remaining challenges in rationally designing catalysts in light of these complex phenomena.
catalytic mechanisms↗
A high-throughput and data-driven computational framework for novel quantum materials
Two-dimensional layered materials, such as transition metal dichalcogenides (TMDs), possess an intrinsic van der Waals gap at the layer interface, allowing for remarkable tunability of the optoelectronic features via external intercalation of foreign guests such as atoms, ions, or molecules. Herein, we introduce a high-throughput, data-driven computational framework for the design of novel quantum materials derived from intercalating planar conjugated organic molecules into bilayer transition metal dichalcogenides and dioxides. By combining first-principles methods, material informatics, and machine learning, we characterize the energetic and mechanical stability of this new class of materials and identify the fifty (50) most stable hybrid materials from a vast configurational space comprising ∼105 materials, employing intercalation energy as the screening criterion.
Kastuar, Srihari M. (ORCID:0000000279001561)↗
Quasiparticle spectroscopy in technologically relevant niobium using London penetration depth measurements: experiment and theory
Abstract The London penetration depth, λ ( T ) , was measured in various forms of niobium, including foils, thin films, single crystals, and samples from superconducting radio-frequency (SRF) cavities. We observed a significant difference in λ ( T ) at low temperatures, T < T c / 3 , due to low-energy quasiparticles. In particular, an unusual downturn of λ ( T ) on cooling in the SRF cavity samples required to take into account deep in-gap bound states. Theoretical modeling using the generalized Dynes density of states shows that such in-gap states lead to a downturn or a peak in λ ( T ) upon cooling. Combined, experimental and theoretical findings provide a method for detecting two-level systems or states related to magnetic impurities in the bulk of niobium. This result is particularly relevant for the quantum informatics sciences technologies used in qubits and circuit quantum electrodynamics architecture based on SRF cavities.
46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
LLaMP v0.1.0
Reducing hallucination of Large Language Models (LLMs) is imperative for use in the sciences, where reliability and reproducibility are crucial. However, LLMs inherently lack long-term memory, making it a nontrivial, ad hoc, and inevitably biased task to fine-tune them on domain-specific literature and data. LLaMP is a multimodal retrieval-augmented generation (RAG) framework of hierarchical reasoning and acting (ReAct) agents that can dynamically and recursively interact with Materials Project to ground large language models on high-fidelity materials informatics.
Riebesell, Janosh [Lawrence Berkeley National Labo↗
Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)
Ontologies are fundamental components of informatics infrastructure in domains such as biomedical, environmental, and food sciences, representing consensus knowledge in an accurate and computable form. However, their construction and maintenance demand substantial resources and necessitate substantial collaboration between domain experts, curators, and ontology experts. We present Dynamic Retrieval Augmented Generation of Ontologies using AI (DRAGON-AI), an ontology generation method employing Large Language Models (LLMs) and Retrieval Augmented Generation (RAG). DRAGON-AI can generate textual and logical ontology components, drawing from existing knowledge in multiple ontologies and unstructured text sources.We assessed performance of DRAGON-AI on de novo term construction across ten diverse ontologies, making use of extensive manual evaluation of results. Our method has high precision for relationship generation, but has slightly lower precision than from logic-based reasoning. Our method is also able to generate definitions deemed acceptable by expert evaluators, but these scored worse than human-authored definitions. Notably, evaluators with the highest level of confidence in a domain were better able to discern flaws in AI-generated definitions. We also demonstrated the ability of DRAGON-AI to incorporate natural language instructions in the form of GitHub issues.These findings suggest DRAGON-AI's potential to substantially aid the manual ontology construction process. However, our results also underscore the importance of having expert curators and ontology editors drive the ontology generation process.
96 KNOWLEDGE MANAGEMENT AND PRESERVATION↗
Remote sensing images, DEM, and point clouds associated with “Accuracy evaluation of cost-effective 3D reconstruction approaches for hydrobiogeochemical processes in non-perennial stream riverbeds”
This data package is associated with the publication “Accuracy evaluation of cost-effective 3D reconstruction approaches for hydrobiogeochemical processes in non-perennial stream riverbeds” published in Frontiers in Environmental Science, Environmental Informatics and Remote Sensing (Bao et al., 2026; doi: 10.3389/fenvs.2026.1725258). This data package includes the drone photos for a section of Umtanum Creek in Washington, Unted States. The photos were used to reconstruct the 3-dimensional (3D) digital elevation model (DEM) of the riverbed for the investigated stream section. The reconstruction results from four approaches are provided: (1) unoccupied aerial vehicle (UAV, colloquially known as drone) imagery-based Structure-from-Motion (SfM), (2) a machine learning-based 3D reconstruction model, Visual Geometry Grounded Deep Structure from Motion (VGGSfM), (3) Visual Geometry Grounded Transformer for long sequence of images (VGGT-Long), and (4) handheld smartphone LiDAR scanning. The ground truth measurements by tripod-mounted optical level kit and ground control points GPS locations for evaluating the accuracy of the four reconstruction approaches are also provided in this data package. A preliminary version of this data package was published in October 2025 at the time of manuscript submission. It was updated in March 2026, at the time of manuscript acceptance, to include additional metadata (this readme, data dictionary, and file level metadata). The data did not change. For details on how to navigate data packages generated by this project, see https://data.ess-dive.lbl.gov/portals/PNNLRiverCorridorSFA/About. In addition to a readme, this data package also includes a file-level metadata (FLMD) file that describes each file and a data dictionary (DD) that describes all column/row headers and variable definitions. This dataset is comprised of (1) 8 folders; (2) the detailed flight configuration html files; (3) field metadata; (4) a readme; (5) a data dictionary; and (6) file-level metadata. The folders “2024_10_18_d01” and “2024_10_18_d02” contain the original drone photos for the two drone flights (d01 and d02) on October 18, 2024. The reconstruction results from each of the approaches are in the folders called “ODM_SfM”, “VGGSfM”, “VGGTLong”, and “LiDAR”. The ground truth measurements are in the folder called “optical_level_kit”. Lastly, results comparing the different approaches are in the folder called “comparisons”. All files are .csv, .html, .jpg, .obj, .txt, and .npy. For information on using the .obj and .npy files, see the readme files within the same folder as the files.
54 ENVIRONMENTAL SCIENCES↗
Chemical Recommender System: Replacement Suggestions for Small Molecules
The Chemical Recommender System (CRS) is an open-source, high-performance toolkit that enables real-time similarity searches across the complete PubChem database (over 50 million molecules) using commodity hardware. The CRS addresses critical limitations in existing chemical informatics platforms through a novel vector database infrastructure, extensible model integration capabilities, and complete algorithmic transparency. The system implements a vector database deployment with partitioned indexing that achieves a ~60x speedup over traditional approaches. A containerized model integration framework allows researchers to seamlessly incorporate custom predictive models into the full-scale search and scoring pipeline, while complete configurability of search parameters, filtering logic, and scoring functions provides capabilities not available in existing black-box solutions. Beyond structural similarity, the CRS integrates OPERA QSAR models for thermophysical and toxicity predictions, RDKit synthetic accessibility scoring, and user-defined models to compute weighted final replacement scores. The complete system is accessible through an interactive web application supporting real-time progress monitoring, post-processing score re-weighting, automated PDF reporting, and batch processing capabilities.
Nair, Parthiv Anand [Sandia National Laboratories ↗