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DOE OSTI2025

Combining Machine Learning and Comparative Effectiveness Methodology to Study Primary Care Pharmacotherapy Pathways for Veterans With Depression

Our objective is to demonstrate an innovative method combining machine learning with comparative effectiveness research techniques and to investigate a hitherto unstudied question about the effectiveness of common prescribing patterns. For Operation Enduring Freedom/Operation Iraqi Freedom veterans with major depressive disorder, we generate pharmacotherapy pathways (of antidepressants) using process mining and machine learning. We select the medication episodes that were started at subtherapeutic doses by the first assigned primary care physician and observe the paths that those medication episodes follow. Using 2-stage least squares, we test the effectiveness of starting at a low dose and staying low for longer versus ramping up fast while balancing observable and unobservable characteristics of patients and providers through instrumental variables. We leverage predetermined provider practice patterns as instruments. We collected outpatient pharmacy data for selective serotonin reuptake inhibitors and selective norepinephrine reuptake inhibitors, patient and provider characteristics (as control variables), and the instruments for our cohort. All data were extracted for the period between 2006 and 2020. There is a statistically significant positive effect (0.68, 95% CI 0.11–1.25) of “ramping up fast” on engagement in care. When we examine the effect of “ramping up slow”, we see an insignificant negative impact on engagement in care (−0.82, 95% CI −1.89 to 0.25). As expected, the probability of drop-out also seems to have a negative effect on engagement in care (−0.39, 95% CI −0.94 to 0.17). We further validate these results by testing with medication possession ratios calculated periodically as an alternative engagement in care metric. Our findings contradict the “Start low, go slow” adage, indicating that ramping up the dose of an antidepressant faster has a significantly positive effect on engagement in care for our population.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2026

Advancing hydrogen production: A comprehensive review of wastewater reforming techniques, feedstocks, and opportunities

Wastewater is produced across nearly all human activities and requires treatment to safeguard human health and the natural environment. Treatment of wastewater often requires a large amount of thermal energy, resulting in wasted heat after the treatment process. Because hydrocarbon reforming needs both water and heat, the integration of wastewater treatment with hydrocarbon reforming, a process that produces synthesis gas rich in hydrogen, offers an excellent opportunity to utilize this waste heat and the impurities in wastewater to produce valuable hydrogen gas, to minimize waste from industrial processes, and to integrate water treatment with the hydrogen economy. Yet, no comprehensive literature review has been conducted to examine the integration of reforming and wastewater. To address this lack, we summarize the variety of catalytic reforming techniques available in the open literature and review the current literature on wastewater reforming with these techniques. Subsequently, we conduct a review of common types of wastewater contaminants and their possible effects on reforming catalyst performance and life. Lastly, three underexamined wastewater sources are identified, namely, oilfield wastewater, geothermal water, and mining and mineral processing wastewater, and their potential for future study as a reforming feedstock is examined.

08 HYDROGEN↗

DOE OSTI2025

AI-powered topic modeling: comparing LDA and BERTopic in analyzing opioid-related cardiovascular risks in women

Topic modeling is a crucial technique in natural language processing (NLP), enabling the extraction of latent themes from large text corpora. Traditional topic modeling, such as Latent Dirichlet Allocation (LDA), faces limitations in capturing the semantic relationships in the text document although it has been widely applied in text mining. BERTopic, created in 2022, leveraged advances in deep learning and can capture the contextual relationships between words. In this work, we integrated Artificial Intelligence (AI) modules to LDA and BERTopic and provided a comprehensive comparison on the analysis of prescription opioid-related cardiovascular risks in women. Opioid use can increase the risk of cardiovascular problems in women such as arrhythmia, hypotension etc. 1,837 abstracts were retrieved and downloaded from PubMed as of April 2024 using three Medical Subject Headings (MeSH) words: “opioid,” “cardiovascular,” and “women.” Machine Learning of Language Toolkit (MALLET) was employed for the implementation of LDA. BioBERT was used for document embedding in BERTopic. Eighteen was selected as the optimal topic number for MALLET and 23 for BERTopic. ChatGPT-4-Turbo was integrated to interpret and compare the results. The short descriptions created by ChatGPT for each topic from LDA and BERTopic were highly correlated, and the performance accuracies of LDA and BERTopic were similar as determined by expert manual reviews of the abstracts grouped by their predominant topics. The results of the t-SNE (t-distributed Stochastic Neighbor Embedding) plots showed that the clusters created from BERTopic were more compact and well-separated, representing improved coherence and distinctiveness between the topics. Our findings indicated that AI algorithms could augment both traditional and contemporary topic modeling techniques. In addition, BERTopic has the connection port for ChatGPT-4-Turbo or other large language models in its algorithm for automatic interpretation, while with LDA interpretation must be manually, and needs special procedures for data pre-processing and stop words exclusion. Therefore, while LDA remains valuable for large-scale text analysis with resource constraints, AI-assisted BERTopic offers significant advantages in providing the enhanced interpretability and the improved semantic coherence for extracting valuable insights from textual data.

Research & Experimental Medicine↗

DOE OSTI2026

Development Fiber Optic Distributed System for Direct Detection of Subsurface Gases Leakages

Carbon, natural gas, and hydrogen gas storage is an emerging solution to safeguard us against pollution, support goals of negative carbon emission, and protect sources of renewable energy. Properly constructed storage wells provide a virtually impervious barrier to any unintended subsurface transmission. The ability to ensure the long-term integrity of such wells is vital to the success of any storage operation and be successful in the public eyes. Therefore, robust monitoring of any gas migration into the subsurface is highly sought. A fiber-optic distributed chemical sensor (DCS) enables monitoring of long-term well integrity along its depth, ensuring the success of any storage operation and bolsters public acceptance of the safety of the reservoir via leak early detection. The same technique can be applied to gas monitoring in pipeline networks and nuclear stockpile monitoring applications. Fiber based Raman spectroscopy enables DCS, as optical fibers can be deployed in virtually any environment and relay spectroscopic information over long distances back to the user. Hollow core fibers (HCF) make excellent DCSs as the air core of the fiber allows gas from the environment to diffuse into the core, which interacts with the laser signal that is carried in the air core. This work builds upon the previous LDRD project, Fiber Optic System for Direct Detection of Carbon Dioxide Leakage in Carbon Storage Wells (21-FS-003), in which the feasibility of Raman spectroscopy detection of Carbon Dioxide (CO2) in HCF detection was demonstrated. We mitigated the risk of this DCS technology by establishing and completing five objectives. The first objective was to model and optically characterize HCF uptake of CO2, establishing the relationship between HCF length, gas diffusion time, detectable gas concentration, and measured Raman intensity. In objective two, we developed a fiber core drilling recipe to enable additional diffusion ports in the fiber core and established a method for maintaining fiber strength and integrity post drilling. Objective three characterized the drilled fibers against the undrilled fibers, establishing the differences in the gas mechanics and optical properties and provided parameters to iterate the drilling process. In objective four, a fusion splicing technique was developed to join the HCF to conventional single-mode fibers, localizing the gas detection point at the drilled HCF hole, emulating a DCS. Lastly, objective five was the testing of the sensor in Edgar Mines at Colorado School of Mines on a CO2 pipeline with a simulated leak, to showcase the ability to detect CO2 leaks. This capstone result showed CO2 leak detection in < 10 minutes, raising the technology readiness level of HCF segments as deployable DCS.

organic↗

DOE OSTI2024

Overview of Quantum Sensing Materials and Techniques for Energy Sector Applications

The energy sector is dependent upon highly sensitive sensing devices for a wide range of applications. Variables such as temperature, pH, electromagnetic fields, and pressure must be measured with high precision, often in harsh conditions (e.g. high temperature, pressure and humidity). These sensors are deployed in infrastructure such as transformers, pipelines, mines, nuclear power plants, and other areas to ensure safe operating conditions and uninterrupted, optimized service. Moreover, new opportunities for sensors have emerged due to the expansion of smart grids/meters, driverless vehicles, and the discovery of new oil/gas deposits. The continued maturation of quantum sensors offers exciting opportunities for quantum-enhanced measurements to improve sensitivity beyond the classical limit. Here, an overview of established and emerging quantum materials and methods for sensing applications will be provided. Opportunities within the energy sector for quantum sensors will then be analyzed, including oil/gas discovery, greenhouse gas emission monitoring, pH and ion sensing, current measurements, and quantum-enhanced spectroscopy, along with barriers such as quantum sensor platform miniaturization and ruggedization. A specific project at the National Energy Technology Laboratory involving the functionalization of qubits using metal-organic frameworks for enhanced quantum sensing will then be highlighted. Here, nitrogen vacancy centers (NV) in nanodiamonds, a commercially available qubit with long coherence times and utilizable quantum properties at room temperature, are encapsulated using the metal-organic framework ZIF-8. Significantly, the ZIF-8 coating increases the longitudinal spin relaxation lifetime of the NV centers, an important parameter for spin relaxometry-based quantum sensing experiments. These results demonstrate the importance of qubit functionalization as a crucial step for rationally designing high performance quantum sensors.

Crawford, Scott↗

DOE OSTI2025

Reinventing wastewater treatment plants: energy neutral treatment and enhanced fertilizer production through a novel resource recovery center

Wastewater treatment plants (WWTPs) are typically energy intensive, mainly due to the secondary treatment processes such as activated sludge (AS) for treatment of organics as well as nutrients like nitrogen. Nitrogen removal presents a big problem for WWTPs. The main form of nitrogen in wastewater is ammonium, and an AS process uses oxygen to convert ammonium into nitrite and nitrate which is then converted to nitrogen through denitrification process. During anaerobic digestion (AD), organic nitrogen gets degraded, resulting in an effluent stream (centrate) with a high nitrogen content, mostly in the form of ammonium. This contributes 15-30% of total nitrogen to the wastewater influent which further increases energy consumption for aeration. The project aims to transform this conventional municipal WWTPs into energy-neutral, resource-recovering facilities by integrating three core technologies: • Cloth Media Filtration (CMF) to replace conventional primary sedimentation (CPS) and increase the diversion of organics from the energy intensive secondary treatment to AD. This results in reduced energy demand for aeration in the secondary process while simultaneously increasing the biogas production in the anaerobic digesters. • Anerobic Digester to increase biogas and ammonia production. • Membrane Evaporation (ME) to recover ammonia from AD centrate and produce marketable fertilizer. The benefits of proposed WWTP process modifications were evaluated using techno economic analysis (TEA) and life cycle assessment (LCA). For CMF portion of the research a statistical analysis was employed to develop data-driven tools that could be used to enhance and optimize its performance in terms of energy savings and effluent quality. The main objective of this project is to reduce the energy demand for secondary treatment at municipal WWTPs by at least 50%, increase anaerobic digester (AD) biogas and ammonia production by 100% and 120%, respectively, and recover 90% of ammonia from the AD. Integrated CMF, AD, and ME was shown to work synergistically toward achieving these decarbonization targets through energy-positive treatment and fertilizer recovery techniques.

42 ENGINEERING↗

DOE OSTI2025

Advances in geophysical forensic event monitoring

Forensic analysis of man-made, non-nuclear events (such as industrial accidents, explosion experiments and mine collapses) has become more frequent and detailed owing to advancements in geophysical monitoring. Here, in this Technical Review, we demonstrate how geophysical forensic monitoring using seismic, infrasound and hydroacoustic recordings provides insights on events in the solid earth, atmosphere and underwater. Advanced techniques, including machine-learning-based models, have been developed to detect, identify and investigate these events, providing information on location, subevents, sources and explosive yield. The increase in data availability, application of advanced methods and computation and the growth of multitechnology approaches have increased the accuracy of forensic event analysis and enabled more realistic characterization of uncertainties. For example, the 2020 Beirut explosion in Lebanon demonstrated that various seismic, acoustic and other methods could be used to estimate explosive yield (and yield uncertainties) of about 1 ktonne, providing confidence in the application of these methods to smaller events where data are available. However, forensic investigations remain largely limited to known events with identified sources. Increased access to data, sophisticated analysis methods and high-resolution earth models will improve forensic event analysis further, enabling civil and scientific applications, such as localization in the search for the lost ARA San Juan submarine.

geophysics↗

DOE OSTI2026

Characterization and effects of impurities on carbonate quantification in heterogenous matrices

Mineral carbonation simulates a natural weathering phenomena by breaking down silicates and oxides to form Ca & Mg carbonates. Various mineralization methods have been demonstrated as a potential technique to improve the quality of slags and tailings through neutralization and stabilization of problematic species to yield a product better suited for use in concrete. This study aims to characterize, quantify and analyze carbonates in various carbonated products such as mineralized CaCO 3 , CO 2 mineralized Steel Slags and Mine Tailings. More than 10 samples were analyzed for carbonate measurement and verification from industrial and academic partners that pioneer commercial CO 2 mineralization technologies. The samples were characterized primarily by using X-ray diffraction (XRD), Thermogravimetric Analyses (TGA), and Scanning Electron Microscopy (SEM) to gain insights into CaCO 3 content. A baseline characterization of lab-grade CaCO 3 and MgCO 3 also revealed important considerations for CaCO 3 measurement using TGA alone. The experiments using synthetic lab-grade samples also revealed that the presence of MgCO 3 /MgO can accelerate the decomposition of CaCO 3 and thus can affect measurement parameters. Lab-grade CaCO 3 samples dosed into steel slag and mine tailing also showed significant deviation in their decomposition behavior. These insights are used to inform the development of a standardized protocol for the measurement and verification of carbonate-bearing products.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2025

Faceted NiO(111) nanosheets: morphological and catalytic evolution for the oxygen evolution reaction

The renaissance of the energy system through the use of green hydrogen by water electrolysis lies behind the development of abundant, active, and scalable catalysts for the oxygen evolution reaction (OER). A fundumental understanding of the surface properties for these materials is of vital importance in producing viable heterogenous catalysts. In this feature article, we summarize several years of collaborative work on a uniquely faceted NiO(111) nanosheet possessing hexagonal holes with a focus on understanding how the evolution of the catalyst surface and bulk composition effects OER performance. The importance of surface faceting, morphological evolution, and metal combination by different doping strategies are all analyzed and summarized to further improve the material's performance. Furthermore, microwave and supercritical synthesis processes are utilized to understand how varying wet-chemical techniques effect the formation of the NiO(111) nanosheet and activity of the material. We discuss our chosen strategies and the difficulties encountered with optimizing a catalyst surface for the OER.

08 HYDROGEN↗

DOE OSTI2026

FY 2026 Midyear Report: Seismic Monitoring of Underground Vibration Sources Using Distributed Acoustic Sensing and Seismometers

Safeguards-relevant temporal changes in underground facilities can be observed using geophysical monitoring techniques. Seismic waves, in particular, provide valuable insights into subsurface activities and can serve as an important tool for detecting anomalous events that may indicate containment breaches at geological repositories. This midyear report summarizes ongoing efforts to automatically and rapidly detect and locate anomalous vibration signals that could be indicative of potential containment breaches. Previous work during FY25 focused on compiling continuous seismic datasets from two underground sites and developing a database of continuous waveforms and ground-truth event data derived from multiple sensing modalities. Building on this foundation, we are adapting anomaly detection and geolocation algorithms to explore methods for monitoring underground activities using two relatively low-maintenance sensing technologies: a dense surface geophone array deployed at the Pleasant Gap mine in Pennsylvania, and a three-dimensional fiber-optic cable array for distributed acoustic sensing (DAS) installed in the subsurface at the Sanford Underground Research Facility (SURF) in South Dakota. This report summarizes work conducted during the first two quarters of FY26, during which we refined a dynamic power spectral density (PSD)-based detector, applied it independently to each geophone station, and then combined the per‑station detections with density-based spatial clustering of applications with noise (DBSCAN) to cluster events and produce spatial maps over a nine‑day interval. In addition, we outline plans for a field trial at the Waste Isolation Pilot Plant (WIPP) in New Mexico to compare traditional seismic monitoring approaches with DAS techniques and to evaluate the benefits of combined data analysis. Activities during the past two quarters have included the preparation and submission of a Field Test Plan to WIPP for approval, as well as submission to headquarters for review and feedback.

58 GEOSCIENCES↗

DOE OSTI2026

First Measurement of Charged Current Muon Neutrino-Induced Kaon Production on Argon using the MicroBooNE Detector

MicroBooNE is an 85-tonne active mass liquid argon time projection chamber (LArTPC) neutrino detector exposed to the Booster Neutrino Beamline (BNB) at Fermilab. One of the key physics goals is the precise measurement of neutrino interactions on argon in the 1 GeV energy regime. The study of strange and heavier meson production in neutrino interactions, in particular final states containing $K^{+}$, will help to improve the background estimates for future nucleon decay searches in experiments such as DUNE, provide valuable input for improving neutrino generator models, and will allow the development of techniques to enhance the particle identification capabilities of LArTPCs. In this work, we present the first-ever cross-section measurements of charged current muon neutrino-induced kaon production on argon at MicroBooNE.

Rodriguez Rondon, Jairo H. [South Dakota Sch. Mine↗

DOE OSTI2024

Bringing Alaska's Carbon Ore, Rare Earth, and Critical Minerals (CORE-CM) into Perspective

The final report outlines the outcomes of the Alaska CORE-CM Program, funded by the U.S. Department of Energy under award DE-FE0032050. Led by the University of Alaska Fairbanks and the Alaska Division of Geological and Geophysical Surveys, with assistance from other organizations, the project assessed Alaska's potential for Carbon Ore, Rare Earth Elements, and Critical Minerals (CORE-CM). Leveraging advanced analytical techniques, the project identified high-potential resource basins, evaluated geochemical and satellite data, and conducted targeted field investigations. Findings revealed promising concentrations of critical minerals in legacy samples and newly collected materials. The project also investigated innovative extraction technologies, including BioExtraction and use of supercritical CO2, which show significant promise for sustainable resource recovery. Additionally, the study explored the reuse of waste streams from active mining operations and coal byproducts such as using alkali-activated coal ash to manufacture concrete. Infrastructure and logistical challenges in Alaska’s remote regions are discussed, alongside strategies to establish a Technology Innovation Center aimed at advancing CORE-CM development in Alaska. The report includes actionable insights to support Alaska’s critical role in securing domestic supplies of essential minerals while addressing economic, environmental, and technological challenges.

01 COAL, LIGNITE, AND PEAT↗

DOE OSTI2025

Materials Engineering for High Performance and Durability Proton Exchange Membrane Water Electrolyzers

Proton exchange membrane water electrolyzers (PEMWEs) are expected to play a crucial role in the global green energy transition during the 21st century. They provide a versatile and sustainable solution for generating hydrogen with very high purity in combination with renewable energies, such as solar and wind. Despite their promise, PEMWEs face several critical problems, including high costs, performance limitations, and durability challenges, particularly at low iridium (Ir) loading on the anode. Advancing next-generation PEMWEs requires extensive work on materials engineering of all cell components, including the catalyst layer (CL), membrane, porous transport layer (PTL), bipolar plate (BPP), and gasket. This task must be performed with the complementary contribution of different modeling and characterization techniques. This review presents a critical perspective from academia, research centers, and industry, mapping main developments, remaining gaps, and strategic pathways to advance PEMWE technology. A focus is devoted to key aspects, such as operation at low Ir loading, membrane durability, multiscale transport layers, porous and non-porous flow fields, multiphysics modeling, and multipurpose characterization techniques, which are thoroughly discussed. By unifying these topics, this review provides readers with the essential knowledge to grasp current developments and tackle tomorrow's challenges in PEMWE engineering.

36 MATERIALS SCIENCE↗

DOE OSTI2026

Time of Flight Secondary Ion Mass Spectrometry for Characterization of Pt-Coated Porous Transport Layers in PEM Water Electrolyzers

Titanium-based porous transport layers (PTLs) and iridium-based catalyst layers (CLs) are two main components of proton exchange membrane water electrolyzers (PEMWEs). PTLs are typically coated with platinum to minimize interfacial losses and to support long-term operation. Optimizing coatings and the PTL-CL interface requires comprehensive characterization. This study establishes time-of-flight secondary ion mass spectrometry (ToF-SIMS) as a valuable technique for PTL characterization, addressing capabilities and limitations related to PTL morphology. A methodology was developed that uses a Cs + sputter beam for dynamic depth profiling, with data collected in both positive-ion (MCs + ) and negative-ion modes to generate depth profiles, 2D ion maps, and 3D ion reconstructions. ToF-SIMS detected relative differences in platinum-layer thickness between samples; these trends were validated by cross-sectional scanning transmission electron microscope (STEM) measurements and flat-titanium substrate controls. Interfacial oxide layers are identified in both ion modes, with enhanced oxide sensitivity in negative mode. The technique’s high sensitivity enables detection of nanometer-scale coatings and trace impurities within the bulk PTL structure. These results provide a methodological framework for analyzing Pt-coated PTLs, with the potential to extend to other components in PEMWEs and other electrolyzer systems.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Detection and Association of Operational Events using DAS and Seismometers (FY 2025 Mid-Year Report)

This mid-year report summarizes ongoing work to identify anomalous vibration signals indicative of potential containment breaches. This work includes compiling continuous seismic datasets and testing and refining underground detection and geolocation techniques. In the first two quarters of FY25, we have completed two project work plan tasks: (1) creating a database of continuous waveforms and ground truth event data from multiple modalities and (2) refining and implementing a detection and association algorithm to create a catalog of anomalous underground activities. This report contains a summary of the seismic database including the continuous seismic data collected by a dense array of surface seismic stations above Pleasant Gap Mine, and continuous seismic data collected using subsurface distributed acoustic sensing (DAS) in the subsurface at Sanford Underground Research Facility (SURF) and the ground truth information gathered from both sites. This report also includes results from refining and applying a dynamic power spectral density detector to both continuous seismic datasets. Finally, the report provides an initial catalog of subsurface operational events from both sensing modalities.

58 GEOSCIENCES↗

DOE OSTI2025

Fabrication of porous transport electrodes: Development of quantitative approach for quality control

This work focuses on porous transport electrodes (PTEs), which integrate the anodic catalyst with the adjacent Ti porous transport layer (PTL). Challenges in catalyst deposition on PTLs, particularly at low loadings, motivated this study to evaluate various fabrication methods and characterization approaches. This work investigated Pt-treated PTLs coated with Ir-based catalysts using several common methods, including airbrush coating, rod coating, ultrasonic spray coating, electrodeposition, and sputter deposition, with catalyst loadings ranging from 2.9 to 0.1 mg/cm 2 , providing the opportunity for comparisons across a large set of samples produced by different methods. Two widely accessible characterization techniques: X-ray computed tomography (XCT) and scanning electron microscopy energy dispersive X-ray spectroscopy (SEM-EDS) were explored. Initial evaluation of selected samples with XCT provided qualitative insights into catalyst distribution, however comprehensive quantitative analysis was limited. SEM-EDS enabled detailed information on the catalyst distribution both qualitatively and quantitatively using two metrics. Atomic and surface area % ratios of Pt:Ir and Ti:Ir revealed trends in catalyst loading and losses into the PTL pores, as well as evaluating the homogeneity of catalyst coatings. The analysis demonstrated that ultrasonic spray coating, electrodeposition, and sputter coating produced the most homogeneous coatings, with minimal catalyst losses observed for electrodeposition and sputter coating. By adapting common techniques with novel, standardized methodologies, this work establishes a universally applicable framework for cross-study comparison of PTEs. The SEM-EDS approach provides a practical, accessible tool for PTE characterization and contributes a reference dataset supporting both research development and rapid quality control.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2024

Multi-Level Structural Damage Characterization Using Sparse Acoustic Sensor Networks and Knowledge Transferred Deep Learning

Standard structural health monitoring techniques face well-known difficulties for comprehensive defect diagnosis in real-world structures that have structural, material, or geometric complexity. This motivates the exploration of machine-learning-based structural health monitoring methods in complex structures. However, creating sufficient training data sets with various defects is an ongoing challenge for data-driven machine (deep) learning algorithms. The ability to transfer the knowledge of a trained neural network from one component to another or to other sections of the same component would drastically reduce the required training data set. Also, it would facilitate computationally inexpensive machine learning based inspection systems. In this work, a machine-learning-based multi-level damage characterization is demonstrated with the ability to transfer trained knowledge within the sparse sensor network. A novel network spatial assistance and an adaptive convolution technique are proposed for efficient knowledge transfer within the deep learning algorithm. Proposed structural health monitoring method is experimentally evaluated on an aluminum plate with artificially induced defects. It was observed that the method improves the performance of knowledge transferred damage characterization by 50% during localization and 24% during severity assessment. Further, experiments using time windows with and without multiple edge reflections are studied. Results reveal that multiply scattered waves contain rich and deterministic defect signatures that can be mined using deep learning neural networks, improving the accuracy of both identification and quantification. In the case of a fixed sensor network, using multiply scattered waves shows 100% prediction accuracy at all levels of damage characterization.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Challenges in predicting protein-protein interactions of understudied viruses: Arenavirus-human interactions

Understanding protein-protein interactions (PPIs) between viruses and host organisms is crucial for uncovering infection mechanisms and identifying potential therapeutic targets. The ability to generalize PPI predictive models across understudied viruses presents a significant challenge. In this work, we use arenavirus-human PPIs to illustrate the difficulties associated with model generalization, which are compounded by a lack of both positive and negative data. We employ a Transfer Learning approach to investigate arenavirus-human PPIs by utilizing models trained on better-studied virus-human and human-human PPIs. Additionally, we curate and assess four types of negative sampling datasets to evaluate their impact on model performance. Despite the overall high accuracies (93–99 %) and AUPRC scores (0.8–0.9) appearing promising, further analysis indicates that these performance metrics can be misleading due to data leakage, data bias, and overfitting, especially concerning under-represented viral proteins. We reveal these gaps and assess the impact of data imbalance using standard k-fold cross-validation and Independent Blind Testing with a Balanced Dataset, resulting in a drop in accuracy below 50 %. We propose a viral protein-specific evaluation framework that categorizes viral proteins into majority and minority classes based on their representation in the dataset, enabling comparison of model performance across these groups using balanced accuracies. This framework offers a more robust evaluation of model generalizability, addressing biases inherent in standard evaluation techniques and paving the way for more reliable PPI prediction models for understudied viruses.

59 BASIC BIOLOGICAL SCIENCES↗