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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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A Data-Agnostic, Continuous Machine Learning Framework for Application in High Energy Physics and Beyond: Phase 1 Final Scientific/Technical Report

This Phase 1 effort has focused on the development of continual learning frameworks for use in machine learning, specifically in the applied context of High Energy Physics (HEP). Machine learning (ML) is a transformative technology by which computers, typically through the use of neural networks, are able to perform tasks with proficiency that rivals or surpasses that of human users. Model Degradation & Catastrophic Forgetting are two undesired phenomena which can occur in ML where the performance of a model degrades when either deployed on novel data streams, or trained on novel data which are sufficiently different than the data the models were initially trained on. A natural example where these sorts of effects can be observed is in the performance of detectors in harsh environments, where the detector signature may change over the lifetime of the detector as it ages and deteriorates — precisely what occurs in the experiments conducted in HEP. Real world HEP data is therefore an excellent test-ground and use-case for Continual Learning paradigms, which are techniques used in ML to counteract these problems. Ensemble learning is one such technique, where multiple smaller models are trained on subsets of the overall data and are ensembled together during inference. The intuition behind this technique is that, although there are shifts in the distributions which govern the incoming data streams, these shifts are not expected to be homogeneous or global. If a sufficient diversity in solutions within the various sub-models has been achieved, then at least one sub-model is expected to retain its performance within the overall ensemble. One further strength of this approach is that the architectures of the various models do not need to be identical, and in fact even different modalities of data can naturally be combined in this way. This work focused on applying ensemble learning techniques to derive results using two main datasets, anomaly detection in HEP data & time-series forecasting in semiconductor manufacturing data. Semiconductor manufacturing involves data with surprising similarity to that of HEP (e.g. wafer maps look very similar to digi-occupancy maps) and Cerium Lab’s prominence within the semiconductor industry makes semiconductor manufacturing a natural opportunity for commercialization of this work. Our efforts have led to two strong results. The first is that we evaluated the proposed ensembling techniques using previously proposed machine learning architectures for use in anomaly detection, namely AutoEncoder based models and their derivatives. We also developed new architectures which have not been evaluated in this context before. In fact, this work marks the first use of Vision Transformers for anomaly detection in HEP. Second, we demonstrated that ensemble learning significantly improves model performance in scenarios prone to degradation, validating its effectiveness across both HEP and semiconductor datasets. These results further support ensemble learning as a powerful strategy for mitigating catastrophic forgetting and maintaining robust performance in evolving data environments.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Hydroboost

HydroBoost is the most realistic revenue optimization tool for the hybridization of hydropower and battery energy storage systems to date. The innovative representation of how operators actually schedule hydropower in practice results in more realistic predictions of revenue and operations. Unlike other optimization tools, HydroBoost generates forecast energy prices with uncertainty to use in the optimization. This allows HydroBoost to give users a range of potential revenue with an upper bound using the perfect foresight pricing and a lower bound using a naive persistence forecast model. Additional forecast can be generated and used in the optimization, such as additive models, random forest, and neural networks to give further insight into potential revenue. HydroBoost has been designed to be applicable for both run-of-river and reservoir storage sites. The primary focus is on the day-ahead market and requires year-long data with an hour time-step. All time-series input and constraints are contained in an Excel worksheet for convince. The user will run the forecasting generation first with a Python script to give the optimization model the necessary requirements. Next the optimization is ran using Julia and results are generated and stored into a directory as csv files. HydroBoost includes an additional module to generate figures based on the results of the optimization simulation. The results help analyze the results and users to draw insights into how the hydro and battery systems are operated and the revenue each is producing. Additionally, the difference between the perfect foresight model and models that include forecast can easily be inspected.

Phillips, TylerB. [Idaho National Laboratory (INL)↗

Evaluation of data driven low-rank matrix factorization for accelerated solutions of the Vlasov equation

Low-rank methods have shown success in accelerating simulations of a collisionless plasma described by the Vlasov equation, but still rely on computationally costly linear algebra every time step. We propose a data-driven factorization method using artificial neural networks, specifically with convolutional layer architecture, that trains on existing simulation data. At inference time, the model outputs a low-rank decomposition of the distribution field of the charged particles, and we demonstrate that this step is faster than the standard linear algebra technique. Numerical experiments show that the method achieves comparable reconstruction accuracy for interpolation tasks, generalizing to unseen test data in a manner beyond just memorizing training data; patterns in factorization also inherently followed the same numerical trend as those within algebraic methods (e.g., truncated singular-value decomposition). However, when training on the first 70% of a time-series data and testing on the remaining 30%, the method fails to meaningfully extrapolate. Despite this limiting result, the technique may have benefits for simulations in a statistical steady-state or otherwise showing temporal stability. These results suggest that while the model offers a computationally efficient alternative for datasets with temporal stability, its current formulation is best suited for interpolation rather than for predicting future states in time-evolving systems. This study thus lays the groundwork for further refinement of neural network-based approaches to low-rank matrix factorization in high-dimensional plasma simulations.

97 MATHEMATICS AND COMPUTING↗

A Data Science and Machine Learning Platform Supporting Large Particle Accelerator Control and Diagnostics Applications Final Report: SBIR Initial Phase II DE-SC0022583

The Machine Learning Data Platform (MLDP) is a product providing full-stack support for data science, Machine Learning, and Artificial Intelligence (ML/AI) applications at particle accelerator and large experimental physics facilities. It supports ML/AI applications from front-end, high-speed acquisition of heterogeneous, time-series data, through data archiving and management, to back-end analysis. The MLDP embodies a “data-science ready” platform for data analysis and ML/AI applications in diagnosis, modelling, control, and optimization of these facilities. It provides data scientists and applications a consistent, datacentric interface to archive data standardizing implementation and deployment of ML/AI algorithms to different operations configurations within the same facility, or between facilities. Being an open-source, public-domain project, the MLDP is intended for broadest possible impact by increasing accessibility and minimizing the required expertise for installation and operation. The MLDP can also be deployed at user facilities for experimental data collection, archiving, and analysis. It is capable of acquisition and archiving of heterogeneous data from experimental equipment (e.g., images, arrays, structures, etc.) along with system hardware configurations (e.g., scalars, tables), control system process variables, and any metadata required for provenance. Thus, the MLDP can manage experimental data through its entire lifecycle, from acquisition and archiving, through analysis and investigation, to release and final publication.

43 PARTICLE ACCELERATORS↗

A digital twin platform for building performance monitoring and optimization: Performance simulation and case studies

Advancements in sensor technology, data analytics, affordable compute, and communication infrastructure have paved the way for Digital Twin technology in optimizing building operations and controls. This study presents the development of an open and interoperable web-based Digital Twin platform for integrating diverse data streams and facilitating effective user interactions. The platform utilizes modern technologies for the web framework and time-series data management, ensuring scalability and responsiveness. The backend supports seamless integration of diverse data sources and emulators, incorporating data from building sensors and meters, external weather Application Programming Interfaces, and advanced EnergyPlus simulation models of the building and its energy systems including the Distributed Energy Resources that are formulated in Functional Mockup Units. A simulation case study was conducted with FlexLab, a test facility on Lawrence Berkeley National Laboratory campus. The case study includes normal operations, Distributed Energy Resource integration, and power outage scenarios, to illustrate the Digital Twin’s ability to provide critical insights into energy performance and thermal resilience. The results demonstrated the platform’s potential as a decision-support tool for optimizing building energy performance and enhancing resilience against extreme weather events. Future work will focus on deploying the Digital Twin platform to a real building for field validation, extending its capabilities to cover more scenarios such as bidirectional Electric Vehicle interactions, and enhancing user engagement.

EnergyPlus↗

ResStock Measure Documentation: Residential Two-Stage Geothermal Heat Pump (4.0 COP, 20.5 EER) With Envelope Improvements and Advanced Air Sealing

The goal of this work is to develop energy efficiency, demand flexibility, and other retrofit end-use load shapes (electricity, gas, propane, or fuel oil) that cover a majority of the high-impact, market-ready (or nearly market-ready) measures. "Measures" refers to retrofits that can be applied to buildings during modeling. An "end-use savings shape" is the difference in energy consumption between a baseline building and a building with an energy efficiency, demand flexibility, or other retrofit measure applied. It results in a time-series profile that is broken down by end use and fuel (electricity or on-site gas, propane, or fuel oil use) at each time step. ResStock is a highly granular, physics-based, bottom-up model that uses multiple data sources, statistical sampling methods, and advanced building energy simulations to estimate the annual subhourly energy consumption of the residential building stock across the United States. The baseline model intends to represent the U.S. residential building stock as it existed in 2018. Technical documentation for the inputs and assumptions in the baseline building stock model is available in Reyna et al. (2025). Calibration and validation of the baseline model results are available in the final technical report of the End-Use Load Profiles project (Wilson, et al. 2022). This document focuses on a single end-use savings shape measure: Residential Two-Stage Geothermal Heat Pump (GHP) (4.0 COP, 20.5 EER) With Envelope Improvements. This measure combines a two-stage GHP with envelope improvements as a single package. As this package is a combination of two other measures, this document focused on documenting the results associated with this combination of technologies, with individual measure documents for two-stage GHPs and envelope improvements providing the information on the details of these measures. When the two technologies are combined, envelope improvements can modestly reduce energy consumption by a further 10%-15%, but also reduce the required size of the ground heat exchanger and heat pump by approximately 33% on average across all sites. The cost of installing envelope improvements in these homes is likely to be more than paid for by the reduction in equipment and drilling costs in these buildings for the majority of the stock.

15 GEOTHERMAL ENERGY↗

ResStock Measure Documentation: Residential Single-Stage Geothermal Heat Pump (3.8 COP, 18.6 EER)

The goal of this work is to develop energy efficiency, demand flexibility, and other retrofit end-use load shapes (electricity, gas, propane, or fuel oil) that cover a majority of the high-impact, market-ready (or nearly market-ready) measures. "Measures" refers to retrofits that can be applied to buildings during modeling. An "end-use savings shape" is the difference in energy consumption between a baseline building and a building with an energy efficiency, demand flexibility, or other retrofit measure applied. It results in a time-series profile that is broken down by end use and fuel (electricity or on-site gas, propane, or fuel oil use) at each time step. ResStock is a highly granular, physics-based, bottom-up model that uses multiple data sources, statistical sampling methods, and advanced building energy simulations to estimate the annual subhourly energy consumption of the residential building stock across the United States. The baseline model intends to represent the U.S. residential building stock as it existed in 2018. Technical documentation for the inputs and assumptions in the baseline building stock model is available in Reyna et al. (2025). Calibration and validation of the baseline model results are available in the final technical report of the End-Use Load Profiles project (Wilson et al. 2022). This documentation focuses on a single end-use savings shape measure: Residential Single-Stage Geothermal Heat Pump (GHP).?Single-stage GHPs are able to reduce energy consumption by 31% for the entire stock. Additional results provided below detail how savings changes for sections of the housing stock with different base heating fuel and in different climate zones, as well as the savings potential by state for both heating and cooling. Utility bills and electric panel impacts are also shown and discussed.

15 GEOTHERMAL ENERGY↗

ResStock Measure Documentation: Residential Variable-Speed Geothermal Heat Pump (4.4 COP, 30.9 EER)

The goal of this work is to develop energy efficiency, demand flexibility, and other retrofit end-use load shapes (electricity, gas, propane, or fuel oil) that cover a majority of the high-impact, market-ready (or nearly market-ready) measures. "Measures" refers to retrofits that can be applied to buildings during modeling. An "end-use savings shape" is the difference in energy consumption between a baseline building and a building with an energy efficiency, demand flexibility, or other retrofit measure applied. It results in a time-series profile that is broken down by end use and fuel (electricity or on-site gas, propane, or fuel oil use) at each time step. ResStock (TM) is a highly granular, physics-based, bottom-up model that uses multiple data sources, statistical sampling methods, and advanced building energy simulations to estimate the annual subhourly energy consumption of the residential building stock across the United States. The baseline model intends to represent the U.S. residential building stock as it existed in 2018. Technical documentation for the inputs and assumptions in the baseline building stock model is available in Reyna et al. (2025). Calibration and validation of the baseline model results are available in the final technical report of the End-Use Load Profiles project (Wilson et al. 2022). This documentation focuses on a single end-use savings shape measure: Residential Variable-Speed Geothermal Heat Pump (GHP). This document provides the relevant new modeling information for variable-speed systems not previously covered in either the single-stage or two-stage documents. Variable-speed GHPs represent the most efficient option available for this technology: They provide the most savings, with up to 46% for the applicable portion of the housing stock, compared to 31% for less efficient single-stage GHPs. Additional results shown here detail how the savings change for sections of the housing stock with different base heating fuels and in different climate zones, and they show the savings potential by state for both heating and cooling. Utility bills and electric panel impacts are also shown and discussed.

15 GEOTHERMAL ENERGY↗

ResStock Measure Documentation: Residential Two-Stage Geothermal Heat Pump (4.0 COP, 20.5 EER)

The goal of this work is to develop energy efficiency, demand flexibility, and other retrofit end-use load shapes (electricity, gas, propane, or fuel oil) that cover a majority of the high-impact, market-ready (or nearly market-ready) measures. "Measures" refers to retrofits that can be applied to buildings during modeling. An "end-use savings shape" is the difference in energy consumption between a baseline building and a building with an energy efficiency, demand flexibility, or other retrofit measure applied. It results in a time-series profile that is broken down by end use and fuel (electricity or on-site gas, propane, or fuel oil use) at each time step. ResStock is a highly granular, physics-based, bottom-up model that uses multiple data sources, statistical sampling methods, and advanced building energy simulations to estimate the annual subhourly energy consumption of the residential building stock across the United States. The baseline model intends to represent the U.S. residential building stock as it existed in 2018. Technical documentation for the inputs and assumptions in the baseline building stock model is available in Reyna et al. (2025). Calibration and validation of the baseline model results are available in the final technical report of the End-Use Load Profiles project (Wilson et al. 2022). This document focuses on a single end-use savings shape measure: Residential Two-Stage Geothermal Heat Pump (4.0 COP, 20.5 EER). This document builds on details established in the single-stage document (Maguire et al. 2025) to detail differences in the approach to modeling this higher efficiency, but more commonly deployed, type of geothermal heat pump. Specific EnergyPlus objects and product specific curves used are highlighted along with showing the results of this measure compared to the baseline and single-speed geothermal heat pumps. Two-speed geothermal heat pumps are able to save even more energy and on utility bills than single-speed products, albeit at the expense of a higher first cost.

15 GEOTHERMAL ENERGY↗

Poster Abstract: Leveraging Large Language Models to Reveal Interpretable Cooling Behaviors from Smart Thermostat Data

Frequent heatwaves and hot summers increasingly challenge occupant comfort, health, and energy grid stability. Addressing these challenges requires a detailed understanding of household cooling behaviors, such as thermostat adjustments and adaptive responses to extreme conditions. Traditional analyses often rely on aggregated numerical metrics that overlook subtle but important household-specific variations. In this study, we introduce a generalizable methodology that integrates large language models (LLMs) with vision capabilities to enable scalable and detailed analysis of residential thermostat data. Using Ecobee's Donate Your Data (DYD) dataset—which provides five-minute records of indoor temperatures, thermostat setpoints, and HVAC runtimes—we focus on two U.S. cities with contrasting summer climates : Austin (TX) and Phoenix (AZ). Because raw time-series data are not well suited for direct LLM analysis, we transform them into visual representations, such as daily indoor temperature trajectories and weekly runtime histograms, to better capture behavioral variations. Leveraging LLMs' visual interpretation, we extract descriptive behavioral features, including temperature preferences, time-of-day cooling orientation, anticipatory versus reactive heatwave responses, and behavioral consistency. These semantic features support unsupervised clustering to identify distinct occupant archetypes at scale, revealing differences—such as morning-centric anticipatory coolers versus households that shift toward warmer setpoints during heatwaves—that can inform demand response, resilience planning, and health-aware interventions. By converting raw numerical data into interpretable behavioral patterns, this methodology enables scalable and practical analysis of occupant behavior, supporting actionable insights for comfort, resilience, and energy management.

Nihar, Kopal↗

Anomaly Detection for Online Monitoring of Thermocouple Sensors in the Advanced Test Reactor

This study explores data-driven anomaly detection methods to analyze sensor fail- ures in the Advanced Gas Reactor (AGR) nuclear fuel irradiation experiments. Specifically, we examine failures of thermocouples (TCs), which are critical for mon- itoring and controlling in-reactor temperatures during operation. Failures were pri- marily observed during abrupt power transitions and manifested as sensor drop-outs, drifts, or unexplained behavior. We applied three time-series analysis techniques— rolling mean smoothing, matrix profile, and vector auto-regression (VAR)—to de- tect anomalies in TC data prior to failure events. The rolling mean method effec- tively highlighted deviations aligned with reported failures, while the matrix profile provided partial early warning but sometimes flagged normal fluctuations during power-down periods. VAR shows potential in capturing multivariate dependencies but requires further calibration. A rare case of TC drift was also documented, which did not result in failure, underscoring the challenge of building predictive models with sparse positive examples. Our findings demonstrate that traditional statistical tools can aid anomaly detection but have limited predictive power without richer training data. We propose future directions including synthetic data generation, real- time surrogate modeling, and multi-modal feature integration. This work provides a foundation for applying robust anomaly detection frameworks to mission-critical sensor systems in experimental settings.

11 - NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Explainable AI for Multivariate Time Series Pattern Exploration: Latent Space Visual Analytics With Temporal Fusion Transformer and Variational Autoencoders in Power Grid Event Diagnosis

Detecting and analyzing complex patterns in multivariate time-series data is crucial for decision-making in urban and environmental system operations. However, challenges arise from the high dimensionality, intricate complexity, and interconnected nature of complex patterns, which hinder the understanding of their underlying physical processes. Existing AI methods often face limitations in interpretability, computational efficiency, and scalability, reducing their applicability in real-world scenarios. This paper proposes a novel visual analytics framework that integrates two generative AI models, Temporal Fusion Transformer (TFT) and Variational Autoencoders (VAEs), to reduce complex patterns into lower-dimensional latent spaces and visualize them in 2D using dimensionality reduction techniques such as PCA, t-SNE, and UMAP with DBSCAN. These visualizations, presented through coordinated and interactive views and tailored glyphs, enable intuitive exploration of complex multivariate temporal patterns, identifying patterns’ similarities and uncover their potential correlations for a better interpretability of the AI outputs. The framework is demonstrated through a case study on power grid signal data, where it identifies multi-label grid event signatures, including faults and anomalies with diverse root causes. Additionally, novel metrics and visualizations are introduced to validate the models and assess the performance, efficiency, and consistency of latent maps generated by VAE, which have been utilized in prior studies for latent space cartography and used as a benchmark in this study, and the emerging TFT architecture under various configurations. These analyses provide actionable insights for model parameter tuning and reliability improvements. Comparative results highlight that TFT achieves shorter run times and superior scalability to diverse time-series data shapes compared to VAE. This work advances fault diagnosis in multivariate time series, fostering explainable AI to support critical system operations.

Explainable AI↗

A Neural Optimizer With Decision-Focused Learning for Optimal Energy Storage Operation

Here, this article introduces a neural optimizer-based framework for optimizing battery energy storage system (BESS) control for grid services, including demand charge and energy cost reduction. By leveraging decision-focused learning (DFL), the proposed framework ensures seamless integration and adaptation, significantly enhancing control performance. A patch time-series transformer is employed for peak load forecasting, incorporating aleatoric uncertainty quantification to account for forecasting uncertainties within the decision-making process. The framework utilizes a solver-in-the-loop approach to generate optimal BESS actions, which are then used to train the neural optimizer-based agent. By co-optimizing both BESS operational modes and output power within the NN, the system achieves improved performance and robustness. After initial training, the forecasting and control models are jointly fine-tuned to account for forecasting errors, further improving decision precision and efficiency through DFL. Case studies are performed to validate the performance of the framework using multiple real-world datasets, demonstrating superior performance in monthly peak load forecasting compared to state-of-the-art models. In addition, the results are compared against existing decision-making approaches. The results demonstrate a reduction in monthly peak forecasting error by approximately 15% across various performance measures and achieve an optimization gap for BESS operation that is about three times smaller compared to existing methods.

Kim, Hyeonjin [Pacific Northwest National Laborato↗

Solving high-dimensional inverse problems using amortized likelihood-free inference with noisy and incomplete data

Here, we present a likelihood-free probabilistic inversion method based on normalizing flows for high-dimensional inverse problems. The proposed method is composed of two complementary networks: a summary network for data compression and an inference network for parameter estimation. The summary network encodes raw observations into a fixed-size vector of summary features, while the inference network generates samples of the approximate posterior distribution of the model parameters based on these summary features. The posterior samples are produced in a deep generative fashion by sampling from a latent Gaussian distribution and passing these samples through an invertible transformation. We construct this invertible transformation by sequentially alternating conditional invertible neural network and conditional neural spline flow layers. The summary and inference networks are trained simultaneously. We apply the proposed method to an inversion problem in groundwater hydrology to estimate the posterior distribution of the log-conductivity field conditioned on spatially sparse time-series observations of the system’s hydraulic head responses. The conductivity field is represented with 706 degrees of freedom in the considered problem. Comparison with the likelihood-based iterative ensemble smoother PEST-IES method demonstrates that the proposed method accurately estimates the parameter posterior distribution and the observations’ predictive posterior distribution at a fraction of the inference time of PEST-IES.

conditional invertible neural network↗

ComStock Measure Scenario Documentation: Chiller Replacement

Building on a 3-year effort to calibrate and validate the U.S. Department of Energy's ResStock (TM) and ComStock (TM) models, this work produces national datasets that empower analysts working for federal, state, utility, city, and manufacturer stakeholders to answer a broad range of questions regarding their commercial building stock. ComStock is a highly granular, bottom-up model that uses multiple data sources, statistical sampling methods, and advanced building energy simulations to estimate the annual energy consumption (at a subhourly resolution) of the commercial building stock across the United States. The baseline model intends to represent the U.S. commercial building stock as it existed in 2018. The methodology and results of the baseline model are discussed in the final technical report of the End-Use Load Profiles project. The goal of this work is to develop energy efficiency and demand flexibility end-use load shapes that cover high-impact, market-ready (or nearly market-ready) measures. "Measures" refers to various "what-if" scenarios that can be applied to buildings. An end-use savings shape is the difference in energy consumption between a baseline building (or collection of buildings) and a building with an energy efficiency or demand flexibility measure applied. It results in a time-series profile broken down by end use and fuel (electricity or on-site gas, propane, or fuel oil use) at each time step, as well as annual aggregations. This report describes the modeling methodology for a single end-use savings shape measure - chiller replacement - and briefly introduces key results. The full public dataset can be accessed on the ComStock (TM) data lake or via the Data Viewer at comstock.nrel.gov. The public data set enables users to create custom aggregations of results for their use case (e.g., filter to a specific county).

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

ComStock Measure Scenario Documentation: Standard Performance Heat Pump Rooftop Unit With New Windows

Building on a 3-year effort to calibrate and validate the U.S. Department of Energy's ResStock (TM) and ComStock (TM) models, this work produces national datasets that empower analysts working for federal, state, utility, city, and manufacturer stakeholders to answer a broad range of questions regarding their commercial building stock. ComStock is a highly granular, bottom-up model that uses multiple data sources, statistical sampling methods, and advanced building energy simulations to estimate the annual energy consumption (at subhourly resolution) of the commercial building stock across the United States. The baseline model intends to represent the U.S. commercial building stock as it existed in 2018. The methodology and results of the baseline model are discussed in the final technical report of the End-Use Load Profiles project. The goal of this work is to develop energy efficiency and demand flexibility end-use load shapes that cover high-impact, market-ready (or nearly market-ready) measures. "Measures" refers to various "what-if" scenarios that can be applied to buildings. An end-use savings shape is the difference in energy consumption between a baseline building (or collection of buildings) and a building with an energy efficiency or demand flexibility measure applied. It results in a time-series profile broken down by end use and fuel (electricity or on-site gas, propane, or fuel oil use) at each time step, as well as annual aggregations.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Uncovering heterogeneous intercommunity disease transmission from neutral allele frequency time series

The COVID-19 pandemic has underscored the need for accurate epidemic forecasting to predict pathogen spread, evolution, and evaluate intervention strategies. Forecast reliability hinges on detailed knowledge of disease transmission across population segments, which may be inferred from contact surveys or mobility data. However, these indirect approaches make it difficult to estimate rare transmissions between socially or geographically distant communities. We show that the steep ramp-up of genome sequencing surveillance during the pandemic can be leveraged to directly identify transmission patterns between geographically defined communities. Our approach uses a hidden Markov model to infer the fraction of infections a community imports from others based on how rapidly allele frequencies in the focal community converge to those in the donor communities. Applying this method to SARS-CoV-2 sequencing data from England and the United States, we uncover networks of intercommunity transmission that reflect geographical relationships while exposing significant long-range interactions. The scaling of importation rate with distance is consistent across both countries, yet weaker than expected based on mobility data, highlighting limitations of indirect inference. We show that transmission patterns can change between waves of variants of concern and analyze how the inferred heterogeneity in intercommunity transmission impacts evolutionary forecasts. While applied here to geographically defined communities, our approach could be applied to those defined by other traits (e.g., age, socioeconomic status), provided time-series data can be stratified accordingly. Overall, our study highlights population genomic time series data as a crucial record of epidemiological interactions, which can be deciphered using tree-free inference methods.

Okada, Takashi [Department of Physics; University ↗