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According to the Centers for Disease Control and Prevention (CDC), one in twenty five hospital patients are infected with at least one healthcare acquired infection (HAI) on any given day. Early detection of possible HAI outbreaks help practitioners implement countermeasures before the infection spreads extensively. Here, we develop an efficient data and model driven method to detect outbreaks with high accuracy. We leverage mechanistic modeling of C. difficile infection, a major HAI disease, to simulate its spread in a hospital wing and design efficient near-optimal algorithms to select people and locations to monitor using an optimization formulation. Results show that our strategy detects up to 95% of \"future\" C. difficile outbreaks. We design our method by incorporating specific hospital practices (like swabbing for infections) as well. As a result, our method outperforms state-of-the-art algorithms for outbreak detection. Finally, a qualitative study of our result shows that the people and locations we select to monitor as sensors are intuitive and meaningful.

Healthcare-associated infections (HAIs) are a major problem in hospital infection control. Although HAIs can be suppressed using contact precautions, such precautions are expensive, and we can only apply them to a small fraction of patients (i.e., a limited budget). In this work, we focus on two clinical problems arising from the limited budget: (a) choosing the best patients to be placed under precaution given a limited budget to minimize the spread (the isolation problem), and (b) choosing the best patients to release when limited budget requires some of the patients to be cleared from precaution (the clearance problem). A critical challenge in addressing them is that HAIs have multiple transmission pathways such that locations can also accumulate ‘load’ and spread the disease. One of the most common practices when placing patients under contact precautions is the regular clearance of pathogen loads. However, standard propagation models like independent cascade (IC)/susceptible-infectious-susceptible (SIS) cannot capture such mechanisms directly. Hence to account for this challenge, using non-linear system theory, we develop a novel spectral characterization of a recently proposed pathogen load based model, 2-Mode-SIS model, on people/location networks to capture spread dynamics of HAIs. We formulate the two clinical problems using this spectral characterization and develop effective and efficient algorithms for them. Our experiments show that our methods outperform several natural structural and clinical approaches on real-world hospital testbeds and pick meaningful solutions.

Given a snapshot of a large graph, in which an infection has been spreading for some time, can we identify those nodes from which the infection started to spread? In other words, can we reliably tell who the culprits are? In this paper, we answer this question affirmatively and give an efficient method called NetSleuth for the well-known susceptible-infected virus propagation model. Essentially, we are after that set of seed nodes that best explain the given snapshot. We propose to employ the minimum description length principle to identify the best set of seed nodes and virus propagation ripple, as the one by which we can most succinctly describe the infected graph. We give an highly efficient algorithm to identify likely sets of seed nodes given a snapshot. Then, given these seed nodes, we show we can optimize the virus propagation ripple in a principled way by maximizing likelihood. With all three combined, NetSleuth can automatically identify the correct number of seed nodes, as well as which nodes are the culprits. Experimentation on our method shows high accuracy in the detection of seed nodes, in addition to the correct automatic identification of their number. Moreover, NetSleuth scales linearly in the number of nodes of the graph.

Healthcare-associated infections (HAIs) from multi-drug resistant organisms (MDROs) pose a significant challenge for healthcare systems. Patients can arrive at hospitals already infected (\"importation”) or acquire infections during their stay (\"nosocomial infection”). Many cases, often asymptomatic, complicate rapid identification due to testing limitations and delays. Although recent advancements in mathematical modeling and machine learning have aimed to identify at-risk patients, these methods face challenges: transmission models often overlook valuable electronic health record (EHR) data, while machine learning approaches typically lack mechanistic insights into underlying processes. To address these issues, we propose NeurABM, a novel framework that integrates neural networks and agent-based models (ABM) to leverage the strengths of both methods. NeurABM simultaneously learns a neural network for patient-level importation predictions and an ABM for infection identification. Our findings show that NeurABM significantly outperforms existing methods, marking a breakthrough in accurately identifying importation cases and forecasting future nosocomial infections in clinical practice.

Distribution and administration strategy are critical to successful population immunization efforts. Agent-based modeling (ABM) can reflect the complexity of real-world populations and can experimentally evaluate vaccine strategy and policy. However, ABMs historically have been limited in their time-to-development, long runtime, and difficulty calibrating. Our team had several technical advances in the development of our GradABMs: a novel class of scalable, fast and differentiable simulations. GradABMs can simulate million-size populations in a few seconds on commodity hardware, integrate with deep neural networks and ingest heterogeneous sources. This allows for rapid and real-world sensitivity analyses. Our first epidemiological GradABM (EpiABMv1) enabled simulation interventions over real million-scale populations and was used in vaccine strategy and policy during the COVID-19 pandemic. Literature suggests decisions aided by evidence from these models saved thousands of lives. Our most recent model (EpiABMv2) extends EpiABMv1 to allow improved regional calibration using deep neural networks to incorporate local population data, and in some cases different policy recommendations versus our prior models. This is an important advance for our model to be more effective at vaccine strategy and policy decisions at the local public health level.

Infectious diseases, like COVID-19, pose serious challenges to university campuses, which typically adopt closure as a non-pharmaceutical intervention to control spread and ensure a gradual return to normalcy. Intervention policies, such as remote instruction ( RI ) where large classes are offered online, reduce potential contact but also have broad side-effects on campus by hampering the local economy, students’ learning outcomes, and community wellbeing. In this paper, we demonstrate that university policymakers can mitigate these tradeoffs by leveraging anonymized data from their WiFi infrastructure to learn community mobility—a methodology we refer to as WiFi mobility models ( WiMob ). This approach enables policymakers to explore more granular policies like localized closures ( LC ). WiMob can construct contact networks that capture behavior in various spaces, highlighting new potential transmission pathways and temporal variation in contact behavior. Additionally, WiMob enables us to design LC policies that close super-spreader locations on campus. By simulating disease spread with contact networks from WiMob , we find that LC maintains the same reduction in cumulative infections as RI while showing greater reduction in peak infections and internal transmission. Moreover, LC reduces campus burden by closing fewer locations, forcing fewer students into completely online schedules, and requiring no additional isolation. WiMob can empower universities to conceive and assess a variety of closure policies to prevent future outbreaks.

Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. Starting in April 2020, the US COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized tens of millions of specific predictions from more than 90 different academic, industry, and independent research groups. A multimodel ensemble forecast that combined predictions from dozens of groups every week provided the most consistently accurate probabilistic forecasts of incident deaths due to COVID-19 at the state and national level from April 2020 through October 2021. The performance of 27 individual models that submitted complete forecasts of COVID-19 deaths consistently throughout this year showed high variability in forecast skill across time, geospatial units, and forecast horizons. Two-thirds of the models evaluated showed better accuracy than a naïve baseline model. Forecast accuracy degraded as models made predictions further into the future, with probabilistic error at a 20-wk horizon three to five times larger than when predicting at a 1-wk horizon. This project underscores the role that collaboration and active coordination between governmental public-health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks.

Accurate forecasts can enable more effective public health responses during seasonal influenza epidemics. For the 2021-22 and 2022-23 influenza seasons, 26 forecasting teams provided national and jurisdiction-specific probabilistic predictions of weekly confirmed influenza hospital admissions for one-to-four weeks ahead. Forecast skill is evaluated using the Weighted Interval Score (WIS), relative WIS, and coverage. Six out of 23 models outperform the baseline model across forecast weeks and locations in 2021-22 and 12 out of 18 models in 2022-23. Averaging across all forecast targets, the FluSight ensemble is the 2 most accurate model measured by WIS in 2021-22 and the 5 most accurate in the 2022-23 season. Forecast skill and 95% coverage for the FluSight ensemble and most component models degrade over longer forecast horizons. In this work we demonstrate that while the FluSight ensemble was a robust predictor, even ensembles face challenges during periods of rapid change.

To evaluate the economic costs of reducing the University of Virginia Hospital's present \"3-negative\" policy, which continues methicillin-resistant (MRSA) contact precautions until patients receive 3 consecutive negative test results, to either 2 or 1 negative. Cost-effective analysis. The University of Virginia Hospital. The study included data from 41,216 patients from 2015 to 2019. We developed a model for MRSA transmission in the University of Virginia Hospital, accounting for both environmental contamination and interactions between patients and providers, which were derived from electronic health record (EHR) data. The model was fit to MRSA incidence over the study period under the current 3-negative clearance policy. A counterfactual simulation was used to estimate outcomes and costs for 2- and 1-negative policies compared with the current 3-negative policy. Our findings suggest that 2-negative and 1-negative policies would have led to 6 (95% CI, -30 to 44; < .001) and 17 (95% CI, -23 to 59; -10.1% to 25.8%; < .001) more MRSA cases, respectively, at the hospital over the study period. Overall, the 1-negative policy has statistically significantly lower costs ($628,452; 95% CI, $513,592-$752,148) annually ( < .001) in US dollars, inflation-adjusted for 2023) than the 2-negative policy ($687,946; 95% CI, $562,522-$812,662) and 3-negative ($702,823; 95% CI, $577,277-$846,605). A single negative MRSA nares PCR test may provide sufficient evidence to discontinue MRSA contact precautions, and it may be the most cost-effective option.

Surveillance of epidemic outbreaks and spread from social media is an important tool for governments and public health authorities. Machine learning techniques for nowcasting the Flu have made significant inroads into correlating social media trends to case counts and prevalence of epidemics in a population. There is a disconnect between data-driven methods for forecasting Flu incidence and epidemiological models that adopt a state based understanding of transitions, that can lead to sub-optimal predictions. Furthermore, models for epidemiological activity and social activity like on Twitter predict different shapes and have important differences. In this paper, we propose two temporal topic models (one unsupervised model as well as one improved weakly-supervised model) to capture hidden states of a user from his tweets and aggregate states in a geographical region for better estimation of trends. We show that our approaches help fill the gap between phenomenological methods for disease surveillance and epidemiological models. We validate our approaches by modeling the Flu using Twitter in multiple countries of South America. We demonstrate that our models can consistently outperform plain vocabulary assessment in Flu case-count predictions, and at the same time get better Flu-peak predictions than competitors. We also show that our fine-grained modeling can reconcile some contrasting behaviors between epidemiological and social models.