arXiv subjects

Moritz U. G. Kraemer

Publications and source records attributed to Moritz U. G. Kraemer.

8 recordsLinked to original sources

arXiv2026

Planetary Geospatial Foundation Models: A New Paradigm for Global Public Health

The efficacy of traditional disease prediction is limited by spatial gaps and temporal lags, which impact the timing and targets of resource deployments. Outbreaks escalate undetected, chronic disease burdens are quantified years later, and at-risk populations in data-sparse regions remain unaddressed. Planetary geospatial foundation models complement existing epidemiological workflows to provide operational improvements, encoding multimodal search, mobility, and environmental signals into generalizable place representations. As illustrations of this complementarity, we present independent global health case studies of Google Earth AI's Population Dynamics Foundation Model (PDFM) -- a foundation model for geospatial inference -- across four domains (vaccine-preventable, communicable, noncommunicable, maternal mental health), five tasks (spatial extrapolation, interpolation/nowcasting, probabilistic forecasting, prospective forecasting, risk stratification), and four countries (USA, Canada, Mexico, and the Democratic Republic of the Congo). Across these case studies, PDFM addresses critical surveillance gaps across domains: improving US-Canada border MMR vaccination coverage predictions by capturing cross-border behavioral spillovers domestic models miss; nowcasting cardiovascular disease to accelerate data availability; enhancing short-term municipal Mexican dengue forecasts for timely outbreak vector control; improving forecasts of cholera hotspots; and adding a transferable signal to individual-level postpartum-depression risk prediction in US states the model had never seen, while not replacing individual socioeconomic data or closing demographic screening gaps. Together, these results showcase capabilities of geospatial foundation models for public health surveillance.

cs.LG↗

arXiv2026

Multi-scale measures of time-varying epidemic spread on human mobility networks

Human movement drives the spatial spread and persistence of many infectious diseases, yet existing theory and real-time operational tools for inferring the instantaneous reproduction number R(t) often assume static and/or homogeneously mixing populations and cannot describe how individuals generate and acquire infections heterogeneously based on their movement patterns within a day. Renewal equations underpin many such popular estimators of R(t), and here, we develop a network-based modelling framework from which we derive new mechanism-led renewal equations and control indicators for outbreaks of infectious diseases. These equations directly integrate within-day human movement to rigorously define a family of instantaneous reproduction numbers; inward, outward, and type R(t) for individual locations, R(t) between locations, R(t) at meeting locations, and R(t) for the entire mobility network. These quantities correct for the unsuitability of existing location-specific R(t) estimators that operate in closed, static populations. Applying our framework to epidemics on diverse types of networks alongside mobile phone data, we demonstrate how our new framework's outputs provide new, multi-scale control indicators at the network, location, and transmission corridor scales, and can be used to design targeted disease control interventions including the strength, type, and length of intervention required across space and time. We capture the biasing effects of different existing ways to measure location-specific and network-level transmission potential without capturing within-day human movements. This generalisable framework redefines reproduction numbers in real-world outbreaks that are shaped by individuals moving across connected locations, enabling more spatially and temporally precise interventions.

q-bio.QM↗

arXiv2026

Sequential Federated Analysis of Early Outbreak Data Applied to Incubation Period Estimation

Early outbreak data analysis is critical for informing about their potential impact and interventions. However, data obtained early in outbreaks are often sensitive and subject to strict privacy restrictions. Thus, federated analysis, which implies decentralised collaborative analysis where no raw data sharing is required, emerged as an attractive paradigm to solve issues around data privacy and confidentiality. In the present study, we propose two approaches which require neither data sharing nor direct communication between devices/servers. The first approach approximates the joint posterior distributions via a multivariate normal distribution and uses this information to update prior distributions sequentially. The second approach uses summaries from parameters' posteriors obtained locally at different locations (sites) to perform a meta-analysis via a hierarchical model. We test these models on simulated and on real outbreak data to estimate the incubation period of multiple infectious diseases. Results indicate that both approaches can recover incubation period parameters accurately, but they present different inferential advantages. While the approximation approach permits to work with full posterior distributions, thus providing a better quantification of uncertainty; the meta-analysis approach allows for an explicit hierarchical structure, which can make some parameters more interpretable. We provide a framework for federated analysis of early outbreak data where the public health contexts are complex.

stat.AP↗

arXiv2026

Non-Linear Drivers of Population Dynamics: a Nonparametric Coalescent Approach

Effective population size (Ne(t)) is a fundamental parameter in population genetics and phylodynamics that quantifies genetic diversity and reveals demographic history. Coalescent-based methods enable the inference of Ne(t) trajectories through time from phylogenies reconstructed from molecular sequence data. Understanding the ecological and environmental drivers of population dynamics requires linking Ne(t) to external covariates. Existing approaches typically impose log-linear relationships between covariates and Ne(t), which may fail to capture complex biological processes and can introduce bias when the true relationship is nonlinear. We present a flexible Bayesian framework that integrates covariates into coalescent models with piecewise-constant Ne(t) through a Gaussian process (GP) prior. The GP, a distribution over functions, naturally accommodates nonlinear covariate effects without restrictive parametric assumptions. This formulation improves estimation of covariate-Ne(t) relationships, mitigates bias under nonlinear associations, and yields interpretable uncertainty quantification that varies across the covariate space. To balance global covariate-driven patterns with local temporal dynamics, we couple the GP prior with a Gaussian Markov random field that enforces smoothness in Ne(t) trajectories. Through simulation studies and three empirical applications - yellow fever virus dynamics in Brazil (2016-2018), late-Quaternary musk ox demography, and HIV-1 CRF02-AG evolution in Cameroon - we demonstrate that our method both confirms linear relationships where appropriate and reveals nonlinear covariate effects that would otherwise be missed or mischaracterized. This framework advances phylodynamic inference by enabling more accurate and biologically realistic modeling of how environmental and epidemiological factors shape population size through time.

stat.AP↗

arXiv2025

Identifying and Characterising Higher Order Interactions in Mobility Networks Using Hypergraphs

Understanding human mobility is essential for applications ranging from urban planning to public health. Traditional mobility models such as flow networks and colocation matrices capture only pairwise interactions between discrete locations, overlooking higher-order relationships among locations (i.e., mobility flow among two or more locations). To address this, we propose co-visitation hypergraphs, a model that leverages temporal observation windows to extract group interactions between locations from individual mobility trajectory data. Using frequent pattern mining, our approach constructs hypergraphs that capture dynamic mobility behaviors across different spatial and temporal scales. We validate our method on a publicly available mobility dataset and demonstrate its effectiveness in analyzing city-scale mobility patterns, detecting shifts during external disruptions such as extreme weather events, and examining how a location's connectivity (degree) relates to the number of points of interest (POIs) within it. Our results demonstrate that our hypergraph-based mobility analysis framework is a valuable tool with potential applications in diverse fields such as public health, disaster resilience, and urban planning.

cs.SI↗

arXiv2024

Renewal equations for vector-borne diseases

During infectious disease outbreaks, estimates of time-varying pathogen transmissibility, such as the instantaneous reproduction number R(t) or epidemic growth rate r(t), are used to inform decision-making by public health authorities. For directly transmitted infectious diseases, the renewal equation framework is a widely used method for measuring time-varying transmissibility. The framework uses information on the typical time elapsing between an infection and the offspring infections (quantified by the generation time distribution), and R(t), to describe the rate at which currently infected individuals generate new infections. For diseases with transmission cycles involving hosts and vectors, however, renewal equation models have been far less used. This is likely due to difficulties in mechanistically defining generation times that can capture the complexity of multi-stage, human-vector relationships. Here, using dengue as an example, we provide general renewal equations that are derived from first principles using age-structured systems of coupled partial differential equations across human and vector sub-populations. Our framework tracks the multi-stage transmission cycle over calendar time and across stage-specific ages, resulting in governing renewal equations that quantify how the rate at which new infections are generated from existing infections depends on stage-specific processes. The framework provides a foundation on which to base inferential frameworks for estimating R(t) and r(t) for infectious diseases with multiple stages in the transmission cycle

q-bio.PE↗

arXiv2023

Spatial scales of COVID-19 transmission in Mexico

During outbreaks of emerging infectious diseases, internationally connected cities often experience large and early outbreaks, while rural regions follow after some delay. This hierarchical structure of disease spread is influenced primarily by the multiscale structure of human mobility. However, during the COVID-19 epidemic, public health responses typically did not take into consideration the explicit spatial structure of human mobility when designing non-pharmaceutical interventions (NPIs). NPIs were applied primarily at national or regional scales. Here we use weekly anonymized and aggregated human mobility data and spatially highly resolved data on COVID-19 cases, deaths and hospitalizations at the municipality level in Mexico to investigate how behavioural changes in response to the pandemic have altered the spatial scales of transmission and interventions during its first wave (March - June 2020). We find that the epidemic dynamics in Mexico were initially driven by SARS-CoV-2 exports from Mexico State and Mexico City, where early outbreaks occurred. The mobility network shifted after the implementation of interventions in late March 2020, and the mobility network communities became more disjointed while epidemics in these communities became increasingly synchronised. Our results provide actionable and dynamic insights into how to use network science and epidemiological modelling to inform the spatial scale at which interventions are most impactful in mitigating the spread of COVID-19 and infectious diseases in general.

physics.soc-ph↗

arXiv2022

Characterizing collective physical distancing in the U.S. during the first nine months of the COVID-19 pandemic

The COVID-19 pandemic offers an unprecedented natural experiment providing insights into the emergence of collective behavioral changes of both exogenous (government mandated) and endogenous (spontaneous reaction to infection risks) origin. Here, we characterize collective physical distancing -- mobility reductions, minimization of contacts, shortening of contact duration -- in response to the COVID-19 pandemic in the pre-vaccine era by analyzing de-identified, privacy-preserving location data for a panel of over 5.5 million anonymized, opted-in U.S. devices. We define five indicators of users' mobility and proximity to investigate how the emerging collective behavior deviates from the typical pre-pandemic patterns during the first nine months of the COVID-19 pandemic. We analyze both the dramatic changes due to the government mandated mitigation policies and the more spontaneous societal adaptation into a new (physically distanced) normal in the fall 2020. The indicators defined here allow the quantification of behavior changes across the rural/urban divide and highlight the statistical association of mobility and proximity indicators with metrics characterizing the pandemic's social and public health impact such as unemployment and deaths. This study provides a framework to study massive social distancing phenomena with potential uses in analyzing and monitoring the effects of pandemic mitigation plans at the national and international level.

physics.soc-ph↗