arXiv subjects

Matthew Scotch

Publications and source records attributed to Matthew Scotch.

6 recordsLinked to original sources

arXiv2026

An Infectious Disease Spread Simulation Based on Large Language Model Decision Making

Modelling individual decision-making during infectious disease outbreaks is crucial for understanding behavioural dynamics and informing effective public health interventions. Prior work has shown that large language models can simulate realistic human behaviour by generating agent decisions based on demographic prompts and situational context. We build on this foundation with a spatially grounded, agent-based simulation framework that integrates LLM-generated decisions about self-reported influenza-like illness into a census-based synthetic population of agents. Location is treated as a central feature: agents are assigned to spatial units within cities, capturing the spatial distributions of different demographic groups using real-world census data and enabling geographically diverse behavioural modelling. We implement and compare three decision scenarios, independent reasoning, household influence, and message framing, and simulate self-reporting outcomes in San Francisco and Atlanta. Results reveal that income and education are the dominant drivers of reporting rate variation, with smaller but consistent effects from geography, LLM model choice, and message framing. Our framework generates synthetic data that captures both social and geographic heterogeneity, supporting spatial epidemiological modelling and bias-aware behavioural analysis.

cs.AI↗

arXiv2026

From Ecological Connectivity to Outbreak Risk: A Heterogeneous Graph Network for Epidemiological Reasoning under Sparse Spatiotemporal Data

Estimating population-level prevalence and transmission dynamics of wildlife pathogens can be challenging, partly because surveillance data is sparse, detection-driven, and unevenly sequenced. Using highly pathogenic avian influenza A/H5 clade 2.3.4.4b as a case study, we develop zooNet, a graph-based epidemiological framework that integrates mechanistic transmission simulation, metadata-driven genetic distance imputation, and spatiotemporal graph learning to reconstruct outbreak dynamics from incomplete observations. Applied to wild bird surveillance data from the United States during 2022, zooNet recovered coherent spatiotemporal structure despite intermittent detections, revealing sustained regional circulation across multiple migratory flyways. The framework consistently identified counties with ongoing transmission weeks to months before confirmed detections, including persistent activity in northeastern regions prior to documented re-emergence. These signals were detectable even in areas with sparse sequencing and irregular reporting. These results show that explicitly representing ecological processes and inferred genomic connectivity within a unified graph structure allows persistence and spatial risk structure to be inferred from detection-driven wildlife surveillance data.

q-bio.PE↗

arXiv2025

A Probabilistic Framework for Imputing Genetic Distances in Spatiotemporal Pathogen Models

Pathogen genome data offers valuable structure for spatial models, but its utility is limited by incomplete sequencing coverage. We propose a probabilistic framework for inferring genetic distances between unsequenced cases and known sequences within defined transmission chains, using time-aware evolutionary distance modeling. The method estimates pairwise divergence from collection dates and observed genetic distances, enabling biologically plausible imputation grounded in observed divergence patterns, without requiring sequence alignment or known transmission chains. Applied to highly pathogenic avian influenza A/H5 cases in wild birds in the United States, this approach supports scalable, uncertainty-aware augmentation of genomic datasets and enhances the integration of evolutionary information into spatiotemporal modeling workflows.

q-bio.GN↗

arXiv2025

Evaluating the Bias in LLMs for Surveying Opinion and Decision Making in Healthcare

Generative agents have been increasingly used to simulate human behaviour in silico, driven by large language models (LLMs). These simulacra serve as sandboxes for studying human behaviour without compromising privacy or safety. However, it remains unclear whether such agents can truly represent real individuals. This work compares survey data from the Understanding America Study (UAS) on healthcare decision-making with simulated responses from generative agents. Using demographic-based prompt engineering, we create digital twins of survey respondents and analyse how well different LLMs reproduce real-world behaviours. Our findings show that some LLMs fail to reflect realistic decision-making, such as predicting universal vaccine acceptance. However, Llama 3 captures variations across race and Income more accurately but also introduces biases not present in the UAS data. This study highlights the potential of generative agents for behavioural research while underscoring the risks of bias from both LLMs and prompting strategies.

cs.CL↗

arXiv2021

Identifying Mitigation Strategies for COVID-19 Superspreading on Flights using Models that Account for Passenger Movement

Despite commercial airlines mandating masks, there have been multiple documented events of COVID-19 superspreading on flights. We used available data from three flights, including cabin layout and seat locations of infected and uninfected passengers, to suggest interventions to mitigate COVID-19 superspreading events during air travel. Specifically, we studied: 1) London to Hanoi with 201 passengers, including 13 secondary infections among passengers; 2) Singapore to Hangzhou with 321 passengers, including 12 to 14 secondary infections; 3) a non-superspreading event on a private jet in Japan with 9 passengers and no secondary infections. We show that inclusion of passenger movement better explains the infection spread patterns than conventional models do. We also found that FFP2/N95 mask usage would have reduced infection by 95-100%, while cloth masks would have reduced it by only 40-80%. This suggests the need for more stringent guidelines to reduce aviation-related superspreading events of COVID-19.

q-bio.PE↗

arXiv2020

Mathematical assessment of the impact of non-pharmaceutical interventions on curtailing the 2019 novel Coronavirus

A novel Coronavirus pandemic emerged in December of 2019, causing devastating public health impact across the world. In the absence of a safe and effective vaccine or antiviral, strategies for mitigating the burden of the pandemic are focused on non-pharmaceutical interventions, such as social-distancing, contact-tracing, quarantine, isolation and the use of face-masks in public. We develop a new mathematical model for assessing the population-level impact of these mitigation strategies. Simulations of the model, using data relevant to COVID-19 transmission in New York state and the entire US, show that the pandemic will peak in mid and late April, respectively. The worst-case scenario projections for cumulative mortality (based on the baseline levels of anti-COVID non-pharmaceutical interventions considered in the study) in New York State and the entire US decrease dramatically by 80% and 64%, respectively, if the strict social-distancing measures implemented are maintained until the end of May or June, 2020. This study shows that early termination of strict social-distancing could trigger a devastating second wave with burden similar to that projected before the onset of strict social-distance. The use of efficacious face-masks (efficacy greater than 70%) could lead to the elimination of the pandemic if at least 70% of the residents of New York state use such masks consistently (nationwide, a compliance of at least 80% will be required using such masks). The use of low efficacy masks, such as cloth masks (of efficacy less than 30%), could also lead to significant reduction of COVID-19 burden (albeit, they are not able to lead to elimination). Combining low efficacy masks with improved levels of other anti-COVID-19 intervention measures can lead to elimination of the pandemic. The mask coverage needed to eliminate COVID-19 decreases if mask-use is combined with strict social-distancing.

q-bio.PE↗