Epidemic Forecasting

Weekly influenza surveillance counts guide vaccine distribution and public-health alerts, yet they are hard to forecast. Each region offers only a few seasons, waves shift in timing and height every year, and information that helps while a wave grows misleads after its peak, whereas last season's shape stays informative for a year. Existing epidemic graph models and general forecasters read a short fixed window and treat all past information alike, so they neither exploit earlier seasons nor discard stale associations when the epidemic phase changes. To address these limitations, we propose TERN, a forecaster built around a delta-rule fast-weight memory that decays channel-wise and erases along a learned address under gates driven by local epidemic-phase features, combined with an explicit seasonal reference and online adaptation. On three Cola-GNN influenza benchmarks, TERN outperformed epidemic graph models and general forecasters, matched or exceeded seasonal references, and a controlled comparison confirmed the contribution of the memory itself.

The COVID-19 pandemic has had profound impacts on global health, social structures, and economies. It disproportionately affected lower socioeconomic groups and those reliant on interaction-based jobs. Regulatory bodies faced the challenge of designing policies that preserve public health while limiting disruption to economic stability and productivity. Epidemiological models such as SIR and agent-based models (ABMs) have been used to study disease dynamics and the socioeconomic impacts of disease and interventions. Population-level models often simplify individual heterogeneity, while detailed ABMs can become computationally expensive as the numbers of agents and interactions increase. We propose ABM-SIRTEM, a hybrid model that incorporates occupation categories, economic productivity, and welfare at the individual level while dynamically modeling compliance with government interventions. We calibrate the model against historical positive and negative test counts from four U.S. states and examine the resulting compliance dynamics. This framework provides a basis for studying the interaction between disease spread and socioeconomic behavior in pandemic-response planning.

Wastewater-based surveillance is an effective tool for disease monitoring and can provide early warning of outbreaks. Although wastewater viral loads (WVL) correlate with disease burden, their utility for improving real-time forecasting remains under investigation. During the early phases of an epidemic, many indicators can effectively monitor disease spread, but their reliability may decline because of reporting fatigue and low prevalence. Hospital burden can vary substantially even during low-prevalence periods, making accurate forecasting of burden indicators essential for minimizing disease impacts. In this paper, we present principled approaches for processing wastewater data, characterizing its relationship with burden indicators, and generating real-time forecasts. We assess the predictability of WVL using entropy measures. We analyze the relationship between WVL and burden indicators using causality tests that capture temporal dynamics and the leading-indicator behavior of WVL. We incorporate these insights into a time-varying forecasting model that accounts for the evolving relationship between the signals. We also evaluate the effects of delays in WVL reporting through simulations. We test the utility of our methods by forecasting COVID-19 hospital admissions across Virginia and its health regions during periods of varying disease prevalence. Incorporating WVL improves forecast accuracy relative to baseline models, particularly during critical epidemic phases, and results in a 20 percentage point improvement in forecast coverage. Our results demonstrate that WVL signals can improve infectious disease forecasting even under conditions of low prevalence or delayed reporting.

Predicting the existence and type of links (edges) between nodes in a multi-relational graph is key for applications from social interaction prediction to knowledge relationship identification. Enhancing local features with relevant global information is crucial for accurate link prediction, yet it remains challenging. We address this by modeling the relationship between node pairs as node influence. That is, whether the node influence can be propagated and what type of influence is propagated indicates where and what type the edge is, which will be the most relevant local and global information to predict the edges. To this end, we extend the Susceptible-Infectious-Recovered (SIR) epidemic model to capture the influence propagation of nodes on a large scale through sub-graph structures. Subsequently, these sub-graphs are compressed using virtual edges, thereby substantially reducing the computation associated with utilizing the global graph structure. Finally, we propose the Influential Graph Neural Predictor, referred to as IGNP, a link prediction framework guided by influence propagation. Extensive experiments demonstrate the superiority of the proposed method, which outperforms strong baselines by a large margin on the widely used and real-world datasets.

Multi-agent collaborative filtering (CF) systems coordinate autonomous LLM-powered user and item agents through natural-language interaction to refine preferences and generate recommendations. These systems inherit vulnerabilities from both their data-driven nature and their multi-agent interactions, which manifest in distinct ways. Understanding how connectivity modulates vulnerability in these systems could facilitate the development of more robust recommendation pipelines. In this work, we adapt attacks and defenses from the general multi-agent systems (MAS) literature to the agent-based CF setting, evaluating them under systematically varied connectivity in the AgentCF framework, where CF connectivity is characterized along two axes: (i) candidate count (the number of item candidates per turn per user, measuring user-side interaction density) and (ii) catalog concentration (the degree of item catalog overlap across users). Our contributions include: (1) Adaptation: we reproduce MAS-inspired attacks and defenses in the agentic CF domain, confirming partial transferability of original observations. (2) Characterization: we characterize how the two aspects of connectivity shape attack and defense outcomes, revealing role asymmetries between user and item agents, non-monotonic temporal dynamics in attack efficacy, and divergent patterns across dissemination and extraction attack goals. Additionally, as an exploratory extension, we assess the applicability of epidemic-inspired static metrics in ranking CF configurations by expected attack outcome, potentially enabling cost-efficient robustness assessment. Implementation is available at https://github.com/anjunhu/ConnACF

Emergency Departments (EDs) are critical access points in healthcare systems, yet they face persistent pressure from unpredictable patient demand, seasonal surges, and non-urgent visits. Effective ED planning requires forecasts at multiple decision-making levels: hospitals need local demand estimates for staffing and bed management, regions require forecasts to coordinate healthcare units, and national authorities need system-wide projections for capacity planning. However, most existing approaches forecast ED demand independently at a single level, ignoring the hierarchy linking hospitals, regions, and national systems. This can produce incoherent predictions, where hospital-level forecasts do not aggregate consistently to regional or national demand. We propose HierSTT, a hierarchical Transformer-based framework for coherent multi-level ED forecasting. HierSTT jointly predicts hospital, regional, and national level demand in a single end-to-end model. A Temporal Fusion Transformer captures national dynamics, while spatio-temporal Transformer encoder-decoder modules model regional and hospital demand conditioned on higher-level forecasts. A coherence-aware loss penalizes cross-level inconsistencies during training. We further introduce a nationwide Portuguese ED dataset covering 81 hospitals across 5 regional health administrations, with heterogeneous covariates at each level. Experiments show that HierSTT reduces average WAPE by 32% relative to the best non-hierarchical deep learning baseline and outperforms all classical hierarchical reconciliation methods, while producing near-coherent predictions across levels. Additional resources associated with this work are available at https://github.com/FilipaLino/HierSTT.

Accurate multi-week dengue forecasting supports timely vector-control interventions, outbreak preparedness, and healthcare resource allocation. However, newly established surveillance systems often lack the historical data needed to train reliable neural forecasting models. Although pretrained time-series models offer promising zero-shot forecasts, their cross-domain training may not capture local epidemiological dynamics. We propose TREA-Net, a Transferable Residual Epidemiological Adaptation Network for dengue forecasting under limited data. TREA-Net augments neural forecasting backbones with projections from an Environmental Time-Series Susceptible-Infected-Recovered model and learns a lightweight gated residual correction transferable from data-rich to data-scarce regions. Its node-invariant design accommodates surveillance systems with different numbers of locations, while target adaptation requires learning only two global parameters. We transfer knowledge from long-running dengue surveillance in Colombia and Nicaragua to 8-week-ahead forecasting in Mexico and Malaysia using only 78 or 104 weeks of target data. Across five neural backbones and ten transfer settings, TREA-Net improves the corresponding backbone in 9 out of 10 settings, with statistically significant gains. When integrated with TiRex, a foundation model for forecasting, it achieves the lowest mean absolute error across all target datasets. Conformal prediction further maintains empirical coverage while reducing 8-week prediction-interval width by 29.6% in Mexico. These results demonstrate TREA-Net's potential as a lightweight and portable early-warning framework for health agencies with limited surveillance data.

Regional surveillance data reflect local transmission, reporting, seeding, and external infection pressure, which are difficult to identify separately. We introduce GeoID-PINN, a physics-informed neural network (PINN) for susceptible-infectious-recovered-deceased (SIRD) dynamics. The model represents spatial dependence with a row-stochastic source-composition matrix whose rows assign nonnegative source weights that sum to one. We regularize this matrix toward a spatial prior constructed from distance, adjacency, commuting, or lead-lag information. In a four-region simulation with known truth, a compatible distance prior gives source-composition error 0.099. The error rises to 0.159 without regularization and 0.577 under a strongly misspecified prior, while trajectory fit and transmission-scale estimates remain similar. Accurate trajectories therefore do not guarantee recovery of the regional dependence structure. We also evaluate GeoID-PINN retrospectively using COVID-19 data from 64 Louisiana counties. Relative to an autoregressive negative-binomial baseline, Forecast-Trained Geo-PINN reduces mean squared error (MSE) from 32,957 to 11,468 and mean absolute error (MAE) from 70.60 to 57.73. The baseline has lower negative log likelihood (NLL), 5.158 versus 5.346, indicating better distributional fit but worse point accuracy. In a controlled 15-county comparison, county adjacency reduces MSE by 6.85 percent and MAE by 3.1 percent. Similar performance across plausible priors supports structured regularization but not unique edge recovery. These results require prior-sensitivity and observation-model checks before interpretation.

Generation of clear and accessible public health narratives is critical for communicating complex epidemiological projections to policymakers and the general public at large. Such narratives require more than simply reporting numbers: projections must be contextualized and quantitatively grounded across multiple dimensions. Further, projections are often derived from large ensemble datasets which combine intervention assumptions, geographic and demographic strata, outcomes, time horizons, and uncertainty quantiles. However, directly using large language models (LLMs) to summarize and contextualize such data often leads to inconsistencies, omissions, and fragile behavior. We introduce an agentic framework (EpiNarrate) for public health report generation that separates structured numerical reasoning from natural-language generation. The framework first extracts scenario axes and organizes them into a partial-order schema, enabling systematic traversal of the underlying multidimensional space. It then constructs an augmented dataset and derives valid quantitative statements through a comparison grammar that enforces semantic and arithmetic consistency. To balance coverage and non-redundancy, we introduce an interestingness-driven selection mechanism based on maximum-entropy principles. Experiments on the COVID-19 Scenario Modeling Hub demonstrate that our model produces narratives with improved factual grounding and broader coverage of salient epidemiological patterns, while preserving the style of expert-written reports.

Abductive reasoning operates in two directions. The synthetic mode builds explanations from available hypotheses; the analytic mode, conversely, identifies the latent factors whose interaction accounts for a complex observed state. This paper develops the analytic mode as a non-greedy, risk-sensitive discipline of commitment, in which candidate factors coexist and interact, resolving into committed conclusions only when explicit governance conditions are met. The formal core is the $κ$-$τ$ apparatus: $κ$ encodes the epistemic interaction among hypotheses, and $τ$ sets a commitment threshold calibrated to the decision's stakes. The central contribution is the causal cluster, a structured object recording which latent factors participate in a decomposition, with what weights and interaction structure, together with a two-level architecture (intra-cluster $κ^*$, inter-cluster $κ^{**}$) that guards against causal misattribution. Demonstrated in epidemiological crisis decomposition and adversarial cyber threat analysis, the framework's contribution to human-AI reasoning is the legibility of suspended decomposition as a shared coordination object, providing structural resistance to premature convergence. In practice, the decision-maker is handed not a single imposed answer but the competing explanatory scenarios, weighted by plausibility and paired with the evidence that would resolve between them, so that sound action is possible even before the ambiguity is resolved.

Numerical integration is a cornerstone of various scientific computing applications, such as engineering simulations and model evidence computations in probabilistic machine learning. Bayesian Quadrature uses Gaussian process surrogates that explicitly encode structural assumptions about the integrand to obtain integral estimates with quantified uncertainty. These surrogates are predominantly based on stationary covariance functions, which results in model misspecification for integrands exhibiting nonstationary behavior. We tackle this issue through an adaptively growing, tree-based partition of the integration domain into local stationary models. Our method recombines the local integral estimates through a hierarchy of GP conditioning that reintroduces cross-subdomain correlations, while model selection criteria control the tree growth to avoid unnecessary partitioning. The resulting algorithm is simple, requires no MCMC, and adapts its evaluation budget to local integrand complexity. On benchmark integration problems and a model evidence computation for an epidemiological model, Hierarchical Bayesian Quadrature achieves substantial gains over standard Bayesian Quadrature on nonstationary integrands while matching its performance on stationary ones.

Agent-based modeling (ABM) has the capability to model millions of individuals and their interactions, which is useful for policy making. However, ABMs have traditionally relied on static prior, which prevents the models from adapting to real-time changes. Our research provides a novel approach to addressing this information gap. Large language models (LLMs) offer new opportunities to predict human decision-making. Here, we introduce a scalable Hybrid Agent-based and Language-driven Epidemic (HALE) modeling framework that leverages LLMs to predict human decision-making in an ABM simulation. As a proof-of-concept, we use HALE to simulate COVID-19 and its effects in Salt Lake County, UT.

Reconstructing who infected whom often relies on case timing and published transmission links. However, two important questions remain: can a temporal pattern learned from other diseases transfer to a new outbreak, and how reliable are the transmission links used as ground truth? We learned a temporal prior from eleven disease groups using logistic regression. The model was locked before any target-outbreak data were accessed and was then tested without refitting on 29 Andes virus (ANDV) parent-ranking tasks. The locked prior achieved a mean reciprocal rank (MRR) of 0.571, compared with 0.274 for the strongest fair source-trained temporal baseline (permutation p<0.001). Its Top-1 accuracy was 37.9%, compared with 13.8%. The MRR advantage remained significant unless 7-8 favorable task outcomes were reversed. We separately examined the reliability of published transmission links. Among 75 epidemiologically linked inter-host pairs from the 2022 New York City mpox outbreak, 54.67% were genomically unresolved or unsupported as direct transmission links (exact 95% CI: 42.75-66.21%). We also tested whether retaining uncertain transmission edges changed source prioritization. In ANDV and Guangdong Delta outbreak graphs, the top-5 priority sets changed, with Jaccard similarity ranging from 0.429 to 0.667. These results show that temporal information learned across diseases can provide a useful ranking signal without target-specific refitting. They also show that uncertainty in published transmission links can affect which source cases are prioritized for investigation.

Characterizing the scenario underlying an epidemic from its disease cascade is an important task in simulation analytics. We propose boundary degree, the count of an infected node's contacts in the underlying contact network that were not infected, as a per-node cascade feature for this task. Through systematic ablation on realistic social contact networks of Tennessee and Virginia, we show that boundary degree alone improves scenario identification accuracy by 19%. Edge features, whose importance was observed empirically by prior work, consistently improve accuracy across all settings; we provide theoretical grounding for this observation. These effects are complementary. We prove that certain epidemic scenarios are indistinguishable without boundary or edge information. Prior feature engineering approaches included aggregate boundary statistics, but these were not among the top-ranked feature groups; the per-node representation we propose reveals their importance clearly. Our results suggest that contact tracing applications should track contacts with non-infected individuals, not only transmissions.

Metric aggregation divergence (MAD) is the silent inconsistency that arises when distinct pipeline stages in an agent-based model coupled with a multi-objective evolutionary algorithm (ABM+MOEA) independently re-implement how an outcome metric is extracted from simulation trajectories. Unlike deliberate analytical choices, MAD operates at the level of pipeline architecture: each stage is internally coherent, and the inconsistency becomes visible only when cross-stage outputs are compared. Code inspection of EpidemiOptim, a JAIR-published epidemic policy toolbox, reveals three structurally independent aggregation paths in peer-reviewed code. A faithful replication of this structure produces champion disagreement in 64.2% of independent runs (n=500, 95% CI: [59.9%, 68.3%]). In a 300-seed policy-flip experiment, divergent aggregation causes the optimizer to recommend the wrong champion in 83% of replications, with a mean welfare gap of 2.19 units and a Gini inequality gap of 0.050 units. In a follow-up inference audit, 3 of 249 flipped seeds cross the significance boundary itself. A complementary enterprise follow-up produces the predicted null under near-commensurable rankings (rho = 0.991), while a public upstream rerun of the Lake Problem DPS workflow shows that the archived published-path recommendation reaches joint-threshold success 0.401 whereas a shared contract-path rule reaches 0.552. We introduce the metric contract - a single shared callable enforced at dispatch time across all pipeline stages - as the remedy. Framed as standard engineering discipline applied to the cross-stage metric interface, the contract eliminates divergence by construction with approximately 3% runtime overhead.

Mechanistic epidemiological models are widely used to support infectious disease forecasting and public-health decision making. Bayesian calibration of such models is commonly performed using Markov chain Monte Carlo (MCMC), which can become computationally expensive for high-dimensional nonlinear systems and repeated near-real-time analyses. Here, we investigate simulation-based inference (SBI) using neural posterior estimation as a scalable alternative for Bayesian calibration of a mechanistic SECIR epidemiological model using COVID-19 intensive care unit (ICU) occupancy data from Germany during 2020. We compared SBI and MCMC across multiple epidemic phases using both 31-day inference windows and a substantially more challenging 201-day reconstruction problem involving multiple transmission change points. Posterior agreement was evaluated quantitatively using Wasserstein distances and Kullback-Leibler divergences together with posterior predictive checks. Across the 31-day windows, SBI recovered posterior distributions in strong agreement with MCMC while accurately reproducing observed ICU trajectories. In the 201-day setting, SBI preserved the dominant posterior structure despite increased uncertainty. SBI, by combining CPU and GPU resources, substantially reduced computational runtime compared with MCMC, which was restricted to running on CPUs. Whereas MCMC required approximately 1000 seconds for the 31-day inference problems, SBI achieved comparable posterior and predictive performance in approximately 60-70 seconds on a single GPU. For the 201-day inference problem, SBI required an average of 157 seconds, while the MCMC runs took over 19,000 seconds. Our results demonstrate that SBI provides a rapid and computationally efficient framework for Bayesian calibration of mechanistic epidemiological models, supporting repeated near-real-time inference and rapid outbreak analysis.

Epidemic forecasting models typically rely on surveillance data reported over administrative regions, treating them as atomic units, thereby obscuring sub-regional spatial structure that shapes disease dynamics. We introduce a spatially structured multimodal epidemic forecasting setting that integrates region-level temporal surveillance data with spatially localized auxiliary signals that are misaligned in resolution and structure, reflecting realistic public health reporting constraints. Building on this formulation, we propose M-SPICE (Multimodal SPatIal Context for Epidemic Forecasting), a structure-aware spatiotemporal forecasting framework that performs joint reasoning over temporal disease dynamics and spatial context via attention-based multimodal fusion, allowing spatial signals to selectively condition temporal representations across forecast horizons. We evaluate our approach on real-world COVID-19, influenza, and influenza-like illness (ILI) forecasting tasks under realistic real-time evaluation protocols. Across all forecasting settings, our method consistently outperforms state-of-the-art multivariate time-series, multimodal, and epidemiological forecasting baselines while maintaining strong probabilistic forecasting performance. Finally, interpretability analyses reveal when, where, and how spatial signals are leveraged, highlighting settings in which purely temporal, region-aggregated models are most likely to fail.

Epidemiological models often rely on survey data to represent how individuals make health-related decisions, such as whether to vaccinate or adopt protective behaviors. However, repeated large-scale surveys are costly, time-consuming, and limited in the range of scenarios they can capture. In this work, we investigate whether large language models (LLMs) can generate synthetic survey responses that reproduce patterns observed in real populations. Using longitudinal data from the FluPaths surveys, we first identify groups associated with broadly positive or negative attitudes toward vaccination through clustering analysis. We then evaluate several LLMs using a cluster-informed prompting approach to generate synthetic survey responses across multiple epidemic waves. Across models, the synthetic data generally reproduce the distributions of demographic characteristics, vaccination-related beliefs, risk perceptions, and health behaviors observed in the survey data. However, they are less successful at capturing how these factors vary together within respondents. Some models reproduce group-level vaccination trends more reliably than others, although performance varies across waves. We also trained a classifier to distinguish real from synthetic records and found that the generated responses remained identifiable as synthetic. Overall, our findings suggest that LLM-generated survey data may provide a useful tool for exploratory data augmentation and we hope that it could support agent-based epidemic modeling approaches. However, the generated data should not be treated as a substitute for human survey data without further methodological improvements and validation.

Seasonal influenza infects millions of people and causes substantial morbidity and mortality in the United States each year, making accurate short-term forecasting a core public-health need. Reliable forecasts of epidemic time series can inform vaccination timing, hospital staffing, and resource allocation, yet the comparative behavior of modern forecasting architectures on infectious-disease surveillance data remains insufficiently characterized. We address this gap through a systematic evaluation of regional influenza forecasting using influenza-like illness surveillance and influenza-associated hospitalization time series under both temporal and spatial generalization settings for 1-4-week-ahead prediction. We compare classical neural network architectures, numerical transformer-based models, pretrained time series foundation models, and LLM-based forecasting approaches. Across tasks, we demonstrate that a mixture-of-experts model that fuses multiple pretrained forecasters achieves the strongest overall performance, indicating that heterogeneous pretrained representations provide complementary predictive information. Our results further show that numerical transformer-based models produce reliable forecasts, while pretraining provides the largest gains at longer horizons, particularly when the pretraining domain is mechanistically aligned with influenza dynamics. In contrast, LLM-based time series methods underperform relative to numerical forecasters in this setting. Finally, we examine hospitalization information as both an auxiliary covariate and a pretraining source. Hospitalization signals provide complementary improvements in selected settings and clarify when additional surveillance streams enhance the robustness of multi-horizon forecasting. These findings provide actionable guidance on model selection, pretraining strategy, and auxiliary-signal use for influenza preparedness.

Wastewater influenza surveillance can reveal community circulation before clinical reporting, but wastewater alone is not a fully identifiable proxy for human burden. Existing wastewater models assume a fixed evidence set, while generic evidence-acquisition methods treat official surveillance streams as interchangeable costly features. We cast wastewater-first influenza monitoring as a selective decision problem: starting from mandatory wastewater evidence, the system must decide whether wastewater is sufficient, which delayed official stream to query next, and when abstention is the only scientifically defensible action under source ambiguity. We propose Bayesian Selective Latent Inference (BSLI), a principled Bayesian method that maintains a posterior over latent burden and identifiability, certifies answerability through explicit scientific gates, and optimizes query-stop decisions with an exact cost-calibrated Bellman policy. We prove the key variational, answerability, Bellman-optimality, and one-dimensional cost-calibration properties. On a fixed public-data benchmark with 5,933 forecasting episodes and 3,102 source-ambiguity episodes, BSLI improves the matched-budget cost-performance frontier while preserving conservative abstention under source ambiguity.

Many important outcomes unfold as dynamic cascades, including product adoption, disease spread, financial distress, and information diffusion. A central challenge is to recover the hidden influence network behind these cascades. Existing methods typically assume a specific diffusion model, and their performance degrades substantially when that assumption is misspecified. We propose CascadeNet, a Jacobian-based machine learning framework for network recovery that does not require specifying a diffusion mechanism. The key idea is that the underlying influence structure can be characterized by the Jacobian of the one-step transition function. CascadeNet first constructs a flexible estimator of the transition function, and further applies Neyman-orthogonal debiasing via the Riesz representer, so that the debiased Jacobian is $\sqrt{n}$-consistent and asymptotically normal, enabling formal inference on the network structure. We validate CascadeNet in both a simulation exercise and a real-world empirical application. In simulations, where the data-generating process is known, CascadeNet achieves the highest network recovery accuracy across nine common data-generating processes. In an empirical application to COVID-19 transmission across Spain's 52 provinces, CascadeNet recovers transmission networks that are significantly correlated with the true inter-province mobility network, whereas networks recovered by baseline methods show no significant alignment with the ground truth.

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.

Deep learning has enabled significant advances in time-series causal inference, yet progress remains constrained by the lack of realistic benchmarks with observable counterfactual outcomes. Existing datasets either rely on real-world observations without ground-truth counterfactuals or on simplified simulations that fail to capture complex causal dynamics. To address this gap, we develop a large-scale benchmark for counterfactual prediction in epidemic time series under dynamic interventions. Unlike existing benchmarks, it supports static and time-varying treatments, as well as both single-policy and multi-policy intervention settings, enabling evaluation of causal inference methods across a broad range of causal inference scenarios. Leveraging a calibrated agent-based model grounded in real-world demographic, mobility, epidemiological, and policy data, we generate realistic counterfactual trajectories across more than 150 U.S. counties. Using this benchmark, we evaluate widely used and state-of-the-art causal inference methods, revealing substantial performance differences and highlighting the challenges of realistic time-series causal reasoning.

Epidemic LLM forecasters are usually trained and evaluated as static supervised models, whereas operational pandemic forecasting is a streaming process in which labels arrive after predictions and disease regimes shift over time. We study this mismatch in weekly COVID-19 hospitalization trend forecasting across five variant regimes. We introduce EpiEvolve, a self-evolving agent that wraps an LLM forecaster trained on the warm-start period and keeps its weights fixed during streaming. EpiEvolve adapts by storing forecast outcomes in a hierarchical episodic memory, reflecting on delayed labels, retrieving cases relevant to the current regime, and distilling recurring errors into strategic rules. The resulting context lets the forecaster reuse its own past predictions and outcomes in later weeks while following a chronological protocol that prevents future leakage. On the streaming dataset, EpiEvolve reaches $0.629$ average accuracy, compared with $0.561$ for the static backbone and $0.325$ for the external CDC ensemble, and reduces recovery lag after regime shifts from $5$ to $2$ weeks. Ablations show that reflection, strategic memory, and regime-aware retrieval each contribute to the gains.

Purpose The WHO's COVID-19 non-pharmaceutical interventions (e.g., lockdowns, vaccinations) effectively curb transmission but impose heavy economic strains. Existing research often neglects individual behaviors and falsely assumes perfect infection tracking and flawless policy execution, failing to account for real-world uncertainties and errors. Methods We propose an integrative approach incorporating uncertainties in both epidemic measurement (infections/hospitalizations) and policy implementation. We built a simulation model of 1,000 individuals making real-time choices regarding mask-wearing, vaccination, and shopping. Concurrently, policymakers deploy interventions (lockdowns, mandates) based on health and economic observations. This framework is driven by hierarchical reinforcement learning agents, utilizing deep Q-networks alongside uncertainty-aware policy gradient variants (DDPG and TD3). Results The simulations effectively managed the epidemic's progression. Masking and vaccinations proved highly effective, significantly reducing both the outbreak's peak height and duration. By integrating individual behaviors, policy uncertainties, and multifaceted interventions, our dynamic control approach successfully mitigated the epidemic's impact. Conclusions Our model overcomes previous research limitations by embedding uncertainty and human behavior into public health policy frameworks. The simulation demonstrates that accounting for individual choices and imperfect data is crucial for designing effective interventions during complex pandemics, with masks and vaccines serving as pivotal tools.

We investigate whether large language models produce different medical triage recommendations for identical neurological symptoms when only the patient's stated gender and age vary. Using three model families--Gemini 3.5 Flash, Claude Sonnet 4.6, and GPT-5.4-mini--we present a standardized symptom profile (persistent headache, blurred vision, morning nausea, visual disturbances) across seven demographic conditions: three age groups (25, 38, 65) x two genders (male, female), plus a gender-unspecified baseline (n = 30 per condition per model, 630 total trials). We find a stark, systemic gender-dependent triage disparity: young women receive significantly lower emergency room (ER) referral rates than age-matched men (Gemini: 0% vs. 23.3%; Claude: 6.7% vs. 96.7%; GPT: 6.7% vs. 66.7%, all p < 0.001). The disparity disappears at age 65 for all models. The primary mechanism is diagnostic substitution: the models anchor on a gender-associated diagnosis, preferentially classifying young women with Idiopathic Intracranial Hypertension (IIH)--a condition epidemiologically linked to women of childbearing age--while diagnosing men with generic increased intracranial pressure with space-occupying lesions in the differential. This diagnostic closure routes female patients to lower-urgency care (outpatient doctor appointments) despite comparable severity ratings (7-9/10). Our findings demonstrate that clinical LLMs replicate documented human clinical biases by using epidemiological priors to suppress triage urgency, suggesting that AI triage engines must decouple urgency assessment from probabilistic diagnostic priors. We release all code, prompts, and raw results.

Human behaviour during epidemics affects infectious disease dynamics, but quantifying this remains deeply challenging. Here we introduce the Epi-LLM framework: a novel integration of agent-based modelling, real-life epigames, and large language models (LLMs) in which a synthetic society of agents reasons and adapts dynamically over an outbreak contact network. Comparing synthetic agent behaviour against a no-intervention SEIR baseline and human participant data from the AUIB epigame study, we find that LLM agents across four different architectures reduced peak active infections, with quarantine compliance peaking at 58-65% on day six of the 15-day simulation. A binomial generalised linear model showed that perceived health severity was the strongest predictor of quarantine behaviour ($β= 0.33, p = 0.002$), yielding a pseudo-$R^2$ of 0.055, comparable to the 0.072 observed in the human trial. LLM architecture is a key determinant of epidemic dynamics: low-variance architectures offer greater internal validity for testing behavioural rules, while high-variance models may better represent real-world decision-making. Geographic labels alone do not induce culturally differentiated behaviour; explicit attitudinal parameterisation is required. This proof-of-principle work lays the groundwork for deploying the Epi-LLM framework as a scalable, risk-free simulation environment for pandemic preparedness research.

Spatio-temporal graph-based models have typically been used to forecast new cases of infectious diseases such as COVID-19 and chickenpox outbreaks. However, the use of stochastic modelling into their learning process has been surprisingly under-investigated and rarely considered entire data sets of large countries. As a result, it is unknown whether these models would provide accurate forecasts in real-world disease spread scenarios. In this work, we propose a spatio-temporal stochastic graph-based architecture that integrates a stochastic formulation and uncertainty approximation process to forecast new infectious disease cases. We find that our approach can adapt to encode large and small population geographical networks within a single model architecture. Using two real-world data sets, COVID-19 in the US and chickenpox in Hungary, we report an enhanced effect of the proposed architecture across predictions of the 2022 first wave for COVID-19 in the US and comparative results of chickenpox waves during 2012-2014 in Hungary. By benchmarking with four spatio-temporal graph-based models, quantitative results show competitive overall weekly performance of the proposed approach on forecasting new cases for all 3,218 US counties and all 20 Hungary counties. The proposed approach can represent overall epidemic progression relative to baselines, though with a one-step delay; while exhibiting a reduced sensitivity to high-frequency and low-amplitude variability.

Disease forecasting models typically rely on a single data stream, making models brittle when histories are short or noisy. Recent top-performing models have shown that synthesizing multiple reporting systems for the same disease improves performance. Other recent work takes this idea a step further, using transfer learning to train a forecasting model for one disease using data from a different disease. We expand upon each of these approaches greatly, training machine learning models on data that span 66 infectious diseases and several data streams. We investigate the value of incorporating different data streams for forecasting 20 different disease data streams. We find that incorporating other data streams improves forecasting in the vast majority (84.9%) of time series and model structures considered. However, our work highlights that the quality of the added data matters, where adding data extremely different from the target data stream can sometimes degrade forecast performance. A major contribution of this work is in compiling a publicly-available database of data for use by the infectious disease forecasting community.

Chart-to-data extraction with vision-language models (VLMs) is increasingly evaluated on benchmarks that show diminishing headroom (frontier VLMs exceed 89% on ChartQA) and with metrics that treat extracted points as unordered key-value pairs, ignoring the temporal structure of time series and penalizing small alignment shifts as catastrophic failures. We address both gaps with EpiCurveBench, a benchmark of 1,000 real-world epidemic curve images curated from diverse public-health sources, and EpiCurveSimilarity (ECS), an evaluation metric that aligns predicted and ground-truth series via dynamic programming, tolerating local temporal shifts and gaps while penalizing them proportionally. Evaluating six methods--three frontier closed VLMs, one open VLM, and two specialized chart-extraction systems--we find the strongest model reaches only 52.3% ECS, and that ECS spreads the four general-purpose VLMs over a 25-point range where key-value metrics (RMS, SCRM) compress them into a 5-point band. We further validate ECS against four downstream epidemiological summary statistics, finding that higher ECS predicts smaller errors in total counts, peak timing, and peak magnitude, and higher growth-rate fidelity; across all four, ECS correlates 1.5--3.6 times more strongly than Dynamic Time Warping, which lacks a gap penalty and therefore cannot distinguish a truncated prediction from a temporally faithful one. EpiCurveBench targets a high-impact public-health application--unlocking decades of outbreak data trapped in published figures--but the benchmark and metric apply directly to any structured time-series chart-extraction setting.

Decentralized learning enhances privacy, scalability, and fault tolerance by distributing data and computation across nodes. A popular approach is Federated learning, which relies on a central aggregator, yet faces challenges such as server vulnerabilities, scalability issues, privacy risks and most importantly, the single point of failure. Alternatively Gossip Learning and Epidemic Learning offer fully decentralization through peer-to-peer exchanges of model updates, ensuring robustness and privacy, at the price of slower model convergence. In this work, we introduce a novel decentralized learning framework called HEAL. HEAL is the first cross-layer decentralized learning framework that exploits an optimized self-organizing and self-healing underlying P2P overlay combining the strengths of Federated Learning, Gossip and Epidemic Learning. Leveraging the recently proposed Elevator algorithm, HEAL promotes dynamically chosen nodes to act as aggregators. Through simulations, we demonstrate that HEAL has similar performances to that of Federated Learning in crash-free settings, while being fully decentralized and fault-tolerant. In crash and churn prone environments HEAL outperforms Gossip and Epidemic Learning.

Epidemic forecasting faces a fundamental challenge: human behavior dynamically responds to disease spread, creating feedback loops that induce distribution shifts at policy intervention points. This renders data-driven models unreliable under distribution shift. We propose \textbf{SL-BiLEM} (Structured Learnable Behavior-in-the-Loop Epidemic Model), leveraging physical constraints as regularization for robust extrapolation. The framework decomposes effective transmission as $β_{\text{eff}}(t,g) = β_0(g) \times m_{\text{policy}}(t) \times m_{\text{media}}(t) \times m_{\text{comp}}(t,g)$, where monotonicity, smoothness, and bounded-jump constraints on the learned compliance function maintain predictive validity under novel policy regimes. Beyond forecasting, SL-BiLEM enables counterfactual analysis for intervention decision support. We validate forecasting on three real-world datasets (cruise ship, school influenza, and school-district COVID-19 surveillance) and evaluate counterfactual recovery on synthetic benchmarks with known ground truth. SL-BiLEM demonstrates: (1) 76% improvement over neural-mechanistic baselines, with only 53% OOD degradation versus 1142% for neural baselines under policy-induced shift; (2) 100% bootstrap CI coverage across 27 synthetic counterfactual experiments; and (3) Treatment Effect Accuracy exceeding 0.85. These results establish SL-BiLEM as an interpretable tool for public health decision-makers seeking accurate prediction and principled intervention planning.

We document inverse scaling in LLMs on forecasting problems whose underlying time series exhibit superlinear growth and tail risk of regime change, a structure common in finance and epidemiology. On these tasks, more capable models produce worse distributional forecasts. The pattern appears on ForecastBench-Sim (FBSim), a contamination-free, simulated-world benchmark we release, in forecasting synthetic SIR epidemics with a matched linear control, and replicates in real-world datasets on COVID-19, measles, housing markets, and hyperinflation. A per-quantile decomposition shows the failure concentrates at the upper tail, which more capable models shift upward to track aggressive extrapolations of growth, while the lower tail stays put. A within-family study of Llama-3.1 shows that both model scale and post-training independently contribute to this effect. Domain knowledge does not reliably rescue calibration. This inverse scaling does not appear on single-threshold metrics common in LLM forecasting benchmarks, reversing the sign of the capability--accuracy relationship on identical outputs. Single-threshold scoring at conventional cutoffs misses the upper-tail cost; tail-inclusive scoring reverses the sign of the capability--accuracy relationship on the same outputs. We recommend that LLM forecasting evaluations use continuous (and unbounded) measures of accuracy alongside bounded binary threshold metrics.

Probabilistic forecasting of infectious diseases is crucial for public health but relies on labor-intensive manual model curation by expert modeling teams. This bespoke development bottlenecks scalability to granular geographic resolutions or emerging pathogens. Here, we present an autonomous system using Large Language Model (LLM)-guided tree search to iteratively generate, evaluate, and optimize executable forecasting software. In a fully prospective, real-time evaluation during the 2025-2026 US respiratory season, the system autonomously discovered methodologically diverse models for influenza, COVID-19, and respiratory syncytial virus (RSV). Aggregating these machine-generated models yielded an ensemble that consistently matched or outperformed the gold-standard, human-curated Centers for Disease Control and Prevention (CDC) hub ensembles out-of-sample. The system successfully navigated data-scarce "cold start" scenarios for RSV. Moreover, controlled retrospective ablations revealed that optimizing log-scale distance metrics prevents reward hacking, while an automated judge-in-the-loop ensures structural fidelity to complex scientific theories. By autonomously translating epidemiological theory into accurate, transparent code, this framework overcomes the modeling labor bottleneck, enabling rapid deployment of expert-level disease forecasting at unprecedented scales.

The increasing adoption of data-driven decision-making in public health has established epidemic forecasting as a critical area of research. Recent advances in multivariate forecasting models better capture complex temporal dependencies than conventional univariate approaches, which model individual series independently. Despite this potential, the development of robust epidemic forecasting methods is constrained by the lack of high-quality benchmarks comprising diverse multivariate datasets across infectious diseases and geographical regions. To address this gap, we present EpiCastBench, a large-scale benchmarking framework featuring 40 curated (correlated) multivariate epidemic datasets. These publicly available datasets span a wide range of infectious diseases and exhibit diverse characteristics in terms of temporal granularity, series length, and sparsity. We analyze these datasets to identify their global features and structural patterns. To ensure reproducibility and fair comparison, we establish standardized evaluation settings, including a unified forecasting horizon, consistent preprocessing pipelines, diverse performance metrics, and statistical significance testing. By leveraging this framework, we conduct a comprehensive evaluation of 15 multivariate forecasting models spanning statistical baselines to state-of-the-art deep learning and foundation models. All datasets and code are publicly available on Kaggle (https://www.kaggle.com/datasets/aimltsf/epicastbench) and GitHub (https://github.com/aimltsf/EpiCastBench).

Accurate spatiotemporal pattern analysis is critical in fields such as urban traffic, meteorology, and public health monitoring. However, existing methods face performance bottlenecks, typically yielding only incremental gains and often exhibiting limited cross-domain transferability. We analyze this bottleneck through spatial and temporal entropy measures, which are used as diagnostic indicators of spatiotemporal complexity mismatch rather than as guarantees that entropy alignment alone yields better forecasting. Empirically, larger mismatch is often accompanied by higher prediction uncertainty, especially under a fixed model-capacity budget. Guided by this diagnostic, we propose a scalable, adaptive framework that harmonizes spatial and temporal feature representations. Spatial dimensionality is compressed via low-rank matrix embedding to preserve essential structure, while an extended temporal horizon captures long-range dependencies and mitigates cumulative errors arising from temporal heterogeneity. Extensive experiments on urban traffic, meteorological, and epidemic datasets demonstrate substantial accuracy gains and broad applicability across the evaluated domains, suggesting that the framework is promising for a wide range of spatiotemporal tasks beyond the current study. The code is available on GitHub at https://github.com/ST-Balance/ST-Balance.

Accurate epidemic forecasting is crucial for public health response, resource allocation, and outbreak intervention, but remains difficult with sparse, noisy, and highly non-stationary data. Because epidemics unfold across interacting regions, spatiotemporal methods are natural candidates for improving forecasts. Despite growing interest in spatial information, no standardized benchmark exists, and current evaluations often use simple chronological train-test splits that do not reflect real-time forecasting practice. We address this gap with SpatialEpiBench, a challenging benchmark for spatiotemporal epidemic forecasting in realistic public-health settings. SpatialEpiBench includes 11 epidemic datasets with standardized rolling evaluations and outbreak-specific metrics. We evaluate adjacency-informed forecasting models with widely used epidemic priors that adapt general models to epidemiology, but find that most methods underperform a simple last-value baseline from 1 day to 1 month ahead, even during outbreaks and with these priors. We identify three major failure modes: (1) poor outbreak anticipation, (2) difficulty handling sparsity and noise, and (3) limited utility of common geographic adjacency for epidemiological spatial information. We release benchmark data, code, and instructions at https://github.com/Rachel-Lyu/SpatialEpiBench to support development of operationally useful epidemic forecasting models.

Agent-based model (ABM) are a kind of computer model that makes it possible to simulate a set of autonomous interacting programs called agents in a shared virtual environment. Among other application field, it has been commonly used to simulate social phenomena such as urban segregation, opinion dynamic or epidemiological crisis [1]. Recently, a research emphasis has been put on ABM to study in silico the impact of non-pharmaceutical interventions to mitigate the SARS-CoV-2 outbreak of 2020, with few of them that had a great impact on global political responses [2]. Among the model used COMOKIT [3] has been design to simulate the every-day-life of inhabitant of various cities in Vietnam and test policy interventions for various COVID-19 spread scenarios. Such endeavor required huge computational power to handle a huge number of simulation replication over a large set of parameters. In this proposal we present a python package that enables to easily generate, explore and build reports for any COMOKIT experiment to be launched over High-Performance Computing (HPC) infrastructure.

This paper presents a Koopman-based framework for early outbreak detection and intervention selection in a multi-agent epidemic simulation. Agents exhibit mobility patterns, heterogeneous susceptibility, immunity-dependent viral load progression, and local transmission through co-location. The goal of the simulation is to study near-critical epidemic regimes in which small changes in exposure or timing can alter the final outcome. Aggregate daily observables from early trajectory windows are encoded into a low-dimensional Koopman latent space whose approximately linear evolution supports short-horizon forecasting and outbreak risk estimation. These representations are combined with a random forest classifier trained to predict whether the final attack rate exceeds a major outbreak threshold. Experiments near the system tipping points show strong early warning performance, with Koopman-derived features contributing to class separation. Counterfactual analysis further shows that minimal interventions, such as keeping a single selected agent at home for one day, can reduce attack rates and, often, shift the trajectory below the outbreak threshold.

Forecasting infectious disease incidence can provide important information to guide public health planning, yet is difficult because epidemic dynamics are complex. Current mechanistic and statistical approaches often struggle to capture multimodal uncertainty or emergent trends. Influpaint adapts denoising diffusion probabilistic models to epidemic forecasting. By encoding influenza seasons as spatiotemporal images in which pixel intensity represents incidence, Influpaint learns a rich distribution of disease dynamics from a hybrid dataset of surveillance and simulated trajectories. Forecasting is formulated as a conditional generation (inpainting) task from partial observations. We show that Influpaint generates realistic, diverse epidemic trajectories and achieves forecast accuracy that is competitive with leading ensemble methods in retrospective evaluation. In real-time evaluation during the 2023--2025 U.S. CDC FluSight challenges, performance improved substantially across seasons, with highly accurate but somewhat overconfident projections in 2024--2025. The best performance was achieved with a training dataset containing 30% surveillance and 70% simulated trajectories. These results show that diffusion models can capture important spatiotemporal structure in influenza dynamics and provide a flexible framework for probabilistic infectious disease forecasting.

Epidemic forecasting has become an integral part of real-time infectious disease outbreak response. While collaborative ensembles composed of statistical and machine learning models have become the norm for real-time forecasting, standardized benchmark datasets for evaluating such methods are lacking. Further, there is limited understanding on performance of these methods for novel outbreaks with limited historical data. In this paper, we propose IDOBE, a curated collection of epidemiological time series focused on outbreak forecasting. IDOBE compiles from multiple data repositories spanning over a century of surveillance and across U.S. states and global locations. We perform derivative-based segmentation to generate over 10,000 outbreaks covering multiple outcomes such as cases and hospitalizations for 13 diseases. We consider a variety of information-theoretic and distributional measures to quantify the epidemiological diversity of the dataset. Finally, we perform multi-horizon short-term forecasting (1- to 4-week-ahead) through the progression of the outbreak using 11 baseline models and report on their performance. In addition to standard metrics such as NMSE and MAPE for point forecasts, we include probabilistic scoring rules such as Normalized Weighted Interval Score (NWIS) to quantify the performance. We find that MLP-based methods have the most robust performance, with statistical methods having a slight edge during the pre-peak phase. IDOBE dataset along with baselines are released publicly on https://github.com/NSSAC/IDOBE to enable standardized, reproducible benchmarking of outbreak forecasting methods.

Rabies remains a major public health concern across many African and Asian countries, where accurate diagnosis is critical for effective epidemiological surveillance. The gold standard diagnostic methods rely heavily on fluorescence microscopy, necessitating skilled laboratory personnel for the accurate interpretation of results. Such expertise is often scarce, particularly in regions with low annual sample volumes. This paper presents an automated, AI-driven diagnostic system designed to address these challenges. We developed a robust pipeline utilizing fluorescent image analysis through transfer learning with four deep learning architectures: EfficientNetB0, EfficientNetB2, VGG16, and Vision Transformer (ViTB16). Three distinct data augmentation strategies were evaluated to enhance model generalization on a dataset of 155 microscopic images (123 positive and 32 negative). Our results demonstrate that TrivialAugmentWide was the most effective augmentation technique, as it preserved critical fluorescent patterns while improving model robustness. The EfficientNetB0 model, utilizing Geometric & Color augmentation and selected through stratified 3fold cross-validation, achieved optimal classification performance on cropped images. Despite constraints posed by class imbalance and a limited dataset size, this work confirms the viability of deep learning for automating rabies diagnosis. The proposed method enables fast and reliable detection with significant potential for further optimization. An online tool was deployed to facilitate practical access, establishing a framework for future medical imaging applications. This research underscores the potential of optimized deep learning models to transform rabies diagnostics and improve public health outcomes.

Large language models are increasingly deployed to simulate patients for clinical training, research, and mental health tools, yet population-level validity remains largely untested. We introduce PsychBench, the first epidemiological audit of LLM patient simulation: 28,800 profiles from four frontier models (GPT-4o-mini, DeepSeek-V3, Gemini-3-Flash, GLM-4.7) evaluated against NHANES and NESARC-III baselines across 120 intersectional cohorts. The central finding is a coherence-fidelity dissociation: models produce clinically plausible individuals while misrepresenting the populations they are drawn from. Variance compression ranges from 14 percent (GLM-4.7) to 62 percent (DeepSeek-V3), eliminating the distributional tails of clinical reality. Despite test-retest correlations above r = 0.90, 36.66 percent of cases cross diagnostic thresholds between runs. Symptom correlation matrices diverge across demographic groups beyond split-half noise, with transgender populations diverging three to five times more than racial differences. Calibration bias is systematic and asymmetric. Models overestimate depression severity for most groups by 3.6 to 6.1 points (Cohen d = 1.13 to 1.91), consistent with training on clinical corpora with elevated base rates. For transgender women the direction inverts: models capture only 8 to 46 percent of documented minority stress elevation, yielding a -5.42 residual (d = -1.55). Models also attribute irritability to Black men and fatigue to women beyond matched controls, encoding racialized and gendered assumptions. Patterns replicate across US and Chinese architectures, indicating failures tied to current training paradigms rather than isolated implementations. For most users, LLM mental health tools risk pathologizing ordinary distress; for transgender users, algorithmic erasure of genuine need. The patients look right. They do not represent real populations.

Accurate and reliable forecasting of epidemic incidences is critical for public health preparedness, yet it remains a challenging task due to complex nonlinear temporal dependencies and heterogeneous spatial interactions. Often, point forecasts generated by spatiotemporal models are unreliable in assigning uncertainty to future epidemic events. Probabilistic forecasting of epidemics is therefore crucial for providing the best or worst-case scenarios rather than a simple, often inaccurate, point estimate. We present deep spatiotemporal engression methods to generate accurate and reliable probabilistic forecasts on low-frequency epidemic datasets. The proposed methods act as distributional lenses, and out-of-sample probabilistic forecasts are generated by sampling from the trained models. Our frameworks encapsulate lightweight deep generative architectures, wherein uncertainty is quantified endogenously, driven by a pre-additive noise component during model construction. We establish geometric ergodicity and asymptotic stationarity of the spatiotemporal engression processes under mild assumptions on the network weights and pre-additive noise process. Comprehensive evaluations across six epidemiological datasets over three forecast horizons demonstrate that the proposal consistently outperforms several temporal and spatiotemporal benchmarks in both point and probabilistic forecasting. Additionally, we explore the explainability of the proposal to enhance the models' practical application for informed, timely public health interventions.

Epidemiological forecasting from surveillance data is a hard problem and hybridizing mechanistic compartmental models with neural models is a natural direction. The mechanistic structure helps keep trajectories epidemiologically plausible, while neural components can capture non-stationary, data-adaptive effects. In practice, however, many seemingly straightforward couplings fail under partial observability and continually shifting transmission dynamics driven by behavior, waning immunity, seasonality, and interventions. We catalog these failure modes and show that robust performance requires making non-stationarity explicit: we extract and extrapolate multi-scale structure from the observed infection series and use it as an interpretable control signal for a controlled neural ODE coupled to an epidemiological model. Concretely, we decompose infections into trend, seasonal, and residual components and use these signals to drive continuous-time latent dynamics while jointly forecasting and inferring time-varying transmission, recovery, and immunity-loss rates. Across early outbreak and multi-wave regimes, our approach attains the lowest RMSE on all five datasets (27-70% reduction over the strongest baseline), achieves the best peak detection accuracy, and recovers time-varying epidemiological rates within ground-truth ranges, without relying on auxiliary covariates.

Reliable epidemiological reasoning requires synthesizing study evidence to infer disease burden, transmission dynamics, and intervention effects at the population level. Existing medical question answering benchmarks primarily emphasize clinical knowledge or patient-level reasoning, yet few systematically evaluate evidence-grounded epidemiological inference. We present EpiQAL, to our knowledge the first diagnostic benchmark for epidemiological question answering over research literature, comprising three subsets built from open-access articles across diverse diseases. The three subsets progressively test factual recall, multi-step inference, and conclusion reconstruction under incomplete information, and are constructed through a quality-controlled pipeline combining taxonomy guidance, multi-model verification, and difficulty screening. Experiments on fifteen models spanning open-source and proprietary systems reveal that current LLMs show limited performance on epidemiological reasoning, with multi-step inference posing the greatest challenge. Model rankings shift across subsets, and scale alone does not predict success. Chain-of-Thought prompting benefits multi-step inference but yields mixed results elsewhere. EpiQAL provides fine-grained diagnostic signals for evidence-grounding, inferential reasoning, and conclusion reconstruction.

With the growing use of large language models, concerns over content authenticity have spurred a variety of watermarking schemes. These schemes use secret keys to detect machine-generated text while remaining imperceptible to readers. Detection typically reduces to statistical hypothesis testing for the presence of watermarks, a topic that is now well studied. In contrast, the finer-grained task of localizing which segments of a text are watermarked is much less explored; existing approaches often lack scalability or guarantees robust to paraphrasing and post-editing. We bring a new perspective to this segmentation problem through the lens of epidemic change-points and, by exploiting this connection, propose WISER, a novel and computationally efficient watermark segmentation algorithm. We establish finite-sample error bounds and consistency for detecting multiple watermarked segments in a single text. Complementing these theoretical results, our extensive numerical experiments show that WISER outperforms state-of-the-art baseline methods, both in terms of computational speed as well as accuracy, on various benchmark datasets embedded with diverse watermarking schemes. Together, these theoretical and empirical results position WISER as an effective tool for watermark localization and illustrate how classical statistical ideas can yield theoretically valid and computationally efficient solutions to a modern problem of immediate importance.

Data fusion, the process of combining observational and experimental data, can enable the identification of causal effects that would otherwise remain non-identifiable. Although identification algorithms have been developed for specific scenarios, do-calculus remains the only general-purpose tool for causal data fusion, particularly when variables are present in some data sources but not others. However, approaches based on do-calculus may encounter computational challenges as the number of variables increases and the causal graph grows in complexity. Consequently, there exists a need to reduce the size of such models while preserving the essential features. For this purpose, we propose pruning (removing unnecessary variables) and clustering (combining variables) as preprocessing operations for causal data fusion. We generalize earlier results on a single data source and derive conditions for applying pruning and clustering in the case of multiple data sources. We give sufficient conditions for inferring the identifiability or non-identifiability of a causal effect in a larger graph based on a smaller graph and show how to obtain the corresponding identifying functional for identifiable causal effects. Examples from epidemiology and social science demonstrate the use of the results.

This paper presents a hybrid modeling approach that couples an Agent-Based Model (ABM) with a partial differential equation (PDE) model in an epidemic setting to simulate the spatial spread of infectious diseases using a compartmental structure with seven health states. The goal is to reduce the computational complexity of a full-ABM by introducing a coupled ABM-PDE model that offers significantly faster simulations while maintaining comparable accuracy. Our results demonstrate that the hybrid model not only reduces the overall simulation runtime (defined as the number of runs required for stable results multiplied by the duration of a single run) but also achieves smaller errors across both 25% and 100% population samples. The coupling mechanism ensures consistency at the model interface: agents crossing from the ABM into the PDE domain are removed and represented as density contributions, while surplus density in the PDE domain is used to generate agents with plausible trajectories derived from mobile phone data. We evaluate the hybrid model using real-world mobility and infection data for the Berlin-Brandenburg region in Germany, showing that it captures the core epidemiological dynamics while enabling efficient large-scale simulations. These results demonstrate that the proposed ABM-PDE framework provides a robust and computationally efficient alternative to full-scale agent-based simulations, making it suitable for realistic epidemic modeling and scenario analysis.