Unified Bayesian-AI framework improves epidemiological risk prediction and uncertainty quantification.
problem Lack of calibrated uncertainty in machine learning models for epidemiology.
method Combines Bayesian prediction with Bayesian hyperparameter optimization using logistic regression and Gaussian-process Bayesian optimization.
result Unified Bayesian-AI framework provides reliable coverage and improved calibration, enhancing epidemiological decision making.
ESOP uses Bayesian optimization to find optimal lock-down schedules.
problem Finding optimal lock-down schedules balancing health and economy.
method Bayesian optimization interacting with epidemiological models.
result ESOP schedules balance public health and economic impacts.
Efficiently calibrates epidemiological models using Bayesian optimization.
problem Calibration of complex epidemiological models is computationally expensive and challenging.
method Graybox Bayesian optimization scheme leveraging Gaussian processes and functional structure of compartmental models.
result Proposed methods achieve efficient calibration and improved performance compared to existing schemes.
Bayesian network modelling is a well adapted approach to study messy and highly correlated datasets which are very common in, e.g., systems epidemiology. A popular approach to learn a Bayesian network from an observational datasets is to identify the maximum a posteriori network in a search-and-score approach. Many sco…
A framework detects nonlinear and interaction effects in epidemiological data with uncertainty quantification.
problem Lack of reliable inference for ML-discovered nonlinearities and interactions in epidemiological data.
method Combines Bayesian sparse regression, tree ensembles, and Shapley values.
result Valid uncertainty quantification for feature effects at the individual level.
Bayesian calibration speeds up ABM for pandemic modeling.
problem Calibrating stochastic ABMs for accurate pandemic predictions is computationally intensive.
method Random forest surrogate modeling for accelerated ABM evaluation.
result Improved predictive performance with random forest calibration compared to previous methods.
A new method combines ANN and Laplace for fast Bayesian inference in ODE models.
problem Bayesian inference for ODE systems with non-analytical solutions is computationally expensive.
method Hybrid approach using ANN for tractable likelihood and Laplace approximation.
result Effective posterior inference with improved computational cost compared to traditional methods.
Cost-aware SBI reduces expensive simulations in complex models.
problem High computational cost in simulating complex models.
method Combination of rejection and self-normalised importance sampling.
result Significant reduction in overall cost of inference.
Simulation-based inference aids in predicting disease dynamics for health policy.
problem Predicting disease dynamics to inform public health interventions.
method Simulation-based inference using machine learning.
result Potential for efficient interpretable Bayesian inference in epidemiological models.
Method estimates parameters for disease spread models robustly.
problem Estimating parameters for disease spread models.
method Statistical Learning applied to Approximate Bayesian Computation.
result Qualitative properties of disease evolution can be assessed.
State-space models (SSMs) provide a flexible framework for modelling time-series data. Consequently, SSMs are ubiquitously applied in areas such as engineering, econometrics and epidemiology. In this paper we provide a fast approach for approximate Bayesian inference in SSMs using the tools of deep learning and variati…
EGDL predicts TB outbreaks with deep learning, integrating epidemiological models.
problem Predicting TB outbreaks with complex spatiotemporal dynamics.
method Modified MN-SIR model with Bayesian inference, deep neural networks.
result EGDL delivers robust and accurate TB outbreak predictions.
A framework for data-driven decision-making in infectious disease control.
problem Optimizing trade-offs between public health and economic impacts.
method Multi-objective model-based reinforcement learning.
result Pareto-optimal policies minimizing long-term costs.
The study examines methods to correct measurement error in nutritional epidemiology studies.
problem Measurement error in nutritional studies leads to biased and underconfident estimates.
method The article reviews various bias-correction models for exposure variables in nutritional epidemiology.
result Bias-correction methods are essential for accurate inference in nutritional studies.
SVI and GP surrogates improve calibration of ABMs in epidemiology.
problem Calibrating stochastic ABMs in epidemiology is computationally expensive.
method Stein Variational Inference (SVI) with Gaussian process (GP) surrogates.
result SVI maintains comparable predictive accuracy and calibration effectiveness to MCMC.
Machine learning aids epidemiologists in analyzing big data.
problem Handling large, complex data in epidemiology.
method Explains principles and methods of supervised and unsupervised learning.
result Develops strategies for model evaluation and hyperparameter optimization.
ARF synthesizes epidemiological data to match original findings.
problem Synthetic data quality and privacy in epidemiology.
method Adversarial Random Forests (ARF) for efficient data synthesis.
result ARF-generated synthetic data consistently matches original epidemiological findings.
Automates infectious disease policy-making via inference in epidemiological models.
problem Improving policy-making for infectious diseases during pandemics.
method Performing inference in existing epidemiological models using a probabilistic programming language.
result Automated inference leads to better disease progression outcomes and policy prescriptions.
Simformer uses transformer models to perform flexible Bayesian inference.
problem Current simulation-based inference methods are inflexible and require fixed priors.
method Trains a probabilistic diffusion model with transformer architectures.
result Outperforms state-of-the-art methods on various benchmarks.
TOO optimizes stochastic epidemiological models by finding both parameter settings and random seeds.
problem Calibrating stochastic epidemiological models to match empirical observations.
method Gaussian process surrogates and Thompson sampling for optimization.
result Produces actual trajectories consistent with ground truth.
BOED improves SBI by optimizing experimental designs and inference functions.
problem Efficiently use experimental resources for better inference on complex models.
method Link mutual information bounds between SBI and BOED, optimizing both design and inference.
result BOED improves inference in real-world simulators in epidemiology and biology.
Optimizes experimental designs for intractable models using mutual information bounds.
problem Finding optimal experimental designs for models with intractable data-generating distributions.
method Maximizes mutual information lower bounds parametrized by neural networks, updating network parameters and designs simultaneously.
result Framework enables experimental design for various tasks including parameter estimation and model discrimination.
Bayesian network (BN) modelling is extensively used in systems epidemiology. Usually it consists in selecting and reporting the best-fitting structure conditional to the data. A major practical concern is avoiding overfitting, on account of its extreme flexibility and its modelling richness. Many approaches have been p…
TMLE improves unbiased estimation in public health studies.
problem Improving unbiased estimation in observational studies.
method Targeted Maximum Likelihood Estimation (TMLE) integrates machine learning and statistical theory.
result TMLE has been adopted by researchers worldwide, especially outside the US.
A new method for experimental design focuses on predicting downstream quantities of interest.
problem Designs that maximize parameter learning may not maximize downstream quantity prediction.
method Likelihood-free goal-oriented optimal experimental design (LF-GO-OED) using ABC density ratio estimation.
result LF-GO-OED maximizes the expected information gain for downstream quantities.
Novel method for estimating SIRD model parameters and forecasting COVID-19 deaths in Poland.
problem Estimating epidemiological parameters for SARS-CoV-2 spread in Poland.
method Modified SIRD model, GPU architecture for computation.
result Effectiveness of short-term forecasts (up to 2 weeks) and stability of the method.
Epidemiological model updates infection rates in China, US, Italy.
problem Evaluate policy interventions for mitigating the 2019-nCov pandemic.
method Custom SITR model with variational data assimilation for real-time updates.
result Model robust to initial conditions, infers infection numbers and parameters.
Neural surrogate predicts SPN rates from token trajectories.
problem Challenging parameter estimation in SPNs with covariates.
method 1D Convolutional Residual Network trained on Gillespie-simulated SPN realizations.
result Surrogate predicts rate-function coefficients with RMSE = 0.043.
BayesMR estimates causal effects and directionality from genetic data.
problem Challenges in finding good genetic instruments and estimating causal effects.
method Bayesian Mendelian randomization approach that accounts for pleiotropy and reverse causation.
result BayesMR provides a posterior distribution over causal effects and uncertainty.
BayesFlow learns complex models using neural networks.
problem Estimating parameters in complex, non-likelihood models.
method Invertible neural networks for global Bayesian inference.
result Global probabilistic mapping from data to parameters.
Paper adapts Bayesian Hui-Walter method for unlabeled data.
problem Lack of labeled data in machine learning.
method Adapted Hui-Walter paradigm for online, unlabeled data.
result Estimates performance metrics without labeled data.
New method detects close contacts to prevent SARS-CoV-2 spread.
problem Detecting close contacts to prevent SARS-CoV-2 spread.
method Machine learning approach using BLE data.
result Reliable detection of close contacts reduces SARS-CoV-2 risk.
Framework extracts symptoms from EHRs for rapid disease outbreak detection.
problem Extracting relevant data from unstructured medical texts.
method Conformal active learning for efficient data mining.
result Framework achieves strong performance with minimal manual labeling.
Bayesian model tackles spatial count data issues with flexible non-parametric techniques.
problem Challenges in traditional parametric models for spatial count data with unbalanced distributions and complex dependencies.
method Bayesian semi-parametric spatial dispersed count model combining non-parametric techniques and adapted count models.
result Demonstrates superior performance in managing dispersion and capturing intricate spatial patterns.
Bayesian quadrature (BQ) is a sample-efficient probabilistic numerical method to solve integrals of expensive-to-evaluate black-box functions, yet so far,active BQ learning schemes focus merely on the integrand itself as information source, and do not allow for information transfer from cheaper, related functions. Here…
Study on financial impacts of zombie outbreak on economy.
problem Financial and economic consequences of a zombie epidemic.
method Epidemiological modeling and financial computation.
result GDP losses of 23.44% and financial market drop of 29.30% in a major industrialized nation.
Modeling infection hotspots to quantify effects of contact tracing and testing.
problem Capturing the role of infection hotspots in disease transmission.
method Temporal point process modeling framework to represent visits and disease transmission.
result Estimation of transmission rates at sites and households using Bayesian optimization.
In record linkage (RL), or exact file matching, the goal is to identify the links between entities with information on two or more files. RL is an important activity in areas including counting the population, enhancing survey frames and data, and conducting epidemiological and follow-up studies. RL is challenging when…
The process of contagiousness spread modelling is well-known in epidemiology. However, the application of spread modelling to banking market is quite recent. In this work, we present a system of ordinary differential equations, simulating data from the largest European banks. Then, an optimal control problem is formula…
New method corrects selection bias in complex models.
problem Selection bias in statistical studies leading to systematic distortions.
method Amortized Bayesian inference with neural posterior estimation.
result Recover well-calibrated posterior distributions across diverse selection mechanisms.
Bayesian inference in state-space models is challenging due to high-dimensional state trajectories. A viable approach is particle Markov chain Monte Carlo, combining MCMC and sequential Monte Carlo to form "exact approximations" to otherwise intractable MCMC methods. The performance of the approximation is limited to t…
Italy's daily COVID-19 cases stratified by age groups.
problem Analyzing the spread and impact of COVID-19 across different age groups.
method Stratified daily data of COVID-19 cases by age classes.
result Detailed insights into how age affects COVID-19 outcomes.
Increasingly complex generative models are being used across disciplines as they allow for realistic characterization of data, but a common difficulty with them is the prohibitively large computational cost to evaluate the likelihood function and thus to perform likelihood-based statistical inference. A likelihood-free…
Epidemiology simulations have become a fundamental tool in the fight against the epidemics of various infectious diseases like AIDS and malaria. However, the complicated and stochastic nature of these simulators can mean their output is difficult to interpret, which reduces their usefulness to policymakers. In this pap…
Model predicts US COVID-19 deaths with quantile estimates.
problem Predicting US COVID-19 deaths at county level.
method Hybrid machine learning and epidemiological approach, minimizing pinball loss.
result Quantile estimates accurately forecast deaths for different forecast periods.
Models for predicting the risk of cardiovascular events based on individual patient characteristics are important tools for managing patient care. Most current and commonly used risk prediction models have been built from carefully selected epidemiological cohorts. However, the homogeneity and limited size of such coho…
Model for valuing options on epidemic spread.
problem Valuation of options on epidemic spread during an outbreak.
method Stochastic differential SIR model for epidemic dynamics.
result Parsimonious model for option valuation on epidemic spread.
Parity calibration aims to predict increase-decrease events, not values.
problem Forecasting future increase-decrease events rather than exact values.
method Online binary calibration method to achieve parity calibration.
result Online binary calibration achieves parity calibration effectively.