# Neural Posterior Estimation for Stochastic Epidemic Models Using Final Outcome Data

arXiv: https://arxiv.org/abs/2606.02874 · HTML: https://mlsanity.com/paper/2606.02874/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 7 of its 29 references that are in the map.
- First posted on arXiv 1 Jun 2026.

## Builds on (most cited first, 7 of 7)

- [Neural Spline Flows](https://mlsanity.com/paper/1906.04032/) (2019)
- [The frontier of simulation-based inference](https://mlsanity.com/paper/1911.01429/) (2019)
- [Sequential Neural Likelihood: Fast Likelihood-free Inference with Autoregressive Flows](https://mlsanity.com/paper/1805.07226/) (2018)
- [Automatic Posterior Transformation for Likelihood-Free Inference](https://mlsanity.com/paper/1905.07488/) (2019)
- [Benchmarking Simulation-Based Inference](https://mlsanity.com/paper/2101.04653/) (2021)
- [Real-time gravitational-wave science with neural posterior estimation](https://mlsanity.com/paper/2106.12594/) (2021)
- [Neural Importance Sampling for Rapid and Reliable Gravitational-Wave Inference](https://mlsanity.com/paper/2210.05686/) (2022)

## Abstract (arXiv)

Neural posterior estimation (NPE) is a simulation-based approach to Bayesian inference that trains a neural network to approximate the posterior distribution from simulated parameter - data pairs, bypassing likelihood evaluation. We apply NPE -- to our knowledge for the first time -- to stochastic susceptible-infectious-removed (SIR) epidemic models observed through final outcome data, considering both homogeneously mixing and household-structured populations. Such data arise naturally in retrospective outbreak investigations and household transmission studies, yet inference is computationally challenging: data-augmentation Markov chain Monte Carlo (MCMC) can be slow to mix in large populations and difficult to implement, while Approximate Bayesian Computation (ABC) suffers from low acceptance rates, particularly for large populations or unlikely outcomes. The discrete, low-dimensional nature of such observations makes this setting particularly well suited to NPE. We show that a logNormal posterior approximation, parameterised by a feed-forward neural network, accurately recovers reference posteriors across a range of population sizes and transmission regimes, and extends naturally to joint inference on global and local transmission rates in the household model. Once trained, the network produces approximate posterior distributions in seconds and generalises reliably to population sizes and structures not seen during training. Performance on both synthetic and real outbreak datasets is consistently strong, with results in close agreement with published analyses.