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Abstract Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are often computationally expensive, which limits the complexity and realism of phylodynamic models and makes them ill-suited for informing policy decisions in real-time during rapidly developing outbreaks. Likelihood-free methods using deep learning are pushing the boundaries of inference beyond these constraints. In this paper, we extend, compare, and contrast a recently developed deep learning method for likelihood-free inference from trees. We trained multiple deep neural networks using phylogenies from simulated outbreaks that spread among 5 locations and found they achieve close to the same levels of accuracy as Bayesian inference under the true simulation model. We compared robustness to model misspecification of a trained neural network to that of a Bayesian method. We found that both models had comparable performance, converging on similar biases. We also implemented a method of uncertainty quantification called conformalized quantile regression that we demonstrate has similar patterns of sensitivity to model misspecification as Bayesian highest posterior density (HPD) and greatly overlap with HPDs, but have lower precision (more conservative). Finally, we trained and tested a neural network against phylogeographic data from a recent study of the SARS-Cov-2 pandemic in Europe and obtained similar estimates of region-specific epidemiological parameters and the location of the common ancestor in Europe. Along with being as accurate and robust as likelihood-based methods, our trained neural networks are on average over 3 orders of magnitude faster after training. Our results support the notion that neural networks can be trained with simulated data to accurately mimic the good and bad statistical properties of the likelihood functions of generative phylogenetic models.
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This content will become publicly available on November 18, 2025
Transfer Learning with Uncertainty Quantification: Random Effect Calibration of Source to Target (RECaST)
Transfer learning uses a data model, trained to make predictions or inferences on data from one population, to make reliable predictions or inferences on data from another population. Most existing transfer learning approaches are based on fine-tuning pre-trained neural network models, and fail to provide crucial uncertainty quantification. We develop a statistical framework for model predictions based on transfer learning, called RECaST. The primary mechanism is a Cauchy random effect that recalibrates a source model to a target population; we mathematically and empirically demonstrate the validity of our RECaST approach for transfer learning between linear models, in the sense that prediction sets will achieve their nominal stated coverage, and we numerically illustrate the method's robustness to asymptotic approximations for nonlinear models. Whereas many existing techniques are built on particular source models, RECaST is agnostic to the choice of source model, and does not require access to source data. For example, our RECaST transfer learning approach can be applied to a continuous or discrete data model with linear or logistic regression, deep neural network architectures, etc. Furthermore, RECaST provides uncertainty quantification for predictions, which is mostly absent in the literature. We examine our method's performance in a simulation study and in an application to real hospital data.
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- Award ID(s):
- 2337943
- PAR ID:
- 10576241
- Publisher / Repository:
- JMLR, Inc.
- Date Published:
- Journal Name:
- Journal of machine learning research
- Volume:
- 25
- Issue:
- 338
- ISSN:
- 1533-7928
- Page Range / eLocation ID:
- 1-40
- Subject(s) / Keyword(s):
- Bayesian transfer learning Electronic health records Informative Bayesian prior Model calibration
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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