Uncovering

Non-Identifiable Demographic Histories

with Generative AI

Ekaterina (Katya) Noskova

PI: Dr. Konrad Lohse

3 June 2025

Demographic History

Demographic History

Demographic History

Demographic history describes how populations evolved over time.

It includes events such as:

  • population size changes
  • splits
  • migrations
  • admixture
  • selection

Why Reconstruct 

Demographic History

?

Understand population history

Why Reconstruct 

Demographic History

?

Conservation biology studies

Demographic Inference

Demographic Inference

Maximum-likelihood

       estimation

Model Non-identifiability Problem

Model Non-identifiability Problem

Model Non-identifiability Problem

There are some known examples of non-identifiable models:

However, generally classes are unknown

Generative AI

Generative AI

Generative AI models learn the underlying probability distribution of the training data, enabling them to generate new samples with similar characteristics.

Existing Applications

  • Variational autoencoder for drug design [Gangwal et al. 2024]:
  • Discrete diffusion-like model for Bayesian sampling of phylogenetic trees [Zhou et al. 2024]

Proposed Approach

Train generative AI model to explore classes of non-identifiable demographic histories.

Applications

Once trained, a generative AI model enables a fast sampling procedure.

It allows to address various problems:

  • Unravel complex admixture history of domesticated species (cattle)
  • Investigate the regions that act as barriers to gene flow in recently diverged species (butterfly)

Team

Konrad
Lohse

Nikolay
Malkin

Gregory
Gorjanc

Thank you!

Slides:
ekaterina.e.noskova@gmail.com                       enoskova.me