# Dynamic causal discovery in Alzheimer's disease through latent pseudotime modelling

arXiv: https://arxiv.org/abs/2511.04619 · HTML: https://mlsanity.com/paper/2511.04619/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 3 of its 57 references that are in the map.
- First posted on arXiv 6 Nov 2025.

## Builds on (most cited first, 3 of 3)

- [Causal Discovery from Heterogeneous/Nonstationary Data with Independent Changes](https://mlsanity.com/paper/1903.01672/) (2019)
- [Constraint-based Causal Discovery for Non-Linear Structural Causal Models with Cycles and Latent Confounders](https://mlsanity.com/paper/1807.03024/) (2018)
- [A Discovery Algorithm for Directed Cyclic Graphs](https://mlsanity.com/paper/1302.3599/) (2013)

## Abstract (arXiv)

The application of causal discovery to diseases like Alzheimer's (AD) is limited by the static graph assumptions of most methods; such models cannot account for an evolving pathophysiology, modulated by a latent disease pseudotime. We propose to apply an existing latent variable model to real-world AD data, inferring a pseudotime that orders patients along a data-driven disease trajectory independent of chronological age, then learning how causal relationships evolve. Pseudotime outperformed age in predicting diagnosis (AUC 0.82 vs 0.59). Incorporating minimal, disease-agnostic background knowledge substantially improved graph accuracy and orientation. Our framework reveals dynamic interactions between novel (NfL, GFAP) and established AD markers, enabling practical causal discovery despite violated assumptions.