AIPD-DC2-UL

Stratification of Clinical Disease Trajectories and Prediction of Individual Rate of Progression

  • Host Institution: University of Luxembourg
  • PhD Enrolment: University of Luxembourg
  • Start Date: October 2025
  • Duration: 36 months
  • Official PhD Supervisor: Jochen Klucken

Research Objectives

Building on prior work by FH, the first main objective of this project is to stratify the trajectories of patients with a confirmed PD diagnosis and to predict the individual rate of disease progression from baseline, using data from PPMI, LuxPARK and ICEBERG. One of the challenges to be addressed in this context is that patients in many cohort studies already demonstrate a high variability of disease progression at study baseline, which can lead to severe biases of models, if they are naively trained. One possibility to address such bias is to rely on a linear mixed modelling framework to interpolate between patient trajectories and align them to a common disease time scale. However, non-linear techniques, including neural networks with mixed effects, have also been devised recently, and these techniques may potentially be better able to capture the long-term behaviour of disease progression.

The specific aims of this project are thus:

  1. To explore the potential benefit of non-linear mixed modelling approaches and to investigate how they can be combined with or embedded into the previously established VaDER trajectory clustering algorithm.
  2. To apply these techniques to identify and statistically characterize clusters of disease progression in different cohorts in terms of clinical features as well as digital gait assessments (LuxPARK).
  3. To develop multimodal predictive AI/ML models combining clinical and genomic factors to predict the likely disease progression subtype on an individual level. XAI techniques such as SHAP will be employed to understand likely influencing factors for a faster versus slower disease progression. 
  4. To carefully assess the reproducibility and generalizability of findings across cohorts. This specifically includes the task to externally validate models trained on data of one study with data from an independent study. 

The second main objective is to study the potential benefit of stratifying patients by disease progression for clinical trial design, as e.g. demonstrated in prior work by FH for other indication areas. We will investigate the sample size reduction that could be achieved using such stratification, and whether future clinical trials for a drug would preferably recruit patients that have been predicted as fast progressors at the screening phase. Different settings will be considered regarding patient inclusion/exclusion criteria, endpoints, control arm/active comparator as well as anticipated effect sizes of a future drug. DC2 focuses on disease progression assessed via traditional clinical assessments, whereas DC4 will explore non-traditional digital speech assessments for monitoring of disease progression. Both DCs will closely work together.

Expected Results

  • Innovative and explainable AI/ML models predicting PD risk on an individual basis.
  • New insights about relevant data modalities and the putative causal effect of lifestyle on disease risk.
  • Pioneering the use of causal AI/ML techniques in the PD field.
     

Planned Secondment(s)

  • Host 1: Petanux
    • Duration: 18 months
    • Purpose: Learning about AI/ML
  • Host 2: Fraunhofer SCAI
    • Duration: 3 months
    • Purpose: Learning about VaDER and its application, and trial simulation.

This project is part of the "Precision Neurology" work package.

References

  • Johann de Jong, Mohammad Asif Emon, Ping Wu, Reagon Karki, Meemansa Sood, Patrice Godard, Ashar Ahmad, Henri Vrooman, Martin Hofmann-Apitius, Holger Fröhlich, Deep learning for clustering of multivariate clinical patient trajectories with missing values, GigaScience, Volume 8, Issue 11, November 2019, giz134. https://doi.org/10.1093/gigascience/giz134
  • Wendland, P., Birkenbihl, C., Gomez-Freixa, M. et al. Generation of realistic synthetic data using Multimodal Neural Ordinary Differential Equations. npj Digit. Med. 5, 122 (2022). https://doi.org/10.1038/s41746-022-00666-x
  • Samuel Iddi, Dan Li, Paul S. Aisen, Michael S. Rafii, Irene Litvan, Wesley K. Thompson, Michael C. Donohue; Estimating the Evolution of Disease in the Parkinson’s Progression Markers Initiative. Neurodegener Dis 24 October 2018; 18 (4): 173–190. https://doi.org/10.1159/000488780
  • Koval, I., Bône, A., Louis, M. et al. AD Course Map charts Alzheimer’s disease progression. Sci Rep 11, 8020 (2021). https://doi.org/10.1038/s41598-021-87434-1
  • Giora Simchoni and Saharon Rosset. 2024. Integrating random effects in deep neural networks. J. Mach. Learn. Res. 24, 1, Article 156 (January 2023). https://dl.acm.org/doi/10.5555/3648699.3648855
  • Johann de Jong, Ioana Cutcutache, Matthew Page, Sami Elmoufti, Cynthia Dilley, Holger Fröhlich, Martin Armstrong, Towards realizing the vision of precision medicine: AI based prediction of clinical drug response, Brain, Volume 144, Issue 6, June 2021, Pages 1738–1750. https://doi.org/10.1093/brain/awab108