Causal Cell Dynamics Lab – A Mila-Helmholtz International Project

Combining Artificial Intelligence (AI) Expertise to Tackle Cellular Processes in Disease

Banner with project name and microscopic view of human tissue.


Mila and its partners are committed to helping researchers in stem cell biology, biomedicine and related fields respond to some of the world’s most urgent health challenges such as cancer, diabetes, and antimicrobial resistance.

As part of this mission, Mila has joined forces with the research institute Helmholtz Munich and the Max Planck Institute for Intelligent Systems to form an international lab that will use big data and artificial intelligence to shed light on the role of cellular processes in the development of diseases.


The goal of this research effort is the modelling of cellular dynamics from single cell genomics as well as the latent causes driving those dynamics. Through this work, the team is developing methods for causally structured deep representation learning to improve understanding of cellular decisions.

Specifically, the aims are to :

  • Develop robust high-dimensional causal inference working on latent spaces
  • Develop causal models for cell dynamics and perturbations
  • Extend to multi-omics data adding biological priors

About the Project

Recent advances in genomics allow researchers to measure individual cellular differences with unprecedented resolution and see more clearly how cell characteristics are influenced by their environment. These breakthroughs have generated a wealth of molecular biology data for which the analysis and interpretation are of critical importance.

To address this challenge, Mila and its partners launched the Causal Cell Dynamics Lab. The initiative merges Mila’s deep learning expertise, Helmholtz’ genomics-specific bioinformatics skills and causal learning specialists from the Max Planck Institute. The Causal Cell Dynamics Lab researchers have a five-year mandate to find ways to identify underlying causal structures that explain cell development and  trajectories and to develop models that improve our of cell responses to environmental changes. The Lab is being co-funded by the Helmholtz Initiative and Networking Fund.

The Canada-Germany collaboration will forge strategic partnerships between leading-edge research institutions, allowing world-renowned researchers and promising PhD students to work abroad and strengthen international connections and networks.

Photo of Yoshua Bengio.

Our diverse consortium will work at the intersection of AI and genomics. This will not only help us to predict important causes of various diseases, but also to make significant advances in AI and basic biology research.

Yoshua Bengio, Full Professor, Université de Montréal, Founder and Scientific Director, Mila


Interview with Yoshua Bengio and Fabian Theis
From the Helmholtz newsroom
Human Cell Atlas
The Human Cell Atlas is an international collaborative consortium that charts the cell types in the healthy body, across time from development to adulthood, and eventually to old age.
Causal Cell Dynamics International Lab on X (formerly Twitter)
Stay informed on the lab's activities.
Causal Cell Dynamics Scientific Symposium
Abstract molecular structure.

Meet the Team

The Causal Cell Dynamics Lab is a collaboration between Helmholtz Munich, the Max Planck Institute for Intelligent Systems and Mila.

Lab Director (Mila)
Core Academic Member
Portrait of Yoshua Bengio
Full Professor, Université de Montréal, Department of Computer Science and Operations Research Department
Canada CIFAR AI Chair
Other Members
Fabian Theis (Lab Director, Helmholtz)
Bernhard Schölkopf (Lab Director, MPI)
Mathieu Blanchette (Mila)
Joseph Paul Cohen (Mila)
Benjamin Schubert (Mila)
Alexander Tong (Mila)
Maria Colomé-Tatché (Helmholtz)
Niki Kilbertus (Helmholtz)
Annalisa Marsico (Helmholtz)


For any inquiry about the project, please contact Mathieu Seyfrid(, Program Manager at Helmholtz. 

Exterior view of Mila's facade.