Informed machine learning for predicting gene expression

Prof. Dr. Katharina Baum 

 

We offer a PhD position in the research group Data Integration in the Life Sciences of Prof. Katharina Baum at the Institute for Computer Sciences of the Free University Berlin. We are a young and dynamic team on the idyllic research campus in Berlin-Dahlem. Our research focuses on computational method development for analyzing data from health and molecular biology. In particular, we combine machine learning with dynamical modeling and graphs in informed machine learning approaches.

In the planned PhD project, the goal is to extend our simulation-based machine learning approach SimbaML to the forecasting of gene expression upon perturbations. This prediction task is key for advancing in personalized medicine as it may allow determining the molecular response of a patient to a given drug or treatment in silico. Therefore, it has received much attention lately and has been approached both on the bulk- as well as single-cell RNAseq measurement level. Using informed machine learning poses a unique opportunity to feed knowledge on underlying regulatory mechanisms acquired from generations of systems biologists into the prediction models.

As the project is purely computational, with collaborations with wet-lab partners, it requires proficiency in Python and a strong background in data analysis, as well as experience with machine learning. First experience with ordinary differential equation modeling will be beneficial.

Be part of this exciting endeavor and apply! You can find more information on other projects on our website.

© Katharina Baum