Homepage of Katharina Baum

Professor at the Institute of Computer Science at the Free University Berlin, head of the research group Data Integration in the Life Sciences (DILiS, see the group's website here). You can also find me on LinkedIn.

Prof. Dr. Katharina Baum
Institut für Informatik | Freie Universität Berlin
Takustr. 9 | 14195 Berlin
katharina.baum@fu-berlin.de
+49 30 838 55850
T9 | R. 161

Research Interests

Networks allow representing interactions between entities and are highly informative. They enable the integrative analysis of different data views. I am interested in combining network-based data analysis approaches and mathematical modeling of dynamic processes with machine learning to bring in prior information. Applications stem mainly from a biomedical background, such as drug response prediction, and we focus on integrating different kinds of data with biomolecular, "multi-omics" data.

Selected projects:

• Multi-omics network-based prediction of differential drug response (DrDimont)
• Drug response prediction using graph-neural networks with uncertainty
• Proteogenomic abundance imputation
• Informing machine learning using simulations from dynamical models

Find more details on some current projects here.

Teaching and theses

I am offering lectures, seminars, software projects in the broad scope of data analysis. Topics and covered methods are frequently motivated by questions from molecular biology and biomedicine. Main themes are machine learning, graphs and dynamical models, but also (biomedical) databases as well as basic maths.

Please find a list of our current and past teaching offers at FU on our group's website.

We offer a broad variety of thesis topics, both on Master and Bachelor level, with varying degree of required expertise and background in programming, data analysis, theory, biology. Of course, we are also happy if you have an idea for a project for your thesis! In any case, please contact us and discuss.

Examples of past and current theses topics are

• The Impact of Synthetic Dataset Size and Diversity on Transfer Learning Model Performance for Time Series Data (Julian Zabbarov, HPI, MA Data Engineering), preprint of a derived publication here
• p-motifs: Non-frequency based relevance metrics for network motifs (Tim Garrels, HPI, MA IT Systems Engineering)
• Graph Neural Networks and a Systematic Evaluation Framework for Missing Value Imputation in Proteomics (Tobias Pietz, HPI, MA Data Engineering), preprint of a derived publication here

Short CV

2023/05: Assistant Professor for Data Integration in the Life Sciences at the Institute of Computer Sciences at Free University Berlin

2023/05: Guest Researcher at Hasso Plattner Institute for Digital Engineering gGmbH

2023/02: Adjunct Assistant Professor at the Windreich Department for AI and Human Health and the Hasso Plattner Institute at Mount Sinai, Icahn School of Medicine at Mount Sinai, New York, USA

2021-2023: Group Leader (Senior Researcher) at Hasso Plattner Institute for Digital Engineering gGmbH

2020-2021: PostDoc at Hasso Plattner Institute for Digital Engineering gGmbH

2017-2019: PostDoc at Luxembourg Institute of Health, joint project with Nanyang Technological University Singapore

2014-2020: PostDoc at Max Delbrück Center for Molecular Medicine in the Helmholtz Association

2009-2014: PhD in Theoretical Biophysics at Humboldt University Berlin and Max Delbrück Center for Molecular Medicine in the Helmholtz Association

2003-2009: studies of Mathematics (diploma), Humboldt University Berlin and École Polytechnique, France

Publications

Please find a list of publications on the group page. In addition, please consult my google scholar profile or records of my ORCID profile.