Karsten Borgwardt

Prof. Dr. Karsten Borgwardt is Director of the Research Department of Machine Learning and Systems Biology at the Max Planck Institute of Biochemistry in Martinsried, Germany. A leading figure in the intersection of machine learning, bioinformatics, and systems biology, he heads a multidisciplinary team that develops novel computational methods to extract knowledge from large biomedical data sets.

Research Mission: The Borgwardt lab converges big data analytics and biomedical research. Two overarching goals drive their work:
(1) Automatically generating new biological and medical knowledge from massive data via state-of-the-art machine-learning algorithms.
(2) Understanding the molecular underpinnings of biological system function, with emphasis on personalized medicine and biomarker discovery.

Their methodological toolbox spans graph neural networks, kernel methods, conformal prediction, deep learning on sequences and structures, and topological data analysis. Application domains include antimicrobial resistance prediction, protease engineering, acute-kidney-injury forecasting, coronary-artery-disease diagnostics, single-cell spatial proteomics, and Long-COVID immune profiling.

Recent Publication Landscape (2023-2025):
The group’s latest articles demonstrate a clear trend toward translationally relevant machine learning. High-impact venues such as Nature Communications, Science, ICLR, and RECOMB feature their work on:

• Data-driven protein engineering using DNA-recorded deep mutational scanning.
• Guaranteed antimicrobial resistance detection from MALDI-TOF spectra via conformal prediction.
• Graph-based biomarker discovery with theoretical guarantees.
• Deep phenotyping of human iPSC-derived neuronal networks to study disease mutations.
• Multi-modal learning that fuses genomics, proteomics, and clinical data for patient stratification.

These contributions collectively advance both the theoretical foundations and real-world deployment of machine learning in medicine.

Scientific Awards & Honors:
While no explicit award list is provided, the breadth and impact of publications, invited book chapters, and keynote-level conference presentations (ICLR, RECOMB, ISMB/ECCB) testify to sustained international recognition.

Laboratory & Collaboration Ecosystem:
The Borgwardt lab operates at the Max Planck Institute of Biochemistry—a world-leading biomedical research campus. Collaborations span multiple Max Planck centers, university hospitals across Europe, and international consortia such as the EyeConic study on optogenetics therapy. The lab’s open-source footprint includes the Multi-SConES R package for multi-task network-regularized feature selection, fostering reproducible science across the community.