Dominika Matus

I am a Master’s student in Computer Science at the University of Freiburg specializing in Artificial Intelligence. My research focus lies at the intersection of deep learning and biology, in particular in RNA structure and interaction prediction. Together with Frederic Runge, Jörg Franke, and Lars Gerne, we have published a workshop paper “RNA-Protein Interaction Prediction via Sequence Embeddings” at the 12th International Conference on Learning Representations in 2024. This work explores the benefit of using embeddings learned from foundation models to predict interactions between RNA and proteins and proposes homology-based splits for the data for a more realistic evaluation of model generalizability. My past work experience includes a Student Assistant position at the Machine Learning Lab at the University of Freiburg and an internship at IBM in Poland. I am currently writing my Master’s thesis on dimensionality reduction for tabular data with a focus on biomedical applications.