CytoBERT: A Foundation Model for Cytometry Data

Cytometry measures the complex characteristics of single cells (e.g., counts and protein expression of immune cells) and is widely used across immunological research and clinical settings. However, cytometry data is highly heterogeneous and unstandardized due to experimental protocols and the choice of measured features. While machine learning methods hold the potential to gain deeper insights into cell biology, these challenges make them difficult to apply and transfer across studies. Recent advances in foundation models can alleviate these issues, but corresponding approaches are still scarce in this field. To address this, we provide CytoBERT, a publicly available, open-source, open-weight foundation model for single-cell cytometry data with variable marker panels. CytoBERT is pretrained in a self-supervised manner on a large-scale cytometry corpus (15 human datasets with heterogeneous marker panels and more than 50 million cells) curated through marker standardization, enabling it to learn transferable inter-marker relationships within cells. Fine-tuning CytoBERT for sample-level classification demonstrates that transfer learning across heterogeneous cytometry datasets is feasible, providing a starting point for scalable, generalizable cytometry analysis. Code is available at GitHub.

Informed, but Not Always Improved: Challenging the Benefit of Background Knowledge in GNNs

In complex and low-data domains such as biomedical research, incorporating background knowledge (BK) graphs, such as protein-protein interaction (PPI) networks, into graph-based machine learning pipelines is a promising research direction. However, while BK is often assumed to improve model performance, its actual contribution and the impact of imperfect knowledge remain poorly understood. In this work, we investigate the role of BK in an important real-world task: cancer subtype classification. Surprisingly, we find that (i) state-of-the-art GNNs using BK perform no better than uninformed models like linear regression, and (ii) their performance remains largely unchanged even when the BK graph is heavily perturbed. To understand these unexpected results, we introduce an evaluation framework, which employs (i) a synthetic setting where the BK is clearly informative and (ii) a set of perturbations that simulate various imperfections in BK graphs. With this, we test the robustness of BK-aware models in both synthetic and real-world biomedical settings. Our findings reveal that careful alignment of GNN architectures and BK characteristics is necessary but holds the potential for significant performance improvements.

SubROC: AUC-Based Discovery of Exceptional Subgroup Performance for Binary Classifiers

Machine learning (ML) is increasingly employed in real-world applications like medicine or economics, thus, potentially affecting large populations. However, ML models often do not perform homogeneously across such populations resulting in subgroups of the population (e.g., sex=female AND marital_status=married) where the model underperforms or, conversely, is particularly accurate. Identifying and describing such subgroups can support practical decisions on which subpopulation a model is safe to deploy or where more training data is required. The potential of identifying and analyzing such subgroups has been recognized, however, an efficient and coherent framework for effective search is missing. Consequently, we introduce SubROC, an open-source, easy-to-use framework based on Exceptional Model Mining for reliably and efficiently finding strengths and weaknesses of classification models in the form of interpretable population subgroups. SubROC incorporates common evaluation measures (ROC and PR AUC), efficient search space pruning for fast exhaustive subgroup search, control for class imbalance, adjustment for redundant patterns, and significance testing. We illustrate the practical benefits of SubROC in case studies as well as in comparative analyses across multiple datasets.