Jens Baumann | Searcharxiv

arXiv2025

From Cells to Survival: Hierarchical Analysis of Cell Inter-Relations in Multiplex Microscopy for Lung Cancer Prognosis

The tumor microenvironment (TME) has emerged as a promising source of prognostic biomarkers. To fully leverage its potential, analysis methods must capture complex interactions between different cell types. We propose HiGINE -- a hierarchical graph-based approach to predict patient survival (short vs. long) from TME characterization in multiplex immunofluorescence (mIF) images and enhance risk stratification in lung cancer. Our model encodes both local and global inter-relations in cell neighborhoods, incorporating information about cell types and morphology. Multimodal fusion, aggregating cancer stage with mIF-derived features, further boosts performance. We validate HiGINE on two public datasets, demonstrating improved risk stratification, robustness, and generalizability.

cs.CV↗

arXiv2025

Diversity Over Scale: Whole-Slide Image Variety Enables H&E Foundation Model Training with Fewer Patches

Rapid progress in computational pathology is increasingly driven by vision foundation models pretrained on vast histopathology datasets. While recent efforts have prioritized training on an ever-larger amount of patches, we take an alternative approach focused on data diversity. Our foundation model, Athena, was initialized from a pretrained model and trained on just 115 million tissue patches, several times fewer than recent histopathology foundation models. Rather than relying on patch volume or complex sampling heuristics, we maximize data diversity by randomly selecting only a moderate number of patches per whole-slide image from our diverse internal repository, which spans multiple countries, institutions, and scanner types. Evaluated on a single patch-level benchmark and four slide-level downstream tasks (two molecular and two morphological), Athena approaches the state-of-the-art and even surpasses several models trained on substantially larger datasets. This indicates that diversity across whole-slide images, rather than patch quantity alone, drives learning in histopathology foundation models.

q-bio.TO↗