Flexible and scalable federated learning with deep feature prompts for digital pathology

Collaborative learning across medical institutions is essential for building robust and generalisable digital pathology models. Federated learning (FL) enables collaboration without centralising data, yet its adoption is limited by high communication costs, model heterogeneity, and privacy concerns. We propose Federated Deep Feature Prompting (FedDFP), an efficient FL framework tailored for heterogeneous clinical environments. FedDFP introduces lightweight, client-specific learnable prompts applied to patch-level embeddings from whole-slide images. By sharing only these compact prompts, FedDFP reduces communication overhead by over 99.9% compared to standard FL while improving classification accuracy. Extensive experiments on TCGA-IDH, CAMELYON16 and CAMELYON17 show that FedDFP consistently outperforms standard and personalised FL baselines, achieving mean AUC gains of 0.11-0.13 over local-only training and up to 0.10 over the strongest federated methods. FedDFP also converges 2-4× faster and remains effective across diverse feature extractors and multiple-instance learning architectures, demonstrating scalability, flexibility and privacy-aware collaboration.