Privacy-Preserving Detection of Rare Disease-Associated Cell Subsets via Secure Multi-Party Computation

The detection of rare disease-associated cell subsets from high-dimensional single-cell measurements is critical for understanding diseases such as leukaemia and viral infections. CellCnn, a convolutional neural network (CNN) designed for this task, has demonstrated the ability to identify phenotype-associated cell populations at frequencies as low as 0.01\%. Training such models reliably requires patient cohorts that are larger and more diverse than any single institution can typically assemble, and the underlying single-cell data is too sensitive to share across institutional boundaries under existing privacy regulations. We propose a secure multi-party computation (MPC) framework that enables the training and inference of CellCnn entirely on secret-shared data. This ensures that neither the participants nor the computing servers ever observe raw patient data or intermediate values. Evaluated on benchmark single-cell datasets for cytomegalovirus infection (CMV) and acute myeloid leukaemia (AML), our implementation preserves accuracy close to its plaintext counterpart while outperforming the prior privacy-preserving baseline. In contrast to earlier privacy-preserving approaches that removed components such as ReLU activations and bias terms, our method retains these key parts of the CellCnn architecture and supports accurate analysis without exposing raw patient data.

From Gradient Clipping to Structural Refinement: Improving DPSGD for Medical Image Segmentation

Medical image segmentation is widely used for disease detection but relies on sensitive data, raising privacy concerns as trained models can leak information. Differential privacy, typically implemented via Differential Private Stochastic Gradient Descent (DPSGD), provides a solution, though at the cost of reduced utility. Recent DPSGD variants, including Automatic clipping (Auto-S), Normalised SGD with perturbation (NSGD), and Per-sample adaptive clipping (PSAC), have shown promise in image classification, but their behavior in medical segmentation remains underexplored. We evaluate these methods across binary and multi-class tasks and analyze gradient alignment, showing that prior assumptions, particularly for PSAC, do not consistently hold. We further demonstrate that combining clipping strategies with morphological refinement improves segmentation quality under privacy constraints. Finally, we propose an adaptive DP-Morph variant that captures class-specific structures and enhances performance in multi-class settings.