Mehmet Yigit Balik

Mehmet Yigit Balik, Arwa Rekik, Islem Rekik

Graph neural networks (GNNs) have achieved extraordinary enhancements in various areas including the fields medical imaging and network neuroscience where they displayed a high accuracy in diagnosing challenging neurological disorders such as autism. In the face of medical data scarcity and high-privacy, training such data-hungry models remains challenging. Federated learning brings an efficient solution to this issue by allowing to train models on multiple datasets, collected independently by different hospitals, in fully data-preserving manner. Although both state-of-the-art GNNs and federated learning techniques focus on boosting classification accuracy, they overlook a critical unsolved problem: investigating the reproducibility of the most discriminative biomarkers (i.e., features) selected by the GNN models within a federated learning paradigm. Quantifying the reproducibility of a predictive medical model against perturbations of training and testing data distributions presents one of the biggest hurdles to overcome in developing translational clinical applications. To the best of our knowledge, this presents the first work investigating the reproducibility of federated GNN models with application to classifying medical imaging and brain connectivity datasets. We evaluated our framework using various GNN models trained on medical imaging and connectomic datasets. More importantly, we showed that federated learning boosts both the accuracy and reproducibility of GNN models in such medical learning tasks. Our source code is available at https://github.com/basiralab/reproducibleFedGNN.

Mehmet Yigit Balik, Harri Lähdesmäki

Single-cell RNA sequencing provides insights into gene expression at single-cell resolution, yet inferring temporal processes from these static snapshot measurements remains a fundamental challenge. Current approaches utilizing neural differential equations and flows are sensitive to overfitting and lack careful considerations of biological variability. In this work, we propose a generative framework that models population trends using a latent heteroscedastic Gaussian process (GP) approximated by Hilbert space methods. To address the absence of genuine cell trajectories, we leverage an optimal transport (OT) objective that aligns generated and observed population distributions. Our method explicitly captures biological heterogeneity by incorporating cell-specific latent time and cell type conditioning to disentangle temporal asynchrony and trajectories to different cell types. We demonstrate state-of-the-art performance on complex interpolation and extrapolation benchmarks and introduce a novel gradient-based strategy for inferring perturbation trajectories.

Mehmet Yigit Balik

Predicting hospital length of stay (LOS) reliably is an essential need for efficient resource allocation at hospitals. Traditional predictive modeling tools frequently have difficulty acquiring sufficient and diverse data because healthcare institutions have privacy rules in place. In our study, we modeled this problem as an empirical graph where nodes are the hospitals. This modeling approach facilitates collaborative model training by modeling decentralized data sources from different hospitals without extracting sensitive data outside of hospitals. A local model is trained on a node (hospital) by aiming the generalized total variation minimization (GTVMin). Moreover, we implemented and compared two different federated learning optimization algorithms named federated stochastic gradient descent (FedSGD) and federated averaging (FedAVG). Our results show that federated learning enables accurate prediction of hospital LOS while addressing privacy concerns without extracting data outside healthcare institutions.