Ziming Gan

Zebin Wang, Ziming Gan, Weijing Tang et al.

Classical probabilistic graphical models face fundamental challenges in modern data environments, which are characterized by high dimensionality, source heterogeneity, and stringent data-sharing constraints. In this work, we revisit the Ising model, a well-established member of the Markov Random Field (MRF) family, and develop a distributed framework that enables scalable and privacy-preserving representation learning from large-scale binary data with inherent low-rank structure. Our approach optimizes a non-convex surrogate loss function via bi-factored gradient descent, offering substantial computational and communication advantages over conventional convex approaches. We evaluate our algorithm on multi-institutional electronic health record (EHR) datasets from 58,248 patients across the University of Pittsburgh Medical Center (UPMC) and Mass General Brigham (MGB), demonstrating superior performance in global representation learning and downstream clinical tasks, including relationship detection, patient phenotyping, and patient clustering. These results highlight a broader potential for statistical inference in federated, high-dimensional settings while addressing the practical challenges of data complexity and multi-institutional integration.

Jessica Gronsbell, Vidul Ayakulangara Panickan, Chris Lin et al.

Integrative analysis of multi-institutional Electronic Health Record (EHR) data enhances the reliability and generalizability of translational research by leveraging larger, more diverse patient cohorts and incorporating multiple data modalities. However, harmonizing EHR data across institutions poses major challenges due to data heterogeneity, semantic differences, and privacy concerns. To address these challenges, we introduce $\textit{PEHRT}$, a standardized pipeline for efficient EHR data harmonization consisting of two core modules: (1) data pre-processing and (2) representation learning. PEHRT maps EHR data to standard coding systems and uses advanced machine learning to generate research-ready datasets without requiring individual-level data sharing. Our pipeline is also data model agnostic and designed for streamlined execution across institutions based on our extensive real-world experience. We provide a complete suite of open source software, accompanied by a user-friendly tutorial, and demonstrate the utility of PEHRT in a variety of tasks using data from diverse healthcare systems.

Doudou Zhou, Han Tong, Linshanshan Wang et al.

The adoption of EHRs has expanded opportunities to leverage data-driven algorithms in clinical care and research. A major bottleneck in effectively conducting multi-institutional EHR studies is the data heterogeneity across systems with numerous codes that either do not exist or represent different clinical concepts across institutions. The need for data privacy further limits the feasibility of including multi-institutional patient-level data required to study similarities and differences across patient subgroups. To address these challenges, we developed the GAME algorithm. Tested and validated across 7 institutions and 2 languages, GAME integrates data in several levels: (1) at the institutional level with knowledge graphs to establish relationships between codes and existing knowledge sources, providing the medical context for standard codes and their relationship to each other; (2) between institutions, leveraging language models to determine the relationships between institution-specific codes with established standard codes; and (3) quantifying the strength of the relationships between codes using a graph attention network. Jointly trained embeddings are created using transfer and federated learning to preserve data privacy. In this study, we demonstrate the applicability of GAME in selecting relevant features as inputs for AI-driven algorithms in a range of conditions, e.g., heart failure, rheumatoid arthritis. We then highlight the application of GAME harmonized multi-institutional EHR data in a study of Alzheimer's disease outcomes and suicide risk among patients with mental health disorders, without sharing patient-level data outside individual institutions.