Clinical informatics, decision support for health professionals, electronic health records, and ehealth infrastructures.

Clinical informatics, decision support for health professionals, electronic health records, and ehealth infrastructures.

Objective The Cox proportional hazards model is a widely used method for analyzing survival data. To achieve sufficient statistical power in a survival analysis, it usually requires a large amount of data. Data sharing across institutions could be a potential workaround for providing this added power. Methods and materials The authors develop a web service for distributed Cox model learning (WebDISCO), which focuses on the proof-of-concept and algorithm development for federated survival analysis. The sensitive patient-level data can be processed locally and only the less-sensitive intermediate statistics are exchanged to build a global Cox model. Mathematical derivation shows that the proposed distributed algorithm is identical to the centralized Cox model. Results The authors evaluated the proposed framework at the University of California, San Diego (UCSD), Emory, and Duke. The experimental results show that both distributed and centralized models result in near-identical model coefficients with differences in the range 10−15 to 10−12 . The results confirm the mathematical derivation and show that the implementation of the distributed model can achieve the same results as the centralized implementation. Limitation The proposed method serves as a proof of concept, in which a publicly available dataset was used to evaluate the performance. The authors do not intend to suggest that this method can resolve policy and engineering issues related to the federated use of institutional data, but they should serve as evidence of the technical feasibility of the proposed approach. Conclusions WebDISCO (Web-based Distributed Cox Regression Model; https://webdisco.ucsd-dbmi.org:8443/cox/) provides a proof-of-concept web service that implements a distributed algorithm to conduct distributed survival analysis without sharing patient level data.

Motivation: Genome-wide association studies (GWAS) have been widely used in discovering the association between genotypes and phenotypes. Human genome data contain valuable but highly sensitive information. Unprotected disclosure of such information might put individual’s privacy at risk. It is important to protect human genome data. Exact logistic regression is a bias-reduction method based on a penalized likelihood to discover rare variants that are associated with disease susceptibility. We propose the HEALER framework to facilitate secure rare variants analysis with a small sample size. Results: We target at the algorithm design aiming at reducing the computational and storage costs to learn a homomorphic exact logistic regression model (i.e. evaluate P-values of coefficients), where the circuit depth is proportional to the logarithmic scale of data size. We evaluate the algorithm performance using rare Kawasaki Disease datasets. Availability and implementation: Download HEALER at http://research.ucsd-dbmi.org/HEALER/ Contact:shw070@ucsd.edu Supplementary information: Supplementary data are available at Bioinformatics online.

We introduce PRINCESS, a privacy-preserving international collaboration framework for analyzing rare disease genetic data that are distributed across different continents. PRINCESS leverages Software Guard Extensions (SGX) and hardware for trustworthy computation. Unlike a traditional international collaboration model, where individual-level patient DNA are physically centralized at a single site, PRINCESS performs a secure and distributed computation over encrypted data, fulfilling institutional policies and regulations for protected health information. To demonstrate PRINCESS’ performance and feasibility, we conducted a family-based allelic association study for Kawasaki Disease, with data hosted in three different continents. The experimental results show that PRINCESS provides secure and accurate analyses much faster than alternative solutions, such as homomorphic encryption and garbled circuits (over 40 000× faster). https://github.com/achenfengb/PRINCESS_opensource Supplementary data are available at Bioinformatics online.

Advances in deep learning have revolutionized medical image segmentation, facilitating the precise delineation of complex anatomical structures. The scarcity of annotated training samples remains a significant bottleneck. To tackle the data limitation, federated learning (FL) offers the promise of pooling data from multiple healthcare institutions. However, as models grow larger, the increase in communication costs restricts FL to fewer nodes, which constrains the volume of data. This situation necessitates the simultaneous achievement of model lightweighting. To address this problem, this study proposes FKD-Med, a novel framework that integrates FL for privacy-sensitive data amalgamation across multiple healthcare institutions, and uses knowledge distillation (KD) to enhance communication efficiency. The "Med" in FKD-Med refers to medical application computational problems. Our principal contributions encompass the design of an open-source framework that seamlessly blends FL and KD, rendering it applicable to a broad spectrum of medical informatics tasks. Our approach substantially augments the computational data volume, thereby boosting both communication efficiency and training throughput. Tested on two datasets of medical image segmentation using TransUNet and ResUNet as teacher models, FKD-Med achieves data privacy, lowers communication costs, and increases accuracy. The parameters of the student models were reduced to 1/127 and 1/1027 of those in the teacher models. Additionally, the models subjected to KD exhibited accuracy improvements of 0.25%, 0.43%, 1.35%, and 1.46% respectively, given the same parameter volume. This positions FKD-Med not only as a pivotal tool for multi-institutional medical research but also as a versatile platform adaptable to a wide array of real-world medical engineering applications. The code is publicly available at https://github.com/SUN-1024/FKD-Med.