Federated deep learning for detecting COVID-19 lung abnormalities in CT: a privacy-preserving multinational validation study.
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ABSTRACT:
SUBMITTER: Dou Q
PROVIDER: S-EPMC8007806 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:ObjectiveWe introduce fold-stratified cross-validation, a validation methodology that is compatible with privacy-preserving federated learning and that prevents data leakage caused by duplicates of electronic health records (EHRs).Materials and methodsFold-stratified cross-validation complements cross-validation with an initial stratification of EHRs in folds containing patients with similar characteristics, thus ensuring that duplicates of a record are jointly present either in training or in validation folds. Monte Carlo simulations are performed to investigate the properties of fold-stratified cross-validation in the case of a model data analysis using both synthetic data and MIMIC-III (Medical Information Mart for Intensive Care-III) medical records.ResultsIn situations in which duplicated EHRs could induce overoptimistic estimations of accuracy, applying fold-stratified cross-validation prevented this bias, while not requiring full deduplication. However, a pessimistic bias might appear if the covariate used for the stratification was strongly associated with the outcome.DiscussionAlthough fold-stratified cross-validation presents low computational overhead, to be efficient it requires the preliminary identification of a covariate that is both shared by duplicated records and weakly associated with the outcome. When available, the hash of a personal identifier or a patient's date of birth provides such a covariate. On the contrary, pseudonymization interferes with fold-stratified cross-validation, as it may break the equality of the stratifying covariate among duplicates.ConclusionFold-stratified cross-validation is an easy-to-implement methodology that prevents data leakage when a model is trained on distributed EHRs that contain duplicates, while preserving privacy.
| S-EPMC7647321 | biostudies-literature
Project description:Federated Learning (FL) is a machine learning framework that enables multiple organizations to train a model without sharing their data with a central server. However, it experiences significant performance degradation if the data is non-identically independently distributed (non-IID). This is a problem in medical settings, where variations in the patient population contribute significantly to distribution differences across hospitals. Personalized FL addresses this issue by accounting for site-specific distribution differences. Clustered FL, a Personalized FL variant, was used to address this problem by clustering patients into groups across hospitals and training separate models on each group. However, privacy concerns remained as a challenge as the clustering process requires exchange of patient-level information. This was previously solved by forming clusters using aggregated data, which led to inaccurate groups and performance degradation. In this study, we propose Privacy-preserving Community-Based Federated machine Learning (PCBFL), a novel Clustered FL framework that can cluster patients using patient-level data while protecting privacy. PCBFL uses Secure Multiparty Computation, a cryptographic technique, to securely calculate patient-level similarity scores across hospitals. We then evaluate PCBFL by training a federated mortality prediction model using 20 sites from the eICU dataset. We compare the performance gain from PCBFL against traditional and existing Clustered FL frameworks. Our results show that PCBFL successfully forms clinically meaningful cohorts of low, medium, and high-risk patients. PCBFL outperforms traditional and existing Clustered FL frameworks with an average AUC improvement of 4.3% and AUPRC improvement of 7.8%.
| S-EPMC11376435 | biostudies-literature
Project description:With the increase in applications of machine learning methods in drug design and related fields, the challenge of designing sound test sets becomes more and more prominent. The goal of this challenge is to have a realistic split of chemical structures (compounds) between training, validation and test set such that the performance on the test set is meaningful to infer the performance in a prospective application. This challenge is by its own very interesting and relevant, but is even more complex in a federated machine learning approach where multiple partners jointly train a model under privacy-preserving conditions where chemical structures must not be shared between the different participating parties. In this work we discuss three methods which provide a splitting of a data set and are applicable in a federated privacy-preserving setting, namely: a. locality-sensitive hashing (LSH), b. sphere exclusion clustering, c. scaffold-based binning (scaffold network). For evaluation of these splitting methods we consider the following quality criteria (compared to random splitting): bias in prediction performance, classification label and data imbalance, similarity distance between the test and training set compounds. The main findings of the paper are a. both sphere exclusion clustering and scaffold-based binning result in high quality splitting of the data sets, b. in terms of compute costs sphere exclusion clustering is very expensive in the case of federated privacy-preserving setting.
| S-EPMC8650276 | biostudies-literature
Project description:Training accurate and robust machine learning models requires a large amount of data that is usually scattered across data silos. Sharing or centralizing the data of different healthcare institutions is, however, unfeasible or prohibitively difficult due to privacy regulations. In this work, we address this problem by using a privacy-preserving federated learning-based approach, PriCell, for complex models such as convolutional neural networks. PriCell relies on multiparty homomorphic encryption and enables the collaborative training of encrypted neural networks with multiple healthcare institutions. We preserve the confidentiality of each institutions' input data, of any intermediate values, and of the trained model parameters. We efficiently replicate the training of a published state-of-the-art convolutional neural network architecture in a decentralized and privacy-preserving manner. Our solution achieves an accuracy comparable with the one obtained with the centralized non-secure solution. PriCell guarantees patient privacy and ensures data utility for efficient multi-center studies involving complex healthcare data.
| S-EPMC9122966 | biostudies-literature
Project description:BackgroundThere is an urgent need for the development of global analytic frameworks that can perform analyses in a privacy-preserving federated environment across multiple institutions without privacy leakage. A few studies on the topic of federated medical analysis have been conducted recently with the focus on several algorithms. However, none of them have solved similar patient matching, which is useful for applications such as cohort construction for cross-institution observational studies, disease surveillance, and clinical trials recruitment.ObjectiveThe aim of this study was to present a privacy-preserving platform in a federated setting for patient similarity learning across institutions. Without sharing patient-level information, our model can find similar patients from one hospital to another.MethodsWe proposed a federated patient hashing framework and developed a novel algorithm to learn context-specific hash codes to represent patients across institutions. The similarities between patients can be efficiently computed using the resulting hash codes of corresponding patients. To avoid security attack from reverse engineering on the model, we applied homomorphic encryption to patient similarity search in a federated setting.ResultsWe used sequential medical events extracted from the Multiparameter Intelligent Monitoring in Intensive Care-III database to evaluate the proposed algorithm in predicting the incidence of five diseases independently. Our algorithm achieved averaged area under the curves of 0.9154 and 0.8012 with balanced and imbalanced data, respectively, in ?-nearest neighbor with ?=3. We also confirmed privacy preservation in similarity search by using homomorphic encryption.ConclusionsThe proposed algorithm can help search similar patients across institutions effectively to support federated data analysis in a privacy-preserving manner.
| S-EPMC5924379 | biostudies-literature
Project description:MotivationIn the realm of precision medicine, effective patient stratification and disease subtyping demand innovative methodologies tailored for multi-omics data. Clustering techniques applied to multi-omics data have become instrumental in identifying distinct subgroups of patients, enabling a finer-grained understanding of disease variability. Meanwhile, clinical datasets are often small and must be aggregated from multiple hospitals. Online data sharing, however, is seen as a significant challenge due to privacy concerns, potentially impeding big data's role in medical advancements using machine learning. This work establishes a powerful framework for advancing precision medicine through unsupervised random forest-based clustering in combination with federated computing.ResultsWe introduce a novel multi-omics clustering approach utilizing unsupervised random forests. The unsupervised nature of the random forest enables the determination of cluster-specific feature importance, unraveling key molecular contributors to distinct patient groups. Our methodology is designed for federated execution, a crucial aspect in the medical domain where privacy concerns are paramount. We have validated our approach on machine learning benchmark datasets as well as on cancer data from The Cancer Genome Atlas. Our method is competitive with the state-of-the-art in terms of disease subtyping, but at the same time substantially improves the cluster interpretability. Experiments indicate that local clustering performance can be improved through federated computing.Availability and implementationThe proposed methods are available as an R-package (https://github.com/pievos101/uRF).
| S-EPMC11373406 | biostudies-literature
Project description:Unsorted retired batteries with varied cathode materials hinder the adoption of direct recycling due to their cathode-specific nature. The surge in retired batteries necessitates precise sorting for effective direct recycling, but challenges arise from varying operational histories, diverse manufacturers, and data privacy concerns of recycling collaborators (data owners). Here we show, from a unique dataset of 130 lithium-ion batteries spanning 5 cathode materials and 7 manufacturers, a federated machine learning approach can classify these retired batteries without relying on past operational data, safeguarding the data privacy of recycling collaborators. By utilizing the features extracted from the end-of-life charge-discharge cycle, our model exhibits 1% and 3% cathode sorting errors under homogeneous and heterogeneous battery recycling settings respectively, attributed to our innovative Wasserstein-distance voting strategy. Economically, the proposed method underscores the value of precise battery sorting for a prosperous and sustainable recycling industry. This study heralds a new paradigm of using privacy-sensitive data from diverse sources, facilitating collaborative and privacy-respecting decision-making for distributed systems.
| S-EPMC10697957 | biostudies-literature
Project description:MotivationGenome-wide association studies (GWAS) benefit from the increasing availability of genomic data and cross-institution collaborations. However, sharing data across institutional boundaries jeopardizes medical data confidentiality and patient privacy. While modern cryptographic techniques provide formal secure guarantees, the substantial communication and computational overheads hinder the practical application of large-scale collaborative GWAS.ResultsThis work introduces an efficient framework for conducting collaborative GWAS on distributed datasets, maintaining data privacy without compromising the accuracy of the results. We propose a novel two-step strategy aimed at reducing communication and computational overheads, and we employ iterative and sampling techniques to ensure accurate results. We instantiate our approach using logistic regression, a commonly used statistical method for identifying associations between genetic markers and the phenotype of interest. We evaluate our proposed methods using two real genomic datasets and demonstrate their robustness in the presence of between-study heterogeneity and skewed phenotype distributions using a variety of experimental settings. The empirical results show the efficiency and applicability of the proposed method and the promise for its application for large-scale collaborative GWAS.Availability and implementationThe source code and data are available at https://github.com/amioamo/TDS.
| S-EPMC10612407 | biostudies-literature
Project description:Privacy protection is paramount in conducting health research. However, studies often rely on data stored in a centralized repository, where analysis is done with full access to the sensitive underlying content. Recent advances in federated learning enable building complex machine-learned models that are trained in a distributed fashion. These techniques facilitate the calculation of research study endpoints such that private data never leaves a given device or healthcare system. We show-on a diverse set of single and multi-site health studies-that federated models can achieve similar accuracy, precision, and generalizability, and lead to the same interpretation as standard centralized statistical models while achieving considerably stronger privacy protections and without significantly raising computational costs. This work is the first to apply modern and general federated learning methods that explicitly incorporate differential privacy to clinical and epidemiological research-across a spectrum of units of federation, model architectures, complexity of learning tasks and diseases. As a result, it enables health research participants to remain in control of their data and still contribute to advancing science-aspects that used to be at odds with each other.
| S-EPMC8423792 | biostudies-literature
Project description:While federated learning (FL) is promising for efficient collaborative learning without revealing local data, it remains vulnerable to white-box privacy attacks, suffers from high communication overhead, and struggles to adapt to heterogeneous models. Federated distillation (FD) emerges as an alternative paradigm to tackle these challenges, which transfers knowledge among clients instead of model parameters. Nevertheless, challenges arise due to variations in local data distributions and the absence of a well-trained teacher model, which leads to misleading and ambiguous knowledge sharing that significantly degrades model performance. To address these issues, this paper proposes a selective knowledge sharing mechanism for FD, termed Selective-FD, to identify accurate and precise knowledge from local and ensemble predictions, respectively. Empirical studies, backed by theoretical insights, demonstrate that our approach enhances the generalization capabilities of the FD framework and consistently outperforms baseline methods. We anticipate our study to enable a privacy-preserving, communication-efficient, and heterogeneity-adaptive federated training framework.
| S-EPMC10774276 | biostudies-literature