Privacy-first health research with federated learning.
Ontology highlight
ABSTRACT:
SUBMITTER: Sadilek A
PROVIDER: S-EPMC8423792 | biostudies-literature |
REPOSITORIES: biostudies-literature
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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:BackgroundThe collection, storage, and analysis of large data sets are relevant in many sectors. Especially in the medical field, the processing of patient data promises great progress in personalized health care. However, it is strictly regulated, such as by the General Data Protection Regulation (GDPR). These regulations mandate strict data security and data protection and, thus, create major challenges for collecting and using large data sets. Technologies such as federated learning (FL), especially paired with differential privacy (DP) and secure multiparty computation (SMPC), aim to solve these challenges.ObjectiveThis scoping review aimed to summarize the current discussion on the legal questions and concerns related to FL systems in medical research. We were particularly interested in whether and to what extent FL applications and training processes are compliant with the GDPR data protection law and whether the use of the aforementioned privacy-enhancing technologies (DP and SMPC) affects this legal compliance. We placed special emphasis on the consequences for medical research and development.MethodsWe performed a scoping review according to the PRISMA-ScR (Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews). We reviewed articles on Beck-Online, SSRN, ScienceDirect, arXiv, and Google Scholar published in German or English between 2016 and 2022. We examined 4 questions: whether local and global models are "personal data" as per the GDPR; what the "roles" as defined by the GDPR of various parties in FL are; who controls the data at various stages of the training process; and how, if at all, the use of privacy-enhancing technologies affects these findings.ResultsWe identified and summarized the findings of 56 relevant publications on FL. Local and likely also global models constitute personal data according to the GDPR. FL strengthens data protection but is still vulnerable to a number of attacks and the possibility of data leakage. These concerns can be successfully addressed through the privacy-enhancing technologies SMPC and DP.ConclusionsCombining FL with SMPC and DP is necessary to fulfill the legal data protection requirements (GDPR) in medical research dealing with personal data. Even though some technical and legal challenges remain, for example, the possibility of successful attacks on the system, combining FL with SMPC and DP creates enough security to satisfy the legal requirements of the GDPR. This combination thereby provides an attractive technical solution for health institutions willing to collaborate without exposing their data to risk. From a legal perspective, the combination provides enough built-in security measures to satisfy data protection requirements, and from a technical perspective, the combination provides secure systems with comparable performance with centralized machine learning applications.
| S-EPMC10131784 | biostudies-literature
Project description:BackgroundThe use of wearables facilitates data collection at a previously unobtainable scale, enabling the construction of complex predictive models with the potential to improve health. However, the highly personal nature of these data requires strong privacy protection against data breaches and the use of data in a way that users do not intend. One method to protect user privacy while taking advantage of sharing data across users is federated learning, a technique that allows a machine learning model to be trained using data from all users while only storing a user's data on that user's device. By keeping data on users' devices, federated learning protects users' private data from data leaks and breaches on the researcher's central server and provides users with more control over how and when their data are used. However, there are few rigorous studies on the effectiveness of federated learning in the mobile health (mHealth) domain.ObjectiveWe review federated learning and assess whether it can be useful in the mHealth field, especially for addressing common mHealth challenges such as privacy concerns and user heterogeneity. The aims of this study are to describe federated learning in an mHealth context, apply a simulation of federated learning to an mHealth data set, and compare the performance of federated learning with the performance of other predictive models.MethodsWe applied a simulation of federated learning to predict the affective state of 15 subjects using physiological and motion data collected from a chest-worn device for approximately 36 minutes. We compared the results from this federated model with those from a centralized or server model and with the results from training individual models for each subject.ResultsIn a 3-class classification problem using physiological and motion data to predict whether the subject was undertaking a neutral, amusing, or stressful task, the federated model achieved 92.8% accuracy on average, the server model achieved 93.2% accuracy on average, and the individual model achieved 90.2% accuracy on average.ConclusionsOur findings support the potential for using federated learning in mHealth. The results showed that the federated model performed better than a model trained separately on each individual and nearly as well as the server model. As federated learning offers more privacy than a server model, it may be a valuable option for designing sensitive data collection methods.
| S-EPMC8044739 | 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: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: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:Thermal comfort is a crucial element of smart buildings that assists in improving, analyzing, and realizing intelligent structures. Energy consumption forecasts for such smart buildings are crucial owing to the intricate decision-making processes surrounding resource efficiency. Machine learning (ML) techniques are employed to estimate energy consumption. ML algorithms, however, require a large amount of data to be adequate. There may be privacy violations due to collecting this data. To tackle this problem, this study proposes a federated deep learning (FDL) architecture developed around a deep neural network (DNN) paradigm. The study employs the ASHRAE RP-884 standard dataset for experimentation and analysis, which is available to the general public. The data is normalized using the min-max normalization approach, and the Synthetic Minority Over-sampling Technique (SMOTE) is used to enhance the minority class's interpretation. The DNN model is trained separately on the dataset after obtaining modifications from two clients. Each client assesses the data greatly to reduce the over-fitting impact. The test result demonstrates the efficiency of the proposed FDL by reaching 82.40% accuracy while securing the data.
| S-EPMC10909213 | 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:The reliance on data donation from citizens as a driver for research, known as citizen science, has accelerated during the Sars-Cov-2 pandemic. An important enabler of this is Internet of Things (IoT) devices, such as mobile phones and wearable devices, that allow continuous data collection and convenient sharing. However, potentially sensitive health data raises privacy and security concerns for citizens, which research institutions and industries must consider. In e-commerce or social network studies of citizen science, a privacy calculus related to user perceptions is commonly developed, capturing the information disclosure intent of the participants. In this study, we develop a privacy calculus model adapted for IoT-based health research using citizen science for user engagement and data collection. Based on an online survey with 85 participants, we make use of the privacy calculus to analyse the respondents' perceptions. The emerging privacy personas are clustered and compared with previous research, resulting in three distinct personas which can be used by designers and technologists who are responsible for developing suitable forms of data collection. These are the 1) Citizen Science Optimist, the 2) Selective Data Donor, and the 3) Health Data Controller. Together with our privacy calculus for citizen science based digital health research, the three privacy personas are the main contributions of this study.
| S-EPMC8716597 | biostudies-literature