Privacy-preserving model learning on a blockchain network-of-networks.

ObjectiveTo facilitate clinical/genomic/biomedical research, constructing generalizable predictive models using cross-institutional methods while protecting privacy is imperative. However, state-of-the-art methods assume a "flattened" topology, while real-world research networks may consist of "network-of-networks" which can imply practical issues including training on small data for rare diseases/conditions, prioritizing locally trained models, and maintaining models for each level of the hierarchy. In this study, we focus on developing a hierarchical approach to inherit the benefits of the privacy-preserving methods, retain the advantages of adopting blockchain, and address practical concerns on a research network-of-networks.Materials and methodsWe propose a framework to combine level-wise model learning, blockchain-based model dissemination, and a novel hierarchical consensus algorithm for model ensemble. We developed an example implementation HierarchicalChain (hierarchical privacy-preserving modeling on blockchain), evaluated it on 3 healthcare/genomic datasets, as well as compared its predictive correctness, learning iteration, and execution time with a state-of-the-art method designed for flattened network topology.ResultsHierarchicalChain improves the predictive correctness for small training datasets and provides comparable correctness results with the competing method with higher learning iteration and similar per-iteration execution time, inherits the benefits of the privacy-preserving learning and advantages of blockchain technology, and immutable records models for each level.DiscussionHierarchicalChain is independent of the core privacy-preserving learning method, as well as of the underlying blockchain platform. Further studies are warranted for various types of network topology, complex data, and privacy concerns.ConclusionWe demonstrated the potential of utilizing the information from the hierarchical network-of-networks topology to improve prediction

Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

Privacy-Preserving Patient Similarity Learning in a Federated Environment: Development and Analysis

Background: There 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. Objective: The 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. Methods: We 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. Results: We 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. Conclusions: The proposed algorithm can help search similar patients across institutions effectively to support federated data analysis in a privacy-preserving manner

Impacts of Data Synthesis: A Metric for Quantifiable Data Standards and Performances

Clinical data analysis could lead to breakthroughs. However, clinical data contain sensitive information about participants that could be utilized for unethical activities, such as blackmailing, identity theft, mass surveillance, or social engineering. Data anonymization is a standard step during data collection, before sharing, to overcome the risk of disclosure. However, conventional data anonymization techniques are not foolproof and also hinder the opportunity for personalized evaluations. Much research has been done for synthetic data generation using generative adversarial networks and many other machine learning methods; however, these methods are either not free to use or are limited in capacity. This study evaluates the performance of an emerging tool named synthpop, an R package producing synthetic data as an alternative approach for data anonymization. This paper establishes data standards derived from the original data set based on the utilities and quality of information and measures variations in the synthetic data set to evaluate the performance of the data synthesis process. The methods to assess the utility of the synthetic data set can be broadly divided into two approaches: general utility and specific utility. General utility assesses whether synthetic data have overall similarities in the statistical properties and multivariate relationships with the original data set. Simultaneously, the specific utility assesses the similarity of a fitted model’s performance on the synthetic data to its performance on the original data. The quality of information is assessed by comparing variations in entropy bits and mutual information to response variables within the original and synthetic data sets. The study reveals that synthetic data succeeded at all utility tests with a statistically non-significant difference and not only preserved the utilities but also preserved the complexity of the original data set according to the data standard established in this study. Therefore, synthpop fulfills all the necessities and unfolds a wide range of opportunities for the research community, including easy data sharing and information protection

Personalized Federated Deep Learning for Pain Estimation From Face Images

Standard machine learning approaches require centralizing the users' data in one computer or a shared database, which raises data privacy and confidentiality concerns. Therefore, limiting central access is important, especially in healthcare settings, where data regulations are strict. A potential approach to tackling this is Federated Learning (FL), which enables multiple parties to collaboratively learn a shared prediction model by using parameters of locally trained models while keeping raw training data locally. In the context of AI-assisted pain-monitoring, we wish to enable confidentiality-preserving and unobtrusive pain estimation for long-term pain-monitoring and reduce the burden on the nursing staff who perform frequent routine check-ups. To this end, we propose a novel Personalized Federated Deep Learning (PFDL) approach for pain estimation from face images. PFDL performs collaborative training of a deep model, implemented using a lightweight CNN architecture, across different clients (i.e., subjects) without sharing their face images. Instead of sharing all parameters of the model, as in standard FL, PFDL retains the last layer locally (used to personalize the pain estimates). This (i) adds another layer of data confidentiality, making it difficult for an adversary to infer pain levels of the target subject, while (ii) personalizing the pain estimation to each subject through local parameter tuning. We show using a publicly available dataset of face videos of pain (UNBC-McMaster Shoulder Pain Database), that PFDL performs comparably or better than the standard centralized and FL algorithms, while further enhancing data privacy. This, has the potential to improve traditional pain monitoring by making it more secure, computationally efficient, and scalable to a large number of individuals (e.g., for in-home pain monitoring), providing timely and unobtrusive pain measurement.Comment: 12 pages, 6 figure

Deep Learning-Based Intrusion Detection Methods for Computer Networks and Privacy-Preserving Authentication Method for Vehicular Ad Hoc Networks

The incidence of computer network intrusions has significantly increased over the last decade, partially attributed to a thriving underground cyber-crime economy and the widespread availability of advanced tools for launching such attacks. To counter these attacks, researchers in both academia and industry have turned to machine learning (ML) techniques to develop Intrusion Detection Systems (IDSes) for computer networks. However, many of the datasets use to train ML classifiers for detecting intrusions are not balanced, with some classes having fewer samples than others. This can result in ML classifiers producing suboptimal results. In this dissertation, we address this issue and present better ML based solutions for intrusion detection. Our contributions in this direction can be summarized as follows: Balancing Data Using Synthetic Data to detect intrusions in Computer Networks: In the past, researchers addressed the issue of imbalanced data in datasets by using over-sampling and under-sampling techniques. In this study, we go beyond such traditional methods and utilize a synthetic data generation method called Con- ditional Generative Adversarial Network (CTGAN) to balance the datasets and in- vestigate its impact on the performance of widely used ML classifiers. To the best of our knowledge, no one else has used CTGAN to generate synthetic samples for balancing intrusion detection datasets. We use two widely used publicly available datasets and conduct extensive experiments and show that ML classifiers trained on these datasets balanced with synthetic samples generated by CTGAN have higher prediction accuracy and Matthew Correlation Coefficient (MCC) scores than those trained on imbalanced datasets by 8% and 13%, respectively. Deep Learning approach for intrusion detection using focal loss function: To overcome the data imbalance problem for intrusion detection, we leverage the specialized loss function, called focal loss, that automatically down-weighs easy ex- amples and focuses on the hard negatives by facilitating dynamically scaled-gradient updates for training ML models effectively. We implement our approach using two well-known Deep Learning (DL) neural network architectures. Compared to training DL models using cross-entropy loss function, our approach (training DL models using focal loss function) improved accuracy, precision, F1 score, and MCC score by 24%, 39%, 39%, and 60% respectively. Efficient Deep Learning approach to detect Intrusions using Few-shot Learning: To address the issue of imbalance the datasets and develop a highly effective IDS, we utilize the concept of few-shot learning. We present a Few-Shot and Self-Supervised learning framework, called FS3, for detecting intrusions in IoT networks. FS3 works in three phases. Our approach involves first pretraining an encoder on a large-scale external dataset in a selfsupervised manner. We then employ few-shot learning (FSL), which seeks to replicate the encoder’s ability to learn new patterns from only a few training examples. During the encoder training us- ing a small number of samples, we train them contrastively, utilizing the triplet loss function. The third phase introduces a novel K-Nearest neighbor algorithm that sub- samples the majority class instances to further reduce imbalance and improve overall performance. Our proposed framework FS3, utilizing only 20% of labeled data, out- performs fully supervised state-of-the-art models by up to 42.39% and 43.95% with respect to the metrics precision and F1 score, respectively. The rapid evolution of the automotive industry and advancements in wireless com- munication technologies will result in the widespread deployment of Vehicular ad hoc networks (VANETs). However, despite the network’s potential to enable intelligent and autonomous driving, it also introduces various attack vectors that can jeopardize its security. In this dissertation, we present efficient privacy-preserving authenticated message dissemination scheme in VANETs. Conditional Privacy-preserving Authentication and Message Dissemination Scheme using Timestamp based Pseudonyms: To authenticate a message sent by a vehicle using its pseudonym, a certificate of the pseudonym signed by the central authority is generally utilized. If a vehicle is found to be malicious, certificates associated with all the pseudonyms assigned to it must be revoked. Certificate revocation lists (CRLs) should be shared with all entities that will be corresponding with the vehicle. As each vehicle has a large pool of pseudonyms allocated to it, the CRL can quickly grow in size as the number of revoked vehicles increases. This results in high storage overheads for storing the CRL, and significant authentication overheads as the receivers must check their CRL for each message received to verify its pseudonym. To address this issue, we present a timestamp-based pseudonym allocation scheme that reduces the storage overhead and authentication overhead by streamlining the CRL management process

sPLINK : a hybrid federated tool as a robust alternative to meta-analysis in genome-wide association studies

Meta-analysis has been established as an effective approach to combining summary statistics of several genome-wide association studies (GWAS). However, the accuracy of meta-analysis can be attenuated in the presence of cross-study heterogeneity. We present sPLINK, a hybrid federated and user-friendly tool, which performs privacy-aware GWAS on distributed datasets while preserving the accuracy of the results. sPLINK is robust against heterogeneous distributions of data across cohorts while meta-analysis considerably loses accuracy in such scenarios. sPLINK achieves practical runtime and acceptable network usage for chi-square and linear/logistic regression tests.Peer reviewe

Garantia de privacidade na exploração de bases de dados distribuídas

Anonymisation is currently one of the biggest challenges when sharing sensitive personal information. Its importance depends largely on the application domain, but when dealing with health information, this becomes a more serious issue. A simpler approach to avoid this disclosure is to ensure that all data that can be associated directly with an individual is removed from the original dataset. However, some studies have shown that simple anonymisation procedures can sometimes be reverted using specific patients’ characteristics, namely when the anonymisation is based on hidden key attributes. In this work, we propose a secure architecture to share information from distributed databases without compromising the subjects’ privacy. The work was initially focused on identifying techniques to link information between multiple data sources, in order to revert the anonymization procedures. In a second phase, we developed the methodology to perform queries over distributed databases was proposed. The architecture was validated using a standard data schema that is widely adopted in observational research studies.A garantia da anonimização de dados é atualmente um dos maiores desafios quando existe a necessidade de partilhar informações pessoais de carácter sensível. Apesar de ser um problema transversal a muitos domínios de aplicação, este torna-se mais crítico quando a anonimização envolve dados clinicos. Nestes casos, a abordagem mais comum para evitar a divulgação de dados, que possam ser associados diretamente a um indivíduo, consiste na remoção de atributos identificadores. No entanto, segundo a literatura, esta abordagem não oferece uma garantia total de anonimato, que pode ser quebrada através de ataques específicos que permitem a reidentificação dos sujeitos. Neste trabalho, é proposta uma arquitetura que permite partilhar dados armazenados em repositórios distribuídos, de forma segura e sem comprometer a privacidade. Numa primeira fase deste trabalho, foi feita uma análise de técnicas que permitam reverter os procedimentos de anonimização. Na fase seguinte, foi proposta uma metodologia que permite realizar pesquisas em bases de dados distribuídas, sem que o anonimato seja quebrado. Esta arquitetura foi validada sobre um esquema de base de dados relacional que é amplamente utilizado em estudos clínicos observacionais.Mestrado em Ciberseguranç