OBJECTIVE: A previous study, PheMAP, combined independent, online resources to enable high-throughput phenotyping (HTP) using electronic health records (EHRs). However, online resources offer distinct quality descriptions of diseases which may affect phenotyping performance. We aimed to evaluate the phenotyping performance of single resource-based PheMAPs and investigate an optimized strategy for HTP. MATERIALS AND METHODS: We compared how each resource produced top-ranked concept unique identifiers (CUIs) by term frequency-inverse document frequency with Jaccard matrices comparing single resources and the original PheMAP. We correlated top-ranked concepts from each resource to features used in established Phenotype KnowledgeBase (PheKB) algorithms for hypothyroidism, type II diabetes mellitus (T2DM), and dementias. Using resources separately, we calculated multiple phenotype risk scores for individuals from Vanderbilt University Medical Center's BioVU DNA Biobank and compared phenotyping performance against rule-based eMERGE algorithms. Lastly, we implemented an ensemble strategy which classified patient case/control status based upon PheMAP resource agreement. RESULTS: Jaccard similarity matrices indicate that the similarity of CUIs comprising single resource-based PheMAPs varies. Single resource-based PheMAPs generated from MedlinePlus and MedicineNet outperformed others but only encompass 81.6% of overall disease phenotypes. We propose the PheMAP-Ensemble which provides higher average accuracy and precision than the combined average accuracy and precision of single resource-based PheMAPs. While offering complete phenotype coverage, PheMAP-Ensemble significantly increases phenotyping recall compared to the original iteration. CONCLUSIONS: Resources comprising the PheMAP produce different phenotyping performance when implemented individually. The ensemble method significantly improves the quality of PheMAP by fully utilizing dissimilar resources to capture accurate phenotyping data from EHRs.

Federated learning is a collaborative/distributed machine learning system which is designed to address the privacy issues in centralized machine learning systems. The transparency and provenance of a machine learning model are important aspects of federated learning systems since they impact peoples’ lives in various domains (e.g., from healthcare to personal finance to employment). However, most of the existing federated learning systems deal with centralized coordinators which are vulnerable to attacks and privacy breaches. Also, they do not provide any standard transparency and provenance mechanisms for the resulting models. In this paper, we propose a blockchain and Model Card-based integrated federated learning system "Bassa-ML" providing enhanced transparency and trust for the models. Model parameter sharing, local model generation, model averaging, and model sharing functions are implemented using smart contracts. The generated models, model training information, and model reports are stored in the blockchain ledger as Model Card Objects. This results in enhanced transparency and auditability to the federated learning process.

OBJECTIVE: We developed and evaluated Drug-Drug Interaction Wide Association Study (DDIWAS). This novel method detects potential drug-drug interactions (DDIs) by leveraging data from the electronic health record (EHR) allergy list. MATERIALS AND METHODS: To identify potential DDIs, DDIWAS scans for drug pairs that are frequently documented together on the allergy list. Using deidentified medical records, we tested 616 drugs for potential DDIs with simvastatin (a common lipid-lowering drug) and amlodipine (a common blood-pressure lowering drug). We evaluated the performance to rediscover known DDIs using existing knowledge bases and domain expert review. To validate potential novel DDIs, we manually reviewed patient charts and searched the literature. RESULTS: DDIWAS replicated 34 known DDIs. The positive predictive value to detect known DDIs was 0.85 and 0.86 for simvastatin and amlodipine, respectively. DDIWAS also discovered potential novel interactions between simvastatin-hydrochlorothiazide, amlodipine-omeprazole, and amlodipine-valacyclovir. A software package to conduct DDIWAS is publicly available. CONCLUSIONS: In this proof-of-concept study, we demonstrate the value of incorporating information mined from existing allergy lists to detect DDIs in a real-world clinical setting. Since allergy lists are routinely collected in EHRs, DDIWAS has the potential to detect and validate DDI signals across institutions.

OBJECTIVE: Developing algorithms to extract phenotypes from electronic health records (EHRs) can be challenging and time-consuming. We developed PheMap, a high-throughput phenotyping approach that leverages multiple independent, online resources to streamline the phenotyping process within EHRs. MATERIALS AND METHODS: PheMap is a knowledge base of medical concepts with quantified relationships to phenotypes that have been extracted by natural language processing from publicly available resources. PheMap searches EHRs for each phenotype's quantified concepts and uses them to calculate an individual's probability of having this phenotype. We compared PheMap to clinician-validated phenotyping algorithms from the Electronic Medical Records and Genomics (eMERGE) network for type 2 diabetes mellitus (T2DM), dementia, and hypothyroidism using 84 821 individuals from Vanderbilt Univeresity Medical Center's BioVU DNA Biobank. We implemented PheMap-based phenotypes for genome-wide association studies (GWAS) for T2DM, dementia, and hypothyroidism, and phenome-wide association studies (PheWAS) for variants in FTO, HLA-DRB1, and TCF7L2. RESULTS: In this initial iteration, the PheMap knowledge base contains quantified concepts for 841 disease phenotypes. For T2DM, dementia, and hypothyroidism, the accuracy of the PheMap phenotypes were >97% using a 50% threshold and eMERGE case-control status as a reference standard. In the GWAS analyses, PheMap-derived phenotype probabilities replicated 43 of 51 previously reported disease-associated variants for the 3 phenotypes. For 9 of the 11 top associations, PheMap provided an equivalent or more significant P value than eMERGE-based phenotypes. The PheMap-based PheWAS showed comparable or better performance to a traditional phecode-based PheWAS. PheMap is publicly available online. CONCLUSIONS: PheMap significantly streamlines the process of extracting research-quality phenotype information from EHRs, with comparable or better performance to current phenotyping approaches.

Network attacks are serious concerns in today’s increasingly interconnected society. Recent studies have applied conventional machine learning to network attack detection by learning the patterns of the network behaviors and training a classification model. These models usually require large labeled datasets; however, the rapid pace and unpredictability of cyber attacks make this labeling impossible in real time. To address these problems, we proposed utilizing transfer learning for detecting new and unseen attacks by transferring the knowledge of the known attacks. In our previous work, we have proposed a transfer learning-enabled framework and approach, called HeTL, which can find the common latent subspace of two different attacks and learn an optimized representation, which was invariant to attack behaviors’ changes. However, HeTL relied on manual pre-settings of hyper-parameters such as relativeness between the source and target attacks. In this paper, we extended this study by proposing a clustering-enhanced transfer learning approach, called CeHTL, which can automatically find the relation between the new attack and known attack. We evaluated these approaches by stimulating scenarios where the testing dataset contains different attack types or subtypes from the training set. We chose several conventional classification models such as decision trees, random forests, KNN, and other novel transfer learning approaches as strong baselines. Results showed that proposed HeTL and CeHTL improved the performance remarkably. CeHTL performed best, demonstrating the effectiveness of transfer learning in detecting new network attacks.

Cyber-physical systems (CPS) including power systems, transportation, industrial control systems, etc. support both advanced control and communications among system components. Frequent data operations could introduce random failures and malicious attacks or even bring down the whole system. The dependency on a central authority increases the risk of single point of failure. To establish an immutable data provenance scheme for CPS, the authors adopt blockchain and propose a decentralized architecture to assure data integrity. In business-driven CPS, end users are required to share their personal information with multiple third parties. To prevent data leakage and preserve user privacy, the authors isolate and feed different information retrieval requests using tokens specifically generated for each type of request. Providing both traceability of data operations, and unlinkability of end user activities, a robust blockchain-based CPS is prototyped. Evaluation indicates the architecture is capable of assured data provenance validation and user privacy preservation at a low overhead.

Enabled by mobile and wearable technology, personal health data delivers immense and increasing value for healthcare, benefiting both care providers and medical research. The secure and convenient sharing of personal health data is crucial to the improvement of the interaction and collaboration of the healthcare industry. Faced with the potential privacy issues and vulnerabilities existing in current personal health data storage and sharing systems, as well as the concept of self-sovereign data ownership, we propose an innovative user-centric health data sharing solution by utilizing a decentralized and permissioned blockchain to protect privacy using channel formation scheme and enhance the identity management using the membership service supported by the blockchain. A mobile application is deployed to collect health data from personal wearable devices, manual input, and medical devices, and synchronize data to the cloud for data sharing with healthcare providers and health insurance companies. To preserve the integrity of health data, within each record, a proof of integrity and validation is permanently retrievable from cloud database and is anchored to the blockchain network. Moreover, for scalable and performance considerations, we adopt a tree-based data processing and batching method to handle large data sets of personal health data collected and uploaded by the mobile platform.

Applying for research funding projects is becoming one of the most important ways for scientists to carry on the research. How to find an appropriate collaborator/applicant is a major concern for scientists. Social networks provide one means of visualizing existing and potential collaborations. In this paper, we study the funding collaborators recommendation problems. We solve the problem by starting with analyzing the researchers' motivations for finding collaboration, which are (i) to form a competitive team (ii) to expand cooperation circle, which little work noticed. We model the funding relation as a complex network called co-applicant network. Based on that, we propose a utility function to take all the aspects of recommendation into account. And we propose a novel recommendation algorithm by modeling the utility function based on the group relations in the co-applicant network. We experiment our approaches on National Science Foundation of China (NSFC) funding projects and achieve effective results.

In this paper, we carry out a knowledge-based scholar network practice towards Research community, named Research Social Networking, shortly DSN, by setting up a large knowledge base of scientists. We discuss key technologies in the paper, including scholar disambiguation and relationship extraction with the better performance evaluation than traditional methods. The DSN system has been implemented and integrated with Duckling cloud service, known as Research Online, with more than 60 thousand scientists and 100 thousand papers.