Systematizing Genome Privacy Research: A Privacy-Enhancing Technologies Perspective

Rapid advances in human genomics are enabling researchers to gain a better understanding of the role of the genome in our health and well-being, stimulating hope for more effective and cost efficient healthcare. However, this also prompts a number of security and privacy concerns stemming from the distinctive characteristics of genomic data. To address them, a new research community has emerged and produced a large number of publications and initiatives. In this paper, we rely on a structured methodology to contextualize and provide a critical analysis of the current knowledge on privacy-enhancing technologies used for testing, storing, and sharing genomic data, using a representative sample of the work published in the past decade. We identify and discuss limitations, technical challenges, and issues faced by the community, focusing in particular on those that are inherently tied to the nature of the problem and are harder for the community alone to address. Finally, we report on the importance and difficulty of the identified challenges based on an online survey of genome data privacy expertsComment: To appear in the Proceedings on Privacy Enhancing Technologies (PoPETs), Vol. 2019, Issue

Big data analytics:Computational intelligence techniques and application areas

Big Data has significant impact in developing functional smart cities and supporting modern societies. In this paper, we investigate the importance of Big Data in modern life and economy, and discuss challenges arising from Big Data utilization. Different computational intelligence techniques have been considered as tools for Big Data analytics. We also explore the powerful combination of Big Data and Computational Intelligence (CI) and identify a number of areas, where novel applications in real world smart city problems can be developed by utilizing these powerful tools and techniques. We present a case study for intelligent transportation in the context of a smart city, and a novel data modelling methodology based on a biologically inspired universal generative modelling approach called Hierarchical Spatial-Temporal State Machine (HSTSM). We further discuss various implications of policy, protection, valuation and commercialization related to Big Data, its applications and deployment

Diabetes Diagnosis by Case-Based Reasoning and Fuzzy Logic

In the medical field, experts’ knowledge is based on experience, theoretical knowledge and rules. Case-based reasoning is a problem-solving paradigm which is based on past experiences. For this purpose, a large number of decision support applications based on CBR have been developed. Cases retrieval is often considered as the most important step of case-based reasoning. In this article, we integrate fuzzy logic and data mining to improve the response time and the accuracy of the retrieval of similar cases. The proposed Fuzzy CBR is composed of two complementary parts; the part of classification by fuzzy decision tree realized by Fispro and the part of case-based reasoning realized by the platform JColibri. The use of fuzzy logic aims to reduce the complexity of calculating the degree of similarity that can exist between diabetic patients who require different monitoring plans. The results of the proposed approach are compared with earlier methods using accuracy as metrics. The experimental results indicate that the fuzzy decision tree is very effective in improving the accuracy for diabetes classification and hence improving the retrieval step of CBR reasoning

Decision support systems for adoption in dental clinics: a survey

While most dental clinicians use some sort of information system, they are involved with administrative functions, despite the advisory potential of some of these systems. This paper outlines some current decision support systems (DSS) and the common barriers facing dentists in adopting them within their workflow. These barriers include lack of perceived usefulness, complicated social and economic factors, and the difficulty for users to interpret the advice given by the system. A survey of current systems found that although there are systems that suggest treatment options, there is no real-time integration with other knowledge bases. Additionally, advice on drug prescription at point-of-care is absent from such systems, which is a significant omission, in consideration of the fact that disease management and drug prescription are common in the workflow of a dentist. This paper also addresses future trends in the research and development of dental clinical DSS, with specific emphasis on big data, standards and privacy issues to fulfil the vision of a robust, user-friendly and scalable personalised DSS for dentists. The findings of this study will offer strategies in design, research and development of a DSS with sufficient perceived usefulness to attract adoption and integration by dentists within their routine clinical workflow, thus resulting in better health outcomes for patients and increased productivity for the clinic

A case-based reasoning framework for prediction of stroke

© Springer Nature Singapore Pte Ltd. 2018. Case-based reasoning (CBR) has been a popular method in health care sector from the last two decades. It is used for analysis, prediction, diagnosis and recommending treatment for patients. This research purposes a conceptual CBR framework for stroke disease prediction that uses previous case-based knowledge. The outcomes of this approach not only assist in stroke disease decision-making, but also will be very useful for prevention and early treatment of patients

geneCBR: a translational tool for multiple-microarray analysis and integrative information retrieval for aiding diagnosis in cancer research

8 pages, 5 figures, 3 additional files.-- Software.[Background] Bioinformatics and medical informatics are two research fields that serve the needs of different but related communities. Both domains share the common goal of providing new algorithms, methods and technological solutions to biomedical research, and contributing to the treatment and cure of diseases. Although different microarray techniques have been successfully used to investigate useful information for cancer diagnosis at the gene expression level, the true integration of existing methods into day-to-day clinical practice is still a long way off. Within this context, case-based reasoning emerges as a suitable paradigm specially intended for the development of biomedical informatics applications and decision support systems, given the support and collaboration involved in such a translational development. With the goals of removing barriers against multi-disciplinary collaboration and facilitating the dissemination and transfer of knowledge to real practice, case-based reasoning systems have the potential to be applied to translational research mainly because their computational reasoning paradigm is similar to the way clinicians gather, analyze and process information in their own practice of clinical medicine.[Results] In addressing the issue of bridging the existing gap between biomedical researchers and clinicians who work in the domain of cancer diagnosis, prognosis and treatment, we have developed and made accessible a common interactive framework. Our geneCBR system implements a freely available software tool that allows the use of combined techniques that can be applied to gene selection, clustering, knowledge extraction and prediction for aiding diagnosis in cancer research. For biomedical researches, geneCBR expert mode offers a core workbench for designing and testing new techniques and experiments. For pathologists or oncologists, geneCBR diagnostic mode implements an effective and reliable system that can diagnose cancer subtypes based on the analysis of microarray data using a CBR architecture. For programmers, geneCBR programming mode includes an advanced edition module for run-time modification of previous coded techniques.[Conclusion] geneCBR is a new translational tool that can effectively support the integrative work of programmers, biomedical researches and clinicians working together in a common framework. The code is freely available under the GPL license and can be obtained at http://www.genecbr.org (webcite).This work is supported in part by the projects Research on Translational Bioinformatics (ref. 08VIB6) from University of Vigo and Development of computational tools for the classification and clustering of gene expression data in order to discover meaningful biological information in cancer diagnosis (ref. VA100A08) from JCyL (Spain). The work of D. Glez-Peña is supported by a "María Barbeito" contract from Xunta de Galicia.Peer reviewe

Content Based Image Retrieval (CBIR) in Remote Clinical Diagnosis and Healthcare

Content-Based Image Retrieval (CBIR) locates, retrieves and displays images alike to one given as a query, using a set of features. It demands accessible data in medical archives and from medical equipment, to infer meaning after some processing. A problem similar in some sense to the target image can aid clinicians. CBIR complements text-based retrieval and improves evidence-based diagnosis, administration, teaching, and research in healthcare. It facilitates visual/automatic diagnosis and decision-making in real-time remote consultation/screening, store-and-forward tests, home care assistance and overall patient surveillance. Metrics help comparing visual data and improve diagnostic. Specially designed architectures can benefit from the application scenario. CBIR use calls for file storage standardization, querying procedures, efficient image transmission, realistic databases, global availability, access simplicity, and Internet-based structures. This chapter recommends important and complex aspects required to handle visual content in healthcare.Comment: 28 pages, 6 figures, Book Chapter from "Encyclopedia of E-Health and Telemedicine

An Extended Semantic Interoperability Model for Distributed Electronic Health Record Based on Fuzzy Ontology Semantics

Semantic interoperability of distributed electronic health record (EHR) systems is a crucial problem for querying EHR and machine learning projects. The main contribution of this paper is to propose and implement a fuzzy ontology-based semantic interoperability framework for distributed EHR systems. First, a separate standard ontology is created for each input source. Second, a unified ontology is created that merges the previously created ontologies. However, this crisp ontology is not able to answer vague or uncertain queries. We thirdly extend the integrated crisp ontology into a fuzzy ontology by using a standard methodology and fuzzy logic to handle this limitation. The used dataset includes identified data of 100 patients. The resulting fuzzy ontology includes 27 class, 58 properties, 43 fuzzy data types, 451 instances, 8376 axioms, 5232 logical axioms, 1216 declarative axioms, 113 annotation axioms, and 3204 data property assertions. The resulting ontology is tested using real data from the MIMIC-III intensive care unit dataset and real archetypes from openEHR. This fuzzy ontology-based system helps physicians accurately query any required data about patients from distributed locations using near-natural language queries. Domain specialists validated the accuracy and correctness of the obtained resultsThis work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korean government (MSIT) (NRF-2021R1A2B5B02002599)S