Health systems data interoperability and implementation

Objective The objective of this study was to use machine learning and health standards to address the problem of clinical data interoperability across healthcare institutions. Addressing this problem has the potential to make clinical data comparable, searchable and exchangeable between healthcare providers. Data sources Structured and unstructured data has been used to conduct the experiments in this study. The data was collected from two disparate data sources namely MIMIC-III and NHanes. The MIMIC-III database stored data from two electronic health record systems which are CareVue and MetaVision. The data stored in these systems was not recorded with the same standards; therefore, it was not comparable because some values were conflicting, while one system would store an abbreviation of a clinical concept, the other would store the full concept name and some of the attributes contained missing information. These few issues that have been identified make this form of data a good candidate for this study. From the identified data sources, laboratory, physical examination, vital signs, and behavioural data were used for this study. Methods This research employed a CRISP-DM framework as a guideline for all the stages of data mining. Two sets of classification experiments were conducted, one for the classification of structured data, and the other for unstructured data. For the first experiment, Edit distance, TFIDF and JaroWinkler were used to calculate the similarity weights between two datasets, one coded with the LOINC terminology standard and another not coded. Similar sets of data were classified as matches while dissimilar sets were classified as non-matching. Then soundex indexing method was used to reduce the number of potential comparisons. Thereafter, three classification algorithms were trained and tested, and the performance of each was evaluated through the ROC curve. Alternatively the second experiment was aimed at extracting patient’s smoking status information from a clinical corpus. A sequence-oriented classification algorithm called CRF was used for learning related concepts from the given clinical corpus. Hence, word embedding, random indexing, and word shape features were used for understanding the meaning in the corpus. Results Having optimized all the model’s parameters through the v-fold cross validation on a sampled training set of structured data ( ), out of 24 features, only ( 8) were selected for a classification task. RapidMiner was used to train and test all the classification algorithms. On the final run of classification process, the last contenders were SVM and the decision tree classifier. SVM yielded an accuracy of 92.5% when the and parameters were set to and . These results were obtained after more relevant features were identified, having observed that the classifiers were biased on the initial data. On the other side, unstructured data was annotated via the UIMA Ruta scripting language, then trained through the CRFSuite which comes with the CLAMP toolkit. The CRF classifier obtained an F-measure of 94.8% for “nonsmoker” class, 83.0% for “currentsmoker”, and 65.7% for “pastsmoker”. It was observed that as more relevant data was added, the performance of the classifier improved. The results show that there is a need for the use of FHIR resources for exchanging clinical data between healthcare institutions. FHIR is free, it uses: profiles to extend coding standards; RESTFul API to exchange messages; and JSON, XML and turtle for representing messages. Data could be stored as JSON format on a NoSQL database such as CouchDB, which makes it available for further post extraction exploration. Conclusion This study has provided a method for learning a clinical coding standard by a computer algorithm, then applying that learned standard to unstandardized data so that unstandardized data could be easily exchangeable, comparable and searchable and ultimately achieve data interoperability. Even though this study was applied on a limited scale, in future, the study would explore the standardization of patient’s long-lived data from multiple sources using the SHARPn open-sourced tools and data scaling platformsInformation ScienceM. Sc. (Computing

Optimizing IETF multimedia signaling protocols and architectures in 3GPP networks : an evolutionary approach

Signaling in Next Generation IP-based networks heavily relies in the family of multimedia signaling protocols defined by IETF. Two of these signaling protocols are RTSP and SIP, which are text-based, client-server, request-response signaling protocols aimed at enabling multimedia sessions over IP networks. RTSP was conceived to set up streaming sessions from a Content / Streaming Server to a Streaming Client, while SIP was conceived to set up media (e.g.: voice, video, chat, file sharing, …) sessions among users. However, their scope has evolved and expanded over time to cover virtually any type of content and media session. As mobile networks progressively evolved towards an IP-only (All-IP) concept, particularly in 4G and 5G networks, 3GPP had to select IP-based signaling protocols for core mobile services, as opposed to traditional SS7-based protocols used in the circuit-switched domain in use in 2G and 3G networks. In that context, rather than reinventing the wheel, 3GPP decided to leverage Internet protocols and the work carried on by the IETF. Hence, it was not surprise that when 3GPP defined the so-called Packet-switched Streaming Service (PSS) for real-time continuous media delivery, it selected RTSP as its signaling protocol and, more importantly, SIP was eventually selected as the core signaling protocol for all multimedia core services in the mobile (All-)IP domain. This 3GPP decision to use off-the-shelf IETF-standardized signaling protocols has been a key cornerstone for the future of All-IP fixed / mobile networks convergence and Next Generation Networks (NGN) in general. In this context, the main goal of our work has been analyzing how such general purpose IP multimedia signaling protocols are deployed and behave over 3GPP mobile networks. Effectively, usage of IP protocols is key to enable cross-vendor interoperability. On the other hand, due to the specific nature of the mobile domain, there are scenarios where it might be possible to leverage some additional “context” to enhance the performance of such protocols in the particular case of mobile networks. With this idea in mind, the bulk of this thesis work has consisted on analyzing and optimizing the performance of SIP and RTSP multimedia signaling protocols and defining optimized deployment architectures, with particular focus on the 3GPP PSS and the 3GPP Mission Critical Push-to-Talk (MCPTT) service. This work was preceded by a detailed analysis work of the performance of underlying IP, UDP and TCP protocol performance over 3GPP networks, which provided the best baseline for the future work around IP multimedia signaling protocols. Our contributions include the proposal of new optimizations to enhance multimedia streaming session setup procedures, detailed analysis and optimizations of a SIP-based Presence service and, finally, the definition of new use cases and optimized deployment architectures for the 3GPP MCPTT service. All this work has been published in the form of one book, three papers published in JCR cited International Journals, 5 articles published in International Conferences, one paper published in a National Conference and one awarded patent. This thesis work provides a detailed description of all contributions plus a comprehensive overview of their context, the guiding principles beneath all contributions, their applicability to different network deployment technologies (from 2.5G to 5G), a detailed overview of the related OMA and 3GPP architectures, services and design principles. Last but not least, the potential evolution of this research work into the 5G domain is also outlined as well.Els mecanismes de Senyalització en xarxes de nova generació es fonamenten en protocols de senyalització definits per IETF. En particular, SIP i RTSP són dos protocols extensibles basats en missatges de text i paradigma petició-resposta. RTSP va ser concebut per a establir sessions de streaming de continguts, mentre SIP va ser creat inicialment per a facilitar l’establiment de sessions multimèdia (veu, vídeo, xat, compartició) entre usuaris. Tot i així, el seu àmbit d’aplicació s’ha anat expandint i evolucionant fins a cobrir virtualment qualsevol tipus de contingut i sessió multimèdia. A mesura que les xarxes mòbils han anat evolucionant cap a un paradigma “All-IP”, particularment en xarxes 4G i 5G, 3GPP va seleccionar els protocols i arquitectures destinats a gestionar la senyalització dels serveis mòbils presents i futurs. En un moment determinat 3GPP decideix que, a diferència dels sistemes 2G i 3G que fan servir protocols basats en SS7, els sistemes de nova generació farien servir protocols estandarditzats per IETF. Quan 3GPP va començar a estandarditzar el servei de Streaming sobre xarxes mòbils PSS (Packet-switched Streaming Service) va escollir el protocol RTSP com a mecanisme de senyalització. Encara més significatiu, el protocol SIP va ser escollit com a mecanisme de senyalització per a IMS (IP Multimedia Subsystem), l’arquitectura de nova generació que substituirà la xarxa telefònica tradicional i permetrà el desplegament de nous serveis multimèdia. La decisió per part de 3GPP de seleccionar protocols estàndards definits per IETF ha representat una fita cabdal per a la convergència del sistemes All-IP fixes i mòbils, i per al desenvolupament de xarxes NGN (Next Generation Networks) en general. En aquest context, el nostre objectiu inicial ha estat analitzar com aquests protocols de senyalització multimèdia, dissenyats per a xarxes IP genèriques, es comporten sobre xarxes mòbils 3GPP. Efectivament, l’ús de protocols IP és fonamental de cara a facilitar la interoperabilitat de solucions diferents. Per altra banda, hi ha escenaris a on és possible aprofitar informació de “context” addicional per a millorar el comportament d’aquests protocols en al cas particular de xarxes mòbils. El cos principal del treball de la tesi ha consistit en l’anàlisi i optimització del rendiment dels protocols de senyalització multimèdia SIP i RTSP, i la definició d’arquitectures de desplegament, amb èmfasi en els serveis 3GPP PSS i 3GPP Mission Critical Push-to-Talk (MCPTT). Aquest treball ha estat precedit per una feina d’anàlisi detallada del comportament dels protocols IP, TCP i UDP sobre xarxes 3GPP, que va proporcionar els fonaments adequats per a la posterior tasca d’anàlisi de protocols de senyalització sobre xarxes mòbils. Les contribucions inclouen la proposta de noves optimitzacions per a millorar els procediments d’establiment de sessions de streaming multimèdia, l’anàlisi detallat i optimització del servei de Presència basat en SIP i la definició de nous casos d’ús i exemples de desplegament d’arquitectures optimitzades per al servei 3GPP MCPTT. Aquestes contribucions ha quedat reflectides en un llibre, tres articles publicats en Revistes Internacionals amb índex JCR, 5 articles publicats en Conferències Internacionals, un article publicat en Congrés Nacional i l’adjudicació d’una patent. La tesi proporciona una descripció detallada de totes les contribucions, així com un exhaustiu repàs del seu context, dels principis fonamentals subjacents a totes les contribucions, la seva aplicabilitat a diferents tipus de desplegaments de xarxa (des de 2.5G a 5G), així una presentació detallada de les arquitectures associades definides per organismes com OMA o 3GPP. Finalment també es presenta l’evolució potencial de la tasca de recerca cap a sistemes 5G.Postprint (published version

Prototyping and Evaluation of Sensor Data Integration in Cloud Platforms

The SFI Smart Ocean centre has initiated a long-running project which consists of developing a wireless and autonomous marine observation system for monitoring of underwater environments and structures. The increasing popularity of integrating the Internet of Things (IoT) with Cloud Computing has led to promising infrastructures that could realize Smart Ocean's goals. The project will utilize underwater wireless sensor networks (UWSNs) for collecting data in the marine environments and develop a cloud-based platform for retrieving, processing, and storing all the sensor data. Currently, the project is in its early stages and the collaborating partners are researching approaches and technologies that can potentially be utilized. This thesis contributes to the centre's ongoing research, focusing on the aspect of how sensor data can be integrated into three different cloud platforms: Microsoft Azure, Amazon Web Services, and the Google Cloud Platform. The goals were to develop prototypes that could successfully send data to the chosen cloud platforms and evaluate their applicability in context of the Smart Ocean project. In order to determine the most suitable option, each platform was evaluated based on set of defined criteria, focusing on their sensor data integration capabilities. The thesis has also investigated the cloud platforms' supported protocol bindings, as well as several candidate technologies for metadata standards and compared them in surveys. Our evaluation results shows that all three cloud platforms handle sensor data integration in very similar ways, offering a set of cloud services relevant for creating diverse IoT solutions. However, the Google Cloud Platform ranks at the bottom due to the lack of IoT focus on their platform, with less service options, features, and capabilities compared to the other two. Both Microsoft Azure and Amazon Web Services rank very close to each other, as they provide many of the same sensor data integration capabilities, making them the most applicable options.Masteroppgave i Programutvikling samarbeid med HVLPROG399MAMN-PRO

Integrating institutional repositories into the Semantic Web

The Web has changed the face of scientific communication; and the Semantic Web promises new ways of adding value to research material by making it more accessible to automatic discovery, linking, and analysis. Institutional repositories contain a wealth of information which could benefit from the application of this technology. In this thesis I describe the problems inherent in the informality of traditional repository metadata, and propose a data model based on the Semantic Web which will support more efficient use of this data, with the aim of streamlining scientific communication and promoting efficient use of institutional research output

Implementing Azure Active Directory Integration with an Existing Cloud Service

Training Simulator (TraSim) is an online, web-based platform for holding crisis management exercises. It simulates epidemics and other exceptional situations to test the functionality of an organization’s operating instructions in the hour of need. The main objective of this thesis is to further develop the service by delegating its existing authentication and user provisioning mechanisms to a centralized, cloud-based Identity and Access Management (IAM) service. Making use of a centralized access control service is widely known as a Single Sign-On (SSO) implementation which comes with multiple benefits such as increased security, reduced administrative overhead and improved user experience. The objective originates from a customer organization’s request to enable SSO for TraSim. The research mainly focuses on implementing SSO by integrating TraSim with Azure Active Directory (AD) from a wide range of IAM services since it is considered as an industry standard and already utilized by the customer. Anyhow, the complexity of the integration is kept as reduced as possible to retain compatibility with other services besides Azure AD. While the integration is a unique operation with an endless amount of software stacks that a service can build on and multiple IAM services to choose from, this thesis aims to provide a general guideline of how to approach a resembling assignment. Conducting the study required extensive search and evaluation of the available literature about terms such as IAM, client-server communication, SSO, cloud services and AD. The literature review is combined with an introduction to the basic technologies that TraSim is built with to justify the choice of OpenID Connect as the authentication protocol and why it was implemented using the mozilla-django-oidc library. The literature consists of multiple online articles, publications and the official documentation of the utilized technologies. The research uses a constructive approach as it focuses into developing and testing a new feature that is merged into the source code of an already existing piece of software

Standards in the data storage industry : emergence, sustainability, and the battle for platform leadership

Thesis (S.M.)--Massachusetts Institute of Technology, System Design and Management Program, 2005.Includes bibliographical references (p. 127-130).In order to cope with the continuous increase of magnetically stored data and of mission critical dependence on this data, storage systems must similarly increase in their functionality offerings, and with that, their complexity. The efficient management of the heterogeneous and complex aggregation of these systems is becoming one of the major challenges to IT customers. At the same time, hardware is becoming commoditized, and the industry is looking towards software for additional revenue generation. This document examines proprietary as well as open-standards attempts at solving the interoperability problem. The first attempt was made by EMC when it developed WideSky, a middleware software layer that would be able to manage third party hardware. It is shown that the aim was to eventually transform this middleware into a de facto standard and with that establish platform leadership in the industry. The WideSky effort failed, and the analysis of this failure attributes it to a lack of industry support and inability at establishing a sustainable value chain. Meanwhile, the industry players rallied around the SNIA body and adopted the SMI specification (SMI-S) as a standard. SMI-S adoption is on the rise, but although it has the formal backing of most of the storage industry firms, it has not yet fulfilled its promise of enabling centralized management of heterogeneous systems. This is partially because of the fact that the functionality that it provides is still lagging behind the functionality that native APIs provide. Moreover, client adoption and the availability of client products that can be directly used by IT customers are still very limited.(cont.) However, an examination of the dynamics surrounding this standard show how SMI-S will benefit greatly from learning effects and network externalities as it continues to grow, and although lagging in traditional functionality, it offers an ancillary functionality of interoperability that is missing from current non- standardized software interfaces. The adoption tipping point is highly dependant on whether or not the value chain can be established before vendors start dropping support for the specification. It is proposed that a positive tipping of the market will make SMI-S a disruptive technology that has the potential of becoming the dominant design for storage management interfaces.by Jean-Claude Jacques Saghbini.S.M

Colorado school safety: an examination of web availability of emergency management information

2016 Spring.Includes bibliographical references.The Colorado legislature declared their commitment to school safety in 2009. Yet, in the years since, there has been no systematic analysis of how Colorado’s 179 public school districts communicate disaster management procedures through various mediums. In order to begin to fill this void, this thesis reviews and analyzes online safety information published by Colorado school districts. In total, 175 (98%) of Colorado’s 179 public school districts have active websites. These 175 available sites were thus analyzed to understand (1) how many of Colorado’s public school districts include emergency management information as part of their websites, (2) how does this online emergency management information vary by region, setting, student enrollment, and socio-economic status of the students and school districts, (3) how many of Colorado’s public school districts publish emergency management documents online, (4) how do these documents vary by region, setting, student enrollment, and socio-economic status of the students and school districts, and (5) how do Colorado public school districts frame emergency management information published online. To answer these research questions, this thesis uses qualitative document analyses to systematically assess emergency management information and documents found on school district websites.This study found that 31% (55 of 175) of all districts in the state publish emergency management information on their website. These districts enroll 87% of all students in Colorado and tend to be larger than those that do not publish online emergency management information. Furthermore, the Metro Educational Region, North Central Educational Region, and Pikes Peak Educational Region, which all have total student enrollments of over 100,000, are also the only educational regions where 50% or more of their districts publish emergency information online. School districts that did not publish any online emergency management information on their website constitute around 69% (120 out of 175) of school districts. These school districts encompass only 13% of enrolled students in Colorado. Importantly, this analysis revealed a “rural-urban” divide, with approximately 90% of school districts that do not publish online emergency management information located in more rural areas of Colorado. On the other hand, nearly 60% of schools that publish online emergency management information on their website are located within the most populous settings including the Denver Metro, urban-suburban, and outlying city regions. In addition to the analysis of the online information, 48 emergency management documents from 35 school district websites were collected for further analysis. Over 70% of these documents encompassed an all-hazards approach, but exhibited relatively low rates of actionable advice for students (5%), teachers/staff (42%), and parents (53%). This runs counter to a growing body of literature that suggests that in order to increase public preparedness, stakeholder groups must be advised regarding what they should actually do in the face of an emergency. This thesis concludes with a discussion of the implications of the findings and suggestions for interventions based on best practices from the field of emergency management. Ultimately, this thesis reveals the lack in uniformity in published online emergency management information across region, setting, socio-economic status, and student enrollment and suggests new pathways for increasing the dissemination of knowledge via school websites to communicate emergency management information