Impliance: A Next Generation Information Management Appliance

ably successful in building a large market and adapting to the changes of the last three decades, its impact on the broader market of information management is surprisingly limited. If we were to design an information management system from scratch, based upon today's requirements and hardware capabilities, would it look anything like today's database systems?" In this paper, we introduce Impliance, a next-generation information management system consisting of hardware and software components integrated to form an easy-to-administer appliance that can store, retrieve, and analyze all types of structured, semi-structured, and unstructured information. We first summarize the trends that will shape information management for the foreseeable future. Those trends imply three major requirements for Impliance: (1) to be able to store, manage, and uniformly query all data, not just structured records; (2) to be able to scale out as the volume of this data grows; and (3) to be simple and robust in operation. We then describe four key ideas that are uniquely combined in Impliance to address these requirements, namely the ideas of: (a) integrating software and off-the-shelf hardware into a generic information appliance; (b) automatically discovering, organizing, and managing all data - unstructured as well as structured - in a uniform way; (c) achieving scale-out by exploiting simple, massive parallel processing, and (d) virtualizing compute and storage resources to unify, simplify, and streamline the management of Impliance. Impliance is an ambitious, long-term effort to define simpler, more robust, and more scalable information systems for tomorrow's enterprises.Comment: This article is published under a Creative Commons License Agreement (http://creativecommons.org/licenses/by/2.5/.) You may copy, distribute, display, and perform the work, make derivative works and make commercial use of the work, but, you must attribute the work to the author and CIDR 2007. 3rd Biennial Conference on Innovative Data Systems Research (CIDR) January 710, 2007, Asilomar, California, US

Distributional Semantic Models for Clinical Text Applied to Health Record Summarization

As information systems in the health sector are becoming increasingly computerized, large amounts of care-related information are being stored electronically. In hospitals clinicians continuously document treatment and care given to patients in electronic health record (EHR) systems. Much of the information being documented is in the form of clinical notes, or narratives, containing primarily unstructured free-text information. For each care episode, clinical notes are written on a regular basis, ending with a discharge summary that basically summarizes the care episode. Although EHR systems are helpful for storing and managing such information, there is an unrealized potential in utilizing this information for smarter care assistance, as well as for secondary purposes such as research and education. Advances in clinical language processing are enabling computers to assist clinicians in their interaction with the free-text information documented in EHR systems. This includes assisting in tasks like query-based search, terminology development, knowledge extraction, translation, and summarization. This thesis explores various computerized approaches and methods aimed at enabling automated semantic textual similarity assessment and information extraction based on the free-text information in EHR systems. The focus is placed on the task of (semi-)automated summarization of the clinical notes written during individual care episodes. The overall theme of the presented work is to utilize resource-light approaches and methods, circumventing the need to manually develop knowledge resources or training data. Thus, to enable computational semantic textual similarity assessment, word distribution statistics are derived from large training corpora of clinical free text and stored as vector-based representations referred to as distributional semantic models. Also resource-light methods are explored in the task of performing automatic summarization of clinical freetext information, relying on semantic textual similarity assessment. Novel and experimental methods are presented and evaluated that focus on: a) distributional semantic models trained in an unsupervised manner from statistical information derived from large unannotated clinical free-text corpora; b) representing and computing semantic similarities between linguistic items of different granularity, primarily words, sentences and clinical notes; and c) summarizing clinical free-text information from individual care episodes. Results are evaluated against gold standards that reflect human judgements. The results indicate that the use of distributional semantics is promising as a resource-light approach to automated capturing of semantic textual similarity relations from unannotated clinical text corpora. Here it is important that the semantics correlate with the clinical terminology, and with various semantic similarity assessment tasks. Improvements over classical approaches are achieved when the underlying vector-based representations allow for a broader range of semantic features to be captured and represented. These are either distributed over multiple semantic models trained with different features and training corpora, or use models that store multiple sense-vectors per word. Further, the use of structured meta-level information accompanying care episodes is explored as training features for distributional semantic models, with the aim of capturing semantic relations suitable for care episode-level information retrieval. Results indicate that such models performs well in clinical information retrieval. It is shown that a method called Random Indexing can be modified to construct distributional semantic models that capture multiple sense-vectors for each word in the training corpus. This is done in a way that retains the original training properties of the Random Indexing method, by being incremental, scalable and distributional. Distributional semantic models trained with a framework called Word2vec, which relies on the use of neural networks, outperform those trained using the classic Random Indexing method in several semantic similarity assessment tasks, when training is done using comparable parameters and the same training corpora. Finally, several statistical features in clinical text are explored in terms of their ability to indicate sentence significance in a text summary generated from the clinical notes. This includes the use of distributional semantics to enable case-based similarity assessment, where cases are other care episodes and their “solutions”, i.e., discharge summaries. A type of manual evaluation is performed, where human experts rates the different aspects of the summaries using a evaluation scheme/tool. In addition, the original clinician-written discharge summaries are explored as gold standard for the purpose of automated evaluation. Evaluation shows a high correlation between manual and automated evaluation, suggesting that such a gold standard can function as a proxy for human evaluations. --- This thesis has been published jointly with Norwegian University of Science and Technology, Norway and University of Turku, Finland.This thesis has beenpublished jointly with Norwegian University of Science and Technology, Norway.Siirretty Doriast

An Analysis of the Evolving Intellectual Structure of Health Information Systems Research in the Information Systems Discipline

The rapid evolution of health information systems (Health IS) research has led to many significantcontributions. However, while the Health IS subset of information systems (IS) scholarship hasconsiderably grown over the past two decades, this growth hasled to questions regarding the currentintellectual structure of this area of inquiry. In an effort to more fully understand how Health ISresearchhas contributed to the IS discipline, and what this may mean for future Health IS researchin the IS domain, we conduct an in-depth evaluation of Health IS research published in mainstreamIS journals. We apply citation analysis, latent semantic analysis (LSA), and social network analysis(SNA) to ourdata setof Health IS articles in order to: (1) identify Health IS research themes andthematic shifts, (2)determine which Health IS research themes are cohesive (versus disparate), (3)identify which Health IS research themes are central (versus peripheral), (4) clarify networks ofresearchers (i.e., thought leaders) contributing to these research themes, and(5) provide insights intothe connection of Health ISresearchto its reference disciplines. Overall, we contribute a systematicdescription and explanation of the intellectual structure ofHealth ISresearchand highlight how theexisting intellectual structure of Health ISresearchprovides opportunities for future research

Yleiskäyttöinen tekstinluokittelija suomenkielisille potilaskertomusteksteille

Medical texts are an underused source of data in clinical analytics. Extracting the relevant information from unstructured texts is difficult and while there are some tools available, they are often targeted for English texts. The situation is worse for smaller languages, such as Finnish. In this work, we reviewed literature in text mining and natural language processing fields in the scope of analyzing medical texts. Using the results of our literature review, we created an algorithm for information extraction from patient record texts. During this thesis work we created a decent text mining tool that works through text classification. This algorithm can be used detect medical conditions solely from medical texts. The usage of the algorithm is limited through the availability of large training data.Potilaskertomustekstejä käytetään kliinisessä analytiikassa huomattavan vähäisessä määrin. Olennaisen tiedon poimiminen tekstin joukosta on vaikeaa, ja vaikka siihen on työkaluja saatavilla, ovat ne useimmiten tehty englanninkielisille teksteille. Pienempien kielten, kuten suomen kohdalla tilanne on heikompi. Tässä työssä tehtiin kirjallisuuskatsaus tekstinlouhintaan ja luonnollisen kielen käsittelyyn liittyvään kirjallisuuteen, keskittyen erityisesti menetelmiin jotka soveltuvat lääketieteellisten tekstien analysointiin. Kirjallisuuskatsauksen pohjalta loimme algoritmin, joka soveltuu yleisesti lääketieteellisten tekstien luokitteluun. Tämän diplomityön osana luotiin tekstinlouhintatyökalu suomenkielisille lääketieteellisille teksteille. Kehitettyä algoritmia voidaan käyttää erilaisten tilojen tunnistamiseen potilaskertomusteksteistä. Algoritmin käyttöä kuitenkin rajoittaa tarve suurehkolle määrälle opetusdataa

Semantic interpretation of events in lifelogging

The topic of this thesis is lifelogging, the automatic, passive recording of a person’s daily activities and in particular, on performing a semantic analysis and enrichment of lifelogged data. Our work centers on visual lifelogged data, such as taken from wearable cameras. Such wearable cameras generate an archive of a person’s day taken from a first-person viewpoint but one of the problems with this is the sheer volume of information that can be generated. In order to make this potentially very large volume of information more manageable, our analysis of this data is based on segmenting each day’s lifelog data into discrete and non-overlapping events corresponding to activities in the wearer’s day. To manage lifelog data at an event level, we define a set of concepts using an ontology which is appropriate to the wearer, applying automatic detection of concepts to these events and then semantically enriching each of the detected lifelog events making them an index into the events. Once this enrichment is complete we can use the lifelog to support semantic search for everyday media management, as a memory aid, or as part of medical analysis on the activities of daily living (ADL), and so on. In the thesis, we address the problem of how to select the concepts to be used for indexing events and we propose a semantic, density- based algorithm to cope with concept selection issues for lifelogging. We then apply activity detection to classify everyday activities by employing the selected concepts as high-level semantic features. Finally, the activity is modeled by multi-context representations and enriched by Semantic Web technologies. The thesis includes an experimental evaluation using real data from users and shows the performance of our algorithms in capturing the semantics of everyday concepts and their efficacy in activity recognition and semantic enrichment

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

Usefulness of social tagging in organizing and providing access to the web: An analysis of indexing consistency and quality

This dissertation research points out major challenging problems with current Knowledge Organization (KO) systems, such as subject gateways or web directories: (1) the current systems use traditional knowledge organization systems based on controlled vocabulary which is not very well suited to web resources, and (2) information is organized by professionals not by users, which means it does not reflect intuitively and instantaneously expressed users’ current needs. In order to explore users’ needs, I examined social tags which are user-generated uncontrolled vocabulary. As investment in professionally-developed subject gateways and web directories diminishes (support for both BUBL and Intute, examined in this study, is being discontinued), understanding characteristics of social tagging becomes even more critical. Several researchers have discussed social tagging behavior and its usefulness for classification or retrieval; however, further research is needed to qualitatively and quantitatively investigate social tagging in order to verify its quality and benefit. This research particularly examined the indexing consistency of social tagging in comparison to professional indexing to examine the quality and efficacy of tagging. The data analysis was divided into three phases: analysis of indexing consistency, analysis of tagging effectiveness, and analysis of tag attributes. Most indexing consistency studies have been conducted with a small number of professional indexers, and they tended to exclude users. Furthermore, the studies mainly have focused on physical library collections. This dissertation research bridged these gaps by (1) extending the scope of resources to various web documents indexed by users and (2) employing the Information Retrieval (IR) Vector Space Model (VSM) - based indexing consistency method since it is suitable for dealing with a large number of indexers. As a second phase, an analysis of tagging effectiveness with tagging exhaustivity and tag specificity was conducted to ameliorate the drawbacks of consistency analysis based on only the quantitative measures of vocabulary matching. Finally, to investigate tagging pattern and behaviors, a content analysis on tag attributes was conducted based on the FRBR model. The findings revealed that there was greater consistency over all subjects among taggers compared to that for two groups of professionals. The analysis of tagging exhaustivity and tag specificity in relation to tagging effectiveness was conducted to ameliorate difficulties associated with limitations in the analysis of indexing consistency based on only the quantitative measures of vocabulary matching. Examination of exhaustivity and specificity of social tags provided insights into particular characteristics of tagging behavior and its variation across subjects. To further investigate the quality of tags, a Latent Semantic Analysis (LSA) was conducted to determine to what extent tags are conceptually related to professionals’ keywords and it was found that tags of higher specificity tended to have a higher semantic relatedness to professionals’ keywords. This leads to the conclusion that the term’s power as a differentiator is related to its semantic relatedness to documents. The findings on tag attributes identified the important bibliographic attributes of tags beyond describing subjects or topics of a document. The findings also showed that tags have essential attributes matching those defined in FRBR. Furthermore, in terms of specific subject areas, the findings originally identified that taggers exhibited different tagging behaviors representing distinctive features and tendencies on web documents characterizing digital heterogeneous media resources. These results have led to the conclusion that there should be an increased awareness of diverse user needs by subject in order to improve metadata in practical applications. This dissertation research is the first necessary step to utilize social tagging in digital information organization by verifying the quality and efficacy of social tagging. This dissertation research combined both quantitative (statistics) and qualitative (content analysis using FRBR) approaches to vocabulary analysis of tags which provided a more complete examination of the quality of tags. Through the detailed analysis of tag properties undertaken in this dissertation, we have a clearer understanding of the extent to which social tagging can be used to replace (and in some cases to improve upon) professional indexing