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Mining association rules from a pediatric primary care decision support system.

The purpose of this study was to apply an unsupervised data mining algorithm to a database containing data collected at the point of care for clinical decision support. The data set was taken from the Child Health Improvement Program (CHIP), a preventive services tracking and reminder system in use at the University of North Carolina. The database contains over 30,000 visits. We used a previously described pattern discovery algorithm to extract 2nd and 3rd order association rules from the data and reviewed the literature two see if the associations had been described before. The algorithm discovered 16 2nd order associations and 103 3rd order associations. The 3rd order associations contained no new information. The 2nd order associations demonstrated a covariance among a range of health risk behaviors. Additionally, the algorithm discovered that both tobacco smoke exposure and chronic cardiopulmonary disease are associated with failure on developmental screens. These relationships have been described before and have been attributed to underlying poverty. The work demonstrates the ability of unsupervised data mining by rule association on sparse clinical data to discover clinically important associations. However, many associations may be previously known or explained by confounding variables.

Algorithms↗

Clinical documents: attribute-values entity representation,context, page layout and communication.

This paper presents how acquisition, storage and communication of clinical documents is implemented at the University Hospitals of Geneva. Careful attention has been given to user-interfaces, in order to support complex layouts, spell checking, and templates management with automatic prefilling. A dual architecture has been developed for storage using an entity-attribute-value unified database and a consolidated, patient-centered, layout-respectful file-based storage, providing both representation power and speed of access. This architecture allows a great flexibility for storing a continuum of data types, ranging from simple typed values to complex clinical reports. Finally, communication is entirely based on HTTP-XML internally, and a HL-7 CDA interface V2 is currently studied for external communication. Some of the problems encountered, mostly related to the typology of documents and the ontology of clinical attributes are evoked.

Computer Systems↗

Medical problem and document model for natural language understanding.

We are developing tools to help maintain a complete, accurate and timely problem list within a general purpose Electronic Medical Record system. As a part of this project, we have designed a system to automatically retrieve medical problems from free-text documents. Here we describe an information model based on XML (eXtensible Markup Language) and compliant with the CDA (Clinical Document Architecture). This model is used to ease the exchange of clinical data between the Natural Language Understanding application that retrieves potential problems from narrative document, and the problem list management application.

Computer Simulation↗

Online identification of viruses.

A computerized animal virus information system is developed in the Sequence Retrieval System (SRS) format. This database is available on the Word Wide Web (WWW) at the site http://bioinfo.ernet.in/www/avis/avis++ +.html. The database has been used to generate large number of identification matrices for each family. The software is developed in C. Unix shell scripts and Hypertext Marked-up Language (HTML) to assign the family to an unknown virus deterministically and to identify the virus probabilistically. It has been shown that such web based virus identification approach provides results with high confidence in those cases where identification matrix uses large number of independent characters. Protein sequence data for animal viruses have been analyzed and oligopeptides specific to each virus family and also specific to each virus species are identified for several viruses. These peptides thus could be used to identify the virus and to assign the virus family with high confidence showing the usefulness of sequence data in virus identification.

Databases as Topic↗

Biomedical knowledge navigation by literature clustering.

There is an urgent need for a system that facilitates surveys by biomedical researchers and the subsequent formulation of hypotheses based on the knowledge stored in literature. One approach is to cluster papers discussing a topic of interest and reveal its sub-topics that allow researchers to acquire an overview of the topic. We developed such a system called McSyBi. It accepts a set of citation data retrieved with PubMed and hierarchically and non-hierarchically clusters them based on the titles and the abstracts using statistical and natural language processing methods. A novel point is that McSyBi allows its users to change the clustering by entering a MeSH term or UMLS Semantic Type, and therefore they can see a set of citation data from multiple aspects. We evaluated McSyBi quantitatively and qualitatively: clustering of 27 sets of citation data (40643 different papers) and scrutiny of several resultant clusters. While non-hierarchical clustering provides us with an overview of the target topic, hierarchical clustering allows us to see more details and relationships among citation data. McSyBi is freely available at http://textlens.hgc.jp/McSyBi/.

Artificial Intelligence↗

Tools for managing image flow in the modality to clinical-image-review chain.

Web-based clinical-image viewing is commonplace in large medical centers. As demands for product and performance escalate, physicians, sold on the concept of "any image, anytime, anywhere," fret when image studies cannot be viewed in a time frame to which they are accustomed. Image delivery pathways in large medical centers are oftentimes complicated by multiple networks, multiple picture archiving and communication systems (PACS), and multiple groups responsible for image acquisition and delivery to multiple destinations. When studies are delayed, it may be difficult to rapidly pinpoint bottlenecks. Described here are the tools used to monitor likely failure points in our modality to clinical-image-viewing chain and tools for reporting volume and throughput trends. Though perhaps unique to our environment, we believe that tools of this type are essential for understanding and monitoring image-study flow, re-configuring resources to achieve better throughput, and planning for anticipated growth. Without such tools, quality clinical-image delivery may not be what it should.

Data Display↗

DICOM structured reporting: Part 1. Overview and characteristics.

Supplement 23 to Digital Imaging and Communications in Medicine (DICOM) is an introduction to the structured reporting (SR) classes, which are used for transmission and storage of clinical documents. The SR classes fully support both conventional free-text reports and structured information, thus enhancing the precision, clarity, and value of clinical documentation. In addition, the SR standard provides the capability to link text and other data to particular images or waveforms and to store the coordinates of findings. In other words, SR documents not only describe the specific features contained in images or waveforms but can also refer to any number of images or waveforms. Accordingly, SR bridges the traditional gap between imaging systems and information systems. Furthermore, SR plays an essential role in Integrating the Healthcare Enterprise by providing healthcare practitioners with an effective tool that encompasses a variety of clinical contexts. Harmonization of DICOM SR and the Health Level Seven clinical document architecture standard is under way.

Abstracting and Indexing↗

Voice-activated retrieval of mammography reference images.

We undertook this project to integrate context sensitive computer-based educational and decision making aids into the film interpretation and reporting process, and to determine the clinical utility of this method as a guide for further system development. An image database of 347 digital mammography images was assembled and image features were coded. An interface was developed to a computerized speech recognition radiology reporting system which was modified to translate reported findings into database search terms. These observations were used to formulate database search strategies which not only retrieved similar cases from the image database, but also other cases that were related to the index case in different ways. The search results were organized into image sets intended to address common questions that arise during image interpretation. An evaluation of the clinical utility of this method was performed as a guide for further system development. We found that voice dictation of prototypical mammographic cases resulted in automatic retrieval of reference images. The retrieved images were organized into sets matching findings, diagnostic hypotheses, diagnosis, spectrum of findings or diagnoses, closest match to dictated case, or user specified parameters. Two mammographers graded the clinical utility of each form of system output. We concluded that case specific and problem specific image sets may be automatically generated from spoken case dictation. A potentially large number of retrieved images may be divided into subsets which anticipate common clinical problems. This automatic method of context sensitive image retrieval may provide a "continuous" form of education integrated into routine case interpretation.

Breast Neoplasms↗

Flying blind: using a digital dashboard to navigate a complex PACS environment.

Radiology workflows have become more distributed and complicated, and fewer tangible cues are available to the radiologist to help optimize task prioritization and selection. Additionally, faster scanners, more detailed exams, and increased demand for imaging services have precipitated a potential image overload for today's radiologists who are pressured to provide efficient, quality service in less time. Radiologists are faced with the task of operating within complex systems but are lacking tools to efficiently and effectively monitor these systems in real time. Dashboard technology can help address this deficiency in radiology and facilitate informed, optimized decisions about workflow. Possible areas of application include workflow consolidation, workload distribution, and urgency evaluation. Dashboards should be optimized, context-sensitive, customizable, and workflow-integrated. Further research is needed to identify the most important dashboard metrics, determine their optimal display, and validate their utility.

Data Display↗

Population groups: indexing, coverage, and retrieval effectiveness of ethnically related health care issues in health sciences databases.

OBJECTIVES: This study examined methods of accessing (for indexing and retrieval purposes) medical research on population groups in the major abstracting and indexing services of the health sciences literature. DESIGN: The study of diseases in specific population groups is facilitated by the indexing of both diseases and populations in a database. The MEDLINE, PsycINFO, and Embase databases were selected for the study. The published thesauri for these databases were examined to establish the vocabulary in use. Indexing terms were identified and examined as to their representation in the current literature. Terms were clustered further into groups thought to reflect an end user's perspective and to facilitate subsequent analysis. The medical literature contained in the three online databases was searched with both controlled vocabulary and natural language terms. RESULTS: The three thesauri revealed shallow pre-coordinated hierarchical structures, rather difficult-to-use terms for post-coordination, and a blurring of cultural, genetic, and racial facets of populations. Post-coordination is difficult because of the system-oriented terminology, which is intended mostly for information professionals. The terminology unintentionally restricts access by the end users who lack the knowledge needed to use the thesauri effectively for information retrieval. CONCLUSIONS: Population groups are not represented adequately in the index languages of health sciences databases. Users of these databases need to be alerted to the difficulties that may be encountered in searching for information on population groups. Information and health professionals may not be able to access the literature if they are not familiar with the indexing policies on population groups. Consequently, the study points to a problem that needs to be addressed, through either the redesign of existing systems or the design of new ones to meet the goals of Healthy People 2000 and beyond.

Abstracting and Indexing↗

An integrated approach to senology education: combination of a hypermedia program with a multimedia archive.

The aim of this work was to demonstrate the computerized system on senology, which combines a hypermedia application to a multimedia didactical archive, integrated with a radiological information system. These applications have been developed on Macintosh computers using the softwares Supercard and 4th Dimension. The hypermedia application deals with basic principles of anatomy as well as the radiologic semeiology and pathology through different imaging techniques in order to illustrate basic principles. Thus, students can modify their learning pathways and the timing as they wish. Limitations are related to time consumption in preparing the programs and technical difficulties in expanding them. Multimedia archive allows to classify a large number of difficult and uncommon clinical cases, creating an easily updatable teaching file in digital format which considerably improves access to stored image data, also reducing loss of films and film degradation. From initial experiences we conclude that these systems are valid devices in information and up to date for physicians dedicated to the study of breast pathology.

Breast↗

Improving access of associated states to advanced concepts in medical telematics--a day before the accession to EU.

Central and Eastern Europe countries (CEEC) undertook considerable efforts to include themselves in the main research and development activities in the area of health telematics in Europe. Countries of this region demonstrate diversified environments of economy transformation and health care systems status. The transition phase to market economy brings essential risks to the healthcare system performance. It seems that efforts of developing e-health environment in CEEC could be substantially accelerated by extended co-operation with partners from current member states of the European Union. The PRO-ACCESS project was initiated in the late phase of fifth Framework Programme as supporting action. It focused on the transfer of current concepts in medical telematics to countries remaining in the pre-accession phase. The process of dissemination of up-to-date approaches to e-health environment development is carried out by the Krakow Centre of Telemedicine and is supported by leading health telematics centres in Europe. To accelerate the dissemination activities the network of co-operating centres in CEEC was established. The strategy employed within the PRO-ACCESS project is supposed to yield "critical mass" necessary for facilitating the e-health development in this region of Europe. The activities employed to reach this objective included publishing activities, events and trainings as well as intake of solutions from supporting centres.

Database Management Systems↗

Data streaming in telepresence environments.

In this paper, we discuss data transmission in telepresence environments for collaborative virtual reality applications. We analyze data streams in the context of networked virtual environments and classify them according to their traffic characteristics. Special emphasis is put on geometry-enhanced (3D) video. We review architectures for real-time 3D video pipelines and derive theoretical bounds on the minimal system latency as a function of the transmission and processing delays. Furthermore, we discuss bandwidth issues of differential update coding for 3D video. In our telepresence system-the blue-c-we use a point-based 3D video technology which allows for differentially encoded 3D representations of human users. While we discuss the considerations which lead to the design of our three-stage 3D video pipeline, we also elucidate some critical implementation details regarding decoupling of acquisition, processing and rendering frame rates, and audio/video synchronization. Finally, we demonstrate the communication and networking features of the blue-c system in its full deployment. We show how the system can possibly be controlled to face processing or networking bottlenecks by adapting the multiple system components like audio, application data, and 3D video.

Computer Communication Networks↗

Informatics in radiology (infoRAD): A complete continuous-availability PACS archive server.

The operational reliability of the picture archiving and communication system (PACS) server in a filmless hospital environment is always a major concern because server failure could cripple the entire PACS operation. A simple, low-cost, continuous-availability (CA) PACS archive server was designed and developed. The server makes use of a triple modular redundancy (TMR) system with a simple majority voting logic that automatically identifies a faulty module and removes it from service. The remaining two modules continue normal operation with no adverse effects on data flow or system performance. In addition, the server is integrated with two external mass storage devices for short- and long-term storage. Evaluation and testing of the server were conducted with laboratory experiments in which hardware failures were simulated to observe recovery time and the resumption of normal data flow. The server provides maximum uptime (99.999%) for end users while ensuring the transactional integrity of all clinical PACS data. Hardware failure has only minimal impact on performance, with no interruption of clinical data flow or loss of data. As hospital PACS become more widespread, the need for CA PACS solutions will increase. A TMR CA PACS archive server can reliably help achieve CA in this setting.

Computer Communication Networks↗

Medical record linkage in health information systems by approximate string matching and clustering.

BACKGROUND: Multiplication of data sources within heterogeneous healthcare information systems always results in redundant information, split among multiple databases. Our objective is to detect exact and approximate duplicates within identity records, in order to attain a better quality of information and to permit cross-linkage among stand-alone and clustered databases. Furthermore, we need to assist human decision making, by computing a value reflecting identity proximity. METHODS: The proposed method is in three steps. The first step is to standardise and to index elementary identity fields, using blocking variables, in order to speed up information analysis. The second is to match similar pair records, relying on a global similarity value taken from the Porter-Jaro-Winkler algorithm. And the third is to create clusters of coherent related records, using graph drawing, agglomerative clustering methods and partitioning methods. RESULTS: The batch analysis of 300,000 "supposedly" distinct identities isolates 240,000 true unique records, 24,000 duplicates (clusters composed of 2 records) and 3,000 clusters whose size is greater than or equal to 3 records. CONCLUSION: Duplicate-free databases, used in conjunction with relevant indexes and similarity values, allow immediate (i.e. real-time) proximity detection when inserting a new identity.

Algorithms↗