PhenDisco: phenotype discovery system for the database of genotypes and phenotypes.

The database of genotypes and phenotypes (dbGaP) developed by the National Center for Biotechnology Information (NCBI) is a resource that contains information on various genome-wide association studies (GWAS) and is currently available via NCBI's dbGaP Entrez interface. The database is an important resource, providing GWAS data that can be used for new exploratory research or cross-study validation by authorized users. However, finding studies relevant to a particular phenotype of interest is challenging, as phenotype information is presented in a non-standardized way. To address this issue, we developed PhenDisco (phenotype discoverer), a new information retrieval system for dbGaP. PhenDisco consists of two main components: (1) text processing tools that standardize phenotype variables and study metadata, and (2) information retrieval tools that support queries from users and return ranked results. In a preliminary comparison involving 18 search scenarios, PhenDisco showed promising performance for both unranked and ranked search comparisons with dbGaP's search engine Entrez. The system can be accessed at http://pfindr.net

User-centered visual analysis using a hybrid reasoning architecture for intensive care units

One problem pertaining to Intensive Care Unit information systems is that, in some cases, a very dense display of data can result. To ensure the overview and readability of the increasing volumes of data, some special features are required (e.g., data prioritization, clustering, and selection mechanisms) with the application of analytical methods (e.g., temporal data abstraction, principal component analysis, and detection of events). This paper addresses the problem of improving the integration of the visual and analytical methods applied to medical monitoring systems. We present a knowledge- and machine learning-based approach to support the knowledge discovery process with appropriate analytical and visual methods. Its potential benefit to the development of user interfaces for intelligent monitors that can assist with the detection and explanation of new, potentially threatening medical events. The proposed hybrid reasoning architecture provides an interactive graphical user interface to adjust the parameters of the analytical methods based on the users' task at hand. The action sequences performed on the graphical user interface by the user are consolidated in a dynamic knowledge base with specific hybrid reasoning that integrates symbolic and connectionist approaches. These sequences of expert knowledge acquisition can be very efficient for making easier knowledge emergence during a similar experience and positively impact the monitoring of critical situations. The provided graphical user interface incorporating a user-centered visual analysis is exploited to facilitate the natural and effective representation of clinical information for patient care

ELVIS: Entertainment-led video summaries

© ACM, 2010. This is the author's version of the work. It is posted here by permission of ACM for your personal use. Not for redistribution. The definitive version was published in ACM Transactions on Multimedia Computing, Communications, and Applications, 6(3): Article no. 17 (2010) http://doi.acm.org/10.1145/1823746.1823751Video summaries present the user with a condensed and succinct representation of the content of a video stream. Usually this is achieved by attaching degrees of importance to low-level image, audio and text features. However, video content elicits strong and measurable physiological responses in the user, which are potentially rich indicators of what video content is memorable to or emotionally engaging for an individual user. This article proposes a technique that exploits such physiological responses to a given video stream by a given user to produce Entertainment-Led VIdeo Summaries (ELVIS). ELVIS is made up of five analysis phases which correspond to the analyses of five physiological response measures: electro-dermal response (EDR), heart rate (HR), blood volume pulse (BVP), respiration rate (RR), and respiration amplitude (RA). Through these analyses, the temporal locations of the most entertaining video subsegments, as they occur within the video stream as a whole, are automatically identified. The effectiveness of the ELVIS technique is verified through a statistical analysis of data collected during a set of user trials. Our results show that ELVIS is more consistent than RANDOM, EDR, HR, BVP, RR and RA selections in identifying the most entertaining video subsegments for content in the comedy, horror/comedy, and horror genres. Subjective user reports also reveal that ELVIS video summaries are comparatively easy to understand, enjoyable, and informative

The National Transport Data Framework

Report by Professor Peter Landshoff (Cambridge University) and Professor John Polak (Imperial College London) on a project for the Department for Transport. emails: [email protected] [email protected] NTDF is designed to be a resource for data owners to deposit descriptions into a central catalogue, so that people can search for data and find data and understand their characteristics. The value of this is to individuals, to commercial organizations, and to public bodies. For example, services that provide better information to travellers will help to make their journey less stressful and persuade them to make more use of public transport. Transport operators need very diverse information to help them plan developments to their services: demographic, geographical, economic etc. And policy makers need a similar range of information to help them decide how to divide their budget and afterwards to evaluate how valuable it has been.This work was supported by the Department for Transport (DfT)

A Generic Approach and Framework for Managing Complex Information

Several application domains, such as healthcare, incorporate domain knowledge into their day-to-day activities to standardise and enhance their performance. Such incorporation produces complex information, which contains two main clusters (active and passive) of information that have internal connections between them. The active cluster determines the recommended procedure that should be taken as a reaction to specific situations. The passive cluster determines the information that describes these situations and other descriptive information plus the execution history of the complex information. In the healthcare domain, a medical patient plan is an example for complex information produced during the disease management activity from specific clinical guidelines. This thesis investigates the complex information management at an application domain level in order to support the day-to-day organization activities. In this thesis, a unified generic approach and framework, called SIM (Specification, Instantiation and Maintenance), have been developed for computerising the complex information management. The SIM approach aims at providing a conceptual model for the complex information at different abstraction levels (generic and entity-specific). In the SIM approach, the complex information at the generic level is referred to as a skeletal plan from which several entity-specific plans are generated. The SIM framework provides comprehensive management aspects for managing the complex information. In the SIM framework, the complex information goes through three phases, specifying the skeletal plans, instantiating entity-specific plans, and then maintaining these entity-specific plans during their lifespan. In this thesis, a language, called AIM (Advanced Information Management), has been developed to support the main functionalities of the SIM approach and framework. AIM consists of three components: AIMSL, AIM ESPDoc model, and AIMQL. The AIMSL is the AIM specification component that supports the formalisation process of the complex information at a generic level (skeletal plans). The AIM ESPDoc model is a computer-interpretable model for the entity-specific plan. AIMQL is the AIM query component that provides support for manipulating and querying the complex information, and provides special manipulation operations and query capabilities, such as replay query support. The applicability of the SIM approach and framework is demonstrated through developing a proof-of-concept system, called AIMS, using the available technologies, such as XML and DBMS. The thesis evaluates the the AIMS system using a clinical case study, which has applied to a medical test request application