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

Formulating MEDLINE queries for article retrieval based on PubMed exemplars

Bibliographic search engines allow endless possibilities for building queries based on specific words or phrases in article titles and abstracts, indexing terms, and other attributes. Unfortunately, deciding which attributes to use in a methodologically sound query is a non-trivial process. In this paper, we describe a system to help with this task, given an example set of PubMed articles to retrieve and a corresponding set of articles to exclude. The system provides the users with unigram and bigram features from the title, abstract, MeSH terms, and MeSH qualifier terms in decreasing order of precision, given a recall threshold. From this information and their knowledge of the domain, users can formulate a query and evaluate its performance. We apply the system to the task of distinguishing original research articles of functional magnetic resonance imaging (fMRI) of sensorimotor function from fMRI studies of higher cognitive functions

Toward automated evaluation of interactive segmentation

We previously described a system for evaluating interactive segmentation by means of user experiments (McGuinness and O’Connor, 2010). This method, while effective, is time-consuming and labor-intensive. This paper aims to make evaluation more practicable by investigating if it is feasible to automate user interactions. To this end, we propose a general algorithm for driving the segmentation that uses the ground truth and current segmentation error to automatically simulate user interactions. We investigate four strategies for selecting which pixels will form the next interaction. The first of these is a simple, deterministic strategy; the remaining three strategies are probabilistic, and focus on more realistically approximating a real user. We evaluate four interactive segmentation algorithms using these strategies, and compare the results with our previous user experiment-based evaluation. The results show that automated evaluation is both feasible and useful

Visual Information Retrieval in Endoscopic Video Archives

In endoscopic procedures, surgeons work with live video streams from the inside of their subjects. A main source for documentation of procedures are still frames from the video, identified and taken during the surgery. However, with growing demands and technical means, the streams are saved to storage servers and the surgeons need to retrieve parts of the videos on demand. In this submission we present a demo application allowing for video retrieval based on visual features and late fusion, which allows surgeons to re-find shots taken during the procedure.Comment: Paper accepted at the IEEE/ACM 13th International Workshop on Content-Based Multimedia Indexing (CBMI) in Prague (Czech Republic) between 10 and 12 June 201

Digital Image Access & Retrieval

The 33th Annual Clinic on Library Applications of Data Processing, held at the University of Illinois at Urbana-Champaign in March of 1996, addressed the theme of "Digital Image Access & Retrieval." The papers from this conference cover a wide range of topics concerning digital imaging technology for visual resource collections. Papers covered three general areas: (1) systems, planning, and implementation; (2) automatic and semi-automatic indexing; and (3) preservation with the bulk of the conference focusing on indexing and retrieval.published or submitted for publicatio