Visualizing latent domain knowledge

Knowledge discovery and data mining commonly rely on finding salient patterns of association from a vast amount of data. Traditional citation analysis of scientific literature draws insights from strong citation patterns. Latent domain knowledge, in contrast to the mainstream domain knowledge, often consists of highly relevant but relatively infrequently cited scientific works. Visualizing latent domain knowledge presents a significant challenge to knowledge discovery and quantitative studies of science. We build upon a citation-based knowledge visualization procedure and develop an approach that not only captures knowledge structures from prominent and highly cited works, but also traces latent domain knowledge through low-frequency citation chains. We apply this approach to two cases: (1) identifying cross-domain applications of Pathfinder networks (PFNETs) and (2) clarifying the current status of scientific inquiry of a possible link between Bovine spongiform encephalopathy (BSE), also known as mad cow disease, and a new variant Creutzfeldt-Jakob disease (vCJD), a type of brain disease in human

Multiple Uncertainties in Time-Variant Cosmological Particle Data

Though the mediums for visualization are limited, the potential dimensions of a dataset are not. In many areas of scientific study, understanding the correlations between those dimensions and their uncertainties is pivotal to mining useful information from a dataset. Obtaining this insight can necessitate visualizing the many relationships among temporal, spatial, and other dimensionalities of data and its uncertainties. We utilize multiple views for interactive dataset exploration and selection of important features, and we apply those techniques to the unique challenges of cosmological particle datasets. We show how interactivity and incorporation of multiple visualization techniques help overcome the problem of limited visualization dimensions and allow many types of uncertainty to be seen in correlation with other variables

BamView: visualizing and interpretation of next-generation sequencing read alignments.

So-called next-generation sequencing (NGS) has provided the ability to sequence on a massive scale at low cost, enabling biologists to perform powerful experiments and gain insight into biological processes. BamView has been developed to visualize and analyse sequence reads from NGS platforms, which have been aligned to a reference sequence. It is a desktop application for browsing the aligned or mapped reads [Ruffalo, M, LaFramboise, T, Koyutürk, M. Comparative analysis of algorithms for next-generation sequencing read alignment. Bioinformatics 2011;27:2790-6] at different levels of magnification, from nucleotide level, where the base qualities can be seen, to genome or chromosome level where overall coverage is shown. To enable in-depth investigation of NGS data, various views are provided that can be configured to highlight interesting aspects of the data. Multiple read alignment files can be overlaid to compare results from different experiments, and filters can be applied to facilitate the interpretation of the aligned reads. As well as being a standalone application it can be used as an integrated part of the Artemis genome browser, BamView allows the user to study NGS data in the context of the sequence and annotation of the reference genome. Single nucleotide polymorphism (SNP) density and candidate SNP sites can be highlighted and investigated, and read-pair information can be used to discover large structural insertions and deletions. The application will also calculate simple analyses of the read mapping, including reporting the read counts and reads per kilobase per million mapped reads (RPKM) for genes selected by the user

Scientific Visualization Using the Flow Analysis Software Toolkit (FAST)

Over the past few years the Flow Analysis Software Toolkit (FAST) has matured into a useful tool for visualizing and analyzing scientific data on high-performance graphics workstations. Originally designed for visualizing the results of fluid dynamics research, FAST has demonstrated its flexibility by being used in several other areas of scientific research. These research areas include earth and space sciences, acid rain and ozone modelling, and automotive design, just to name a few. This paper describes the current status of FAST, including the basic concepts, architecture, existing functionality and features, and some of the known applications for which FAST is being used. A few of the applications, by both NASA and non-NASA agencies, are outlined in more detail. Described in the Outlines are the goals of each visualization project, the techniques or 'tricks' used lo produce the desired results, and custom modifications to FAST, if any, done to further enhance the analysis. Some of the future directions for FAST are also described

Visualizing pain data for wheelchair users: A ubiquitous approach

Copyright @ 2005 Rinton PressWe describe a wireless enabled solution for the vizualisation of pain data. Our approach uses pain drawings to record spatial location and type of pain and enables data collection with appropriate time stamping, thus providing a means for the seldom-recorded (but often attested) time-varying nature of pain, with consequential impact on monitoring the effectiveness of patient treatment regimes. Moreover, since the implementation platform of our solution is that of a Personal Digital Assistant (PDA), data collection takes place ubiquitously, providing back pain sufferers with mobility problems (such as wheelchair users) with a convenient means of logging their pain data and of seamlessly uploading it to a hospital server using WiFi technology. Stakeholder results show that, notwithstanding problems related to PDA data input, our approach is generally perceived to be an easy to use and convenient solution to the challenges of anywhere/anytime data collection