Topic Similarity Networks: Visual Analytics for Large Document Sets

We investigate ways in which to improve the interpretability of LDA topic models by better analyzing and visualizing their outputs. We focus on examining what we refer to as topic similarity networks: graphs in which nodes represent latent topics in text collections and links represent similarity among topics. We describe efficient and effective approaches to both building and labeling such networks. Visualizations of topic models based on these networks are shown to be a powerful means of exploring, characterizing, and summarizing large collections of unstructured text documents. They help to "tease out" non-obvious connections among different sets of documents and provide insights into how topics form larger themes. We demonstrate the efficacy and practicality of these approaches through two case studies: 1) NSF grants for basic research spanning a 14 year period and 2) the entire English portion of Wikipedia.Comment: 9 pages; 2014 IEEE International Conference on Big Data (IEEE BigData 2014

A signaling visualization toolkit to support rational design of combination therapies and biomarker discovery: SiViT

Targeted cancer therapy aims to disrupt aberrant cellular signalling pathways. Biomarkers are surrogates of pathway state, but there is limited success in translating candidate biomarkers to clinical practice due to the intrinsic complexity of pathway networks. Systems biology approaches afford better understanding of complex, dynamical interactions in signalling pathways targeted by anticancer drugs. However, adoption of dynamical modelling by clinicians and biologists is impeded by model inaccessibility. Drawing on computer games technology, we present a novel visualisation toolkit, SiViT, that converts systems biology models of cancer cell signalling into interactive simulations that can be used without specialist computational expertise. SiViT allows clinicians and biologists to directly introduce for example loss of function mutations and specific inhibitors. SiViT animates the effects of these introductions on pathway dynamics, suggesting further experiments and assessing candidate biomarker effectiveness. In a systems biology model of Her2 signalling we experimentally validated predictions using SiViT, revealing the dynamics of biomarkers of drug resistance and highlighting the role of pathway crosstalk. No model is ever complete: the iteration of real data and simulation facilitates continued evolution of more accurate, useful models. SiViT will make accessible libraries of models to support preclinical research, combinatorial strategy design and biomarker discovery

Rexplore: unveiling the dynamics of scholarly data

Rexplore is a novel system that integrates semantic technologies, data mining techniques, and visual analytics to provide an innovative environment for making sense of scholarly data. Its functionalities include: i) a variety of views to make sense of important trends in research; ii) a novel semantic approach for characterising research topics; iii) a very fine-grained expert search with detailed multi-dimensional parameters; iv) an innovative graph view to relate a variety of academic entities; iv) the ability to detect and explore the main communities within a research topic; v) the ability to analyse research performance at different levels of abstraction, including individual researchers, organizations, countries, and research communities

Fast filtering and animation of large dynamic networks

Detecting and visualizing what are the most relevant changes in an evolving network is an open challenge in several domains. We present a fast algorithm that filters subsets of the strongest nodes and edges representing an evolving weighted graph and visualize it by either creating a movie, or by streaming it to an interactive network visualization tool. The algorithm is an approximation of exponential sliding time-window that scales linearly with the number of interactions. We compare the algorithm against rectangular and exponential sliding time-window methods. Our network filtering algorithm: i) captures persistent trends in the structure of dynamic weighted networks, ii) smoothens transitions between the snapshots of dynamic network, and iii) uses limited memory and processor time. The algorithm is publicly available as open-source software.Comment: 6 figures, 2 table

A computer-assisted motivational social network intervention to reduce alcohol, drug and HIV risk behaviors among Housing First residents.

BackgroundIndividuals transitioning from homelessness to housing face challenges to reducing alcohol, drug and HIV risk behaviors. To aid in this transition, this study developed and will test a computer-assisted intervention that delivers personalized social network feedback by an intervention facilitator trained in motivational interviewing (MI). The intervention goal is to enhance motivation to reduce high risk alcohol and other drug (AOD) use and reduce HIV risk behaviors.Methods/designIn this Stage 1b pilot trial, 60 individuals that are transitioning from homelessness to housing will be randomly assigned to the intervention or control condition. The intervention condition consists of four biweekly social network sessions conducted using MI. AOD use and HIV risk behaviors will be monitored prior to and immediately following the intervention and compared to control participants' behaviors to explore whether the intervention was associated with any systematic changes in AOD use or HIV risk behaviors.DiscussionSocial network health interventions are an innovative approach for reducing future AOD use and HIV risk problems, but little is known about their feasibility, acceptability, and efficacy. The current study develops and pilot-tests a computer-assisted intervention that incorporates social network visualizations and MI techniques to reduce high risk AOD use and HIV behaviors among the formerly homeless. CLINICALTRIALS.Gov identifierNCT02140359