OncoThreads: visualization of large-scale longitudinal cancer molecular data.

MOTIVATION: Molecular profiling of patient tumors and liquid biopsies over time with next-generation sequencing technologies and new immuno-profile assays are becoming part of standard research and clinical practice. With the wealth of new longitudinal data, there is a critical need for visualizations for cancer researchers to explore and interpret temporal patterns not just in a single patient but across cohorts. RESULTS: To address this need we developed OncoThreads, a tool for the visualization of longitudinal clinical and cancer genomics and other molecular data in patient cohorts. The tool visualizes patient cohorts as temporal heatmaps and Sankey diagrams that support the interactive exploration and ranking of a wide range of clinical and molecular features. This allows analysts to discover temporal patterns in longitudinal data, such as the impact of mutations on response to a treatment, for example, emergence of resistant clones. We demonstrate the functionality of OncoThreads using a cohort of 23 glioma patients sampled at 2-4 timepoints. AVAILABILITY AND IMPLEMENTATION: Freely available at http://oncothreads.gehlenborglab.org. Implemented in Java Script using the cBioPortal web API as a backend. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Evaluating Cartogram Effectiveness.

Cartograms are maps in which areas of geographic regions, such as countries and states, appear in proportion to some variable of interest, such as population or income. Cartograms are popular visualizations for geo-referenced data that have been used for over a century to illustrate patterns and trends in the world around us. Despite the popularity of cartograms, and the large number of cartogram types, there are few studies evaluating the effectiveness of cartograms in conveying information. Based on a recent task taxonomy for cartograms, we evaluate four major types of cartograms: contiguous, non-contiguous, rectangular, and Dorling cartograms. We first evaluate the effectiveness of these cartogram types by quantitative performance analysis (time and error). Second, we collect qualitative data with an attitude study and by analyzing subjective preferences. Third, we compare the quantitative and qualitative results with the results of a metrics-based cartogram evaluation. Fourth, we analyze the results of our study in the context of cartography, geography, visual perception, and demography. Finally, we consider implications for design and possible improvements.

Cartogram Visualization for Bivariate Geo-Statistical Data.

We describe bivariate cartograms, a technique specifically designed to allow for the simultaneous comparison of two geo-statistical variables. Traditional cartograms are designed to show only a single statistical variable, but in practice, it is often useful to show two variables (e.g., the total sales for two competing companies) simultaneously. We illustrate bivariate cartograms using Dorling-style cartograms, yet the technique is simple and generalizable to other cartogram types, such as contiguous cartograms, rectangular cartograms, and non-contiguous cartograms. An interactive feature makes it possible to switch between bivariate cartograms, and the traditional (monovariate) cartograms. Bivariate cartograms make it easy to find more geographic patterns and outliers in a pre-attentive way than previous approaches, as shown in Fig. 2 . They are most effective for showing two variables from the same domain (e.g., population in two different years, sales for two different companies), although they can also be used for variables from different domains (e.g., population and income). We also describe a small-scale evaluation of the proposed techniques that indicates bivariate cartograms are especially effective for finding geo-statistical patterns, trends and outliers.

Calorie Estimation From Pictures of Food: Crowdsourcing Study.

BACKGROUND: Software designed to accurately estimate food calories from still images could help users and health professionals identify dietary patterns and food choices associated with health and health risks more effectively. However, calorie estimation from images is difficult, and no publicly available software can do so accurately while minimizing the burden associated with data collection and analysis. OBJECTIVE: The aim of this study was to determine the accuracy of crowdsourced annotations of calorie content in food images and to identify and quantify sources of bias and noise as a function of respondent characteristics and food qualities (eg, energy density). METHODS: We invited adult social media users to provide calorie estimates for 20 food images (for which ground truth calorie data were known) using a custom-built webpage that administers an online quiz. The images were selected to provide a range of food types and energy density. Participants optionally provided age range, gender, and their height and weight. In addition, 5 nutrition experts provided annotations for the same data to form a basis of comparison. We examined estimated accuracy on the basis of expertise, demographic data, and food qualities using linear mixed-effects models with participant and image index as random variables. We also analyzed the advantage of aggregating nonexpert estimates. RESULTS: A total of 2028 respondents agreed to participate in the study (males: 770/2028, 37.97%, mean body mass index: 27.5 kg/m2). Average accuracy was 5 out of 20 correct guesses, where "correct" was defined as a number within 20% of the ground truth. Even a small crowd of 10 individuals achieved an accuracy of 7, exceeding the average individual and expert annotator's accuracy of 5. Women were more accurate than men (P<.001), and younger people were more accurate than older people (P<.001). The calorie content of energy-dense foods was overestimated (P=.02). Participants performed worse when images contained reference objects, such as credit cards, for scale (P=.01). CONCLUSIONS: Our findings provide new information about how calories are estimated from food images, which can inform the design of related software and analyses.