Flud: a hybrid crowd-algorithm approach for visualizing biological networks

Modern experiments in many disciplines generate large quantities of network (graph) data. Researchers require aesthetic layouts of these networks that clearly convey the domain knowledge and meaning. However, the problem remains challenging due to multiple conflicting aesthetic criteria and complex domain-specific constraints. In this paper, we present a strategy for generating visualizations that can help network biologists understand the protein interactions that underlie processes that take place in the cell. Specifically, we have developed Flud, an online game with a purpose (GWAP) that allows humans with no expertise to design biologically meaningful graph layouts with the help of algorithmically generated suggestions. Further, we propose a novel hybrid approach for graph layout wherein crowdworkers and a simulated annealing algorithm build on each other's progress. To showcase the effectiveness of Flud, we recruited crowd workers on Amazon Mechanical Turk to lay out complex networks that represent signaling pathways. Our results show that the proposed hybrid approach outperforms state-of-the-art techniques for graphs with a large number of feedback loops. We also found that the algorithmically generated suggestions guided the players when they are stuck and helped them improve their score. Finally, we discuss broader implications for mixed-initiative interactions in human computation games.Comment: This manuscript is currently under revie

A New Era in Epicardial Access for the Ablation of Ventricular Arrhythmias: The Epi-Co(2) Registry

OBJECTIVES: This multicenter registry aimed to assess the reproducibility and safety of intentional coronary vein exit and carbon dioxide insufflation to facilitate subxiphoid epicardial access in the setting of ventricular tachycardia ablation. BACKGROUND: Epicardial ablation for ventricular tachycardia is not a widespread technique due to the significant potential complications associated with subxiphoid puncture. The first experience in 12 patients showed that intentional coronary vein exit and carbon dioxide insufflation was technically feasible. METHODS: A branch of the coronary sinus was cannulated by means of a diagnostic JR4 coronary catheter. Intentional perforation at the distal portion of that branch was performed with a high tip load 0.014-inch angioplasty wire. A microcatheter was advanced over the wire into the pericardial space. Carbon dioxide was then insufflated into the pericardial space, allowing direct visualization of the anterior pericardial space to facilitate subxiphoid puncture. RESULTS: Intentional coronary vein exit was attempted in 102 consecutive patients in 16 different centers and successfully completed in 101 patients. Significant pericardial adhesions were confirmed in 3 patients, preventing carbon dioxide insufflation and epicardial ablation. None of the punctures were complicated with inadvertent right ventricular puncture or damage to a coronary artery. Significant bleeding (>80 ml) due to coronary vein exit occurred in 5 patients, without hemodynamic compromise. None of the patients required surgery. CONCLUSIONS: Coronary vein exit and carbon dioxide insufflation can be safely and reproducibly achieved to facilitate subxiphoid pericardial access in the setting of ventricular tachycardia ablation.Not heldPublished version, accepted version (12 month embargo