ICCS 2018 Main Track (MT) Session 7
Time and Date: 13:35 - 15:15 on 11th June 2018
Chair: Roberto Ribeiro
| A Computational Model-Based Framework to Plan Clinical Experiments – an Application to Vascular Adaptation Biology [abstract]
Abstract: Several computational models have been developed in order to improve the outcome of Vein Graft Bypasses in response to arterial occlusions and they all share a common property: their accuracy relies on a winning choice of the coefficients’ value related to biological functions that drive them. Our goal is to optimize the retrieval of these unknown coefficients on the base of experimental data and accordingly, as biological experiments are noisy in terms of statistical analysis and the models are typically stochastic and complex, this work wants first to elucidate which experimental measurements might be sufficient to retrieve the targeted coefficients and second how many specimens would constitute a good dataset to guarantee a sufficient level of accuracy. Since experiments are often costly and time consuming, the planning stage is critical to the success of the operation and, on the base of this consideration, the present work shows how, thanks to an ad hoc use of a computational model of vascular adaptation, it is possible to estimate in advance the entity and the quantity of resources needed in order to efficiently repro-duce the experimental reality.
|Stefano Casarin, Scott Berceli and Marc Garbey
| Accelerating Data Analysis in Simulation Neuroscience with Big Data Technologies [abstract]
Abstract: Important progress in computational sciences has been made possible recently thanks to the increasing computing power of high performance systems. Following this trend, larger scientific studies, like brain tissue simulations, will continue to grow in the future. In addition to the challenges of conducting these experiments, we foresee an explosion of the amount of data generated and the consequent unfeasibility of analyzing and understanding the results with the current techniques. This paper proposes Neurolytics, a new data analysis framework, together with a new data layout. The implementation of Neurolytics is mainly focused on simulation neuroscience, although we believe that our design can be applied to other science domains. The framework relies on big data technologies, like Apache Spark, to enable fast, reliable and distributed analyses of brain simulation data in this case. Our experimental evaluation on a cluster of 100 nodes shows that Neurolytics gets up to 374x speed-up compared to a thread-parallel Python implementation and is on par with a highly optimized Spark code. This demonstrates the suitability of our proposal to help scientists structure and understand the results of their experiments in a fast and efficient way.
|Judit Planas, Fabien Delalondre and Felix Schuermann
| Spiral wave drift induced by high-frequency forcing. Parallel simulation in the Luo-Rudy anisotropic model of cardiac tissue [abstract]
Abstract: Non-linear waves occur in various physical, chemical and biological media. One of the most important examples is electrical excitation waves in the myocardium, which initiate contraction of the heart. Abnormal wave propagation in the heart, such as the formation of spiral waves, causes dangerous arrhythmias, and thus methods of elimination of such waves are of great interest. One of the most promising methods is so-called low-voltage cardioversion and defibrillation, which is believed to be achieved by inducing the drift and disappearance of spiral waves using external high-frequency electrical stimulation of the heart. In this paper, we perform a computational analysis of the interaction of spiral waves and trains of high-frequency plane waves in 2D models of cardiac tissue. We investigate the effectiveness and safety of the treatment. We also identify the dependency of drift velocity on the period of plane waves. The simulations were carried out using a parallel computing system with OpenMP technology.
|Timofey Epanchintsev, Sergei Pravdin and Alexander Panfilov
| Understanding Malaria induced red blood cell deformation using data-driven Lattice Boltzmann Simulations [abstract]
Abstract: Malaria remains a deadly disease that affected millions of people in 2016. Among the five Plasmodium (P.) parasites which contribute to malaria dis-eases in humans. P. falciparum is a lethal one which is responsible for the majority of the world-wide-malaria-related deaths. Since the banana-shaped stage V gametocytes play a crucial role in disease transmission, understand-ing the deformation of single stage V gametocytes may offer deeper insights into the development of the disease and provide possible targets for new treatment methods. In this study we used lattice Boltzmann-based simula-tions to investigate the effects of the stretching forces acting on infected red blood cells inside a slit-flow cytometer. The parameters that represent the cellular deformability of healthy and malaria infected red blood cells are chosen such that they mimic the deformability of these cells in a slit-flow cy-tometer. The simulation results show good agreement with experimental data and allow for studying the transportation of malaria infected red blood cell in blood circulation.
|Joey Sing Yee Tan, Gabor Zavodszky and Peter M. A. Sloot
| Towards Model-based Policy Elaboration on City Scale using Game Theory: Application to Ambulance Dispatching [abstract]
Abstract: The paper presents early results on the development of a generalized approach for modeling and analysis of the interaction of multiple stakeholders in city environ-ment while providing services to citizens under the regulation of city authorities. The approach considers the interaction between main stakeholders (organizations of various kind, citizens, and city authorities) including information and finances exchange, activities taken and services or goods provided. The developed ap-proach is based on a combination of game-theoretic modeling and simulation of service providers interaction. Such combination enables consideration of con-fronting stakeholders as well as determined (e.g., scheduled) and stochastic varia-tion in characteristics of system’s elements. The goal of this approach develop-ment is supporting of analysis and optimization of city-level regulation through legislative, financial, and informational interaction with organizations and envi-ronment of a city. An example of ambulance dispatching during providing emer-gent care for acute coronary syndrome (ACS) patients is considered. The exam-ple is analyzed in a simplified linear case and in practical application to dispatch-ing ambulances providing service for ACS patients in Saint Petersburg.
|Sergey Kovalchuk, Mariia Moskalenko and Alexey Yakovlev