NNVA: Neural Network Assisted Visual Analysis of Yeast Cell Polarization Simulation

Complex computational models are often designed to simulate real-world physical phenomena in many scientific disciplines. However, these simulation models tend to be computationally very expensive and involve a large number of simulation input parameters which need to be analyzed and properly calibrated before the models can be applied for real scientific studies. We propose a visual analysis system to facilitate interactive exploratory analysis of high-dimensional input parameter space for a complex yeast cell polarization simulation. The proposed system can assist the computational biologists, who designed the simulation model, to visually calibrate the input parameters by modifying the parameter values and immediately visualizing the predicted simulation outcome without having the need to run the original expensive simulation for every instance. Our proposed visual analysis system is driven by a trained neural network-based surrogate model as the backend analysis framework. Surrogate models are widely used in the field of simulation sciences to efficiently analyze computationally expensive simulation models. In this work, we demonstrate the advantage of using neural networks as surrogate models for visual analysis by incorporating some of the recent advances in the field of uncertainty quantification, interpretability and explainability of neural network-based models. We utilize the trained network to perform interactive parameter sensitivity analysis of the original simulation at multiple levels-of-detail as well as recommend optimal parameter configurations using the activation maximization framework of neural networks. We also facilitate detail analysis of the trained network to extract useful insights about the simulation model, learned by the network, during the training process.Comment: Published at IEEE Transactions on Visualization and Computer Graphic

Interactive Visual Analysis of Networked Systems: Workflows for Two Industrial Domains

We report on a first study of interactive visual analysis of networked systems. Working with ABB Corporate Research and Ericsson Research, we have created workflows which demonstrate the potential of visualization in the domains of industrial automation and telecommunications. By a workflow in this context, we mean a sequence of visualizations and the actions for generating them. Visualizations can be any images that represent properties of the data sets analyzed, and actions typically either change the selection of data visualized or change the visualization by choice of technique or change of parameters

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

Facilitating insight into a simulation model using visualization and dynamic model previews

This paper shows how model simplification, by replacing iterative steps with unitary predictive equations, can enable dynamic interaction with a complex simulation process. Model previews extend the techniques of dynamic querying and query previews into the context of ad hoc simulation model exploration. A case study is presented within the domain of counter-current chromatography. The relatively novel method of insight evaluation was applied, given the exploratory nature of the task. The evaluation data show that the trade-off in accuracy is far outweighed by benefits of dynamic interaction. The number of insights gained using the enhanced interactive version of the computer model was more than six times higher than the number of insights gained using the basic version of the model. There was also a trend for dynamic interaction to facilitate insights of greater domain importance

Soft set theory based decision support system for mining electronic government dataset

Electronic government (e-gov) is applied to support performance and create more efficient and effective public services. Grouping data in soft-set theory can be considered as a decision-making technique for determining the maturity level of e-government use. So far, the uncertainty of the data obtained through the questionnaire has not been maximally used as an appropriate reference for the government in determining the direction of future e-gov development policy. This study presents the maximum attribute relative (MAR) based on soft set theory to classify attribute options. The results show that facilitation conditions (FC) are the highest variable in influencing people to use e-government, followed by performance expectancy (PE) and system quality (SQ). The results provide useful information for decision makers to make policies about their citizens and potentially provide recommendations on how to design and develop e-government systems in improving public services

Discrete event simulation and virtual reality use in industry: new opportunities and future trends

This paper reviews the area of combined discrete event simulation (DES) and virtual reality (VR) use within industry. While establishing a state of the art for progress in this area, this paper makes the case for VR DES as the vehicle of choice for complex data analysis through interactive simulation models, highlighting both its advantages and current limitations. This paper reviews active research topics such as VR and DES real-time integration, communication protocols, system design considerations, model validation, and applications of VR and DES. While summarizing future research directions for this technology combination, the case is made for smart factory adoption of VR DES as a new platform for scenario testing and decision making. It is put that in order for VR DES to fully meet the visualization requirements of both Industry 4.0 and Industrial Internet visions of digital manufacturing, further research is required in the areas of lower latency image processing, DES delivery as a service, gesture recognition for VR DES interaction, and linkage of DES to real-time data streams and Big Data sets