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HD Physiology Project-Japanese efforts to promote multilevel integrative systems biology and physiome research.
The HD Physiology Project is a Japanese research consortium that aimed to develop methods and a computational platform in which physiological and pathological information can be described in high-level definitions across multiple scales of time and size. During the 5 years of this project, an appropriate software platform for multilevel functional simulation was developed and a whole-heart model including pharmacokinetics for the assessment of the proarrhythmic risk of drugs was developed. In this article, we outline the description and scientific strategy of this project and present the achievements and influence on multilevel integrative systems biology and physiome research
Route Planning in Transportation Networks
We survey recent advances in algorithms for route planning in transportation
networks. For road networks, we show that one can compute driving directions in
milliseconds or less even at continental scale. A variety of techniques provide
different trade-offs between preprocessing effort, space requirements, and
query time. Some algorithms can answer queries in a fraction of a microsecond,
while others can deal efficiently with real-time traffic. Journey planning on
public transportation systems, although conceptually similar, is a
significantly harder problem due to its inherent time-dependent and
multicriteria nature. Although exact algorithms are fast enough for interactive
queries on metropolitan transit systems, dealing with continent-sized instances
requires simplifications or heavy preprocessing. The multimodal route planning
problem, which seeks journeys combining schedule-based transportation (buses,
trains) with unrestricted modes (walking, driving), is even harder, relying on
approximate solutions even for metropolitan inputs.Comment: This is an updated version of the technical report MSR-TR-2014-4,
previously published by Microsoft Research. This work was mostly done while
the authors Daniel Delling, Andrew Goldberg, and Renato F. Werneck were at
Microsoft Research Silicon Valle
Multilayer Networks
In most natural and engineered systems, a set of entities interact with each
other in complicated patterns that can encompass multiple types of
relationships, change in time, and include other types of complications. Such
systems include multiple subsystems and layers of connectivity, and it is
important to take such "multilayer" features into account to try to improve our
understanding of complex systems. Consequently, it is necessary to generalize
"traditional" network theory by developing (and validating) a framework and
associated tools to study multilayer systems in a comprehensive fashion. The
origins of such efforts date back several decades and arose in multiple
disciplines, and now the study of multilayer networks has become one of the
most important directions in network science. In this paper, we discuss the
history of multilayer networks (and related concepts) and review the exploding
body of work on such networks. To unify the disparate terminology in the large
body of recent work, we discuss a general framework for multilayer networks,
construct a dictionary of terminology to relate the numerous existing concepts
to each other, and provide a thorough discussion that compares, contrasts, and
translates between related notions such as multilayer networks, multiplex
networks, interdependent networks, networks of networks, and many others. We
also survey and discuss existing data sets that can be represented as
multilayer networks. We review attempts to generalize single-layer-network
diagnostics to multilayer networks. We also discuss the rapidly expanding
research on multilayer-network models and notions like community structure,
connected components, tensor decompositions, and various types of dynamical
processes on multilayer networks. We conclude with a summary and an outlook.Comment: Working paper; 59 pages, 8 figure
Modelling and Design of Resilient Networks under Challenges
Communication networks, in particular the Internet, face a variety of challenges that can disrupt our daily lives resulting in the loss of human lives and significant financial costs in the worst cases. We define challenges as external events that trigger faults that eventually result in service failures. Understanding these challenges accordingly is essential for improvement of the current networks and for designing Future Internet architectures. This dissertation presents a taxonomy of challenges that can help evaluate design choices for the current and Future Internet. Graph models to analyse critical infrastructures are examined and a multilevel graph model is developed to study interdependencies between different networks. Furthermore, graph-theoretic heuristic optimisation algorithms are developed. These heuristic algorithms add links to increase the resilience of networks in the least costly manner and they are computationally less expensive than an exhaustive search algorithm. The performance of networks under random failures, targeted attacks, and correlated area-based challenges are evaluated by the challenge simulation module that we developed. The GpENI Future Internet testbed is used to conduct experiments to evaluate the performance of the heuristic algorithms developed
Deep D-Bar: Real-Time Electrical Impedance Tomography Imaging With Deep Neural Networks
The mathematical problem for electrical impedance tomography (EIT) is a highly nonlinear ill-posed inverse problem requiring carefully designed reconstruction procedures to ensure reliable image generation. D-bar methods are based on a rigorous mathematical analysis and provide robust direct reconstructions by using a low-pass filtering of the associated nonlinear Fourier data. Similarly to low-pass filtering of linear Fourier data, only using low frequencies in the image recovery process results in blurred images lacking sharp features, such as clear organ boundaries. Convolutional neural networks provide a powerful framework for post-processing such convolved direct reconstructions. In this paper, we demonstrate that these CNN techniques lead to sharp and reliable reconstructions even for the highly nonlinear inverse problem of EIT. The network is trained on data sets of simulated examples and then applied to experimental data without the need to perform an additional transfer training. Results for absolute EIT images are presented using experimental EIT data from the ACT4 and KIT4 EIT systems
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