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In recent years, considerable research efforts have been directed to micro-array technologies and their role in providing simultaneous information on expression profiles for thousands of genes. These data, when subjected to clustering and classification procedures, can assist in identifying patterns and providing insight on biological processes. To understand the properties of complex gene expression datasets, graphical representations can be used. Intuitively, the data can be represented in terms of a bipartite graph, with weighted edges corresponding to gene-sample node couples in the dataset. Biologically meaningful subgraphs can be sought, but performance can be influenced both by the search algorithm, and, by the graph-weighting scheme and both merit rigorous investigation. In this paper, we focus on edge-weighting schemes for bipartite graphical representation of gene expression. Two novel methods are presented: the first is based on empirical evidence; the second on a geometric distribution. The schemes are compared for several real datasets, assessing efficiency of performance based on four essential properties: robustness to noise and missing values, discrimination, parameter influence on scheme efficiency and reusability. Recommendations and limitations are briefly discussed. Keywords: Edge-weighting; weighted graphs; gene expression; bi-clustering

The formation of complex patterns in chemical systems is discussed in the following cases: relations of pattern formation to thermodynamics theories; unusually complex pattern formation in very simple experimental chemical systems; and numerical simulation of patterns that develop in multicellular chemical systems. The paper concludes with a discussion on future technological applications.

The evolution of road expansion and traffic growth (motor vehicle) of urban system is a quite complex process. To investigate the interaction between them, a coevolution dynamics model is proposed in this paper to capture the relationships among traveler, vehicle and road. Then stability analysis and numerical simulation are conducted. The results show that the coevolution model can be stable under certain conditions and there exists a dynamic equilibrium in the evolution process. In order to verify the proposed model, Beijing as a case study is analyzed. Results show that the proposed model provides a new perspective for capturing the characteristic of road and urban traffic and contributes to the coordinated development of the whole transportation system.

In this paper, we report on the theoretical foundations, empirical context and technical implementation of an agent-based modeling (ABM) framework, that uses a high-performance computing (HPC) approach to investigate human population dynamics on a global scale, and on evolutionary time scales. The ABM-HPC framework provides an in silico testbed to explore how short-term/small-scale patterns of individual human behavior and long-term/large-scale patterns of environmental change act together to influence human dispersal, survival and extinction scenarios. These topics are currently at the center of the Neanderthal debate, i.e., the question why Neanderthals died out during the Late Pleistocene, while modern humans dispersed over the entire globe. To tackle this and similar questions, simulations typically adopt one of two opposing approaches, top-down (equation-based) and bottom-up (agent-based) models of population dynamics. We propose HPC technology as an essential computational tool to bridge the gap between these approaches. Using the numerical simulation of worldwide human dispersals as an example, we show that integrating different levels of model hierarchy into an ABM-HPC simulation framework provides new insights into emergent properties of the model, and into the potential and limitations of agent-based versus continuum models.