Consensus clustering in complex networks

The community structure of complex networks reveals both their organization and hidden relationships among their constituents. Most community detection methods currently available are not deterministic, and their results typically depend on the specific random seeds, initial conditions and tie-break rules adopted for their execution. Consensus clustering is used in data analysis to generate stable results out of a set of partitions delivered by stochastic methods. Here we show that consensus clustering can be combined with any existing method in a self-consistent way, enhancing considerably both the stability and the accuracy of the resulting partitions. This framework is also particularly suitable to monitor the evolution of community structure in temporal networks. An application of consensus clustering to a large citation network of physics papers demonstrates its capability to keep track of the birth, death and diversification of topics.Comment: 11 pages, 12 figures. Published in Scientific Report

An exploration and validation of computer modeling of evolution, natural selection, and evolutionary biology with cellular automata for secondary students.

The Evolutionary Tool Kit, a new software package, is the prototype of a concept simulator providing an environment for students to create microworlds of populations of artificial organisms. Its function is to model processes, concepts and arguments in natural selection and evolutionary biology, using either Mendelian asexual or sexual reproduction, or counterfactual systems such as \u27paint pot\u27 or blending inheritance. In this environment students can explore a conceptual What if? in evolutionary biology, test misconceptions and deepen understanding of inheritance and changes in populations. Populations can be defined either with typological, or with populational thinking, to inquire into the role and necessity of variation in natural selection. The approach is generative not tutorial. The interface is highly graphic with twenty traits set as icons that are moved onto the \u27phenotypes\u27. Activities include investigations of evolutionary theory of aging, reproductive advantage, sexual selection and mimicry. Design of the activities incorporates Howard Gardner\u27s Theory of Multiple Intelligences. Draft of a teacher and student manual are included

Using MapReduce Streaming for Distributed Life Simulation on the Cloud

Distributed software simulations are indispensable in the study of large-scale life models but often require the use of technically complex lower-level distributed computing frameworks, such as MPI. We propose to overcome the complexity challenge by applying the emerging MapReduce (MR) model to distributed life simulations and by running such simulations on the cloud. Technically, we design optimized MR streaming algorithms for discrete and continuous versions of Conway’s life according to a general MR streaming pattern. We chose life because it is simple enough as a testbed for MR’s applicability to a-life simulations and general enough to make our results applicable to various lattice-based a-life models. We implement and empirically evaluate our algorithms’ performance on Amazon’s Elastic MR cloud. Our experiments demonstrate that a single MR optimization technique called strip partitioning can reduce the execution time of continuous life simulations by 64%. To the best of our knowledge, we are the first to propose and evaluate MR streaming algorithms for lattice-based simulations. Our algorithms can serve as prototypes in the development of novel MR simulation algorithms for large-scale lattice-based a-life models.https://digitalcommons.chapman.edu/scs_books/1014/thumbnail.jp

An Initial Framework Assessing the Safety of Complex Systems

Trabajo presentado en la Conference on Complex Systems, celebrada online del 7 al 11 de diciembre de 2020.Atmospheric blocking events, that is large-scale nearly stationary atmospheric pressure patterns, are often associated with extreme weather in the mid-latitudes, such as heat waves and cold spells which have significant consequences on ecosystems, human health and economy. The high impact of blocking events has motivated numerous studies. However, there is not yet a comprehensive theory explaining their onset, maintenance and decay and their numerical prediction remains a challenge. In recent years, a number of studies have successfully employed complex network descriptions of fluid transport to characterize dynamical patterns in geophysical flows. The aim of the current work is to investigate the potential of so called Lagrangian flow networks for the detection and perhaps forecasting of atmospheric blocking events. The network is constructed by associating nodes to regions of the atmosphere and establishing links based on the flux of material between these nodes during a given time interval. One can then use effective tools and metrics developed in the context of graph theory to explore the atmospheric flow properties. In particular, Ser-Giacomi et al. [1] showed how optimal paths in a Lagrangian flow network highlight distinctive circulation patterns associated with atmospheric blocking events. We extend these results by studying the behavior of selected network measures (such as degree, entropy and harmonic closeness centrality)at the onset of and during blocking situations, demonstrating their ability to trace the spatio-temporal characteristics of these events.This research was conducted as part of the CAFE (Climate Advanced Forecasting of sub-seasonal Extremes) Innovative Training Network which has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 813844

多細胞組織のメゾスコピックレベルでの分解と再構成 : 複雑適応系の非平衡相転移理論に向けて

学位の種別: 課程博士審査委員会委員 : （主査）東京大学准教授 陳 昱, 東京大学教授 飛原 英治, 東京大学教授 奥田 洋司, 東京大学教授 大橋 弘忠, 京都大学准教授 井上 康博University of Tokyo(東京大学

A Complex Systems Simulation Study for Increasing Adaptive-Capacity

Examination of empirical research confirmed that climate change is a complex problem of anthropological origin and revealed the need for a management framework to facilitate strategic decisions aimed at mitigating a rise in global temperatures of 2-°C linked to irresponsible and unsustainable business practices. The purpose of this simulation study was to develop a management framework of resilience, robustness, sustainability, and adaptive-capacity (RRSA) for organizations viewed as complex systems to address the current unsustainable state. As such, the evolutionary-RRSA prisoner\u27s dilemma (PD) simulation was developed using an evolutionary game theory approach to agent based modeling and simulation, to generate data. Regression analyses tested the relationships between organizational resilience (x1), robustness (x2), and sustainability (x3) as independent variables, and the dependent variable of adaptive capacity (y) for cooperative and defective strategies. The findings were that complex nonlinear relationships exist between resilience, robustness, sustainability, and adaptive-capacity, which is sensitive to initial conditions and may emerge and evolve from combinations of cooperative and defective decisions within the evolutionary RRSA PD management tool. This study resulted in the RRSA management framework, a cyclical 4-phased approach, which may be used by climate governance leaders, negotiators, and policy-makers to facilitate strategy to move global climate change policy forward by guiding bottom-up consumption and production of GHGs, thereby improving adaptive-capacity, while mitigating an increase in global temperatures of 2-°C, which in turn would improve global socio-economic conditions

Optimisation algorithms inspired from modelling of bacterial foraging patterns and their applications

Research in biologically-inspired optimisation has been fl<;lurishing over the past decades. This approach adopts a bott0!ll-up viewpoint to understand and mimic certain features of a biological system. It has been proved useful in developing nondeterministic algorithms, such as Evolutionary Algorithms (EAs) and Swarm Intelligence (SI). Bacteria, as the simplest creature in nature, are of particular interest in recent studies. In the past thousands of millions of years, bacteria have exhibited a self-organising behaviour to cope with the natural selection. For example, bacteria have developed a number of strategies to search for food sources with a very efficient manner. This thesis explores the potential of understanding of a biological system by modelling the' underlying mechanisms of bacterial foraging patterns and investigates their applicability to engineering optimisation problems. :rvlodelling plays a significant role in understanding bacterial foraging behaviour. Mathematical expressions and experimental observations have been utilised to represent biological systems. However, difficulties arise from the lack of systematic analysis of the developed models and experimental data. Recently, Systems Biology has be,en proposed to overcome this barrier, with the effort from a number of research fields, including Computer Science and Systems Engineering. At the same time, Individual-based Modelling (IbM) has emerged to assist the modelling of a biological system. Starting from a basic model of foraging and proliferation of bacteria, the development of an IbM of bacterial systems of this thesis focuses on a Varying Environment BActerial Model (VEBAM). Simulation results demonstrate that VEBAM is able to provide a new perspective to describe interactions between the bacteria and their food environment. Knowledge transfer from modelling of bacterial systems to solving optimisation problems also composes an important part of this study. Three Bacteriainspired Algorithms (BalAs) have been developed to bridge the gap between modelling and optimisation. These algorithms make use of the. self-adaptability of individual bacteria in the group searching activities described in VEBAM, while incorporating a variety of additional features. In particular, the new bacterial foraging algorithm with varying population (BFAVP) takes bacterial metabolism into consideration. The group behaviour in Particle Swarm Optimiser (PSO) is adopted in Bacterial Swarming Algorithm (BSA) to enhance searching ability. To reduce computational time, another algorithm, a Paired-bacteria Optimiser (PBO) is designed specifically to further explore the capability of BalAs. Simulation studies undertaken against a wide range of benchmark functions demonstrate a satisfying performance with a reasonable convergence speed. To explore the potential of bacterial searching ability in optimisation undertaken in a varying environment, a dynamic bacterial foraging algorithm (DBFA) is developed with the aim of solving optimisation in a time-varying environment. In this case, the balance between its convergence and exploration abilities is investigated, and a new scheme of reproduction is developed which is different froin that used for static optimisation problems. The simulation studies have been undertaken and the results show that the DBFA can adapt to various environmental changes rapidly. One of the challenging large-scale complex optimisation problems is optimal power flow (OPF) computation. BFAVP shows its advantage in solving this problem. A simulation study has been performed on an IEEE 30-bus system, and the results are compared with PSO algorithm and Fast Evolutionary Programming (FEP) algorithm, respectively. Furthermore, the OPF problem is extended for consideration in varying environments, on which DBFA has been evaluated. A simulation study has been undertaken on both the IEEE 30-bus system and the IEEE l1S-bus system, in compariso~ with a number of existing algorithms. The dynamic OPF problem has been tackled for the first time in the area of power systems, and the results obtained are encouraging, with a significant amount of energy could possibly being saved. Another application of BaIA in this thesis is concerned with estimating optimal parameters of a power transformer winding model using BSA. Compared with Genetic Algorithm (GA), BSA is able to obtain a more satisfying result in modelling the transformer winding, which could not be achieved using a theoretical transfer function model