Computation in Complex Networks

Complex networks are one of the most challenging research focuses of disciplines, including physics, mathematics, biology, medicine, engineering, and computer science, among others. The interest in complex networks is increasingly growing, due to their ability to model several daily life systems, such as technology networks, the Internet, and communication, chemical, neural, social, political and financial networks. The Special Issue “Computation in Complex Networks" of Entropy offers a multidisciplinary view on how some complex systems behave, providing a collection of original and high-quality papers within the research fields of: • Community detection • Complex network modelling • Complex network analysis • Node classification • Information spreading and control • Network robustness • Social networks • Network medicin

Sustaining Glasgow's Urban Networks: the Link Communities of Complex Urban Systems

As cities grow in population size and became more crowded (UN DESA, 2018), the main future challenges around the world will remain to be accommodating the growing urban population while drastically reducing environmental pressure. Contemporary urban agglomerations (large or small) constantly impose burden on the natural environment by conveying ecosystem services to close and distant places, through coupled human nature [infrastructure] systems (CHANS). Tobler’s first law in geography (1970) that states that “everything is related to everything else, but near things are more related than distant things” is now challenged by globalization. When this law was first established, the hypothesis referred to geological processes (Campbell and Shin, 2012, p.194) that were predominantly observed in pre-globalized economy, where freight was costly and mainly localized (Zhang et al., 2018). With the recent advances and modernisation made in transport technologies, most of them in the sea and air transportation (Zhang et al., 2018) and the growth of cities in population, natural resources and bi-products now travel great distances to infiltrate cities (Neuman, 2006) and satisfy human demands. Technical modernisation and the global hyperconnectivity of human interactions and trading, in the last thirty years alone resulted with staggering 94 per cent growth of resource extraction and consumption (Giljum et al., 2015). Local geographies (Kennedy, Cuddihy and Engel-Yan, 2007) will remain affected by global urbanisation (Giljum et al., 2015), and as a corollary, the operational inefficiencies of their local infrastructure networks, will contribute even more to the issues of environmental unsustainability on a global scale. Another challenge for future city-regions is the equity of public infrastructure services and policy creation that promote the same (Neuman and Hull, 2009). Public infrastructure services refer to services provisioned by networked infrastructure, which are subject to both public obligation and market rules. Therefore, their accessibility to all citizens needs to be safeguarded. The disparity of growth between networked infrastructure and socio-economic dynamics affects the sustainable assimilation and equal access to infrastructure in various districts in cities, rendering it as a privilege. Yet, the empirical evidence of whether the place of residence acts as a disadvantage to public service access and use, remains rather scarce (Clifton et al., 2016). The European Union recognized (EU, 2011) the issue of equality in accessibility (i.e. equity) critical for territorial cohesion and sustainable development across districts, municipalities and regions with diverse economic performance. Territorial cohesion, formally incorporated into the Treaty of Lisbon, now steers the policy frameworks of territorial development within the Union. Subsequently, the European Union developed a policy paradigm guided by equal access (Clifton et al., 2016) to public infrastructure services, considering their accessibility as instrumental aspect in achieving territorial cohesion across and within its member states. A corollary of increasing the equity to public infrastructure services among growing global population is the potential increase in environmental pressure they can impose, especially if this pressure is not decentralised and surges at unsustainable rate (Neuman, 2006). This danger varies across countries and continents, and is directly linked to the increase of urban population due to; [1] improved quality of life and increased life expectancy and/or [2] urban in-migration of rural population and/or [3] global political or economic immigration. These three rising urban trends demand new approaches to reimagine planning and design practices that foster infrastructure equity, whilst delivering environmental justice. Therefore, this research explores in depth the nature of growth of networked infrastructure (Graham and Marvin, 2001) as a complex system and its disparity from the socio-economic growth (or decline) of Glasgow and Clyde Valley city-region. The results of this research gain new understanding in the potential of using emerging tools from network science for developing optimization strategy that supports more cecentralized, efficient, fair and (as an outcome) sustainable enlargement of urban infrastructure, to accommodate new and empower current residents of the city. Applying the novel link clustering community detection algorithm (Ahn et al., 2010) in this thesis I have presented the potential for better understanding the complexity behind the urban system of networked infrastructure, through discovering their overlapping communities. As I will show in the literature review (Chapter 2), the long standing tradition of centralised planning practice relying on zoning and infiltrating infrastructure, left us with urban settlements which are failing to respond to the environmental pressure and the socio-economic inequalities. Building on the myriad of knowledge from planners, geographers, sociologists and computer scientists, I developed a new element (i.e. link communities) within the theory of urban studies that defines cities as complex systems. After, I applied a method borrowed from the study of complex networks to unpack their basic elements. Knowing the link (i.e. functional, or overlapping) communities of metropolitan Glasgow enabled me to evaluate the current level of communities interconnectedness and reveal the gaps as well as the potentials for improving the studied system’s performance. The complex urban system in metropolitan Glasgow was represented by its networked infrastructure, which essentially was a system of distinct sub-systems, one of them mapped by a physical and the other one by a social graph. The conceptual framework for this methodological approach was formalised from the extensively reviewed literature and methods utilising network science tools to detect community structure in complex networks. The literature review led to constructing a hypothesis claiming that the efficiency of the physical network’s topology is achieved through optimizing the number of nodes with high betweenness centrality, while the efficiency of the logical network’s topology is achieved by optimizing the number of links with high edge betweenness. The conclusion from the literature review presented through the discourse on to the primal problem in 7.4.1, led to modelling the two network topologies as separate graphs. The bipartite graph of their primal syntax was mirrored to be symmetrical and converted to dual. From the dual syntax I measured the complete accessibility (i.e. betweenness centrality) of the entire area and not only of the streets. Betweenness centrality of a node measures the number of shortest paths that pass through the node connecting pairs of nodes. The betweenness centrality is same as the integration of streets in space syntax, where the streets are analysed in their dual syntax representation. Street integration is the number of intersections the street shares with other streets and a high value means high accessibility. Edges with high betweenness are shared between strong communities. Based on the theoretical underpinnings of the network’s modularity and community structure analysed herein, it can be concluded that a complex network that is both robust and efficient (and in urban planning terminology ‘sustainable’) is consisted of numerous strong communities connected with each other by optimal number of links with high edge betweenness. To get this insight, the study detected the edge cut-set and vertex cut-set of the complex network. The outcome was a statistical model developed in the open source software R (Ihaka and Gentleman, 1996). The model empirical detects the network’s overlapping communities, determining the current sustainability of its physical and logical topologies. Initially, an assumption was that the number of communities within the infrastructure (physical) network layer were different from the one in the logical. They were detected using the Louvain method that performs graph partitioning on the hierarchical streets structure. Further, the number of communities in the relational network layer (i.e. accessibility to locations) was detected based on the OD accessibility matrix established from the functional dependency between the household locations and predefined points of interest. The communities from the graph of the ‘relational layer' were discovered with the single-link hierarchical clustering algorithm. The number of communities observed in the physical and the logical topologies of the eight shires significantly deviated

Statistical Inference for Propagation Processes on Complex Networks

Die Methoden der Netzwerktheorie erfreuen sich wachsender Beliebtheit, da sie die Darstellung von komplexen Systemen durch Netzwerke erlauben. Diese werden nur mit einer Menge von Knoten erfasst, die durch Kanten verbunden werden. Derzeit verfügbare Methoden beschränken sich hauptsächlich auf die deskriptive Analyse der Netzwerkstruktur. In der hier vorliegenden Arbeit werden verschiedene Ansätze für die Inferenz über Prozessen in komplexen Netzwerken vorgestellt. Diese Prozesse beeinflussen messbare Größen in Netzwerkknoten und werden durch eine Menge von Zufallszahlen beschrieben. Alle vorgestellten Methoden sind durch praktische Anwendungen motiviert, wie die Übertragung von Lebensmittelinfektionen, die Verbreitung von Zugverspätungen, oder auch die Regulierung von genetischen Effekten. Zunächst wird ein allgemeines dynamisches Metapopulationsmodell für die Verbreitung von Lebensmittelinfektionen vorgestellt, welches die lokalen Infektionsdynamiken mit den netzwerkbasierten Transportwegen von kontaminierten Lebensmitteln zusammenführt. Dieses Modell ermöglicht die effiziente Simulationen verschiedener realistischer Lebensmittelinfektionsepidemien. Zweitens wird ein explorativer Ansatz zur Ursprungsbestimmung von Verbreitungsprozessen entwickelt. Auf Grundlage einer netzwerkbasierten Redefinition der geodätischen Distanz können komplexe Verbreitungsmuster in ein systematisches, kreisrundes Ausbreitungsschema projiziert werden. Dies gilt genau dann, wenn der Ursprungsnetzwerkknoten als Bezugspunkt gewählt wird. Die Methode wird erfolgreich auf den EHEC/HUS Epidemie 2011 in Deutschland angewandt. Die Ergebnisse legen nahe, dass die Methode die aufwändigen Standarduntersuchungen bei Lebensmittelinfektionsepidemien sinnvoll ergänzen kann. Zudem kann dieser explorative Ansatz zur Identifikation von Ursprungsverspätungen in Transportnetzwerken angewandt werden. Die Ergebnisse von umfangreichen Simulationsstudien mit verschiedenstensten Übertragungsmechanismen lassen auf eine allgemeine Anwendbarkeit des Ansatzes bei der Ursprungsbestimmung von Verbreitungsprozessen in vielfältigen Bereichen hoffen. Schließlich wird gezeigt, dass kernelbasierte Methoden eine Alternative für die statistische Analyse von Prozessen in Netzwerken darstellen können. Es wurde ein netzwerkbasierter Kern für den logistischen Kernel Machine Test entwickelt, welcher die nahtlose Integration von biologischem Wissen in die Analyse von Daten aus genomweiten Assoziationsstudien erlaubt. Die Methode wird erfolgreich bei der Analyse genetischer Ursachen für rheumatische Arthritis und Lungenkrebs getestet. Zusammenfassend machen die Ergebnisse der vorgestellten Methoden deutlich, dass die Netzwerk-theoretische Analyse von Verbreitungsprozessen einen wesentlichen Beitrag zur Beantwortung verschiedenster Fragestellungen in unterschiedlichen Anwendungen liefern kann

Challenges and prospects of spatial machine learning

The main objective of this thesis is to improve the usefulness of spatial machine learning for the spatial sciences and to allow its unused potential to be exploited. To achieve this objective, this thesis addresses several important but distinct challenges which spatial machine learning is facing. These are the modeling of spatial autocorrelation and spatial heterogeneity, the selection of an appropriate model for a given spatial problem, and the understanding of complex spatial machine learning models.Das wesentliche Ziel dieser Arbeit ist es, die Nützlichkeit des räumlichen maschinellen Lernens für die Raumwissenschaften zu verbessern und es zu ermöglichen, ungenutztes Potenzial auszuschöpfen. Um dieses Ziel zu erreichen, befasst sich diese Arbeit mit mehreren wichtigen Herausforderungen, denen das räumliche maschinelle Lernen gegenübersteht. Diese sind die Modellierung von räumlicher Autokorrelation und räumlicher Heterogenität, die Auswahl eines geeigneten Modells für ein gegebenes räumliches Problem und das Verständnis komplexer räumlicher maschineller Lernmodelle

Computational studies of vascularized tumors

Cancer is a hard problem touching numerous branches of life science. One reason for the complexity of cancer is that tumors act across many different time and length scales ranging from the subcellular to the macroscopic level. Modern sciences still lack an integral understanding of cancer, however in recent years, increasing computational power enabled computational models to accompany and support conventional medical and biological methods bridging the scales from micro to macro. Here I report a multiscale computational model simulating the progression of solid tumors comprising the vasculature mimicked by artificial arterio-venous blood vessel networks. I present a numerical optimization procedure to determine radii of blood vessels in an artificial microcirculation based on physiological stimuli independently of Murray’s law. Comprising the blood vessels, the reported model enables the inspection of blood vessel remodeling dynamics (angiogenesis, vaso-dilation, vessel regression and collapse) during tumor growth. We successfully applied the method to simulated tumor blood vessel networks guided by optical mammography data. In subsequent model development, I included cellular details into the method enabling a computational study of the tumor microenvironment at cellular resolution. I found that small vascularized tumors at the angiogenic switch exhibit a large ecological niche diversity resulting in high evolutionary pressure favoring the colonal selecion hypothesis.Krebs ist ein schwieriges Thema und tritt in zahlreichen Gebieten auf. Ein Grund für die Komplexität des Tumorwachstums sind die unterschiedlichen Zeit- und Längenskalen. In der aktuellen Forschung fehlt immernoch ein ganzheitliches Verständnis von Krebs, obwohl die computergestützten Methoden in den vergangenen Jahren die konventionellen Methoden der Medizin und der Biologie erweitern und unterstützen. Damit wird die Kluft zwischen subzellulären und makroskopischen Prozessen bereits verringert. In der vorliegenden Arbeit dokumentiere ich ein computergestütztes Verfahren, welches das Tumorwachstum auf mehreren Skalen simuliert. Insbesondere wird das Blutgefäßsystem durch künstliche Gefäße nachgeahmt. Es wurde ein numerisches Optimierungsverfahren zur Bestimmung der Gefäßradien eines künstlichen Blutkreislaufes entwickelt, welches auf physiologischen Reizen basiert und unabhängig von Murray‘s Gesetz ist. Da das beschriebene Verfahren zur Simulation von Tumoren Blutgefäße beinhaltet, kann die Umbildung des Gefäßbaumes während des Tumorwachstums untersucht werden. Das Modell wurde erfolgreich mit krankhaften Gefäßsystemen verglichen. In der darauffolgenden Weiterentwicklung des Modells berücksichtigte ich zelluläre Feinheiten, die es mir erlaubten das Mikromilieu in zellulärer Auflösung zu untersuchen. Meine Resultate zeigen, dass bereits kleine Tumore eine hohe ökologische Vielfalt besitzen, was den Selektionsdruck erhöht und damit die Klon-Selektionstheorie begünstigt

Ensimmäinen ja toinen käsikirjoitusversio väitöskirjaa varten

This publication contains the first and the second manuscript version for LauriLahti’s doctoral dissertation in 2015 "Computer-assisted learning based on cumulative vocabularies, conceptual networks and Wikipedia linkage".Tämä julkaisu sisältää ensimmäisen ja toisen käsikirjoitusversion Lauri Lahden väitöskirjaan vuonna 2015 "Tietokoneavusteinen oppiminen perustuen karttuviin sanastoihin, käsiteverkostoihin ja Wikipedian linkitykseen".Not reviewe

Application of Geographic Information Systems

The importance of Geographic Information Systems (GIS) can hardly be overemphasized in today’s academic and professional arena. More professionals and academics have been using GIS than ever – urban & regional planners, civil engineers, geographers, spatial economists, sociologists, environmental scientists, criminal justice professionals, political scientists, and alike. As such, it is extremely important to understand the theories and applications of GIS in our teaching, professional work, and research. “The Application of Geographic Information Systems” presents research findings that explain GIS’s applications in different subfields of social sciences. With several case studies conducted in different parts of the world, the book blends together the theories of GIS and their practical implementations in different conditions. It deals with GIS’s application in the broad spectrum of geospatial analysis and modeling, water resources analysis, land use analysis, infrastructure network analysis like transportation and water distribution network, and such. The book is expected to be a useful source of knowledge to the users of GIS who envision its applications in their teaching and research. This easy-to-understand book is surely not the end in itself but a little contribution to toward our understanding of the rich and wonderful subject of GIS