Multifractal characterisation and analysis of complex networks

Complex networks have been studied extensively due to their relevance to many real-world systems such as the world-wide web, the internet, biological and social systems. During the past two decades, studies of such networks in different fields have produced many significant results concerning their structures, topological properties, and dynamics. Three well-known properties of complex networks are scale-free degree distribution, small-world effect and self-similarity. The search for additional meaningful properties and the relationships among these properties is an active area of current research. This thesis investigates a newer aspect of complex networks, namely their multifractality, which is an extension of the concept of selfsimilarity. The first part of the thesis aims to confirm that the study of properties of complex networks can be expanded to a wider field including more complex weighted networks. Those real networks that have been shown to possess the self-similarity property in the existing literature are all unweighted networks. We use the proteinprotein interaction (PPI) networks as a key example to show that their weighted networks inherit the self-similarity from the original unweighted networks. Firstly, we confirm that the random sequential box-covering algorithm is an effective tool to compute the fractal dimension of complex networks. This is demonstrated on the Homo sapiens and E. coli PPI networks as well as their skeletons. Our results verify that the fractal dimension of the skeleton is smaller than that of the original network due to the shortest distance between nodes is larger in the skeleton, hence for a fixed box-size more boxes will be needed to cover the skeleton. Then we adopt the iterative scoring method to generate weighted PPI networks of five species, namely Homo sapiens, E. coli, yeast, C. elegans and Arabidopsis Thaliana. By using the random sequential box-covering algorithm, we calculate the fractal dimensions for both the original unweighted PPI networks and the generated weighted networks. The results show that self-similarity is still present in generated weighted PPI networks. This implication will be useful for our treatment of the networks in the third part of the thesis. The second part of the thesis aims to explore the multifractal behavior of different complex networks. Fractals such as the Cantor set, the Koch curve and the Sierspinski gasket are homogeneous since these fractals consist of a geometrical figure which repeats on an ever-reduced scale. Fractal analysis is a useful method for their study. However, real-world fractals are not homogeneous; there is rarely an identical motif repeated on all scales. Their singularity may vary on different subsets; implying that these objects are multifractal. Multifractal analysis is a useful way to systematically characterize the spatial heterogeneity of both theoretical and experimental fractal patterns. However, the tools for multifractal analysis of objects in Euclidean space are not suitable for complex networks. In this thesis, we propose a new box covering algorithm for multifractal analysis of complex networks. This algorithm is demonstrated in the computation of the generalized fractal dimensions of some theoretical networks, namely scale-free networks, small-world networks, random networks, and a kind of real networks, namely PPI networks of different species. Our main finding is the existence of multifractality in scale-free networks and PPI networks, while the multifractal behaviour is not confirmed for small-world networks and random networks. As another application, we generate gene interactions networks for patients and healthy people using the correlation coefficients between microarrays of different genes. Our results confirm the existence of multifractality in gene interactions networks. This multifractal analysis then provides a potentially useful tool for gene clustering and identification. The third part of the thesis aims to investigate the topological properties of networks constructed from time series. Characterizing complicated dynamics from time series is a fundamental problem of continuing interest in a wide variety of fields. Recent works indicate that complex network theory can be a powerful tool to analyse time series. Many existing methods for transforming time series into complex networks share a common feature: they define the connectivity of a complex network by the mutual proximity of different parts (e.g., individual states, state vectors, or cycles) of a single trajectory. In this thesis, we propose a new method to construct networks of time series: we define nodes by vectors of a certain length in the time series, and weight of edges between any two nodes by the Euclidean distance between the corresponding two vectors. We apply this method to build networks for fractional Brownian motions, whose long-range dependence is characterised by their Hurst exponent. We verify the validity of this method by showing that time series with stronger correlation, hence larger Hurst exponent, tend to have smaller fractal dimension, hence smoother sample paths. We then construct networks via the technique of horizontal visibility graph (HVG), which has been widely used recently. We confirm a known linear relationship between the Hurst exponent of fractional Brownian motion and the fractal dimension of the corresponding HVG network. In the first application, we apply our newly developed box-covering algorithm to calculate the generalized fractal dimensions of the HVG networks of fractional Brownian motions as well as those for binomial cascades and five bacterial genomes. The results confirm the monoscaling of fractional Brownian motion and the multifractality of the rest. As an additional application, we discuss the resilience of networks constructed from time series via two different approaches: visibility graph and horizontal visibility graph. Our finding is that the degree distribution of VG networks of fractional Brownian motions is scale-free (i.e., having a power law) meaning that one needs to destroy a large percentage of nodes before the network collapses into isolated parts; while for HVG networks of fractional Brownian motions, the degree distribution has exponential tails, implying that HVG networks would not survive the same kind of attack.

Bayesian mixtures for modelling complex medical data : a case study in Parkinson’s disease

Mixture models are a flexible tool for unsupervised clustering that have found popularity in a vast array of research areas. In studies of medicine, the use of mixtures holds the potential to greatly enhance our understanding of patient responses through the identification of clinically meaningful clusters that, given the complexity of many data sources, may otherwise by intangible. Furthermore, when developed in the Bayesian framework, mixture models provide a natural means for capturing and propagating uncertainty in different aspects of a clustering solution, arguably resulting in richer analyses of the population under study. This thesis aims to investigate the use of Bayesian mixture models in analysing varied and detailed sources of patient information collected in the study of complex disease. The first aim of this thesis is to showcase the flexibility of mixture models in modelling markedly different types of data. In particular, we examine three common variants on the mixture model, namely, finite mixtures, Dirichlet Process mixtures and hidden Markov models. Beyond the development and application of these models to different sources of data, this thesis also focuses on modelling different aspects relating to uncertainty in clustering. Examples of clustering uncertainty considered are uncertainty in a patient’s true cluster membership and accounting for uncertainty in the true number of clusters present. Finally, this thesis aims to address and propose solutions to the task of comparing clustering solutions, whether this be comparing patients or observations assigned to different subgroups or comparing clustering solutions over multiple datasets. To address these aims, we consider a case study in Parkinson’s disease (PD), a complex and commonly diagnosed neurodegenerative disorder. In particular, two commonly collected sources of patient information are considered. The first source of data are on symptoms associated with PD, recorded using the Unified Parkinson’s Disease Rating Scale (UPDRS) and constitutes the first half of this thesis. The second half of this thesis is dedicated to the analysis of microelectrode recordings collected during Deep Brain Stimulation (DBS), a popular palliative treatment for advanced PD. Analysis of this second source of data centers on the problems of unsupervised detection and sorting of action potentials or "spikes" in recordings of multiple cell activity, providing valuable information on real time neural activity in the brain.

Chaos or complex systems? Identifying factors influencing the success of international and NESB graduate research students in Engineering and Information Technology Fields

The paper explores the results an on-going research project to identify factors influencing the success of international and non-English speaking background (NESB) gradúate students in the fields of Engineering and IT at three Australian universities: the Queensland University of Technology (QUT), the University of Western Australia (UWA), and Curtin University (CU). While the larger study explores the influence of factors from both sides of the supervision equation (e.g., students and supervisors), this paper focusses primarily on the results of an online survey involving 227 international and/or NESB graduate students in the areas of Engineering and IT at the three universities. The study reveals cross-cultural differences in perceptions of student and supervisor roles, as well as differences in the understanding of the requirements of graduate study within the Australian Higher Education context. We argue that in order to assist international and NESB research students to overcome such culturally embedded challenges, it is important to develop a model which recognizes the complex interactions of factors from both sides of the supervision relationship, in order to understand this cohort‟s unique pedagogical needs and develop intercultural sensitivity within postgraduate research supervision.

Design and implementation of a virtual world training simulation of ICU first hour handover processes

Nursing training for an Intensive Care Unit (ICU) is a resource intensive process. High demands are made on staff, students and physical resources. Interactive, 3D computer simulations, known as virtual worlds, are increasingly being used to supplement training regimes in the health sciences; especially in areas such as complex hospital ward processes. Such worlds have been found to be very useful in maximising the utilisation of training resources. Our aim is to design and develop a novel virtual world application for teaching and training Intensive Care nurses in the approach and method for shift handover, to provide an independent, but rigorous approach to teaching these important skills. In this paper we present a virtual world simulator for students to practice key steps in handing over the 24/7 care requirements of intensive care patients during the commencing first hour of a shift. We describe the modelling process to provide a convincing interactive simulation of the handover steps involved. The virtual world provides a practice tool for students to test their analytical skills with scenarios previously provided by simple physical simulations, and live on the job training. Additional educational benefits include facilitation of remote learning, high flexibility in study hours and the automatic recording of a reviewable log from the session. To the best of our knowledge, we believe this is a novel and original application of virtual worlds to an ICU handover process. The major outcome of the work was a virtual world environment for training nurses in the shift handover process, designed and developed for use by postgraduate nurses in training.

Cyclin-dependent kinase-mediated phosphorylation of RBP1 and pRb promotes their dissociation to mediate release of the SAP30·mSin3·HDAC transcriptional repressor complex

Eukaryotic cell cycle progression is mediated by phosphorylation of protein substrates by cyclin-dependent kinases (CDKs). A critical substrate of CDKs is the product of the retinoblastoma tumor suppressor gene, pRb, which inhibits G1-S phase cell cycle progression by binding and repressing E2F transcription factors. CDK-mediated phosphorylation of pRb alleviates this inhibitory effect to promote G1-S phase cell cycle progression. pRb represses transcription by binding to the E2F transactivation domain and recruiting the mSin3·histone deacetylase (HDAC) transcriptional repressor complex via the retinoblastoma-binding protein 1 (RBP1). RBP1 binds to the pocket region of pRb via an LXCXE motif and to the SAP30 subunit of the mSin3·HDAC complex and, thus, acts as a bridging protein in this multisubunit complex. In the present study we identified RBP1 as a novel CDK substrate. RBP1 is phosphorylated by CDK2 on serines 864 and 1007, which are N- and C-terminal to the LXCXE motif, respectively. CDK2-mediated phosphorylation of RBP1 or pRb destabilizes their interaction in vitro, with concurrent phosphorylation of both proteins leading to their dissociation. Consistent with these findings, RBP1 phosphorylation is increased during progression from G 1 into S-phase, with a concurrent decrease in its association with pRb in MCF-7 breast cancer cells. These studies provide new mechanistic insights into CDK-mediated regulation of the pRb tumor suppressor during cell cycle progression, demonstrating that CDK-mediated phosphorylation of both RBP1 and pRb induces their dissociation to mediate release of the mSin3·HDAC transcriptional repressor complex from pRb to alleviate transcriptional repression of E2F.

The reliability, accuracy and minimal detectable difference of a multi-segment kinematic model of the foot-shoe complex

Kinematic models are commonly used to quantify foot and ankle kinematics, yet no marker sets or models have been proven reliable or accurate when wearing shoes. Further, the minimal detectable difference of a developed model is often not reported. We present a kinematic model that is reliable, accurate and sensitive to describe the kinematics of the foot–shoe complex and lower leg during walking gait. In order to achieve this, a new marker set was established, consisting of 25 markers applied on the shoe and skin surface, which informed a four segment kinematic model of the foot–shoe complex and lower leg. Three independent experiments were conducted to determine the reliability, accuracy and minimal detectable difference of the marker set and model. Inter-rater reliability of marker placement on the shoe was proven to be good to excellent (ICC = 0.75–0.98) indicating that markers could be applied reliably between raters. Intra-rater reliability was better for the experienced rater (ICC = 0.68–0.99) than the inexperienced rater (ICC = 0.38–0.97). The accuracy of marker placement along each axis was <6.7 mm for all markers studied. Minimal detectable difference (MDD90) thresholds were defined for each joint; tibiocalcaneal joint – MDD90 = 2.17–9.36°, tarsometatarsal joint – MDD90 = 1.03–9.29° and the metatarsophalangeal joint – MDD90 = 1.75–9.12°. These thresholds proposed are specific for the description of shod motion, and can be used in future research designed at comparing between different footwear.

Complex events in business processes

Flow-oriented process modeling languages have a long tradition in the area of Business Process Management and are widely used for capturing activities with their behavioral and data dependencies. Individual events were introduced for triggering process instantiation and activities. However, real-world business cases drive the need for also covering complex event patterns as they are known in the field of Complex Event Processing. Therefore, this paper puts forward a catalog of requirements for handling complex events in process models, which can be used as reference framework for assessing process definition languages and systems. An assessment of BPEL and BPMN is provided.

Infrastructure transitions toward sustainability : a complex adaptive systems perspective

To ensure infrastructure assets are procured and maintained by government on behalf of citizens, appropriate policy and institutional architecture is needed, particularly if a fundamental shift to more sustainable infrastructure is the goal. The shift in recent years from competitive and resource-intensive procurement to more collaborative and sustainable approaches to infrastructure governance is considered a major transition in infrastructure procurement systems. In order to better understand this transition in infrastructure procurement arrangements, the concept of emergence from Complex Adaptive Systems (CAS) theory is offered as a key construct. Emergence holds that micro interactions can result in emergent macro order. Applying the concept of emergence to infrastructure procurement, this research examines how interaction of agents in individual projects can result in different industry structural characteristics. The paper concludes that CAS theory, and particularly the concept of ‘emergence’, provides a useful construct to understand infrastructure procurement dynamics and progress towards sustainability.

Do perceptions mirror reality? Student perceptions of learning versus grade outcomes

This research addresses whether educators should consider measuring if students have learned what was intended, as recommended by education researchers. Students in an Introductory Marketing subject were asked to complete a voluntary survey rating their own progress on the intended learning outcomes for the course. One hundred and one surveys were completed by students in the second-last teaching week of the semester. Student identification numbers were used to link student perceptions with their grade outcomes. Regression analysis was used to ascertain whether student perceptions of their progress on the intended learning outcomes for the course could be used to predict their grades. While the results were significant, student perceptions of their progress on learning outcomes were a poor predictor of grade outcomes. The results of this study suggest that student perceptions may not mirror the reality. These results are somewhat surprising and future research examining the degree of change in the learning outcomes perceived by students is warranted. This will further contribute to decisions surrounding whether educators should measure if students have learned what was intended.

Some reflections about P2M : the place of the mirror

The purpose of this paper is to provide some insights about P2M, and more specifically, to develop some thoughts about Project Management seen as a Mirror, a place for reflection…, between the Mission of organisation and its actual creation of Values (with s: a source of value for people, organisations and society). This place is the realm of complexity, of interactions between multiple variables, each of them having a specific time horizon and occupying a specific place, playing a specific role. Before developing this paper I would like to borrow to my colleague and friend, Professor Ohara, the following, part of a paper going to be presented at IPMA World Congress, in New Delhi later this year in November 2005. “P2M is the Japanese version of project & program management, which is the first standard guide for education and certification developed in 2001. A specific finding of P2M is characterized by “mission driven management of projects” or a program which harness complexity of problem solving observed in the interface between technical system and business model.” (Ohara, 2005, IPMA Conference, New Delhi) “The term of “mission” is a key word in the field of corporate strategy, where it expresses raison d’être or “value of business”. It is more specifically used for expressing “the client needs” in terms of a strategic business unit. The concept of mission is deemed to be a useful tool to share essential content of value and needs in message for complex project.” (Ohara, 2005, IPMA Conference, New Delhi) “Mission is considered as a significant “metamodel representation” by several reasons. First, it represents multiple values for aspiration. The central objective of mission initiative is profiling of ideality in the future from reality, which all stakeholders are glad to accept and share. Second, it shall be within a stretch of efforts, and not beyond or outside of the realization. Though it looks like unique, it has to depict a solid foundation. The pragmatic sense of equilibrium between innovation and adaptation is required for the mission. Third, it shall imply a rough sketch for solution to critical issues for problems in reality.” (Ohara, 2005, IPMA Conference, New Delhi) “Project modeling” idea has been introduced in P2M program management. A package of three project models of “scheme”, “system” and “service” are given as a reference type program. (Ohara, 2005, IPMA Conference, New Delhi) If these quotes apply to P2M, they are fully congruent with the results of the research undertaken and the resulting meta-model & meta-method developed by the CIMAP, ESC Lille Research Centre in Project & Program Management, since the 80’s. The paper starts by questioning the common Project Management (PM) paradigm. Then discussing the concept of Project, it argues that an alternative epistemological position should be taken to capture Page 2 / 11 the very nature of the PM field. Based on this, a development about “the need of modelling to understand” is proposed grounded on two theoretical roots. This leads to the conclusion that, in order to enables this modelling, a standard approach is necessary, but should be understood under the perspective of the Theory of Convention in order to facilitate a situational and contextual application.

Using virtual reality modelling in cultural management, archiving and research

This paper outlines how the Ortelia project’s 3D virtual reality models have the capacity to assist our understanding of sites of cultural heritage. The VR investigation of such spaces can be a valuable tool in 'real world' empirical research in theatre and spatiality. Through a demonstration of two of Ortelia's VR models (an art gallery and a theatre), we suggest how we might consider interpreting cultural space and sites as contributing significantly to cultural capital. We also introduce the potential for human interaction in such venues through motion-capture to discuss the potential for assessing how humans interact in such contexts.

Taxation of multinational banks : using formulary apportionment to reflect economic reality (Part 1)

Formulary apportionment does not attempt to undertake a transactional division of a highly integrated multinational entity. Rather, it allocates income to the jurisdictions based on an economically justifiable formula. Opposition to formulary apportionment is generally based on the argument that it is not a theoretically superior (or optimal) model because of the implementation difficulties. The conclusion that the unitary taxation model may be theoretically superior to the current arm's-length model that applies to multinational banks, despite significant implementation, compliance, and enforcement issues, is based on the unitary taxation model providing greater alignment with the unique features of these banks. The formulary apportionment model looks to the economic substance of the multinational entity and, in this sense, adopts a substance-over- form approach. Formulary apportionment further recognizes the impossibility of using arm's-length pricing for economically interdependent multinational entities. A final advantage to formulary apportionment, which is also a consequence of this model achieving greater inter-nation equity, is the elimination of double taxation.

The taxation of multinational banks : alternative apportionment through a unitary taxation regime aligning with economic reality

The taxation of multinational banks currently is governed by the general principles of international tax. However, it is arguable that there are characteristics exclusive to multinational banks that may warrant the consideration of a separate taxing regime. This article argues that because of the unique nature of multinational banks, the traditional international tax rules governing jurisdiction to tax and allocation of income do not produce a result which is optimal, as it does not reflect economic reality. That is, the current system does not produce a result that accurately reflects the economic source of the income or the location of the economic activity. The suggested alternative is unitary taxation using global formulary apportionment. Formulary apportionment is considered as an alternative that reflects economic reality by recognising the unique nature of multinational banks and allocating the income to the location of the economic activity. The unique nature of multinational banking is recognised in the fact that formulary apportionment does not attempt to undertake a transactional division of a highly integrated multinational entity. Rather, it allocates income to the jurisdictions based on an economically justifiable formula. Starting from this recognition, the purpose of this article is to demonstrate that formulary apportionment is a theoretically superior (or optimal) model for the taxation of multinational banks. An optimal regime, for the purposes of this article, is considered to be one that distributes the taxing rights in an equitable manner between the relevant jurisdictions, while, simultaneously allowing decisions of the international banks to be tax neutral. In this sense, neutrality is viewed as an economic concept and equity is regarded as a legal concept. A neutral tax system is one in which tax rules do not affect economic choices about commercial activities. Neutrality will ideally be across jurisdictions as well as across traditional and non-traditional industries. The primary focus of this article is jurisdictional neutrality. A system that distributes taxing rights in an equitable manner between the relevant jurisdictions ensures that each country receives its fair share of tax revenue. Given the increase in multinational banking, jurisdictions should be concerned that they are receiving their fair share. Inter-nation equity is concerned with re-determining the proper division of the tax base among countries. Richard and Peggy Musgrave argue that sharing of the tax base by countries of source should be seen as a matter of inter-nation equity requiring international cooperation. The rights of the jurisdiction of residency will also be at issue. To this extent, while it is agreed that inter-nation equity is an essential attribute to an international tax regime, there is no universal agreement as to how to achieve it. The current system attempts to achieve such equity through a combined residency and source regime, with the transfer pricing rules used to apportion income between the relevant jurisdictions. However, this article suggests, that as an alternative to the current regime, equity would be achieved through formulary apportionment. Opposition to formulary apportionment is generally based on the argument that it is not a theoretically superior (or optimal) model because of the implementation difficulties. Yet these are two separate issues. As such, this article is divided into two core parts. The first part examines the theoretical soundness of the formulary apportionment model concluding that it is theoretically superior to the arm’s length pricing requirement of the traditional transfer pricing regime. The second part examines the practical implications of accepting formulary apportionment as an optimal model with a view to disclosing the issues that arise when a formulary apportionment regime is adopted. Prior to an analysis of the theoretical and practical application of formulary apportionment to multinational banks, the unique nature of these banks is considered. The article concludes that, while there are significant implementation, compliance, and enforcement issues to overcome, the unitary taxation model may be theoretically superior to the current arm’s length model which applies to multinational banks. This conclusion is based on the unitary taxation model providing greater alignment with the unique features of these banks.

A review of models and model usage scenarios for an airport complex system

Airports represent the epitome of complex systems with multiple stakeholders, multiple jurisdictions and complex interactions between many actors. The large number of existing models that capture different aspects of the airport are a testament to this. However, these existing models do not consider in a systematic sense modelling requirements nor how stakeholders such as airport operators or airlines would make use of these models. This can detrimentally impact on the verification and validation of models and makes the development of extensible and reusable modelling tools difficult. This paper develops from the Concept of Operations (CONOPS) framework a methodology to help structure the review and development of modelling capabilities and usage scenarios. The method is applied to the review of existing airport terminal passenger models. It is found that existing models can be broadly categorised according to four usage scenarios: capacity planning, operational planning and design, security policy and planning, and airport performance review. The models, the performance metrics that they evaluate and their usage scenarios are discussed. It is found that capacity and operational planning models predominantly focus on performance metrics such as waiting time, service time and congestion whereas performance review models attempt to link those to passenger satisfaction outcomes. Security policy models on the other hand focus on probabilistic risk assessment. However, there is an emerging focus on the need to be able to capture trade-offs between multiple criteria such as security and processing time. Based on the CONOPS framework and literature findings, guidance is provided for the development of future airport terminal models.

Taxation of multinational banks : using formulary apportionment to reflect economic reality (Part 2)

As stated in Part 1 of this article, formulary appointment does not attempt to undertake a transactional division of a highly integrated multinational entity; rather, it allocates income to the jurisdictions based on economically justifiable formula. This article argues that the unitary taxation model is superior to the current arms-lenght model for the taxation of multinational banks despite significant implementation, complicance and enforcement issues. Part one of the article gave some background on the taxation of multinational banks, followed by a discussion of their uniqueness, and the theoretical benefits of the unitary tax model for multinational banking. Part 2 below covers the practical implications of accepting formulary apportionment as an 'optimal' regime for taxing multinational banks.