Fuzzy methods for analysis of microarrays and networks

Bioinformatics involves analyses of biological data such as DNA sequences, microarrays and protein-protein interaction (PPI) networks. Its two main objectives are the identification of genes or proteins and the prediction of their functions. Biological data often contain uncertain and imprecise information. Fuzzy theory provides useful tools to deal with this type of information, hence has played an important role in analyses of biological data. In this thesis, we aim to develop some new fuzzy techniques and apply them on DNA microarrays and PPI networks. We will focus on three problems: (1) clustering of microarrays; (2) identification of disease-associated genes in microarrays; and (3) identification of protein complexes in PPI networks. The first part of the thesis aims to detect, by the fuzzy C-means (FCM) method, clustering structures in DNA microarrays corrupted by noise. Because of the presence of noise, some clustering structures found in random data may not have any biological significance. In this part, we propose to combine the FCM with the empirical mode decomposition (EMD) for clustering microarray data. The purpose of EMD is to reduce, preferably to remove, the effect of noise, resulting in what is known as denoised data. We call this method the fuzzy C-means method with empirical mode decomposition (FCM-EMD). We applied this method on yeast and serum microarrays, and the silhouette values are used for assessment of the quality of clustering. The results indicate that the clustering structures of denoised data are more reasonable, implying that genes have tighter association with their clusters. Furthermore we found that the estimation of the fuzzy parameter m, which is a difficult step, can be avoided to some extent by analysing denoised microarray data. The second part aims to identify disease-associated genes from DNA microarray data which are generated under different conditions, e.g., patients and normal people. We developed a type-2 fuzzy membership (FM) function for identification of diseaseassociated genes. This approach is applied to diabetes and lung cancer data, and a comparison with the original FM test was carried out. Among the ten best-ranked genes of diabetes identified by the type-2 FM test, seven genes have been confirmed as diabetes-associated genes according to gene description information in Gene Bank and the published literature. An additional gene is further identified. Among the ten best-ranked genes identified in lung cancer data, seven are confirmed that they are associated with lung cancer or its treatment. The type-2 FM-d values are significantly different, which makes the identifications more convincing than the original FM test. The third part of the thesis aims to identify protein complexes in large interaction networks. Identification of protein complexes is crucial to understand the principles of cellular organisation and to predict protein functions. In this part, we proposed a novel method which combines the fuzzy clustering method and interaction probability to identify the overlapping and non-overlapping community structures in PPI networks, then to detect protein complexes in these sub-networks. Our method is based on both the fuzzy relation model and the graph model. We applied the method on several PPI networks and compared with a popular protein complex identification method, the clique percolation method. For the same data, we detected more protein complexes. We also applied our method on two social networks. The results showed our method works well for detecting sub-networks and give a reasonable understanding of these communities.

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.

Anonymity and one-way authentication in key exchange protocols

Key establishment is a crucial cryptographic primitive for building secure communication channels between two parties in a network. It has been studied extensively in theory and widely deployed in practice. In the research literature a typical protocol in the public-key setting aims for key secrecy and mutual authentication. However, there are many important practical scenarios where mutual authentication is undesirable, such as in anonymity networks like Tor, or is difficult to achieve due to insufficient public-key infrastructure at the user level, as is the case on the Internet today. In this work we are concerned with the scenario where two parties establish a private shared session key, but only one party authenticates to the other; in fact, the unauthenticated party may wish to have strong anonymity guarantees. We present a desirable set of security, authentication, and anonymity goals for this setting and develop a model which captures these properties. Our approach allows for clients to choose among different levels of authentication. We also describe an attack on a previous protocol of Øverlier and Syverson, and present a new, efficient key exchange protocol that provides one-way authentication and anonymity.

How quantum theory is developing the field of information retrieval

This position paper provides an overview of work conducted and an outlook of future directions within the field of Information Retrieval (IR) that aims to develop novel models, methods and frameworks inspired by Quantum Theory (QT).

Community protest groups' perceptions of environmental risks using social contagion theory

Local communities are vulnerable to the potential environmental risks associated with construction activity. Currently, little is understood about how perceptions of environmental risks are shaped and spread within a community. A better understanding of this process can help bridge the gap between developers and communities and bring about more sustainable development practices. This paper reports a research methodology which uses social contagion theory to investigate this process. The research adopts a single case study approach of a highly controversial housing project in the greater Sydney metropolitan area. The case study is particularly significant as it investigates an extensive and on-going community-based protest campaign (dating back almost 20 years) that has generated the longest standing 24 hour community picket in the New South Wales.

Civil applications in the Magistrates Court are often set down for hearing by a judicial registrar, but there is now some uncertainty on the limitation of this practice

The decision of the District Court of Queensland in Mark Treherne & Associates -v- Murray David Hopkins [2010] QDC 36 will have particular relevance for early career lawyers. This decision raises questions about the limits of the jurisdiction of judicial registrars in the Magistrates Court.

A framework for analysing system intelligence of the building control system: a study of the integrated building management system

The lack of satisfactory consensus for characterizing the system intelligence and structured analytical decision models has inhibited the developers and practitioners to understand and configure optimum intelligent building systems in a fully informed manner. So far, little research has been conducted in this aspect. This research is designed to identify the key intelligent indicators, and develop analytical models for computing the system intelligence score of smart building system in the intelligent building. The integrated building management system (IBMS) was used as an illustrative example to present a framework. The models presented in this study applied the system intelligence theory, and the conceptual analytical framework. A total of 16 key intelligent indicators were first identified from a general survey. Then, two multi-criteria decision making (MCDM) approaches, the analytic hierarchy process (AHP) and analytic network process (ANP), were employed to develop the system intelligence analytical models. Top intelligence indicators of IBMS include: self-diagnostic of operation deviations; adaptive limiting control algorithm; and, year-round time schedule performance. The developed conceptual framework was then transformed to the practical model. The effectiveness of the practical model was evaluated by means of expert validation. The main contribution of this research is to promote understanding of the intelligent indicators, and to set the foundation for a systemic framework that provide developers and building stakeholders a consolidated inclusive tool for the system intelligence evaluation of the proposed components design configurations.

Teacher educators mediating curricular reform : anticipating the Australian curriculum

Many education systems are experiencing a re-scaling and consolidation of governance through rolling national agendas of standardisation and centralisation. This paper considers the case of Australia as it moves towards implementing its first national curriculum, to explore how teacher educators plan to retain pedagogical space for debate, diversity and contestation of such systemic curricular reform. This paper reports on an interview study conducted with nine teacher educators across the four curriculum areas included in the first wave of the Australian Curriculum: English, Science, Mathematics and History. The analysis reveals how teacher educators reported professional dilemmas around curricular design, and planned to resolve such dilemmas between the anticipated changes and their preferences for what might have been. While different curricular areas displayed different patterns of professional dilemma, the teacher educators are shown to construe their role as one of active curriculum mediators, who, in recontextualising curricular reforms, will use the opportunity to reinsert both residualised and emergent alternatives in their students’ professional value sets. The study also identifies a new set of dilemmas emerging around the politicisation and standardisation of curriculum, and its impact on the teaching profession and teacher educators.

A strategy for delayed research method selection : deciding between grounded theory and phenomenology

This paper presents a strategy for delayed research method selection in a qualitative interpretivist research. An exemplary case details how explorative interviews were designed and conducted in accordance with a paradigm prior to deciding whether to adopt grounded theory or phenomenology for data analysis. The focus here is to determine the most appropriate research strategy in this case the methodological framing to conduct research and represent findings, both of which are detailed. Research addressing current management issues requires both a flexible framework and the capability to consider the research problem from various angles, to derive tangible results for academia with immediate application to business demands. Researchers, and in particular novices, often struggle to decide on an appropriate research method suitable to address their research problem. This often applies to interpretative qualitative research where it is not always immediately clear which is the most appropriate method to use, as the research objectives shift and crystallize over time. This paper uses an exemplary case to reveal how the strategy for delayed research method selection contributes to deciding whether to adopt grounded theory or phenomenology in the initial phase of a PhD research project. In this case, semi-structured interviews were used for data generation framed in an interpretivist approach, situated in a business context. Research questions for this study were thoroughly defined and carefully framed in accordance with the research paradigm‟s principles, while at the same time ensuring that the requirements of both potential research methods were met. The grounded theory and phenomenology methods were compared and contrasted to determine their suitability and whether they meet the research objectives based on a pilot study. The strategy proposed in this paper is an alternative to the more „traditional‟ approach, which initially selects the methodological formulation, followed by data generation. In conclusion, the suggested strategy for delayed research method selection intends to help researchers identify and apply the most appropriate method to their research. This strategy is based on explorations of data generation and analysis in order to derive faithful results from the data generated.

Do balanced skills help nascent entrepreneurs to make progress in the venture creation process?

We apply Lazear’s jack-of-all-trades theory to investigate the effect of nascent entrepreneurs´ balanced skill set across various functional areas on the performance of nascent projects. Analyzing longitudinal data on innovative nascent projects, we find that nascent entrepreneurs with a more balanced skill set are more successful in that they progress faster in the venture creation process.

Third-order theory of spectacle lenses applied to correction of peripheral refractive errors

Purpose: To demonstrate that relatively simple third-order theory can provide a framework which shows how peripheral refraction can be manipulated by altering the forms of spectacle lenses. Method: Third-order equations were used to yield lens forms that correct peripheral power errors, either for the lenses alone or in combination with typical peripheral refractions of myopic eyes. These results were compared with those of finite ray-tracing. Results: The approximate forms of spherical and conicoidal lenses provided by third-order theory were flatter over a moderate myopic range than the forms obtained by rigorous raytracing. Lenses designed to correct peripheral refractive errors produced large errors when used with foveal vision and a rotating eye. Correcting astigmatism tended to give large errors in mean oblique error and vice versa. When only spherical lens forms are used, correction of the relative hypermetropic peripheral refractions of myopic eyes which are observed experimentally, or the provision of relative myopic peripheral refractions in such eyes, seems impossible in the majority of cases. Conclusion: The third-order spectacle lens design approach can readily be used to show trends in peripheral refraction.

Balanced skills among nascent entrepreneurs

This paper examines the effects and origins of balanced skills among nascent entrepreneurs. In a first step we apply Lazear’s jack-of-all-trades theory to investigate performance effects of a balanced skill set. Second, we investigate potential sources of balanced skills, thereby testing the investment hypothesis against the endowment hypothesis. Analyzing data on high-potential nascent projects, we find support for the notion that balanced skills are important for making progress in the venture creation process. Regarding the origins of balanced skills, the data support both hypotheses. In line with the investment hypothesis an early interest in an entrepreneurial career, prior managerial and entrepreneurial experience are significantly related with a more balanced skill set. Supporting the endowment hypothesis, an entrepreneurial personality profile indicating entrepreneurial talent is correlated with a balanced skill set. Our results thus hint at the need for theories on the origins of a balanced skill set that integrate both views.

Speeding by young novice drivers : what can personal characteristics and psychosocial theory add to our understanding?

Purpose: Young novice drivers continue to be overrepresented in fatalities and injuries arising from crashes even with the introduction of countermeasures such as graduated driver licensing (GDL). Enhancing countermeasures requires a better understanding of the variables influencing risky driving. One of the most common risky behaviours performed by drivers of all ages is speeding, which is particularly risky for young novice drivers who, due to their driving inexperience, have difficulty in identifying and responding appropriately to road hazards. Psychosocial theory can improve our understanding of contributors to speeding, thereby informing countermeasure development and evaluation. This paper reports an application of Akers’ social learning theory (SLT), augmented by Gerrard and Gibbons’ prototype/willingness model (PWM), in addition to personal characteristics of age, gender, car ownership, and psychological traits/states of anxiety, depression, sensation seeking propensity and reward sensitivity, to examine the influences on self-reported speeding of young novice drivers with a Provisional (intermediate) licence in Queensland, Australia. Method: Young drivers (n = 378) recruited in 2010 for longitudinal research completed two surveys containing the Behaviour of Young Novice Drivers Scale, and reported their attitudes and behaviours as pre-Licence/Learner (Survey 1) and Provisional (Survey 2) drivers and their sociodemographic characteristics. Results: An Akers’ measurement model was created. Hierarchical multiple regressions revealed that (1) personal characteristics (PC) explained 20.3%; (2) the combination of PC and SLT explained 41.1%; and (3) the combination of PC, SLT and PWM explained 53.7% of variance in self-reported speeding. Whilst there appeared to be considerable shared variance, the significant predictors in the final model included gender, car ownership, reward sensitivity, depression, personal attitudes, and Learner speeding. Conclusions: These results highlight the capacity for psychosocial theory to improve our understanding of speeding by young novice drivers, revealing relationships between previous behaviour, attitudes, psychosocial characteristics and speeding. The findings suggest multi-faceted countermeasures should target the risky behaviour of Learners, and Learner supervisors should be encouraged to monitor their Learners’ driving speed. Novice drivers should be discouraged from developing risky attitudes towards speeding.

Collaborative academic/practitioner research in project management : theory and models

Purpose – The purpose of this paper is to provide of a review of the theory and models underlying project management (PM) research degrees that encourage reflective learning. Design/methodology/approach – Review of the literature and reflection on the practice of being actively involved in conducting and supervising academic research and disseminating academic output. The paper argues the case for the potential usefulness of reflective academic research to PM practitioners. It also highlights theoretical drivers of and barriers to reflective academic research by PM practitioners. Findings – A reflective learning approach to research can drive practical results though it requires a great deal of commitment and support by both academic and industry partners. Practical implications – This paper suggests how PM practitioners can engage in academic research that has practical outcomes and how to be more effective at disseminating these research outcomes. Originality/value – Advanced academic degrees, in particular those completed by PM practitioners, can validate a valuable source of innovative ideas and approaches that should be more quickly absorbed into the PM profession’s sources of knowledge. The value of this paper is to critically review and facilitate a reduced adaptation time for implementation of useful reflective academic research to industry.

Understanding the very nature of Project Management : a praxiological approach

Foreword: In this paper I call upon a praxiological approach. Praxeology (early alteration of praxiology) is the study of human action and conduct. The name praxeology/praxiologyakes is root in praxis, Medieval Latin, from Greek, doing, action, from prassein to do, practice (Merriam-Webster Dictionary). Having been involved in project management education, research and practice for the last twenty years, I have constantly tried to improve and to provide a better understanding/knowledge of the field and related practice, and as a consequence widen and deepen the competencies of the people I was working with (and my own competencies as well!), assuming that better project management lead to more efficient and effective use of resources, development of people and at the end to a better world. For some time I have perceived a need to clarify the foundations of the discipline of project management, or at least elucidate what these foundations could be. An immodest task, one might say! But not a neutral one! I am constantly surprised by the way the world (i.e., organizations, universities, students and professional bodies) sees project management: as a set of methods, techniques, tools, interacting with others fields – general management, engineering, construction, information systems, etc. – bringing some effective ways of dealing with various sets of problems – from launching a new satellite to product development through to organizational change.