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.

Perceiving and pursuing novelty : a grounded theory of adolescent creativity

Creativity plays an increasingly important role in our personal, social, educational, and community lives. For adolescents, creativity can enable self-expression, be a means of pushing boundaries, and assist learning, achievement, and completion of everyday tasks. Moreover, adolescents who demonstrate creativity can potentially enhance their capacity to face unknown future challenges, address mounting social and ecological issues in our global society, and improve their career opportunities and contribution to the economy. For these reasons, creativity is an essential capacity for young people in their present and future, and is highlighted as a priority in current educational policy nationally and internationally. Despite growing recognition of creativity’s importance and attention to creativity in research, the creative experience from the perspectives of the creators themselves and the creativity of adolescents are neglected fields of study. Hence, this research investigated adolescents’ self-reported experiences of creativity to improve understandings of their creative processes and manifestations, and how these can be supported or inhibited. Although some aspects of creativity have been extensively researched, there were no comprehensive, multidisciplinary theoretical frameworks of adolescent creativity to provide a foundation for this study. Therefore, a grounded theory methodology was adopted for the purpose of constructing a new theory to describe and explain adolescents’ creativity in a range of domains. The study’s constructivist-interpretivist perspective viewed the data and findings as interpretations of adolescents’ creative experiences, co-constructed by the participants and the researcher. The research was conducted in two academically selective high schools in Australia: one arts school, and one science, mathematics, and technology school. Twenty adolescent participants (10 from each school) were selected using theoretical sampling. Data were collected via focus groups, individual interviews, an online discussion forum, and email communications. Grounded theory methods informed a process of concurrent data collection and analysis; each iteration of analysis informed subsequent data collection. Findings portray creativity as it was perceived and experienced by participants, presented in a Grounded Theory of Adolescent Creativity. The Grounded Theory of Adolescent Creativity comprises a core category, Perceiving and Pursuing Novelty: Not the Norm, which linked all findings in the study. This core category explains how creativity involved adolescents perceiving stimuli and experiences differently, approaching tasks or life unconventionally, and pursuing novel ideas to create outcomes that are not the norm when compared with outcomes by peers. Elaboration of the core category is provided by the major categories of findings. That is, adolescent creativity entailed utilising a network of Sub-Processes of Creativity, using strategies for Managing Constraints and Challenges, and drawing on different Approaches to Creativity – adaptation, transfer, synthesis, and genesis – to apply the sub-processes and produce creative outcomes. Potentially, there were Effects of Creativity on Creators and Audiences, depending on the adolescent and the task. Three Types of Creativity were identified as the manifestations of the creative process: creative personal expression, creative boundary pushing, and creative task achievement. Interactions among adolescents’ dispositions and environments were influential in their creativity. Patterns and variations of these interactions revealed a framework of four Contexts for Creativity that offered different levels of support for creativity: high creative disposition–supportive environment; high creative disposition–inhibiting environment; low creative disposition–supportive environment; and low creative disposition–inhibiting environment. These contexts represent dimensional ranges of how dispositions and environments supported or inhibited creativity, and reveal that the optimal context for creativity differed depending on the adolescent, task, domain, and environment. This study makes four main contributions, which have methodological and theoretical implications for researchers, as well as practical implications for adolescents, parents, teachers, policy and curriculum developers, and other interested stakeholders who aim to foster the creativity of adolescents. First, this study contributes methodologically through its constructivist-interpretivist grounded theory methodology combining the grounded theory approaches of Corbin and Strauss (2008) and Charmaz (2006). Innovative data collection was also demonstrated through integration of data from online and face-to-face interactions with adolescents, within the grounded theory design. These methodological contributions have broad applicability to researchers examining complex constructs and processes, and with populations who integrate multimedia as a natural form of communication. Second, applicable to creativity in diverse domains, the Grounded Theory of Adolescent Creativity supports a hybrid view of creativity as both domain-general and domain-specific. A third major contribution was identification of a new form of creativity, educational creativity (ed-c), which categorises creativity for learning or achievement within the constraints of formal educational contexts. These theoretical contributions inform further research about creativity in different domains or multidisciplinary areas, and with populations engaged in formal education. However, the key contribution of this research is that it presents an original Theory and Model of Adolescent Creativity to explain the complex, multifaceted phenomenon of adolescents’ creative experiences.

A hierarchical evolutionary algorithmic design (HEAD) system for generating and evolving building design models

This thesis develops a detailed conceptual design method and a system software architecture defined with a parametric and generative evolutionary design system to support an integrated interdisciplinary building design approach. The research recognises the need to shift design efforts toward the earliest phases of the design process to support crucial design decisions that have a substantial cost implication on the overall project budget. The overall motivation of the research is to improve the quality of designs produced at the author's employer, the General Directorate of Major Works (GDMW) of the Saudi Arabian Armed Forces. GDMW produces many buildings that have standard requirements, across a wide range of environmental and social circumstances. A rapid means of customising designs for local circumstances would have significant benefits. The research considers the use of evolutionary genetic algorithms in the design process and the ability to generate and assess a wider range of potential design solutions than a human could manage. This wider ranging assessment, during the early stages of the design process, means that the generated solutions will be more appropriate for the defined design problem. The research work proposes a design method and system that promotes a collaborative relationship between human creativity and the computer capability. The tectonic design approach is adopted as a process oriented design that values the process of design as much as the product. The aim is to connect the evolutionary systems to performance assessment applications, which are used as prioritised fitness functions. This will produce design solutions that respond to their environmental and function requirements. This integrated, interdisciplinary approach to design will produce solutions through a design process that considers and balances the requirements of all aspects of the design. Since this thesis covers a wide area of research material, 'methodological pluralism' approach was used, incorporating both prescriptive and descriptive research methods. Multiple models of research were combined and the overall research was undertaken following three main stages, conceptualisation, developmental and evaluation. The first two stages lay the foundations for the specification of the proposed system where key aspects of the system that have not previously been proven in the literature, were implemented to test the feasibility of the system. As a result of combining the existing knowledge in the area with the newlyverified key aspects of the proposed system, this research can form the base for a future software development project. The evaluation stage, which includes building the prototype system to test and evaluate the system performance based on the criteria defined in the earlier stage, is not within the scope this thesis. The research results in a conceptual design method and a proposed system software architecture. The proposed system is called the 'Hierarchical Evolutionary Algorithmic Design (HEAD) System'. The HEAD system has shown to be feasible through the initial illustrative paper-based simulation. The HEAD system consists of the two main components - 'Design Schema' and the 'Synthesis Algorithms'. The HEAD system reflects the major research contribution in the way it is conceptualised, while secondary contributions are achieved within the system components. The design schema provides constraints on the generation of designs, thus enabling the designer to create a wide range of potential designs that can then be analysed for desirable characteristics. The design schema supports the digital representation of the human creativity of designers into a dynamic design framework that can be encoded and then executed through the use of evolutionary genetic algorithms. The design schema incorporates 2D and 3D geometry and graph theory for space layout planning and building formation using the Lowest Common Design Denominator (LCDD) of a parameterised 2D module and a 3D structural module. This provides a bridge between the standard adjacency requirements and the evolutionary system. The use of graphs as an input to the evolutionary algorithm supports the introduction of constraints in a way that is not supported by standard evolutionary techniques. The process of design synthesis is guided as a higher level description of the building that supports geometrical constraints. The Synthesis Algorithms component analyses designs at four levels, 'Room', 'Layout', 'Building' and 'Optimisation'. At each level multiple fitness functions are embedded into the genetic algorithm to target the specific requirements of the relevant decomposed part of the design problem. Decomposing the design problem to allow for the design requirements of each level to be dealt with separately and then reassembling them in a bottom up approach reduces the generation of non-viable solutions through constraining the options available at the next higher level. The iterative approach, in exploring the range of design solutions through modification of the design schema as the understanding of the design problem improves, assists in identifying conflicts in the design requirements. Additionally, the hierarchical set-up allows the embedding of multiple fitness functions into the genetic algorithm, each relevant to a specific level. This supports an integrated multi-level, multi-disciplinary approach. The HEAD system promotes a collaborative relationship between human creativity and the computer capability. The design schema component, as the input to the procedural algorithms, enables the encoding of certain aspects of the designer's subjective creativity. By focusing on finding solutions for the relevant sub-problems at the appropriate levels of detail, the hierarchical nature of the system assist in the design decision-making process.

The theory and practice on pre-qualification in bidding procedure

资格预审是招标程序中重要环节.通过对投标人的资质和业绩等审查既能保证不符合 要求的投标人尽可能早地退出无谓竞争的行列,避免了大量人力"物力的损失和浪费, 又能促进建筑市场优胜劣汰,提高企业竞争力.同时鉴于目前资格预审和建筑市场存在 的问题,笔者以为通过强化资格预审可以有效推进建筑市场信用体系建设,促进行业健康发展,并且深入探讨了资格预审体系建立的具体对策和措施.

The neglected dimension of community liveability : impact on social connectedness and active ageing in higher density accommodation

Purpose This thesis is about liveability, place and ageing in the high density urban landscape of Brisbane, Australia. As with other major developed cities around the globe, Brisbane has adopted policies to increase urban residential densities to meet the main liveability and sustainability aim of decreasing car dependence and therefore pollution, as well as to minimise the loss of greenfield areas and habitats to developers. This objective hinges on urban neighbourhoods/communities being liveable places, which residents do not have to leave for everyday living. Community/neighbourhood liveability is an essential ingredient in healthy ageing in place and has a substantial impact upon the safety, independence and well-being of older adults. It is generally accepted that ageing in place is optimal for both older people and the state. The optimality of ageing in place generally assumes that there is a particular quality to environments or standard of liveability in which people successfully age in place. The aim of this thesis was to examine if there are particular environmental qualities or aspects of liveability that test optimality and to better understand the key liveability factors that contribute to successful ageing in place. Method A strength of this thesis is that it draws on two separate studies to address the research question of what makes high density liveable for older people. In Chapter 3, the two methods are identified and differentiated as Method 1 (used in Paper 1) and Method 2 (used in Papers 2, 3, 4 and 5). Method 1 involved qualitative interviews with 24 inner city high density Brisbane residents. The major strength of this thesis is the innovative methodology outlined in the thesis as Method 2. Method 2 involved a case study approach employing qualitative and quantitative methods. Qualitative data was collected using semi-structured, in-depth interviews and time-use diaries completed by participants during the week of tracking. The quantitative data was gathered using Global Positioning Systems for tracking and Geographical Information Systems for mapping and analysis of participants’ activities. The combination of quantitative and qualitative analysis captured both participants’ subjective perceptions of their neighbourhoods and their patterns of movement. This enhanced understanding of how neighbourhoods and communities function and of the various liveability dimensions that contribute to active ageing and ageing in place for older people living in high density environments. Both studies’ participants were inner-city high density residents of Brisbane. The study based on Method 1 drew on a wider age demographic than the study based on Method 2. Findings The five papers presented in this thesis by publication indicate a complex inter-relationship of the factors that make a place liveable. The first three papers identify what is comparable and different between the physical and social factors of high density communities/neighbourhoods. The last two papers explore relationships between social engagement and broader community variables such as infrastructure and the physical built environments that are risk or protective factors relevant to community liveability, active ageing and ageing in place in high density. The research highlights the importance of creating and/or maintaining a barrier-free environment and liveable community for ageing adults. Together, the papers promote liveability, social engagement and active ageing in high density neighbourhoods by identifying factors that constitute liveability and strategies that foster active ageing and ageing in place, social connections and well-being. Recommendations There is a strong need to offer more support for active ageing and ageing in place. While the data analyses of this research provide insight into the lived experience of high density residents, further research is warranted. Further qualitative and quantitative research is needed to explore in more depth, the urban experience and opinions of older people living in urban environments. In particular, more empirical research and theory-building is needed in order to expand understanding of the particular environmental qualities that enable successful ageing in place in our cities and to guide efforts aimed at meeting this objective. The results suggest that encouraging the presence of more inner city retail outlets, particularly services that are utilised frequently in people’s daily lives such as supermarkets, medical services and pharmacies, would potentially help ensure residents fully engage in their local community. The connectivity of streets, footpaths and their role in facilitating the reaching of destinations are well understood as an important dimension of liveability. To encourage uptake of sustainable transport, the built environment must provide easy, accessible connections between buildings, walkways, cycle paths and public transport nodes. Wider streets, given that they take more time to cross than narrow streets, tend to .compromise safety - especially for older people. Similarly, the width of footpaths, the level of buffering, the presence of trees, lighting, seating and design of and distance between pedestrian crossings significantly affects the pedestrian experience for older people and impacts upon their choice of transportation. High density neighbourhoods also require greater levels of street fixtures and furniture for everyday life to make places more useable and comfortable for regular use. The importance of making the public realm useful and habitable for older people cannot be over-emphasised. Originality/value While older people are attracted to high density settings, there has been little empirical evidence linking liveability satisfaction with older people’s use of urban neighbourhoods. The current study examined the relationships between community/neighbourhood liveability, place and ageing to better understand the implications for those adults who age in place. The five papers presented in this thesis add to the understanding of what high density liveable age-friendly communities/ neighbourhoods are and what makes them so for older Australians. Neighbourhood liveability for older people is about being able to age in place and remain active. Issues of ageing in Australia and other areas of the developed world will become more critical in the coming decades. Creating livable communities for all ages calls for partnerships across all levels of government agencies and among different sectors within communities. The increasing percentage of older people in the community will have increasing political influence and it will be a foolish government who ignores the needs of an older society.

Graph-based concept weighting for medical information retrieval

This paper presents a graph-based method to weight medical concepts in documents for the purposes of information retrieval. Medical concepts are extracted from free-text documents using a state-of-the-art technique that maps n-grams to concepts from the SNOMED CT medical ontology. In our graph-based concept representation, concepts are vertices in a graph built from a document, edges represent associations between concepts. This representation naturally captures dependencies between concepts, an important requirement for interpreting medical text, and a feature lacking in bag-of-words representations. We apply existing graph-based term weighting methods to weight medical concepts. Using concepts rather than terms addresses vocabulary mismatch as well as encapsulates terms belonging to a single medical entity into a single concept. In addition, we further extend previous graph-based approaches by injecting domain knowledge that estimates the importance of a concept within the global medical domain. Retrieval experiments on the TREC Medical Records collection show our method outperforms both term and concept baselines. More generally, this work provides a means of integrating background knowledge contained in medical ontologies into data-driven information retrieval approaches.

Design and analysis of key management schemes for distributed wireless sensor networks

Secure communications in distributed Wireless Sensor Networks (WSN) operating under adversarial conditions necessitate efficient key management schemes. In the absence of a priori knowledge of post-deployment network configuration and due to limited resources at sensor nodes, key management schemes cannot be based on post-deployment computations. Instead, a list of keys, called a key-chain, is distributed to each sensor node before the deployment. For secure communication, either two nodes should have a key in common in their key-chains, or they should establish a key through a secure-path on which every link is secured with a key. We first provide a comparative survey of well known key management solutions for WSN. Probabilistic, deterministic and hybrid key management solutions are presented, and they are compared based on their security properties and re-source usage. We provide a taxonomy of solutions, and identify trade-offs in them to conclude that there is no one size-fits-all solution. Second, we design and analyze deterministic and hybrid techniques to distribute pair-wise keys to sensor nodes before the deployment. We present novel deterministic and hybrid approaches based on combinatorial design theory and graph theory for deciding how many and which keys to assign to each key-chain before the sensor network deployment. Performance and security of the proposed schemes are studied both analytically and computationally. Third, we address the key establishment problem in WSN which requires key agreement algorithms without authentication are executed over a secure-path. The length of the secure-path impacts the power consumption and the initialization delay for a WSN before it becomes operational. We formulate the key establishment problem as a constrained bi-objective optimization problem, break it into two sub-problems, and show that they are both NP-Hard and MAX-SNP-Hard. Having established inapproximability results, we focus on addressing the authentication problem that prevents key agreement algorithms to be used directly over a wireless link. We present a fully distributed algorithm where each pair of nodes can establish a key with authentication by using their neighbors as the witnesses.

Adaptive dynamic path re-planning RRT algorithms with game theory for UAVs

The main aim of this paper is to describe an adaptive re-planning algorithm based on a RRT and Game Theory to produce an efficient collision free obstacle adaptive Mission Path Planner for Search and Rescue (SAR) missions. This will provide UAV autopilots and flight computers with the capability to autonomously avoid static obstacles and No Fly Zones (NFZs) through dynamic adaptive path replanning. The methods and algorithms produce optimal collision free paths and can be integrated on a decision aid tool and UAV autopilots.

A semi-supervised graph-based algorithm for detecting outliers in online-social-networks

In this paper, we propose a semi-supervised approach of anomaly detection in Online Social Networks. The social network is modeled as a graph and its features are extracted to detect anomaly. A clustering algorithm is then used to group users based on these features and fuzzy logic is applied to assign degree of anomalous behavior to the users of these clusters. Empirical analysis shows effectiveness of this method.

A people-to-people matching system using graph mining techniques

A people-to-people matching system (or a match-making system) refers to a system in which users join with the objective of meeting other users with the common need. Some real-world examples of these systems are employer-employee (in job search networks), mentor-student (in university social networks), consume-to-consumer (in marketplaces) and male-female (in an online dating network). The network underlying in these systems consists of two groups of users, and the relationships between users need to be captured for developing an efficient match-making system. Most of the existing studies utilize information either about each of the users in isolation or their interaction separately, and develop recommender systems using the one form of information only. It is imperative to understand the linkages among the users in the network and use them in developing a match-making system. This study utilizes several social network analysis methods such as graph theory, small world phenomenon, centrality analysis, density analysis to gain insight into the entities and their relationships present in this network. This paper also proposes a new type of graph called “attributed bipartite graph���. By using these analyses and the proposed type of graph, an efficient hybrid recommender system is developed which generates recommendation for new users as well as shows improvement in accuracy over the baseline methods.

Postmodern Theory and the Choreography of Michael Clark

This study addresses two interrelated questions: Can postmodern ‘theory��� illuminate an understanding of Michael Clark’s work? and, a sub-question, In which ways, if at all, does Clark’s work demonstrate a postmodern sensibility? Chapter one, the introduction to this study, provides a ‘portrait’ of postmodernism, that is, it addresses the question What is postmodernism? Chapter two is a biography of Michael Clark. The seminal sections to this study, however, are chapters three and four. Here the author blends a discussion of a) subject matter, treatment and meanings in Clark’s choreography, b) journalistic criticisms of those features of his work, and c) postmodern theory. The outcome of these chapters is to demonstrate that Clark’s works do indeed require re-interpretation and re-evaluation, and to illustrate how these factors might be achieved.

Anomaly detection in online social networks : using data-mining techniques and fuzzy logic

This research is a step forward in improving the accuracy of detecting anomaly in a data graph representing connectivity between people in an online social network. The proposed hybrid methods are based on fuzzy machine learning techniques utilising different types of structural input features. The methods are presented within a multi-layered framework which provides the full requirements needed for finding anomalies in data graphs generated from online social networks, including data modelling and analysis, labelling, and evaluation.

The monadic environment : evoking emotion and memory in participatory performance

This practice-led research project examined the audience experience of immersive environments in participatory performance. Drawing upon the work of artist Ilya Kabakov, Gaston Bachelard's Poetics of Space (1964) and Leibniz's theory of the monad, the study investigated how an immersive space can be constructed to evoke emotion and memory recall in participants. The research consisted of two cycles of creative experimentation resulting in the presentation of a final piece entitled Dulcet. The research contributes new terminology to the discourse surrounding the participant experience in immersive environments, specifically space-as-memory, the role of ambiguity in spatial design and the construct of the monadic environment.

Navigating theory, negotiating difference and beating the system : a critical how-to of media assistance evaluation

The wave of democratisation across Europe, Africa, Asia and Latin America in the early 1990s triggered an increase in donor funding to media assistance initiatives, primarily within good governance policy frameworks. However, few media assistance projects have managed to effectively evaluate the impacts of their work. This thesis explores how the impacts of Australian media assistance on social change and governance can be most effectively evaluated and understood. The findings of this research suggest the importance of early investment in participatory planning of evaluation designs, which are then periodically revisited. These evaluation designs should be based on a theoretically sound link between models of change, evaluative questions and methods.

Tubule detection in testis images using boundary weighting and circular shortest path

In studies of germ cell transplantation, measureing tubule diameters and counting cells from different populations using antibodies as markers are very important. Manual measurement of tubule sizes and cell counts is a tedious and sanity grinding work. In this paper, we propose a new boundary weighting based tubule detection method. We first enhance the linear features of the input image and detect the approximate centers of tubules. Next, a boundary weighting transform is applied to the polar transformed image of each tubule region and a circular shortest path is used for the boundary detection. Then, ellipse fitting is carried out for tubule selection and measurement. The algorithm has been tested on a dataset consisting of 20 images, each having about 20 tubules. Experiments show that the detection results of our algorithm are very close to the results obtained manually. © 2013 IEEE.