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.

Knowledge management and Dublin Core

This paper is concerned with investigating existing and potential scope of Dublin Core metadata in Knowledge Management contexts. Modelling knowledge is identified as a conceptual prerequisite in this investigation, principally for the purpose of clarifying scope prior to identifying the range of tasks associated with organising knowledge. A variety of models is presented and relationships between data, information, and knowledge discussed. It is argued that the two most common modes of organisation, hierarchies and networks, influence the effectiveness and flow of knowledge. Practical perspective is provided by reference to implementations and projects providing evidence of how DC metadata is applied in such contexts. A sense-making model is introduced that can be used as a shorthand reference for identifying useful facets of knowledge that might be described using metadata. Discussion is aimed at presenting this model in a way that both validates current applications and points to potential novel applications.

An information literacy integration model and its application in higher education

Purpose - The purpose of this paper is to present a model for curricular integration of information literacy for undergraduate programs in higher education. Design/methodology/approach - Data are drawn from individual interviews at three universities in Australia and curricular integration working experience at a New Zealand university. Sociocultural theories are adopted in the research process and in the development of the model, Findings - Key characteristics of the curriculum integration of information literacy were identified and an information literacy integration model was developed. The S2J2 key behaviours for campus-wide multi-partner collaboration in information literacy integration were also identified. Research limitations/implications - The model was developed without including the employer needs. Through the process of further research, the point of view of the employer on how to provide information literacy education needs to be explored in order to strengthen the model in curricular design. Practical implications - The information literacy integration model was developed based on practical experience in higher education and has been applied in different undergraduate curricular programs. The model could be used or adapted by both librarians and academics when they integrate information literacy into an undergraduate curriculum from a lower level to a higher level. Originality/value - The information literacy integration model was developed based on recent PhD research. The model integrates curriculum, pedagogy and learning theories, information literacy theories, information literacy guidelines, people and collaborative together. The model provides a framework of how information literacy can be integrated into multiple courses across an undergraduate academic degree in higher education.

Information Accountability Framework for a Trusted Health Care System

Trusted health care outcomes are patient centric. Requirements to ensure both the quality and sharing of patients’ health records are a key for better clinical decision making. In the context of maintaining quality health, the sharing of data and information between professionals and patients is paramount. This information sharing is a challenge and costly if patients’ trust and institutional accountability are not established. Establishment of an Information Accountability Framework (IAF) is one of the approaches in this paper. The concept behind the IAF requirements are: transparent responsibilities, relevance of the information being used, and the establishment and evidence of accountability that all lead to the desired outcome of a Trusted Health Care System. Upon completion of this IAF framework the trust component between the public and professionals will be constructed. Preservation of the confidentiality and integrity of patients’ information will lead to trusted health care outcomes.

Structural damage detection using frequency response functions and neural networks

This paper illustrates the damage identification and condition assessment of a three story bookshelf structure using a new frequency response functions (FRFs) based damage index and Artificial Neural Networks (ANNs). A major obstacle of using measured frequency response function data is a large size input variables to ANNs. This problem is overcome by applying a data reduction technique called principal component analysis (PCA). In the proposed procedure, ANNs with their powerful pattern recognition and classification ability were used to extract damage information such as damage locations and severities from measured FRFs. Therefore, simple neural network models are developed, trained by Back Propagation (BP), to associate the FRFs with the damage or undamaged locations and severity of the damage of the structure. Finally, the effectiveness of the proposed method is illustrated and validated by using the real data provided by the Los Alamos National Laboratory, USA. The illustrated results show that the PCA based artificial Neural Network method is suitable and effective for damage identification and condition assessment of building structures. In addition, it is clearly demonstrated that the accuracy of proposed damage detection method can also be improved by increasing number of baseline datasets and number of principal components of the baseline dataset.

Sociocultural theories and their application in information literacy research and education

Drawing on the example of a recent study (Wang, 2010), this paper discusses the application of a sociocultural approach to information literacy research and curriculat design. First, it describes the foundation of this research approach in sociocultural theories, in particular Vygotsky's sociocultural theory. Then it presents key theoretical principles arising from the research and describes how the sociocultural approach enabled the establishment of collaborative partnerships between information professionals and academic and teaching support staff in a community of practice for information literacy integration.

Diversified service provisioning in global business networks

Companies and their services are being increasingly exposed to global business networks and Internet-based ondemand services. Much of the focus is on flexible orchestration and consumption of services, beyond ownership and operational boundaries of services. However, ways in which third-parties in the “global village” can seamlessly self-create new offers out of existing services remains open. This paper proposes a framework for service provisioning in global business networks that allows an open-ended set of techniques for extending services through a rich, multi-tooling environment. The Service Provisioning Management Framework, as such, supports different modeling techniques, through supportive tools, allowing different parts of services to be integrated into new contexts. Integration of service user interfaces, business processes, operational interfaces and business object are supported. The integration specifications that arise from service extensions are uniformly reflected through a kernel technique, the Service Integration Technique. Thus, the framework preserves coherence of service provisioning tasks without constraining the modeling techniques needed for extending different aspects of services.

A quantum information retrieval approach to memory

As computers approach the physical limits of information storable in memory, new methods will be needed to further improve information storage and retrieval. We propose a quantum inspired vector based approach, which offers a contextually dependent mapping from the subsymbolic to the symbolic representations of information. If implemented computationally, this approach would provide exceptionally high density of information storage, without the traditionally required physical increase in storage capacity. The approach is inspired by the structure of human memory and incorporates elements of Gardenfors’ Conceptual Space approach and Humphreys et al.’s matrix model of memory.

Finding and matching communities in social networks using data mining

The rapid growth in the number of users using social networks and the information that a social network requires about their users make the traditional matching systems insufficiently adept at matching users within social networks. This paper introduces the use of clustering to form communities of users and, then, uses these communities to generate matches. Forming communities within a social network helps to reduce the number of users that the matching system needs to consider, and helps to overcome other problems from which social networks suffer, such as the absence of user activities' information about a new user. The proposed system has been evaluated on a dataset obtained from an online dating website. Empirical analysis shows that accuracy of the matching process is increased using the community information.

Information sharing in Onesocialweb using a multiple profile manager to better informed medical decision making processes

The study shows an alternative solution to existing efforts at solving the problem of how to centrally manage and synchronise users’ Multiple Profiles (MP) across multiple discrete social networks. Most social network users hold more than one social network account and utilise them in different ways depending on the digital context (Iannella, 2009a). They may, for example, enjoy friendly chat on Facebook1, professional discussion on LinkedIn2, and health information exchange on PatientsLikeMe3 In this thesis the researcher proposes a framework for the management of a user’s multiple online social network profiles. A demonstrator, called Multiple Profile Manager (MPM), will be showcased to illustrate how effective the framework will be. The MPM will achieve the required profile management and synchronisation using a free, open, decentralized social networking platform (OSW) that was proposed by the Vodafone Group in 2010. The proposed MPM will enable a user to create and manage an integrated profile (IP) and share/synchronise this profile with all their social networks. The necessary protocols to support the prototype are also proposed by the researcher. The MPM protocol specification defines an Extensible Messaging and Presence Protocol (XMPP) extension for sharing vCard and social network accounts information between the MPM Server, MPM Client, and social network sites (SNSs). . Therefore many web users need to manage disparate profiles across many distributed online sources. Maintaining these profiles is cumbersome, time-consuming, inefficient, and may lead to lost opportunity. The writer of this thesis adopted a research approach and a number of use cases for the implementation of the project. The use cases were created to capture the functional requirements of the MPM and to describe the interactions between users and the MPM. In the research a development process was followed in establishing the prototype and related protocols. The use cases were subsequently used to illustrate the prototype via the screenshots taken of the MPM client interfaces. The use cases also played a role in evaluating the outcomes of the research such as the framework, prototype, and the related protocols. An innovative application of this project is in the area of public health informatics. The researcher utilised the prototype to examine how the framework might benefit patients and physicians. The framework can greatly enhance health information management for patients and more importantly offer a more comprehensive personal health overview of patients to physicians. This will give a more complete picture of the patient’s background than is currently available and will prove helpful in providing the right treatment. The MPM prototype and related protocols have a high application value as they can be integrated into the real OSW platform and so serve users in the modern digital world. They also provide online users with a real platform for centrally storing their complete profile data, efficiently managing their personal information, and moreover, synchronising the overall complete profile with each of their discrete profiles stored in their different social network sites.

Exploring health information use by older Australians within everyday life

Exploring information use within everyday or community contexts is a recent area of interest for information literacy research endeavors. Within this domain, health information literacy (HIL) has emerged as a focus of interest due to identified synergies between information use and health status. However, while HIL has been acknowledged as a core ingredient that can assist people to take responsibility for managing and improving their own health, limited research has explored how HIL is experienced in everyday community life. This article will present the findings of ongoing research undertaken using phenomenography to explore how HIL is experienced among older Australians within everyday contexts. It will also discuss how these findings may be used to inform policy formulation in health communication and as an evidence base for the design and delivery of consumer health information resources and services.

SOA for business networks - service delivery framework

The next generation of SOA needs to scale for flexible service consumption, beyond organizational boundaries and current B2B applications, into communities, eco-systems, and business networks. In the wider and, ultimately, global settings, new capabilities are needed so that business partners can efficiently and reliably enable, adapt, and expose services where they can be discovered, ordered, consumed, metered, and paid for, through new applications and opportunities, driven by third parties in the global "village". This trend is already underway, in different ways, through various early adopter market segments. For the small medium enterprises segment, Google, Intuit-Microsoft, and others have launched appstores, through which an open-ended array of hosted applications are sourced from the development community and procured as maketplace commondities. In the corporate sector, the marketplace model and business network hubs are being put in place on top of connectivity and network orchestration investments for capitalizing services as tradable assets, seen in banking/finance (e.g. American Express Intelligent Marketplace), logistics (e.g., the E2open hub), and the public sector (e.g., UK DirectGov whole-of-government citizen services delivery).

Information technology and business value in a global economy : do information technology investments pay off in a developing economy?

Understanding the business value of IT has mostly been studied in developed countries, but because most investment in developing countries is derived from external sources, the influence of that investment on business value is likely to be different. We test this notion using a two-layer model. We examine the impact of IT investments on firm processes, and the relationship of these processes to firm performance in a developing country. Our findings suggest that investment in different areas of IT positively relates to improvements in intermediate business processes and these intermediate business processes positively relate to the overall financial performance of firms in a developing country.

Information technology resources,complementaries and capabilities : towards a deeper understanding of leveraging business value from IT

Organisations devote substantial resources to acquire information technology (IT), and explaining the important issue of how IT can affect performance has posed a significant challenge to information system (IS) researchers. Owing to the importance of expanding our understanding on how and where IT and IT-related resources impact organisational performance, this study investigates the differential effects of IT resources and IT-related capabilities, in the presence of platform-related complementarities, on business process performance. We test these relationships empirically via a field survey of 216 firms. The findings suggest that IT resources and IT-related capabilities explain variance in performance. Of interest is the finding that IT resources and IT-related capabilities ability to explain variance in business process is further enhanced by the presence of the platform-related complementarities. Our findings are largely consistent with the resource-based and complementarity arguments of sources of IT-related business value.

Information technology and business value: how complementary IT usage platform and capable resources explain IT business value variation

Understanding information technology’s (ITs) contribution to business value is an imperative issue, and while we have attempted to untangle the relationship between IT and business value with some success, our knowledge of specific factors leading to ITs contribution to business value still remains limited. In this paper we propose that complementing IT resources, by establishing a sound IT platform with capable organisational resources may aid in ITs ability to contribute to business value. We suggest that performance measurement of this contribution be undertaken at the business process level first, and then mapped through to firm level performance measurement to obtain a better understanding of the path of IT business value contribution.