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.

Developing a fuzzy multi-criteria decision-making model for selecting design-build operational variations

Many academic researchers have conducted studies on the selection of design-build (DB) delivery method; however, there are few studies on the selection of DB operational variations, which poses challenges to many clients. The selection of DB operational variation is a multi-criteria decision making process that requires clients to objectively evaluate the performance of each DB operational variation with reference to the selection criteria. This evaluation process is often characterized by subjectivity and uncertainty. In order to resolve this deficiency, the current investigation aimed to establish a fuzzy multicriteria decision-making (FMCDM) model for selecting the most suitable DB operational variation. A three-round Delphi questionnaire survey was conducted to identify the selection criteria and their relative importance. A fuzzy set theory approach, namely the modified horizontal approach with the bisector error method, was applied to establish the fuzzy membership functions, which enables clients to perform quantitative calculations on the performance of each DB operational variation. The FMCDM was developed using the weighted mean method to aggregate the overall performance of DB operational variations with regard to the selection criteria. The proposed FMCDM model enables clients to perform quantitative calculations in a fuzzy decision-making environment and provides a useful tool to cope with different project attributes.

Development of distributed fuzzy systems with a runtime-adaptable mobile components framework

A distributed fuzzy system is a real-time fuzzy system in which the input, output and computation may be located on different networked computing nodes. The ability for a distributed software application, such as a distributed fuzzy system, to adapt to changes in the computing network at runtime can provide real-time performance improvement and fault-tolerance. This paper introduces an Adaptable Mobile Component Framework (AMCF) that provides a distributed dataflow-based platform with a fine-grained level of runtime reconfigurability. The execution location of small fragments (possibly as little as few machine-code instructions) of an AMCF application can be moved between different computing nodes at runtime. A case study is included that demonstrates the applicability of the AMCF to a distributed fuzzy system scenario involving multiple physical agents (such as autonomous robots). Using the AMCF, fuzzy systems can now be developed such that they can be distributed automatically across multiple computing nodes and are adaptable to runtime changes in the networked computing environment. This provides the opportunity to improve the performance of fuzzy systems deployed in scenarios where the computing environment is resource-constrained and volatile, such as multiple autonomous robots, smart environments and sensor networks.

See-and-avoid quadcopter using fuzzy control optimized by cross-entropy

In this work we present an optimized fuzzy visual servoing system for obstacle avoidance using an unmanned aerial vehicle. The cross-entropy theory is used to optimise the gains of our controllers. The optimization process was made using the ROS-Gazebo 3D simulation with purposeful extensions developed for our experiments. Visual servoing is achieved through an image processing front-end that uses the Camshift algorithm to detect and track objects in the scene. Experimental flight trials using a small quadrotor were performed to validate the parameters estimated from simulation. The integration of cross- entropy methods is a straightforward way to estimate optimal gains achieving excellent results when tested in real flights.

Quadcopter see and avoid using a fuzzy controller

Unmanned Aerial Vehicles (UAVs) industry is a fast growing sector. Nowadays, the market offers numerous possibilities for off-the-shelf UAVs such as quadrotors or fixed-wings. Until UAVs demonstrate advance capabilities such as autonomous collision avoidance they will be segregated and restricted to flight in controlled environments. This work presents a visual fuzzy servoing system for obstacle avoidance using UAVs. To accomplish this task we used the visual information from the front camera. Images are processed off-board and the result send to the Fuzzy Logic controller which then send commands to modify the orientation of the aircraft. Results from flight test are presented with a commercial off-the-shelf platform.

UAS See-and-Avoid using two different approaches of Fuzzy Control

This work presents two UAS See and Avoid approaches using Fuzzy Control. We compare the performance of each controller when a Cross-Entropy method is applied to optimase the parameters for one of the controllers. Each controller receive information from an image processing front-end that detect and track targets in the environment. Visual information is then used under a visual servoing approach to perform autonomous avoidance. Experimental flight trials using a small quadrotor were performed to validate and compare the behaviour of both controllers

Using digital storytelling as a change agent for women’s participation in the Turkish public sphere

This thesis builds on the scholarship and practical know-how that have emerged from digital storytelling projects around the world with diverse groups of participants in a range of institutions. I have used the results of these projects to explore the opportunities Digital Storytelling workshop practice may hold for women’s participation in the public sphere in Turkey. Through theoretical discussion and practical experimentation, I examine the potential of Digital Storytelling workshop practice as a means to promote agency and self-expression in a feminist activist organisation, focusing in particular on whether Digital Storytelling can be used as a change agent – as a tool for challenging the idea of public sphere in ways that make it more inclusive of women’s participation. The thesis engages with feminist scholarship’s critiques of the public/private dichotomy, as well as the concept of gender, to seek connections with narrative identity in the light of the analysis of the Digital Storytelling workshops and the digital stories that were created in a feminist context. The study on which this thesis is based saw the introduction of Digital Storytelling to Turkey for the first time through workshops in Istanbul and Antakya, conducted in partnership with the feminist activist organisation Amargi Women’s Academy. Applying the principles of feminist post-structuralist discourse analysis as used by Judith Baxter (2003), I examine two sets of data collected in this project. First, I analyse the interactions during the Digital Storytelling workshops, where women from Amargi created their digital stories in a collaborative setting. This is done through participatory observation notes and in-depth interviews with the workshop participants and facilitators. Second, I seek to uncover the strategies that these women used to ‘speak back to power’ in their digital stories, reading these as texts. I conclude that women from the Amargi network used the workshops to create digital content in order to communicate their concerns about issues that can be classified as gender-specific matters. During this process, they also cooperated, established new connections, and at the end of the process even defined new ways of using, circulating and repurposing their digital stories for feminist activism in Turkey. My research thereby contributes equally to feminist discourse analysis, the study of new-media usage and uptake among non-professionals, and the study of media–public sphere interactions in a particular national setting: Turkey. My conclusion indicates that the process of production is as important as the product itself, and from that I am able to draw out some strategies for developing digitally equipped women’s activism in Turkey.

Intuitionistic fuzzy Choquet integral operator-based approach for black-start decision-making

Determining the optimal of black-start strategies is very important for speeding the restoration speed of a power system after a global blackout. Most existing black-start decision-making methods are based on the assumption that all indexes are independent of each other, and little attention has been paid to the group decision-making method which is more reliable. Given this background, the intuitionistic fuzzy set and further intuitionistic fuzzy Choquet integral operator are presented, and a black-start decision-making method based on this integral operator is presented. Compared to existing methods, the proposed algorithm cannot only deal with the relevance among the indexes, but also overcome some shortcomings of the existing methods. Finally, an example is used to demonstrate the proposed method. © 2012 The Institution of Engineering and Technology.

Rough fuzzy control of SVC for power system stability enhancement

This paper presents a new approach to the design of a rough fuzzy controller for the control loop of the SVC (static VAR system) in a two area power system for stability enhancement with particular emphasis on providing effective damping for oscillatory instabilities. The performances of the rough fuzzy and the conventional fuzzy controller are compared with that of the conventional PI controller for a variety of transient disturbances, highlighting the effectiveness of the rough fuzzy controller in damping the inter-area oscillations. The effect of the rough fuzzy controller in improving the CCT (critical clearing time) of the two area system is elaborated in this paper as well.

Evaluating stakeholder satisfaction during public participation in major infrastructure and construction projects : a fuzzy approach

Numerous different and sometimes discrepant interests can be affected, both positively and negatively, throughout the course of a major infrastructure and construction (MIC) project. Failing to address and meet the concerns and expectations of the stakeholders involved has resulted in many project failures. One way to address this issue is through a participatory approach to project decision making. Whether the participation mechanism is effective or not depends largely on the client/owner. This paper provides a means of systematically evaluating the effectiveness of the public participation exercise, or even the whole project, through the measurement of stakeholder satisfaction. Since the process of satisfaction measurement is complicated and uncertain, requiring approximate reasoning involving human intuition, a fuzzy approach is adopted. From this, a multi-factor hierarchical fuzzy comprehensive evaluation model is established to facilitate the evaluation of satisfaction in both single stakeholder group and overall MIC project stakeholders.

Cross-entropy optimization for scaling factors of a fuzzy controller : a see-and-avoid approach for unmanned aerial systems

The Cross-Entropy (CE) is an efficient method for the estimation of rare-event probabilities and combinatorial optimization. This work presents a novel approach of the CE for optimization of a Soft-Computing controller. A Fuzzy controller was designed to command an unmanned aerial system (UAS) for avoiding collision task. The only sensor used to accomplish this task was a forward camera. The CE is used to reach a near-optimal controller by modifying the scaling factors of the controller inputs. The optimization was realized using the ROS-Gazebo simulation system. In order to evaluate the optimization a big amount of tests were carried out with a real quadcopter.

TS-fuzzy controlled DFIG based wind energy conversion system

This paper focuses on the implementation of the TS (Tagaki-Sugino) fuzzy controller for the active power and the DC capacitor voltage control of the Doubly Fed Induction Generator (DFIG) based wind generator. DFIG system is represented by a third-order model where electromagnetic transients of the stator are neglected. The effectiveness of the TS-fuzzy controller on the rotor speed oscillations and the DC capacitor voltage variations of the DFIG damping controller on converter ratings of the DFIG system is also investigated. The results of the time domain simulation studies are presented to elucidate the effectiveness of the TS-fuzzy controller compared with conventional PI controller in the DFIG system. The proposed TS-fuzzy controller can improve the fault ride through capability of DFIG compared to the conventional PI controller

Conflict and seduction in the public sphere

In a critical but sympathetic reading of Habermas’s work (1984, 1987a, 1987b, 2003), Luke Goode (2005) recently sought to rework his theory of deliberative democracy in an age of mediated and increasingly digital public spheres. Taking a different approach, Alan McKee (2005) challenged the culture- and class-bound strictures of Habermasian rationalism, instead pursuing a more radically pluralist account of postmodern public spheres. The editors of this special section of Media, Culture & Society invited us to discuss our differing approaches to the public sphere. Goode holds that the institutional bases of contemporary public spheres (political parties, educational institutions or public media) remain of critical importance, albeit in the context of a kaleidoscopic array of unofficial and informal micro-publics, both localized and de-territorialized. In contrast, McKee sustains a ‘hermeneutics of suspicion’ toward the official, hegemonic institutions of the public sphere since they tend to exclude and delegitimize discourses and practices that challenge their polite middle-class norms. McKee’s recent research has focused on sexual cultures, particularly among youth (McKee, 2011). Goode’s recent work has examined new social media spaces, particularly in relation to news and public debate (e.g. Goode, 2009; Goode et al., 2011). Consequently, our discussion turned to a domain which links our interests: after Goode discussed some of his recent research on (in)civility on YouTube as a new media public sphere, McKee challenged him to consider the case of pornographic websites modelled on social media sites.1 He identifies a greater degree of ‘civility’ in these pornographic sibling sites than on YouTube, requiring careful consideration of what constitutes a ‘public sphere’ in contemporary digital culture. Such sites represent an environment that shatters the opposition of public and private interest, affording public engagement on matters of the body, of intimacy, of gender politics, of pleasure and desire – said by many critics to be ruled out of court in Habermasian theory. Such environments also trouble traditional binaries between the cognitive and the affective, and between the performative and the deliberative. In what follows we explore the differences between our approaches in the form of a dialogue. As is often the case, our approaches seemed less at odds after engaging in conversation than may have initially appeared. But important differences of emphasis remain.