A novel Boolean kernels family for categorical data

Kernel based classifiers, such as SVM, are considered state-of-the-art algorithms and are widely used on many classification tasks. However, this kind of methods are hardly interpretable and for this reason they are often considered as black-box models. In this paper, we propose a new family of Boolean kernels for categorical data where features correspond to propositional formulas applied to the input variables. The idea is to create human-readable features to ease the extraction of interpretation rules directly from the embedding space. Experiments on artificial and benchmark datasets show the effectiveness of the proposed family of kernels with respect to established ones, such as RBF, in terms of classification accuracy

The Reasonable Effectiveness of Randomness in Scalable and Integrative Gene Regulatory Network Inference and Beyond

Gene regulation is orchestrated by a vast number of molecules, including transcription factors and co-factors, chromatin regulators, as well as epigenetic mechanisms, and it has been shown that transcriptional misregulation, e.g., caused by mutations in regulatory sequences, is responsible for a plethora of diseases, including cancer, developmental or neurological disorders. As a consequence, decoding the architecture of gene regulatory networks has become one of the most important tasks in modern (computational) biology. However, to advance our understanding of the mechanisms involved in the transcriptional apparatus, we need scalable approaches that can deal with the increasing number of large-scale, high-resolution, biological datasets. In particular, such approaches need to be capable of efficiently integrating and exploiting the biological and technological heterogeneity of such datasets in order to best infer the underlying, highly dynamic regulatory networks, often in the absence of sufficient ground truth data for model training or testing. With respect to scalability, randomized approaches have proven to be a promising alternative to deterministic methods in computational biology. As an example, one of the top performing algorithms in a community challenge on gene regulatory network inference from transcriptomic data is based on a random forest regression model. In this concise survey, we aim to highlight how randomized methods may serve as a highly valuable tool, in particular, with increasing amounts of large-scale, biological experiments and datasets being collected. Given the complexity and interdisciplinary nature of the gene regulatory network inference problem, we hope our survey maybe helpful to both computational and biological scientists. It is our aim to provide a starting point for a dialogue about the concepts, benefits, and caveats of the toolbox of randomized methods, since unravelling the intricate web of highly dynamic, regulatory events will be one fundamental step in understanding the mechanisms of life and eventually developing efficient therapies to treat and cure diseases

Investigating the attainment of optimum data quality for EHR Big Data: proposing a new methodological approach

The value derivable from the use of data is continuously increasing since some years. Both commercial and non-commercial organisations have realised the immense benefits that might be derived if all data at their disposal could be analysed and form the basis of decision taking. The technological tools required to produce, capture, store, transmit and analyse huge amounts of data form the background to the development of the phenomenon of Big Data. With Big Data, the aim is to be able to generate value from huge amounts of data, often in non-structured format and produced extremely frequently. However, the potential value derivable depends on general level of governance of data, more precisely on the quality of the data. The field of data quality is well researched for traditional data uses but is still in its infancy for the Big Data context. This dissertation focused on investigating effective methods to enhance data quality for Big Data. The principal deliverable of this research is in the form of a methodological approach which can be used to optimize the level of data quality in the Big Data context. Since data quality is contextual, (that is a non-generalizable field), this research study focuses on applying the methodological approach in one use case, in terms of the Electronic Health Records (EHR). The first main contribution to knowledge of this study systematically investigates which data quality dimensions (DQDs) are most important for EHR Big Data. The two most important dimensions ascertained by the research methods applied in this study are accuracy and completeness. These are two well-known dimensions, and this study confirms that they are also very important for EHR Big Data. The second important contribution to knowledge is an investigation into whether Artificial Intelligence with a special focus upon machine learning could be used in improving the detection of dirty data, focusing on the two data quality dimensions of accuracy and completeness. Regression and clustering algorithms proved to be more adequate for accuracy and completeness related issues respectively, based on the experiments carried out. However, the limits of implementing and using machine learning algorithms for detecting data quality issues for Big Data were also revealed and discussed in this research study. It can safely be deduced from the knowledge derived from this part of the research study that use of machine learning for enhancing data quality issues detection is a promising area but not yet a panacea which automates this entire process. The third important contribution is a proposed guideline to undertake data repairs most efficiently for Big Data; this involved surveying and comparing existing data cleansing algorithms against a prototype developed for data reparation. Weaknesses of existing algorithms are highlighted and are considered as areas of practice which efficient data reparation algorithms must focus upon. Those three important contributions form the nucleus for a new data quality methodological approach which could be used to optimize Big Data quality, as applied in the context of EHR. Some of the activities and techniques discussed through the proposed methodological approach can be transposed to other industries and use cases to a large extent. The proposed data quality methodological approach can be used by practitioners of Big Data Quality who follow a data-driven strategy. As opposed to existing Big Data quality frameworks, the proposed data quality methodological approach has the advantage of being more precise and specific. It gives clear and proven methods to undertake the main identified stages of a Big Data quality lifecycle and therefore can be applied by practitioners in the area. This research study provides some promising results and deliverables. It also paves the way for further research in the area. Technical and technological changes in Big Data is rapidly evolving and future research should be focusing on new representations of Big Data, the real-time streaming aspect, and replicating same research methods used in this current research study but on new technologies to validate current results

Reliable and energy efficient resource provisioning in cloud computing systems

Cloud Computing has revolutionized the Information Technology sector by giving computing a perspective of service. The services of cloud computing can be accessed by users not knowing about the underlying system with easy-to-use portals. To provide such an abstract view, cloud computing systems have to perform many complex operations besides managing a large underlying infrastructure. Such complex operations confront service providers with many challenges such as security, sustainability, reliability, energy consumption and resource management. Among all the challenges, reliability and energy consumption are two key challenges focused on in this thesis because of their conflicting nature. Current solutions either focused on reliability techniques or energy efficiency methods. But it has been observed that mechanisms providing reliability in cloud computing systems can deteriorate the energy consumption. Adding backup resources and running replicated systems provide strong fault tolerance but also increase energy consumption. Reducing energy consumption by running resources on low power scaling levels or by reducing the number of active but idle sitting resources such as backup resources reduces the system reliability. This creates a critical trade-off between these two metrics that are investigated in this thesis. To address this problem, this thesis presents novel resource management policies which target the provisioning of best resources in terms of reliability and energy efficiency and allocate them to suitable virtual machines. A mathematical framework showing interplay between reliability and energy consumption is also proposed in this thesis. A formal method to calculate the finishing time of tasks running in a cloud computing environment impacted with independent and correlated failures is also provided. The proposed policies adopted various fault tolerance mechanisms while satisfying the constraints such as task deadlines and utility values. This thesis also provides a novel failure-aware VM consolidation method, which takes the failure characteristics of resources into consideration before performing VM consolidation. All the proposed resource management methods are evaluated by using real failure traces collected from various distributed computing sites. In order to perform the evaluation, a cloud computing framework, 'ReliableCloudSim' capable of simulating failure-prone cloud computing systems is developed. The key research findings and contributions of this thesis are: 1. If the emphasis is given only to energy optimization without considering reliability in a failure prone cloud computing environment, the results can be contrary to the intuitive expectations. Rather than reducing energy consumption, a system ends up consuming more energy due to the energy losses incurred because of failure overheads. 2. While performing VM consolidation in a failure prone cloud computing environment, a significant improvement in terms of energy efficiency and reliability can be achieved by considering failure characteristics of physical resources. 3. By considering correlated occurrence of failures during resource provisioning and VM allocation, the service downtime or interruption is reduced significantly by 34% in comparison to the environments with the assumption of independent occurrence of failures. Moreover, measured by our mathematical model, the ratio of reliability and energy consumption is improved by 14%

Impact of assistive technologies in supporting people with dementia.

In recent decades, many Assistive Technologies (ATs) have been developed to promote independence among people with dementia (PWD). Although there is a high rate of AT abandonment, only a handful of studies have focused on AT usability evaluation from the user point of view. The aim of this thesis is to empirically investigate the usability of ATs from the PWD and to measure its impacts on their lives. Following the Multi-methods research approach, the first part of the thesis uses secondary research methods including literature review and systematic mapping studies. The second part uses primary research methods including interviews (N=20) and questionnaire (N=327) based surveys for data collection and requirements elicitation. The third part is based on the design, development, and testing of an assistive software application through case studies (N=8). The first mapping study categorised existing general ATs into five major categories: robotics, monitoring, reminders, communication, and software. The second mapping study categorised software-based ATs into nine categories: cognitive help, reminders, health/activity monitoring, socialization, leisure, travel help, dementia detection, dementia prevention, and rehabilitation. The qualitative results showed that most of the PWD use ATs for socialization, and highlighted user interface efficacy, tailoring individual needs, and simplified functions as the major limitations of existing ATs. The quantitative results identified eleven factors for ATs usage: operational support, physical support, psychological support, social support, cultural match, reduced external help, affordability, travel help, compatibility, effectiveness, and retention. The statistical analysis showed that improved (social, psychological and travel) support and reduced need of external help for operating ATs, greatly impact AT effectiveness and retention. Based on PWD requirements, an assistive software application named E-Community for Dementia (ECD) was developed and tested through case studies involving 8 PWD and 40 volunteers. The participants were able to get their daily needed items in less time and with a friendlier manner through the help of their neighbours. The involvement of the caregivers for medication, meals, prayers etc. reduced significantly. The painting function helped evoke their memories, and encouraged them to perform activities from their youth. The news and weather functions kept them updated about the world around them. The travel tutor guided them in safe travel outside home and made sure that they got back home independently. The enhanced interaction between the PWD and their neighbours significantly reduced their social isolation. The results support the idea to create dementia-friendly communities at street levels, which is a cost-effective and reliable solution. The major outcomes from this thesis are AT categorization, evaluation of user experiences, factor identification and ranking, user requirements elicitation, assistive software application development, and case studies. This thesis helps considerably towards empirical investigation of the impact of ATs in supporting the PWD. The implementation of the ECD contributes towards the wellbeing of the PWD and saves costs spent on caregivers and carer companies. In future, the same study could be conducted in other settings to analyse the role of culture in AT acceptance