Machine Learning and Integrative Analysis of Biomedical Big Data.

Recent developments in high-throughput technologies have accelerated the accumulation of massive amounts of omics data from multiple sources: genome, epigenome, transcriptome, proteome, metabolome, etc. Traditionally, data from each source (e.g., genome) is analyzed in isolation using statistical and machine learning (ML) methods. Integrative analysis of multi-omics and clinical data is key to new biomedical discoveries and advancements in precision medicine. However, data integration poses new computational challenges as well as exacerbates the ones associated with single-omics studies. Specialized computational approaches are required to effectively and efficiently perform integrative analysis of biomedical data acquired from diverse modalities. In this review, we discuss state-of-the-art ML-based approaches for tackling five specific computational challenges associated with integrative analysis: curse of dimensionality, data heterogeneity, missing data, class imbalance and scalability issues

New Fundamental Technologies in Data Mining

The progress of data mining technology and large public popularity establish a need for a comprehensive text on the subject. The series of books entitled by "Data Mining" address the need by presenting in-depth description of novel mining algorithms and many useful applications. In addition to understanding each section deeply, the two books present useful hints and strategies to solving problems in the following chapters. The contributing authors have highlighted many future research directions that will foster multi-disciplinary collaborations and hence will lead to significant development in the field of data mining

Adversarial Robustness in Unsupervised Machine Learning: A Systematic Review

As the adoption of machine learning models increases, ensuring robust models against adversarial attacks is increasingly important. With unsupervised machine learning gaining more attention, ensuring it is robust against attacks is vital. This paper conducts a systematic literature review on the robustness of unsupervised learning, collecting 86 papers. Our results show that most research focuses on privacy attacks, which have effective defenses; however, many attacks lack effective and general defensive measures. Based on the results, we formulate a model on the properties of an attack on unsupervised learning, contributing to future research by providing a model to use.Comment: 38 pages, 11 figure

Ensembles of Pruned Deep Neural Networks for Accurate and Privacy Preservation in IoT Applications

The emergence of the AIoT (Artificial Intelligence of Things) represents the powerful convergence of Artificial Intelligence (AI) with the expansive realm of the Internet of Things (IoT). By integrating AI algorithms with the vast network of interconnected IoT devices, we open new doors for intelligent decision-making and edge data analysis, transforming various domains from healthcare and transportation to agriculture and smart cities. However, this integration raises pivotal questions: How can we ensure deep learning models are aptly compressed and quantised to operate seamlessly on devices constrained by computational resources, without compromising accuracy? How can these models be effectively tailored to cope with the challenges of statistical heterogeneity and the uneven distribution of class labels inherent in IoT applications? Furthermore, in an age where data is a currency, how do we uphold the sanctity of privacy for the sensitive data that IoT devices incessantly generate while also ensuring the unhampered deployment of these advanced deep learning models? Addressing these intricate challenges forms the crux of this thesis, with its contributions delineated as follows: Ensyth: A novel approach designed to synthesise pruned ensembles of deep learning models, which not only makes optimal use of limited IoT resources but also ensures a notable boost in predictability. Experimental evidence gathered from CIFAR-10, CIFAR-5, and MNIST-FASHION datasets solidify its merit, especially given its capacity to achieve high predictability. MicroNets: Venturing into the realms of efficiency, this is a multi-phase pruning pipeline that fuses the principles of weight pruning, channel pruning. Its objective is clear: foster efficient deep ensemble learning, specially crafted for IoT devices. Benchmark tests conducted on CIFAR-10 and CIFAR-100 datasets demonstrate its prowess, highlighting a compression ratio of nearly 92%, with these pruned ensembles surpassing the accuracy metrics set by conventional models. FedNets: Recognising the challenges of statistical heterogeneity in federated learning and the ever-growing concerns of data privacy, this innovative federated learning framework is introduced. It facilitates edge devices in their collaborative quest to train ensembles of pruned deep neural networks. More than just training, it ensures data privacy remains uncompromised. Evaluations conducted on the Federated CIFAR-100 dataset offer a testament to its efficacy. In this thesis, substantial contributions have been made to the AIoT application domain. Ensyth, MicroNets, and FedNets collaboratively tackle the challenges of efficiency, accuracy, statistical heterogeneity arising from distributed class labels, and privacy concerns inherent in deploying AI applications on IoT devices. The experimental results underscore the effectiveness of these approaches, paving the way for their practical implementation in real-world scenarios. By offering an integrated solution that satisfies multiple key requirements simultaneously, this research brings us closer to the realisation of effective and privacy-preserved AIoT systems

Macro-micro approach for mining public sociopolitical opinion from social media

During the past decade, we have witnessed the emergence of social media, which has prominence as a means for the general public to exchange opinions towards a broad range of topics. Furthermore, its social and temporal dimensions make it a rich resource for policy makers and organisations to understand public opinion. In this thesis, we present our research in understanding public opinion on Twitter along three dimensions: sentiment, topics and summary. In the first line of our work, we study how to classify public sentiment on Twitter. We focus on the task of multi-target-specific sentiment recognition on Twitter, and propose an approach which utilises the syntactic information from parse-tree in conjunction with the left-right context of the target. We show the state-of-the-art performance on two datasets including a multi-target Twitter corpus on UK elections which we make public available for the research community. Additionally we also conduct two preliminary studies including cross-domain emotion classification on discourse around arts and cultural experiences, and social spam detection to improve the signal-to-noise ratio of our sentiment corpus. Our second line of work focuses on automatic topical clustering of tweets. Our aim is to group tweets into a number of clusters, with each cluster representing a meaningful topic, story, event or a reason behind a particular choice of sentiment. We explore various ways of tackling this challenge and propose a two-stage hierarchical topic modelling system that is efficient and effective in achieving our goal. Lastly, for our third line of work, we study the task of summarising tweets on common topics, with the goal to provide informative summaries for real-world events/stories or explanation underlying the sentiment expressed towards an issue/entity. As most existing tweet summarisation approaches rely on extractive methods, we propose to apply state-of-the-art neural abstractive summarisation model for tweets. We also tackle the challenge of cross-medium supervised summarisation with no target-medium training resources. To the best of our knowledge, there is no existing work on studying neural abstractive summarisation on tweets. In addition, we present a system for providing interactive visualisation of topic-entity sentiments and the corresponding summaries in chronological order. Throughout our work presented in this thesis, we conduct experiments to evaluate and verify the effectiveness of our proposed models, comparing to relevant baseline methods. Most of our evaluations are quantitative, however, we do perform qualitative analyses where it is appropriate. This thesis provides insights and findings that can be used for better understanding public opinion in social media

Methods for improving robustness against adversarial machine learning attacks

Machine learning systems can improve the efficiency of real-world tasks, including in the cyber security domain; however, these models are susceptible to adversarial attacks; indeed, an arms race exists between adversaries and defenders. The benefits of these systems have been accepted without fully considering their vulnerabilities, resulting in the deployment of vulnerable machine learning models in adversarial environments. For example, intrusion detection systems are relied upon to accurately discern between malicious and benign traffic but can be fooled into allowing malware onto a networks. Robustness is the stability of performance in well-trained models facing adversarial examples. This thesis tackles the urgent problem of improving the robustness of machine learning models, enabling safer deployments in adversarial domains. The logical outputs of this research are countermeasures against adversarial examples. Original contributions to knowledge are: a survey of adversarial machine learning in the cyber security domain, a generalizable approach for feature vulnerability and robustness assessment, and a constraint-based method of generating transferable functionality-preserving adversarial examples in an intrusion detection domain. Novel defences against adversarial examples are presented: Feature selection with recursive feature elimination, and hierarchical classification. Machine learning classifiers can be used in both visual and non-visual domains. Most research in adversarial machine learning considers the visual domain. A primary focus of this work is how adversarial attacks can be effectively used in non-visual domains, such as cyber security. For example, attackers may exploit weaknesses in an intrusion detection system classifier, enabling an intrusion to masquerade as benign traffic. Easily fooled systems are of limited use in critical areas such as cyber security. In future, more sophisticated adversarial attacks could be used by ransomware and malware authors to evade detection by machine learning Intrusion Detection Systems. Experiments in this thesis focus on intrusion detection case studies and use Python code and Python libraries: the CleverHans API, and the Adversarial Robustness Toolkit libraries to generate adversarial examples, and the HiClass library to facilitate Hierarchical Classification. An adversarial arms race is playing out in cyber security. Every time defences are improved, adversaries find new ways to breach networks. Currently, one of the most critical holes in defences are adversarial examples. This thesis examines the problem of robustness against adversarial examples for machine learning systems and contributes novel countermeasures, aiming to enable the deployment of machine learning in critical domains

Feature Space Modeling for Accurate and Efficient Learning From Non-Stationary Data

A non-stationary dataset is one whose statistical properties such as the mean, variance, correlation, probability distribution, etc. change over a specific interval of time. On the contrary, a stationary dataset is one whose statistical properties remain constant over time. Apart from the volatile statistical properties, non-stationary data poses other challenges such as time and memory management due to the limitation of computational resources mostly caused by the recent advancements in data collection technologies which generate a variety of data at an alarming pace and volume. Additionally, when the collected data is complex, managing data complexity, emerging from its dimensionality and heterogeneity, can pose another challenge for effective computational learning. The problem is to enable accurate and efficient learning from non-stationary data in a continuous fashion over time while facing and managing the critical challenges of time, memory, concept change, and complexity simultaneously. Feature space modeling is one of the most effective solutions to address this problem. For non-stationary data, selecting relevant features is even more critical than stationary data due to the reduction of feature dimension which can ensure the best use a computational resource to produce higher accuracy and efficiency by data mining algorithms. In this dissertation, we investigated a variety of feature space modeling techniques to improve the overall performance of data mining algorithms. In particular, we built Relief based feature sub selection method in combination with data complexity iv analysis to improve the classification performance using ovarian cancer image data collected in a non-stationary batch mode. We also collected time series health sensor data in a streaming environment and deployed feature space transformation using Singular Value Decomposition (SVD). This led to reduced dimensionality of feature space resulting in better accuracy and efficiency produced by Density Ration Estimation Method in identifying potential change points in data over time. We have also built an unsupervised feature space modeling using matrix factorization and Lasso Regression which was successfully deployed in conjugate with Relative Density Ratio Estimation to address the botnet attacks in a non-stationary environment. Relief based feature model improved 16% accuracy of Fuzzy Forest classifier. For change detection framework, we observed 9% improvement in accuracy for PCA feature transformation. Due to the unsupervised feature selection model, for 2% and 5% malicious traffic ratio, the proposed botnet detection framework exhibited average 20% better accuracy than One Class Support Vector Machine (OSVM) and average 25% better accuracy than Autoencoder. All these results successfully demonstrate the effectives of these feature space models. The fundamental theme that repeats itself in this dissertation is about modeling efficient feature space to improve both accuracy and efficiency of selected data mining models. Every contribution in this dissertation has been subsequently and successfully employed to capitalize on those advantages to solve real-world problems. Our work bridges the concepts from multiple disciplines ineffective and surprising ways, leading to new insights, new frameworks, and ultimately to a cross-production of diverse fields like mathematics, statistics, and data mining

Extracting and Harnessing Interpretation in Data Mining

Machine learning, especially the recent deep learning technique, has aroused significant development to various data mining applications, including recommender systems, misinformation detection, outlier detection, and health informatics. Unfortunately, while complex models have achieved unprecedented prediction capability, they are often criticized as ``black boxes'' due to multiple layers of non-linear transformation and the hardly understandable working mechanism. To tackle the opacity issue, interpretable machine learning has attracted increasing attentions. Traditional interpretation methods mainly focus on explaining predictions of classification models with gradient based methods or local approximation methods. However, the natural characteristics of data mining applications are not considered, and the internal mechanisms of models are not fully explored. Meanwhile, it is unknown how to utilize interpretation to improve models. To bridge the gap, I developed a series of interpretation methods that gradually increase the transparency of data mining models. First, a fundamental goal of interpretation is providing the attribution of input features to model outputs. To adapt feature attribution to explaining outlier detection, I propose Contextual Outlier Interpretation (COIN). Second, to overcome the limitation of attribution methods that do not explain internal information inside models, I further propose representation interpretation methods to extract knowledge as a taxonomy. However, these post-hoc methods may suffer from interpretation accuracy and the inability to directly control model training process. Therefore, I propose an interpretable network embedding framework to explicitly control the meaning of latent dimensions. Finally, besides obtaining explanation, I propose to use interpretation to discover the vulnerability of models in adversarial circumstances, and then actively prepare models using adversarial training to improve their robustness against potential threats. My research of interpretable machine learning enables data scientists to better understand their models and discover defects for further improvement, as well as improves the experiences of customers who benefit from data mining systems. It broadly impacts fields such as Information Retrieval, Information Security, Social Computing, and Health Informatics