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

An evaluation of feature selection methods on multi-class imbalance and high dimensionality shape-based leaf image features

Multi-class imbalance shape-based leaf image features requires feature subset that appropriately represent the leaf shape.Multi-class imbalance data is a type of data classification problem in which some data classes is highly underrepresented compared to others.This occurs when at least one data class is represented by just a few numbers of training samples known as the minority class compared to other classes that make up the majority class.To address this issue in shapebased leaf image feature extraction, this paper discusses the evaluation of several methods available in Weka and a wrapperbased genetic algorithm feature selection

A Hybrid Multi-Filter Wrapper Feature Selection Method for Software Defect Predictors

Software Defect Prediction (SDP) is an approach used for identifying defect-prone software modules or components. It helps software engineer to optimally, allocate limited resources to defective software modules or components in the testing or maintenance phases of software development life cycle (SDLC). Nonetheless, the predictive performance of SDP models reckons largely on the quality of dataset utilized for training the predictive models. The high dimensionality of software metric features has been noted as a data quality problem which negatively affects the predictive performance of SDP models. Feature Selection (FS) is a well-known method for solving high dimensionality problem and can be divided into filter-based and wrapper-based methods. Filter-based FS has low computational cost, but the predictive performance of its classification algorithm on the filtered data cannot be guaranteed. On the contrary, wrapper-based FS have good predictive performance but with high computational cost and lack of generalizability. Therefore, this study proposes a hybrid multi-filter wrapper method for feature selection of relevant and irredundant features in software defect prediction. The proposed hybrid feature selection will be developed to take advantage of filter-filter and filter-wrapper relationships to give optimal feature subsets, reduce its evaluation cycle and subsequently improve SDP models overall predictive performance in terms of Accuracy, Precision and Recall values

Network Traffic Based Botnet Detection Using Machine Learning

The field of information and computer security is rapidly developing in today’s world as the number of security risks is continuously being explored every day. The moment a new software or a product is launched in the market, a new exploit or vulnerability is exposed and exploited by the attackers or malicious users for different motives. Many attacks are distributed in nature and carried out by botnets that cause widespread disruption of network activity by carrying out DDoS (Distributed Denial of Service) attacks, email spamming, click fraud, information and identity theft, virtual deceit and distributed resource usage for cryptocurrency mining. Botnet detection is still an active area of research as no single technique is available that can detect the entire ecosystem of a botnet like Neris, Rbot, and Virut. They tend to have different configurations and heavily armored by malware writers to evade detection systems by employing sophisticated evasion techniques. This report provides a detailed overview of a botnet and its characteristics and the existing work that is done in the domain of botnet detection. The study aims to evaluate the preprocessing techniques like variance thresholding and one-hot encoding to clean the botnet dataset and feature selection technique like filter, wrapper and embedded method to boost the machine learning model performance. This study addresses the dataset imbalance issues through techniques like undersampling, oversampling, ensemble learning and gradient boosting by using random forest, decision tree, AdaBoost and XGBoost. Lastly, the optimal model is then trained and tested on the dataset of different attacks to study its performance

Computational intelligence contributions to readmisision risk prediction in Healthcare systems

136 p.The Thesis tackles the problem of readmission risk prediction in healthcare systems from a machine learning and computational intelligence point of view. Readmission has been recognized as an indicator of healthcare quality with primary economic importance. We examine two specific instances of the problem, the emergency department (ED) admission and heart failure (HF) patient care using anonymized datasets from three institutions to carry real-life computational experiments validating the proposed approaches. The main difficulties posed by this kind of datasets is their high class imbalance ratio, and the lack of informative value of the recorded variables. This thesis reports the results of innovative class balancing approaches and new classification architectures

Machine Learning Approaches for Improving Prediction Performance of Structure-Activity Relationship Models

In silico bioactivity prediction studies are designed to complement in vivo and in vitro efforts to assess the activity and properties of small molecules. In silico methods such as Quantitative Structure-Activity/Property Relationship (QSAR) are used to correlate the structure of a molecule to its biological property in drug design and toxicological studies. In this body of work, I started with two in-depth reviews into the application of machine learning based approaches and feature reduction methods to QSAR, and then investigated solutions to three common challenges faced in machine learning based QSAR studies. First, to improve the prediction accuracy of learning from imbalanced data, Synthetic Minority Over-sampling Technique (SMOTE) and Edited Nearest Neighbor (ENN) algorithms combined with bagging as an ensemble strategy was evaluated. The Friedman’s aligned ranks test and the subsequent Bergmann-Hommel post hoc test showed that this method significantly outperformed other conventional methods. SMOTEENN with bagging became less effective when IR exceeded a certain threshold (e.g., \u3e40). The ability to separate the few active compounds from the vast amounts of inactive ones is of great importance in computational toxicology. Deep neural networks (DNN) and random forest (RF), representing deep and shallow learning algorithms, respectively, were chosen to carry out structure-activity relationship-based chemical toxicity prediction. Results suggest that DNN significantly outperformed RF (p \u3c 0.001, ANOVA) by 22-27% for four metrics (precision, recall, F-measure, and AUPRC) and by 11% for another (AUROC). Lastly, current features used for QSAR based machine learning are often very sparse and limited by the logic and mathematical processes used to compute them. Transformer embedding features (TEF) were developed as new continuous vector descriptors/features using the latent space embedding from a multi-head self-attention. The significance of TEF as new descriptors was evaluated by applying them to tasks such as predictive modeling, clustering, and similarity search. An accuracy of 84% on the Ames mutagenicity test indicates that these new features has a correlation to biological activity. Overall, the findings in this study can be applied to improve the performance of machine learning based Quantitative Structure-Activity/Property Relationship (QSAR) efforts for enhanced drug discovery and toxicology assessments

A machine learning-based investigation of cloud service attacks

In this thesis, the security challenges of cloud computing are investigated in the Infrastructure as a Service (IaaS) layer, as security is one of the major concerns related to Cloud services. As IaaS consists of different security terms, the research has been further narrowed down to focus on Network Layer Security. Review of existing research revealed that several types of attacks and threats can affect cloud security. Therefore, there is a need for intrusion defence implementations to protect cloud services. Intrusion Detection (ID) is one of the most effective solutions for reacting to cloud network attacks. [Continues.