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

A review of ensemble learning and data augmentation models for class imbalanced problems: combination, implementation and evaluation

Class imbalance (CI) in classification problems arises when the number of observations belonging to one class is lower than the other. Ensemble learning combines multiple models to obtain a robust model and has been prominently used with data augmentation methods to address class imbalance problems. In the last decade, a number of strategies have been added to enhance ensemble learning and data augmentation methods, along with new methods such as generative adversarial networks (GANs). A combination of these has been applied in many studies, and the evaluation of different combinations would enable a better understanding and guidance for different application domains. In this paper, we present a computational study to evaluate data augmentation and ensemble learning methods used to address prominent benchmark CI problems. We present a general framework that evaluates 9 data augmentation and 9 ensemble learning methods for CI problems. Our objective is to identify the most effective combination for improving classification performance on imbalanced datasets. The results indicate that combinations of data augmentation methods with ensemble learning can significantly improve classification performance on imbalanced datasets. We find that traditional data augmentation methods such as the synthetic minority oversampling technique (SMOTE) and random oversampling (ROS) are not only better in performance for selected CI problems, but also computationally less expensive than GANs. Our study is vital for the development of novel models for handling imbalanced datasets

Fault Detection and Diagnosis with Imbalanced and Noisy Data: A Hybrid Framework for Rotating Machinery

Fault diagnosis plays an essential role in reducing the maintenance costs of rotating machinery manufacturing systems. In many real applications of fault detection and diagnosis, data tend to be imbalanced, meaning that the number of samples for some fault classes is much less than the normal data samples. At the same time, in an industrial condition, accelerometers encounter high levels of disruptive signals and the collected samples turn out to be heavily noisy. As a consequence, many traditional Fault Detection and Diagnosis (FDD) frameworks get poor classification performances when dealing with real-world circumstances. Three main solutions have been proposed in the literature to cope with this problem: (1) the implementation of generative algorithms to increase the amount of under-represented input samples, (2) the employment of a classifier being powerful to learn from imbalanced and noisy data, (3) the development of an efficient data pre-processing including feature extraction and data augmentation. This paper proposes a hybrid framework which uses the three aforementioned components to achieve an effective signal-based FDD system for imbalanced conditions. Specifically, it first extracts the fault features, using Fourier and wavelet transforms to make full use of the signals. Then, it employs Wasserstein Generative Adversarial Networks (WGAN) to generate synthetic samples to populate the rare fault class and enhance the training set. Moreover, to achieve a higher performance a novel combination of Convolutional Long Short-term Memory (CLSTM) and Weighted Extreme Learning Machine (WELM) is proposed. To verify the effectiveness of the developed framework, different datasets settings on different imbalance severities and noise degrees were used. The comparative results demonstrate that in different scenarios GAN-CLSTM-ELM outperforms the other state-of-the-art FDD frameworks.Comment: 23 pages, 11 figure

A New Large Scale SVM for Classification of Imbalanced Evolving Streams

Classification from imbalanced evolving streams possesses a combined challenge of class imbalance and concept drift (CI-CD). However, the state of imbalance is dynamic, a kind of virtual concept drift. The imbalanced distributions and concept drift hinder the online learner’s performance as a combined or individual problem. A weighted hybrid online oversampling approach,”weighted online oversampling large scale support vector machine (WOOLASVM),” is proposed in this work to address this combined problem. The WOOLASVM is an SVM active learning approach with new boundary weighing strategies such as (i) dynamically oversampling the current boundary and (ii) dynamic weighing of the cost parameter of the SVM objective function. Thus at any time step, WOOLASVM maintains balanced class distributions so that the CI-CD problem does not hinder the online learner performance. Over extensive experiments on synthetic and real-world streams with the static and dynamic state of imbalance, the WOOLASVM exhibits better online classification performances than other state-of-the-art methods

Evolving Ensemble Fuzzy Classifier

The concept of ensemble learning offers a promising avenue in learning from data streams under complex environments because it addresses the bias and variance dilemma better than its single model counterpart and features a reconfigurable structure, which is well suited to the given context. While various extensions of ensemble learning for mining non-stationary data streams can be found in the literature, most of them are crafted under a static base classifier and revisits preceding samples in the sliding window for a retraining step. This feature causes computationally prohibitive complexity and is not flexible enough to cope with rapidly changing environments. Their complexities are often demanding because it involves a large collection of offline classifiers due to the absence of structural complexities reduction mechanisms and lack of an online feature selection mechanism. A novel evolving ensemble classifier, namely Parsimonious Ensemble pENsemble, is proposed in this paper. pENsemble differs from existing architectures in the fact that it is built upon an evolving classifier from data streams, termed Parsimonious Classifier pClass. pENsemble is equipped by an ensemble pruning mechanism, which estimates a localized generalization error of a base classifier. A dynamic online feature selection scenario is integrated into the pENsemble. This method allows for dynamic selection and deselection of input features on the fly. pENsemble adopts a dynamic ensemble structure to output a final classification decision where it features a novel drift detection scenario to grow the ensemble structure. The efficacy of the pENsemble has been numerically demonstrated through rigorous numerical studies with dynamic and evolving data streams where it delivers the most encouraging performance in attaining a tradeoff between accuracy and complexity.Comment: this paper has been published by IEEE Transactions on Fuzzy System

An Ensemble of Deep Learning-Based Multi-Model for ECG Heartbeats Arrhythmia Classification

An automatic system for heart arrhythmia classification can perform a substantial role inmanaging and treating cardiovascular diseases. In this paper, a deep learning-based multi-model system is proposed for the classification of electrocardiogram (ECG) signals. Two different deep learning bagging models are introduced to classify heartbeats into different arrhythmias types. The first model (CNN-LSTM) is based on a combination of a convolutional neural network (CNN) and long short-term memory (LSTM) network to capture local features and temporal dynamics in the ECG data. The second model (RRHOS-LSTM) integrates some classical features, i.e. RR intervals and higher-order statistics (HOS), with LSTM model to effectively highlight abnormality heartbeats classes. We create a bagging model from the CNN-LSTM and RRHOS-LSTM networks by training each model on a different sub-sampling dataset to handle the high imbalance distribution of arrhythmias classes in the ECG data. Each model is also trained using a weighted loss function to provide high weight for not sufficiently represented classes. These models are then combined using a meta-classifier to form a strong coherent model. The meta-classifier is a feedforward fully connected neural network that takes the different predictions of bagging models as an input and combines them into a final prediction. The result of the meta-classifier is then verified by another CNN-LSTM model to decrease the false positive of the overall system. The experimental results are acquired by evaluating the proposed method on ECG data from the MIT-BIH arrhythmia database. The proposedmethod achieves an overall accuracy of 95.81% in the ‘‘subject-oriented’’ patient independent evaluation scheme. The averages of F1 score and positive predictive value are higher than all other methods by more than 3% and 8% respectively. The experimental results show the superiority of the proposed method for ECG heartbeats classification compared to many state-of-the-art methods

Concept Drift Detection in Data Stream Mining: The Review of Contemporary Literature

Mining process such as classification, clustering of progressive or dynamic data is a critical objective of the information retrieval and knowledge discovery; in particular, it is more sensitive in data stream mining models due to the possibility of significant change in the type and dimensionality of the data over a period. The influence of these changes over the mining process termed as concept drift. The concept drift that depict often in streaming data causes unbalanced performance of the mining models adapted. Hence, it is obvious to boost the mining models to predict and analyse the concept drift to achieve the performance at par best. The contemporary literature evinced significant contributions to handle the concept drift, which fall in to supervised, unsupervised learning, and statistical assessment approaches. This manuscript contributes the detailed review of the contemporary concept-drift detection models depicted in recent literature. The contribution of the manuscript includes the nomenclature of the concept drift models and their impact of imbalanced data tuples

Class-Level Refactoring Prediction by Ensemble Learning with Various Feature Selection Techniques

Background: Refactoring is changing a software system without affecting the software functionality. The current researchers aim i to identify the appropriate method(s) or class(s) that needs to be refactored in object-oriented software. Ensemble learning helps to reduce prediction errors by amalgamating different classifiers and their respective performances over the original feature data. Other motives are added in this paper regarding several ensemble learners, errors, sampling techniques, and feature selection techniques for refactoring prediction at the class level. Objective: This work aims to develop an ensemble-based refactoring prediction model with structural identification of source code metrics using different feature selection techniques and data sampling techniques to distribute the data uniformly. Our model finds the best classifier after achieving fewer errors during refactoring prediction at the class level. Methodology: At first, our proposed model extracts a total of 125 software metrics computed from object-oriented software systems processed for a robust multi-phased feature selection method encompassing Wilcoxon significant text, Pearson correlation test, and principal component analysis (PCA). The proposed multi-phased feature selection method retains the optimal features characterizing inheritance, size, coupling, cohesion, and complexity. After obtaining the optimal set of software metrics, a novel heterogeneous ensemble classifier is developed using techniques such as ANN-Gradient Descent, ANN-Levenberg Marquardt, ANN-GDX, ANN-Radial Basis Function; support vector machine with different kernel functions such as LSSVM-Linear, LSSVM-Polynomial, LSSVM-RBF, Decision Tree algorithm, Logistic Regression algorithm and extreme learning machine (ELM) model are used as the base classifier. In our paper, we have calculated four different errors i.e., Mean Absolute Error (MAE), Mean magnitude of Relative Error (MORE), Root Mean Square Error (RMSE), and Standard Error of Mean (SEM). Result: In our proposed model, the maximum voting ensemble (MVE) achieves better accuracy, recall, precision, and F-measure values (99.76, 99.93, 98.96, 98.44) as compared to the base trained ensemble (BTE) and it experiences less errors (MAE = 0.0057, MORE = 0.0701, RMSE = 0.0068, and SEM = 0.0107) during its implementation to develop the refactoring model. Conclusions: Our experimental result recommends that MVE with upsampling can be implemented to improve the performance of the refactoring prediction model at the class level. Furthermore, the performance of our model with different data sampling techniques and feature selection techniques has been shown in the form boxplot diagram of accuracy, F-measure, precision, recall, and area under the curve (AUC) parameters.publishedVersio