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 low variance error boosting algorithm

This paper introduces a robust variant of AdaBoost, cw-AdaBoost, that uses weight perturbation to reduce variance error, and is particularly effective when dealing with data sets, such as microarray data, which have large numbers of features and small number of instances. The algorithm is compared with AdaBoost, Arcing and MultiBoost, using twelve gene expression datasets, using 10-fold cross validation. The new algorithm consistently achieves higher classification accuracy over all these datasets. In contrast to other AdaBoost variants, the algorithm is not susceptible to problems when a zero-error base classifier is encountered

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

A survey of outlier detection methodologies

Outlier detection has been used for centuries to detect and, where appropriate, remove anomalous observations from data. Outliers arise due to mechanical faults, changes in system behaviour, fraudulent behaviour, human error, instrument error or simply through natural deviations in populations. Their detection can identify system faults and fraud before they escalate with potentially catastrophic consequences. It can identify errors and remove their contaminating effect on the data set and as such to purify the data for processing. The original outlier detection methods were arbitrary but now, principled and systematic techniques are used, drawn from the full gamut of Computer Science and Statistics. In this paper, we introduce a survey of contemporary techniques for outlier detection. We identify their respective motivations and distinguish their advantages and disadvantages in a comparative review

ADIC: Anomaly Detection Integrated Circuit in 65nm CMOS utilizing Approximate Computing

In this paper, we present a low-power anomaly detection integrated circuit (ADIC) based on a one-class classifier (OCC) neural network. The ADIC achieves low-power operation through a combination of (a) careful choice of algorithm for online learning and (b) approximate computing techniques to lower average energy. In particular, online pseudoinverse update method (OPIUM) is used to train a randomized neural network for quick and resource efficient learning. An additional 42% energy saving can be achieved when a lighter version of OPIUM method is used for training with the same number of data samples lead to no significant compromise on the quality of inference. Instead of a single classifier with large number of neurons, an ensemble of K base learner approach is chosen to reduce learning memory by a factor of K. This also enables approximate computing by dynamically varying the neural network size based on anomaly detection. Fabricated in 65nm CMOS, the ADIC has K = 7 Base Learners (BL) with 32 neurons in each BL and dissipates 11.87pJ/OP and 3.35pJ/OP during learning and inference respectively at Vdd = 0.75V when all 7 BLs are enabled. Further, evaluated on the NASA bearing dataset, approximately 80% of the chip can be shut down for 99% of the lifetime leading to an energy efficiency of 0.48pJ/OP, an 18.5 times reduction over full-precision computing running at Vdd = 1.2V throughout the lifetime.Comment: 1

An investigation of ensemble learning methods in classification problems and an application on non-small-cell lung cancer data

This study aims to classify NSCLC death status and consists of patient records of 24 variables created by the open-source dataset of the cancer data site. Besides, basic classifiers such as SMO (Sequential Minimal Optimization), K-NN (K-Nearest Neighbor), random forest, and XGBoost (Extreme Gradient Boosting), which are machine learning methods, and their performances, and voting, bagging, boosting, and stacking methods from ensemble learning methods were used. Performance evaluation of models was compared in terms of accuracy, specificity, sensitivity, precision, and Roc curve. The basic classifier performances of random forest, SMO, K-NN, and XGBoost classifiers, their performances in the bagging ensemble learning method, and their performances in the boosting ensemble learning method are evaluated. In addition, Model 1 (random forest + SMO), Model 2 (XGBoost + K-NN), Model 3 (random forest + K-NN), Model 4 (XGBoost+SMO), Model 5 (SMO+K-NN + random forest), Model 6 (SMO+K-NN+XGBoost) and Model 7 (SMO+K-NN + random forest + XGBoost) the performances of in different metrics were expressed. The boosting ensemble learning method, which provides the maximum classification performance with XGBoost, achieved a 0.982 accuracy value, 0.971 sensitivity value, 0.989 precision value, 0.989 specificity value, and 0.998 ROC curve. It is recommended to use ensemble learning methods for classification problems in patients with a high prevalence of cancer to achieve successful results