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

Multi-class protein fold classification using a new ensemble machine learning approach.

Protein structure classification represents an important process in understanding the associations between sequence and structure as well as possible functional and evolutionary relationships. Recent structural genomics initiatives and other high-throughput experiments have populated the biological databases at a rapid pace. The amount of structural data has made traditional methods such as manual inspection of the protein structure become impossible. Machine learning has been widely applied to bioinformatics and has gained a lot of success in this research area. This work proposes a novel ensemble machine learning method that improves the coverage of the classifiers under the multi-class imbalanced sample sets by integrating knowledge induced from different base classifiers, and we illustrate this idea in classifying multi-class SCOP protein fold data. We have compared our approach with PART and show that our method improves the sensitivity of the classifier in protein fold classification. Furthermore, we have extended this method to learning over multiple data types, preserving the independence of their corresponding data sources, and show that our new approach performs at least as well as the traditional technique over a single joined data source. These experimental results are encouraging, and can be applied to other bioinformatics problems similarly characterised by multi-class imbalanced data sets held in multiple data sources

A Cost-Sensitive Ensemble Method for Class-Imbalanced Datasets

In imbalanced learning methods, resampling methods modify an imbalanced dataset to form a balanced dataset. Balanced data sets perform better than imbalanced datasets for many base classifiers. This paper proposes a cost-sensitive ensemble method based on cost-sensitive support vector machine (SVM), and query-by-committee (QBC) to solve imbalanced data classification. The proposed method first divides the majority-class dataset into several subdatasets according to the proportion of imbalanced samples and trains subclassifiers using AdaBoost method. Then, the proposed method generates candidate training samples by QBC active learning method and uses cost-sensitive SVM to learn the training samples. By using 5 class-imbalanced datasets, experimental results show that the proposed method has higher area under ROC curve (AUC), F-measure, and G-mean than many existing class-imbalanced learning methods

A big data MapReduce framework for fault diagnosis in cloud-based manufacturing

This research develops a MapReduce framework for automatic pattern recognition based on fault diagnosis by solving data imbalance problem in a cloud-based manufacturing (CBM). Fault diagnosis in a CBM system significantly contributes to reduce the product testing cost and enhances manufacturing quality. One of the major challenges facing the big data analytics in cloud-based manufacturing is handling of datasets, which are highly imbalanced in nature due to poor classification result when machine learning techniques are applied on such datasets. The framework proposed in this research uses a hybrid approach to deal with big dataset for smarter decisions. Furthermore, we compare the performance of radial basis function based Support Vector Machine classifier with standard techniques. Our findings suggest that the most important task in cloud-based manufacturing, is to predict the effect of data errors on quality due to highly imbalance unstructured dataset. The proposed framework is an original contribution to the body of literature, where our proposed MapReduce framework has been used for fault detection by managing data imbalance problem appropriately and relating it to firm’s profit function. The experimental results are validated using a case study of steel plate manufacturing fault diagnosis, with crucial performance matrices such as accuracy, specificity and sensitivity. A comparative study shows that the methods used in the proposed framework outperform the traditional ones

Multilevel Weighted Support Vector Machine for Classification on Healthcare Data with Missing Values

This work is motivated by the needs of predictive analytics on healthcare data as represented by Electronic Medical Records. Such data is invariably problematic: noisy, with missing entries, with imbalance in classes of interests, leading to serious bias in predictive modeling. Since standard data mining methods often produce poor performance measures, we argue for development of specialized techniques of data-preprocessing and classification. In this paper, we propose a new method to simultaneously classify large datasets and reduce the effects of missing values. It is based on a multilevel framework of the cost-sensitive SVM and the expected maximization imputation method for missing values, which relies on iterated regression analyses. We compare classification results of multilevel SVM-based algorithms on public benchmark datasets with imbalanced classes and missing values as well as real data in health applications, and show that our multilevel SVM-based method produces fast, and more accurate and robust classification results.Comment: arXiv admin note: substantial text overlap with arXiv:1503.0625