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

Labeling the Features Not the Samples: Efficient Video Classification with Minimal Supervision

Feature selection is essential for effective visual recognition. We propose an efficient joint classifier learning and feature selection method that discovers sparse, compact representations of input features from a vast sea of candidates, with an almost unsupervised formulation. Our method requires only the following knowledge, which we call the \emph{feature sign}---whether or not a particular feature has on average stronger values over positive samples than over negatives. We show how this can be estimated using as few as a single labeled training sample per class. Then, using these feature signs, we extend an initial supervised learning problem into an (almost) unsupervised clustering formulation that can incorporate new data without requiring ground truth labels. Our method works both as a feature selection mechanism and as a fully competitive classifier. It has important properties, low computational cost and excellent accuracy, especially in difficult cases of very limited training data. We experiment on large-scale recognition in video and show superior speed and performance to established feature selection approaches such as AdaBoost, Lasso, greedy forward-backward selection, and powerful classifiers such as SVM.Comment: arXiv admin note: text overlap with arXiv:1411.771

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