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

Sparsity in Dynamics of Spontaneous Subtle Emotions: Analysis \& Application

Spontaneous subtle emotions are expressed through micro-expressions, which are tiny, sudden and short-lived dynamics of facial muscles; thus poses a great challenge for visual recognition. The abrupt but significant dynamics for the recognition task are temporally sparse while the rest, irrelevant dynamics, are temporally redundant. In this work, we analyze and enforce sparsity constrains to learn significant temporal and spectral structures while eliminate irrelevant facial dynamics of micro-expressions, which would ease the challenge in the visual recognition of spontaneous subtle emotions. The hypothesis is confirmed through experimental results of automatic spontaneous subtle emotion recognition with several sparsity levels on CASME II and SMIC, the only two publicly available spontaneous subtle emotion databases. The overall performances of the automatic subtle emotion recognition are boosted when only significant dynamics are preserved from the original sequences.Comment: IEEE Transaction of Affective Computing (2016

BagStack Classification for Data Imbalance Problems with Application to Defect Detection and Labeling in Semiconductor Units

abstract: Despite the fact that machine learning supports the development of computer vision applications by shortening the development cycle, finding a general learning algorithm that solves a wide range of applications is still bounded by the ”no free lunch theorem”. The search for the right algorithm to solve a specific problem is driven by the problem itself, the data availability and many other requirements. Automated visual inspection (AVI) systems represent a major part of these challenging computer vision applications. They are gaining growing interest in the manufacturing industry to detect defective products and keep these from reaching customers. The process of defect detection and classification in semiconductor units is challenging due to different acceptable variations that the manufacturing process introduces. Other variations are also typically introduced when using optical inspection systems due to changes in lighting conditions and misalignment of the imaged units, which makes the defect detection process more challenging. In this thesis, a BagStack classification framework is proposed, which makes use of stacking and bagging concepts to handle both variance and bias errors. The classifier is designed to handle the data imbalance and overfitting problems by adaptively transforming the multi-class classification problem into multiple binary classification problems, applying a bagging approach to train a set of base learners for each specific problem, adaptively specifying the number of base learners assigned to each problem, adaptively specifying the number of samples to use from each class, applying a novel data-imbalance aware cross-validation technique to generate the meta-data while taking into account the data imbalance problem at the meta-data level and, finally, using a multi-response random forest regression classifier as a meta-classifier. The BagStack classifier makes use of multiple features to solve the defect classification problem. In order to detect defects, a locally adaptive statistical background modeling is proposed. The proposed BagStack classifier outperforms state-of-the-art image classification techniques on our dataset in terms of overall classification accuracy and average per-class classification accuracy. The proposed detection method achieves high performance on the considered dataset in terms of recall and precision.Dissertation/ThesisDoctoral Dissertation Computer Engineering 201