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

Multimodal Multipart Learning for Action Recognition in Depth Videos

The articulated and complex nature of human actions makes the task of action recognition difficult. One approach to handle this complexity is dividing it to the kinetics of body parts and analyzing the actions based on these partial descriptors. We propose a joint sparse regression based learning method which utilizes the structured sparsity to model each action as a combination of multimodal features from a sparse set of body parts. To represent dynamics and appearance of parts, we employ a heterogeneous set of depth and skeleton based features. The proper structure of multimodal multipart features are formulated into the learning framework via the proposed hierarchical mixed norm, to regularize the structured features of each part and to apply sparsity between them, in favor of a group feature selection. Our experimental results expose the effectiveness of the proposed learning method in which it outperforms other methods in all three tested datasets while saturating one of them by achieving perfect accuracy

Learning Bodily and Temporal Attention in Protective Movement Behavior Detection

For people with chronic pain, the assessment of protective behavior during physical functioning is essential to understand their subjective pain-related experiences (e.g., fear and anxiety toward pain and injury) and how they deal with such experiences (avoidance or reliance on specific body joints), with the ultimate goal of guiding intervention. Advances in deep learning (DL) can enable the development of such intervention. Using the EmoPain MoCap dataset, we investigate how attention-based DL architectures can be used to improve the detection of protective behavior by capturing the most informative temporal and body configurational cues characterizing specific movements and the strategies used to perform them. We propose an end-to-end deep learning architecture named BodyAttentionNet (BANet). BANet is designed to learn temporal and bodily parts that are more informative to the detection of protective behavior. The approach addresses the variety of ways people execute a movement (including healthy people) independently of the type of movement analyzed. Through extensive comparison experiments with other state-of-the-art machine learning techniques used with motion capture data, we show statistically significant improvements achieved by using these attention mechanisms. In addition, the BANet architecture requires a much lower number of parameters than the state of the art for comparable if not higher performances.Comment: 7 pages, 3 figures, 2 tables, code available, accepted in ACII 201