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

MapReduce is Good Enough? If All You Have is a Hammer, Throw Away Everything That's Not a Nail!

Hadoop is currently the large-scale data analysis "hammer" of choice, but there exist classes of algorithms that aren't "nails", in the sense that they are not particularly amenable to the MapReduce programming model. To address this, researchers have proposed MapReduce extensions or alternative programming models in which these algorithms can be elegantly expressed. This essay espouses a very different position: that MapReduce is "good enough", and that instead of trying to invent screwdrivers, we should simply get rid of everything that's not a nail. To be more specific, much discussion in the literature surrounds the fact that iterative algorithms are a poor fit for MapReduce: the simple solution is to find alternative non-iterative algorithms that solve the same problem. This essay captures my personal experiences as an academic researcher as well as a software engineer in a "real-world" production analytics environment. From this combined perspective I reflect on the current state and future of "big data" research

Deep Extreme Multi-label Learning

Extreme multi-label learning (XML) or classification has been a practical and important problem since the boom of big data. The main challenge lies in the exponential label space which involves $2^L$ possible label sets especially when the label dimension $L$ is huge, e.g., in millions for Wikipedia labels. This paper is motivated to better explore the label space by originally establishing an explicit label graph. In the meanwhile, deep learning has been widely studied and used in various classification problems including multi-label classification, however it has not been properly introduced to XML, where the label space can be as large as in millions. In this paper, we propose a practical deep embedding method for extreme multi-label classification, which harvests the ideas of non-linear embedding and graph priors-based label space modeling simultaneously. Extensive experiments on public datasets for XML show that our method performs competitive against state-of-the-art result