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

Mining the Demographics of Political Sentiment from Twitter Using Learning from Label Proportions

Opinion mining and demographic attribute inference have many applications in social science. In this paper, we propose models to infer daily joint probabilities of multiple latent attributes from Twitter data, such as political sentiment and demographic attributes. Since it is costly and time-consuming to annotate data for traditional supervised classification, we instead propose scalable Learning from Label Proportions (LLP) models for demographic and opinion inference using U.S. Census, national and state political polls, and Cook partisan voting index as population level data. In LLP classification settings, the training data is divided into a set of unlabeled bags, where only the label distribution in of each bag is known, removing the requirement of instance-level annotations. Our proposed LLP model, Weighted Label Regularization (WLR), provides a scalable generalization of prior work on label regularization to support weights for samples inside bags, which is applicable in this setting where bags are arranged hierarchically (e.g., county-level bags are nested inside of state-level bags). We apply our model to Twitter data collected in the year leading up to the 2016 U.S. presidential election, producing estimates of the relationships among political sentiment and demographics over time and place. We find that our approach closely tracks traditional polling data stratified by demographic category, resulting in error reductions of 28-44% over baseline approaches. We also provide descriptive evaluations showing how the model may be used to estimate interactions among many variables and to identify linguistic temporal variation, capabilities which are typically not feasible using traditional polling methods

BDGS: A Scalable Big Data Generator Suite in Big Data Benchmarking

Data generation is a key issue in big data benchmarking that aims to generate application-specific data sets to meet the 4V requirements of big data. Specifically, big data generators need to generate scalable data (Volume) of different types (Variety) under controllable generation rates (Velocity) while keeping the important characteristics of raw data (Veracity). This gives rise to various new challenges about how we design generators efficiently and successfully. To date, most existing techniques can only generate limited types of data and support specific big data systems such as Hadoop. Hence we develop a tool, called Big Data Generator Suite (BDGS), to efficiently generate scalable big data while employing data models derived from real data to preserve data veracity. The effectiveness of BDGS is demonstrated by developing six data generators covering three representative data types (structured, semi-structured and unstructured) and three data sources (text, graph, and table data)