Big Data Science and its Applications in Healthcare and Medical Research: Challenges and Opportunities

Review Article

Austin Biom and Biostat. 2016; 3(1): 1030.

Big Data Science and its Applications in Healthcare and Medical Research: Challenges and Opportunities

Liang Y¹* and Kelemen A²

¹Department of Family and Community Health, University of Maryland, Baltimore, USA

²Department of Organizational Systems and Adult Health, University of Maryland, USA

*Corresponding author: Liang Y, Department of Family and Community Health, University of Maryland, Baltimore, MD 21201, USA

Received: May 06, 2016; Accepted: June 02, 2016; Published: June 09, 2016

Abstract

Recently, Big Data science has been a hot topic in the scientific, industrial and the business worlds. The healthcare and biomedical sciences have rapidly become data-intensive as investigators are generating and using large, complex, high dimensional and diverse domain specific datasets. This paper provides a general survey of recent progress and advances in Big Data science, healthcare, and biomedical research. Big Data science impacts, important features, infrastructures, and basic and advanced analytical tools are presented in detail. Additionally, various challenges, debates, and opportunities inside this quickly emerging scientific field are explored. The human genome and omics research, one of the most promising medical and health areas as an example and application of Big Data science, is discussed to demonstrate how the adaptive advanced computational analytical tools could be utilized for transforming millions of data points into predictions and diagnostics for precision medicine and personalized healthcare with better patient outcomes.

Keywords: Big data science; Big data infrastructure; Advanced analytics; Human genomics and OMICS; Precision medicine; Healthcare

Introduction

The big data impact and potentials in healthcare and medical sciences

Big Data is more than a decade old term that became very popular recently in life sciences and other fields. The healthcare industry has always been a large generator of biomedical data, with the U.S. healthcare system expected to reach the zettabyte (10²¹) scale from electronic health records, scientific instruments, clinical decision support systems, or even research articles in medical journals [1- 3]. Biomedical enterprises including the fields of human genomics (e.g., NIH 1000 Genome project), medical imaging (e.g., BRAIN initiative), the growth of mHealth, telehealth, and telemedicine, have generated trillions of data points resulting from the recent advances in biotechnology and advent of new computing sources (such as cloud) [4-14]. Big Data and its practices in health or medical science become even more prominent due to new social arenas/media and networks (such as Facebook and Twitter), sensory/digital technology, and mobile devices with smartphone apps and personal sensor health data with real time digital data accumulations [15,16].

The National Institutes of Health announced the Big Data to Knowledge (BD2K) Initiative with its long-term goals in 2014. As an important exemplar, NIH recently announced the “Precision Medicine Initiative”, which intends to assemble a longitudinal “cohort” of 1 million Americans, and characterize extensively with cell populations, proteins, metabolites, RNA, DNA and whole genome sequencing along with behavioral data; all linked to electronic health records, and eventually develop genetically guided therapy in the personalized and precision medicine for better preventive solution, early detections and treatment of common complex diseases [14,17- 21]. In the healthcare public health domains, AHRQ and Patient Centered Outcome Research (PCORI) have launched the PCORnet initiative to support an effective, sustainable national research infrastructure that advances data collection from very large study populations, shares and uses of electronic health data in Comparative Effectiveness Research (CER) and other evidence based practice/ medicine research [22-25].

For the educational standard, Big Data are gradually driving higher education from data poor to data rich domain, from hypothesis driven to data driven, and the movements of the online or web based educations as “Wind Tunnels” promote more students getting involved in learning Big Data science worldwide. For example, at the University of London, UK, the Big Data Society forum, related journal, and the Big Data school certificate that trains next generation Big Data science researchers have been established [26-29]. Big Data science has been gradually recognized as an emerging field and discipline and could be one of the most valuable assets not only in the life sciences such as medical and healthcare, but also other domains including educational standards, government prospective, social sciences, financial industry and business opportunities [4-6,30-34]. The lessons learned from all those related domains and fields could be potentially applied to the healthcare and medical fields, e.g., from business field for the lowered cost, improved quality outcomes (fewer medical errors and readmissions), increased efficiency, productivity, effectiveness, and performance of healthcare providers and associated systems.

Big data science features and infrastructure

Big Data science refers to the massive amounts of multiple digital data sets that are captured, collected, integrated, and analyzed. The important features of Big Data include: 1) size/ scale in terms of Volume, Velocity, Variety (known as three V’s): mass of measures increased from petabytes to exabytes, zettabytes, yottabytes; 2) evolving, varied, distributed, timeliness, dynamic, not static, change with real time; 3) complexity and heterogeneity (structured, unstructured, semi-structured data); 4) data sharing and privacy [7,35-39] Due to these unique properties, in order to maximize Big Data potentials for knowledge discovery, and make it actionable and operational for better life science solutions, Big Data science infrastructure, the intelligent fundamental analytical tools, and advanced computational approaches that could conceptualize, theorize, and model the Big Data with the grounded theory method need to be established, understood and available by both Data analysts and domain researchers [40,41]. Therefore, a top layer question for Big Data scientists is what the important framework for good Big Data governance and implementation is in order to make it actionable and operational. There are four critical hierarchical domains/levels for the infrastructure of the Big Data governance [42].

First, in the software, hardware, and physical capacity domains, Big Data requires parallel-distributed architectures with a high performance multicore and clustering or cloud computing platforms that can access hundreds or even thousands of processors. The Hadoop system is an example, and is a distributed computing environment using a Map-Reduce framework. Hadoop tools and related software including HDFS distributed file systems allow for the storage, backup and computing resources for complex workloads [43-49]. Software-defined data center or software-defined network is open flow application programming to interfaces or a virtual network overlay for controlling, understanding and dealing with Big Data, which could also create agility and automation with a centrally programmable network [50,51]. Big data Script is an example of scripting language for complex big data processing pipeline, which improve the hardware abstraction and execution from wide ranges of computer architecture from laptop, to multicore servers, to cloud computing [52].

A few other examples of popular computing software include i) the open source R statistical language and related packages such as bioconductor has been well utilized in the past decades for analyzing Big genomic data [53]; ii) open source pbdR software is a series of R packages and an environment for statistical computing and programming with Big Data in R (http://r-pbd.org) [54,55]. Note that the difference between pbdR and R codes is that R system focuses on single multi-core machines for data analysis via an interactive mode such as GUI interface; while pbdR focuses on distributed memory system, where data are distributed across several processors and analyzed in a batch mode, and communications between processors are utilized in large High-Performance Computing (HPC) systems; iii) Revolution Analytics is a free and premium software and services that brings high-performance, productive, and ease-of-use to R and enables data scientists to derive greater meaning from large sets of critical data in record time; iv) Tableau Software, Tableau Desktop and Tableau Server uses visual analytics, ease-of-use approach and flexibility connecting to live data and perform visual, rapid-fire analysis.

Second, in the databases level/domain, to manage large volume unstructured (e.g., text contents in an electronic Health Record (HER) systems) real time data which cannot be handled by standard database management systems like DBMS or RDBMS, an innovative database structure need be placed in order to streamline and eliminate redundancy, inaccuracy, and enable to have a single version of the truth of data. One of the fundamental issue in working with very large healthcare data, e.g. in the terabyte or petabyte range, small inefficiencies in storing data can have a large effect on ability to retrieve and process these data for other analysis. Third, in the knowledge/data process and logical capacity domain, the traditional operational focus needs to be shifted to a more analytic focus that could manipulate and convert various types of unstructured data and metadata into information context and actionable knowledge [56,57].

Last, but not least, in the resources domain and from the culture perspective, an integrative level has to be reached and shifted from personal/individual level with organizational and systematic approach where data is viewed as an asset with analytical culture and high predictive value [59,60]. Note that above four level hierarchical infrastructures of Big Data science determines it as a connection and systematic science merging and integrating cutting edge diverse multidisciplinary fields for better informed and shared decisionmaking (Table 1 for more examples, cases, software and relevant references).