Using R and Spark for health care

Use of R with regard to healthcare field case study by Pereira and Noronha (2016):

R and RStudio have been used to look at patient health and diseases records located in Electronic Medical Records (EMR) for fraud detection.  Anomaly detection revolves around using a mapping code that filters data based on geo-locations.  Secondly, a reducer code which aggregates the data based on extreme values of cost claims per disease along with calculating the difference.  Finally, a code that analyzed the data that meets a 60% cost fraud threshold. It was found that as the geo-location resolution increased, the anomalies detected increased.

R and RStudio have been able to use big data analytics to predict diabetes from the Health Information System (HIS) which houses patient information, based on symptoms. For predicting diabetes, the authors used a classification algorithm (decision tree) with a 70%-30% training-test dataset split, to eventually plot the false positive rate v. True positive rate.  This plot showed skill in predicting diabetes.

Use of Spark about the healthcare field case study by Pita et al. (2015):

Data quality in healthcare data is poor and in particular that from the Brazilian Public Health System.  Spark was used to help in data processing to improve quality through deterministic and probabilistic record linking within multiple databases.  Record linking is a technique that uses common attributes across multiple databases and identifies a 1-to-1 match.  Spark workflows were created to help do record linking by (1) analyzing all data in each database and common attributes with high probabilities of linkage; (2) pre-processing data where data is transformed, anonymization, and cleaned to a single format so that all the attributes can be compared to each other for a 1-to-1 match; (3) record linking based on deterministic and probabilistic algorithms; and (4) statistical analysis to evaluate the accuracy. Over 397M comparisons were made in 12 hours.  They concluded that accuracy depends on the size of the data, where the bigger the data, the more accuracy in record linking.

References

  • Pereira, J. P., & Noronha, V. (2016). Anomalies Detection and Disease Prediction in Healthcare Systems using Big Data Analytics. Retrieved from http://www.aijet.in/v3/1608001.pdf
  • Pita, R., Pinto, C., Melo, P., Silva, M., Barreto, M., & Rasella, D. (2015). A Spark-based Workflow for Probabilistic Record Linkage of Healthcare Data. In EDBT/ICDT Workshops (pp. 17-26).

Big Data Analytics: Health Care Industry

Since its inception 25 years ago, the human genome project has been trying to sequence its first 3B base pair of the human genome over a 13 year period (Green, Watson, & Collins, 2015).  This 3B base pair is about 100 GB uncompressed and by 2011, 13 quadrillion bases were sequenced (O’Driscoll, Daugelaite, & Sleator, 2013).  With the advancement in technology and software as a service, the cost of sequencing a human genome has been drastically cut from $1M to $1K in 2012 (Green et al., 2015 and O’Driscoll et al., 2013).  It is so cheap now that 23andMe and others were formed as a consumer drove genetic testing industry that has been developed (McEwen, Boyer, & Sun, 2013).  At the beginning of this project, the researcher was wondering what insights the sequencing could bring to understanding decease, to the now explosion of research dealing with studying millions of other genomes from biological pathways, cancerous tumors, microbiomes, etc. (Green et al., 2015 and O’Driscoll et al., 2013).  Storing 1M genomes will exceed 1 Exabyte (O’Driscoll et al., 2013).  Based on the definition of Volume (size like 1 EB), Variety (different types of genomes), and Velocity (processing huge amounts of genomic data), we can classify that the whole genomic project in the health care industry as big data.

This project has paved the way for other projects like sharing MRI data from 511 participants, (exceeding 18 TB) to be shared and analyzed (Poldrak & Gorgolewski, 2014).  Green et al. (2015) have stated that the genome project has led to huge innovation in tangent fields, not directly related to biology, like chemistry, physics, robotics, computer science, etc.  It was due to this type of research that a capillary-based DNA sequencing instruments were invented to be used for sequencing genomes (Green et al., 2015).  The Ethical, legal and Social Implication project, got 5% of the National Institute of Health Budget, to study ethical implications of this data, opening up a new field of study (Green et al., 2015 & O’Driscoll et al., 2013).  O’Driscoll et al. (2013), suggested that solutions like Hadoop’s MapReduce would greatly advance this field.  However, he argues that current java intensive knowledge is needed, which can be a bottleneck on the biologist.   Luckily, this field is helping to provide a need to create a Guided User Interface, which will allow scientist to conduct research and not learn to program.  O’Driscoll et al. (2013), also state that the biggest drawback of using Hadoop MapReduce function is that it reduces data line by line, whereas genomic data needs to be reduced in groups.  This project, should, with time improve the service offering of Hadoop to other fields outside of biomedical research.

In the medical field, cancer diagnosis and treatments will now be possible due to this project (Green et al., 2015).  Green et al. (2015) also predict that a maturation of the microbiome science, routine use of stem-cell therapies could result from this.  These predictions are not far from becoming reality and are the foundation of predictive and preventative medicine.  This is not so far into the future that McEwen et al. (2013) have stated what are the ethical issues, for people who have submitted their genomic data 25 years ago, and they found data that could help the participants take preventative measures for adverse health conditions.  Mostly because clinical versions of this data are starting to become available like from companies like 23andMe. This information so far has yield genealogy data, a few predictive medical measures (to a certain confidence interval).  Predictive and preventative medical advances are still primary and currently in the research phase (McEwen et al., 2013).  Finally, genomics research will pave the way for metagenomics, which is the study of microbiome data of as many of the ~4-6* 10^30 bacterial cells (O’Driscoll et al., 2013).

From this discussion, there is no doubt that genomic data can fall under the classification of big data.  The analysis of this data has yielded advances in the medical fields and other tangential fields.  Future work, to expanding the predictive and preventative medicine is still needed; it is only in research studies, where the participants can learn about their genomic indicators that may lead them to certain types of adverse health conditions.

Resources:

  • Green, E. D., Watson, J. D., & Collins, F. S. (2015). Twenty-five years of big biology. Nature, 526.
  • McEwen, J. E., Boyer, J. T., & Sun, K. Y. (2013). Evolving approaches to the ethical management of genomic data. Trends in Genetics, 29(6), 375-382.
  • O’Driscoll, A., Daugelaite, J., & Sleator, R. D. (2013). ‘Big data,’ Hadoop and cloud computing in genomics. Journal of biomedical informatics, 46(5), 774-781.
  • Poldrack, R. A., & Gorgolewski, K. J. (2014). Making big data open: data sharing in neuroimaging. Nature neuroscience, 17(11), 1510-1517.