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One-Pass Diversified Sampling with Application to Terabyte-Scale Genomic Sequence Streams
Benjamin Coleman · Benito Geordie · Li Chou · R. A. Leo Elworth · Todd Treangen · Anshumali Shrivastava

Wed Jul 20 07:35 AM -- 07:40 AM (PDT) @ Hall G

A popular approach to reduce the size of a massive dataset is to apply efficient online sampling to the stream of data as it is read or generated. Online sampling routines are currently restricted to variations of reservoir sampling, where each sample is selected uniformly and independently of other samples. This renders them unsuitable for large-scale applications in computational biology, such as metagenomic community profiling and protein function annotation, which suffer from severe class imbalance. To maintain a representative and diverse sample, we must identify and preferentially select data that are likely to belong to rare classes. We argue that existing schemes for diversity sampling have prohibitive overhead for large-scale problems and high-throughput streams. We propose an efficient sampling routine that uses an online representation of the data distribution as a prefilter to retain elements from rare groups. We apply this method to several genomic data analysis tasks and demonstrate significant speedup in downstream analysis without sacrificing the quality of the results. Because our algorithm is 2x faster and uses 1000x less memory than coreset, reservoir and sketch-based alternatives, we anticipate that it will become a useful preprocessing step for applications with large-scale streaming data.

Author Information

Benjamin Coleman (Rice University)
Benito Geordie (S01290073)
Li Chou (Rice University)
R. A. Leo Elworth (Rice University)
Todd Treangen (Rice University)
Anshumali Shrivastava (Rice University)

Anshumali Shrivastava is an associate professor in the computer science department at Rice University. His broad research interests include randomized algorithms for large-scale machine learning. In 2018, Science news named him one of the Top-10 scientists under 40 to watch. He is a recipient of National Science Foundation CAREER Award, a Young Investigator Award from Air Force Office of Scientific Research, and machine learning research award from Amazon. His research on hashing inner products has won Best Paper Award at NIPS 2014 while his work on representing graphs got the Best Paper Award at IEEE/ACM ASONAM 2014. Anshumali finished his Ph.D. in 2015 from Cornell University.

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