Distinct counting with a self-learning bitmap

Counting the number of distinct elements (cardinality) in a dataset is a fundamental problem in database management. In recent years, due to many of its modern applications, there has been significant interest to address the distinct counting problem in a data stream setting, where each incoming data can be seen only once and cannot be stored for long periods of time. Many probabilistic approaches based on either sampling or sketching have been proposed in the computer science literature, that only require limited computing and memory resources. However, the performances of these methods are not scale-invariant, in the sense that their relative root mean square estimation errors (RRMSE) depend on the unknown cardinalities. This is not desirable in many applications where cardinalities can be very dynamic or inhomogeneous and many cardinalities need to be estimated. In this paper, we develop a novel approach, called self-learning bitmap (S-bitmap) that is scale-invariant for cardinalities in a specified range. S-bitmap uses a binary vector whose entries are updated from 0 to 1 by an adaptive sampling process for inferring the unknown cardinality, where the sampling rates are reduced sequentially as more and more entries change from 0 to 1. We prove rigorously that the S-bitmap estimate is not only unbiased but scale-invariant. We demonstrate that to achieve a small RRMSE value of $\epsilon$ or less, our approach requires significantly less memory and consumes similar or less operations than state-of-the-art methods for many common practice cardinality scales. Both simulation and experimental studies are reported.Comment: Journal of the American Statistical Association (accepted

The Parallelism Motifs of Genomic Data Analysis

Genomic data sets are growing dramatically as the cost of sequencing continues to decline and small sequencing devices become available. Enormous community databases store and share this data with the research community, but some of these genomic data analysis problems require large scale computational platforms to meet both the memory and computational requirements. These applications differ from scientific simulations that dominate the workload on high end parallel systems today and place different requirements on programming support, software libraries, and parallel architectural design. For example, they involve irregular communication patterns such as asynchronous updates to shared data structures. We consider several problems in high performance genomics analysis, including alignment, profiling, clustering, and assembly for both single genomes and metagenomes. We identify some of the common computational patterns or motifs that help inform parallelization strategies and compare our motifs to some of the established lists, arguing that at least two key patterns, sorting and hashing, are missing