RAMBO: Repeated And Merged BloOm Filter for Ultra-fast Multiple Set Membership Testing (MSMT) on Large-Scale Data

Abstract

Multiple Set Membership Testing (MSMT) is a well-known problem in a variety of search and query applications. Given a dataset of K different sets and a query q, it aims to find all of the sets containing the query. Trivially, an MSMT instance can be reduced to K membership testing instances, each with the same q, leading to O(K) query time with a simple array of Bloom Filters. We propose a data-structure called RAMBO (Repeated And Merged BloOm Filter) that achieves O(\sqrt{K} log K) query time in expectation with an additional worst-case memory cost factor of O(log K) beyond the array of Bloom Filters. Due to this, RAMBO is a very fast and accurate data-structure. Apart from being embarrassingly parallel, supporting cheap updates for streaming inputs, zero false-negative rate, and low false-positive rate, RAMBO beats the state-of-the-art approaches for genome indexing methods: COBS (Compact bit-sliced signature index), Sequence Bloom Trees (a Bloofi based implementation), HowDeSBT, SSBT, and document indexing methods like BitFunnel. The proposed data-structure is simply a count-min sketch type arrangement of a membership testing utility (Bloom Filter in our case). It indexes k-grams and provides an approximate membership testing based search utility. The simplicity of the algorithm and embarrassingly parallel architecture allows us to index a 170 TB genome dataset in a mere 14 hours on a cluster of 100 nodes while competing methods require weeks.