Todd Treangen

David Torres Ramos, Vihan Lakshman, Chen Luo et al.

We study the problem of building space-efficient, in-memory indexes for massive key-value datasets with highly skewed value distributions. This challenge arises in many data-intensive domains and is particularly acute in computational genomics, where $k$-mer count tables can contain billions of entries dominated by a single frequent value. While recent work has proposed to address this problem by augmenting compressed static functions (CSFs) with pre-filters, existing approaches rely on complex heuristics and lack formal guarantees. In this paper, we introduce a principled algorithm, called AutoCSF, for combining CSFs with pre-filtering to provably handle skewed distributions with near-optimal space usage. We improve upon prior CSF pre-filtering constructions by (1) deriving a mathematically rigorous decision criterion for when filter augmentation is beneficial; (2) presenting a general algorithmic framework for integrating CSFs with modern set membership data structures beyond the classic Bloom filter; and (3) establishing theoretical guarantees on the overall space usage of the resulting indexes. Our open-source implementation of AutoCSF demonstrates space savings over baseline methods while maintaining low query latency.

Gaurav Gupta, Minghao Yan, Benjamin Coleman et al.

DNA sequencing, especially of microbial genomes and metagenomes, has been at the core of recent research advances in large-scale comparative genomics. The data deluge has resulted in exponential growth in genomic datasets over the past years and has shown no sign of slowing down. Several recent attempts have been made to tame the computational burden of sequence search on these terabyte and petabyte-scale datasets, including raw reads and assembled genomes. However, no known implementation provides both fast query and construction time, keeps the low false-positive requirement, and offers cheap storage of the data structure. We propose a data structure for search called RAMBO (Repeated And Merged BloOm Filter) which is significantly faster in query time than state-of-the-art genome indexing methods- COBS (Compact bit-sliced signature index), Sequence Bloom Trees, HowDeSBT, and SSBT. Furthermore, it supports insertion and query process parallelism, cheap updates for streaming inputs, has a zero false-negative rate, a low false-positive rate, and a small index size. RAMBO converts the search problem into set membership testing among $K$ documents. Interestingly, it is a count-min sketch type arrangement of a membership testing utility (Bloom Filter in our case). The simplicity of the algorithm and embarrassingly parallel architecture allows us to stream and index a 170TB whole-genome sequence dataset in a mere 9 hours on a cluster of 100 nodes while competing methods require weeks.

Gaurav Gupta, Minghao Yan, Benjamin Coleman et al.

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.