Genomics is the foundation of precision medicine, global food security and virus surveillance. Exact-match is one of the most essential operations widely used in almost every step of genomics such as alignment, assembly, annotation, and compression. Modern genomics adopts Ferragina-Manzini Index (FMIndex) augmenting space-efficient Burrows-Wheeler transform (BWT) with additional data structures to permit ultra-fast exact-match operations. However, FM-Index is notorious for its poor spatial locality and random memory access pattern. Prior works create GPU-, FPGA-, ASIC- and even process-in-memory (PIM)based accelerators to boost FM-Index search throughput. Though they achieve the state-of-the-art FM-Index search throughput, the same as all prior conventional accelerators, FM-Index PIMs process only one DNA symbol after each DRAM row activation, thereby suffering from poor memory bandwidth utilization. In this paper, we propose a hardware accelerator, EXMA, to enhance FM-Index search throughput. We first create a novel EXMA table with a multi-task-learning (MTL)-based index to process multiple DNA symbols with each DRAM row activation. We then build an accelerator to search over an EXMA table. We propose 2-stage scheduling to increase the cache hit rate of our accelerator. We introduce dynamic page policy to improve the row buffer hit rate of DRAM main memory. We also present CHAINmore »
FindeR: Accelerating FM-Index-Based Exact Pattern Matching in Genomic Sequences through ReRAM Technology
Genomics is the critical key to enabling precision medicine, ensuring global food security and enforcing wildlife conservation. The massive genomic data produced by various genome sequencing technologies presents a significant challenge for genome analysis. Because of errors from sequencing machines and genetic variations, approximate pattern matching (APM) is a must for practical genome analysis. Recent work proposes FPGA, ASIC and even process-in-memory-based accelerators to boost the APM throughput by accelerating dynamic-programming-based algorithms (e.g., Smith-Waterman). However, existing accelerators lack the efficient hardware acceleration for the exact pattern matching (EPM) that is an even more critical and essential function widely used in almost every step of genome analysis including assembly, alignment, annotation and compression. State-of-the-art genome analysis adopts the FM-Index that augments the space-efficient BWT with additional data structures permitting fast EPM operations. But the FM-Index is notorious for poor spatial locality and massive random memory accesses. In this paper, we propose a ReRAM-based process-in-memory architecture, FindeR, to enhance the FM-Index EPM search throughput in genomic sequences. We build a reliable and energy-efficient Hamming distance unit to accelerate the computing kernel of FM-Index search using commodity ReRAM chips without introducing extra CMOS logic. We further architect a full-fledged FM-Index search pipeline and more »
- Award ID(s):
- 1909509
- Publication Date:
- NSF-PAR ID:
- 10167925
- Journal Name:
- International Conference on Parallel Architectures and Compilation Techniques
- Page Range or eLocation-ID:
- 284 to 295
- Sponsoring Org:
- National Science Foundation
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Classified as a complex big data analytics problem, DNA short read alignment serves as a major sequential bottleneck to massive amounts of data generated by next-generation sequencing platforms. With Von-Neumann computing architectures struggling to address such computationally-expensive and memory-intensive task today, Processing-in-Memory (PIM) platforms are gaining growing interests. In this paper, an energy-efficient and parallel PIM accelerator (AlignS) is proposed to execute DNA short read alignment based on an optimized and hardware-friendly alignment algorithm. We first develop AlignS platform that harnesses SOT-MRAM as computational memory and transforms it to a fundamental processing unit for short read alignment. Accordingly, we present a novel, customized, highly parallel read alignment algorithm that only seeks the proposed simple and parallel in-memory operations (i.e. comparisons and additions). AlignS is then optimized through a new correlated data partitioning and mapping methodology that allows local storage and processing of DNA sequence to fully exploit the algorithm-level's parallelism, and to accelerate both exact and inexact matches. The device-to-architecture co-simulation results show that AlignS improves the short read alignment throughput per Watt per mm^2 by ~12X compared to the ASIC accelerator. Compared to recent FM-index-based ReRAM platform, AlignS achieves 1.6X higher throughput per Watt.
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Abstract Motivation Indexing reference sequences for search—both individual genomes and collections of genomes—is an important building block for many sequence analysis tasks. Much work has been dedicated to developing full-text indices for genomic sequences, based on data structures such as the suffix array, the BWT and the FM-index. However, the de Bruijn graph, commonly used for sequence assembly, has recently been gaining attention as an indexing data structure, due to its natural ability to represent multiple references using a graphical structure, and to collapse highly-repetitive sequence regions. Yet, much less attention has been given as to how to best index such a structure, such that queries can be performed efficiently and memory usage remains practical as the size and number of reference sequences being indexed grows large.
Results We present a novel data structure for representing and indexing the compacted colored de Bruijn graph, which allows for efficient pattern matching and retrieval of the reference information associated with each k-mer. As the popularity of the de Bruijn graph as an index has increased over the past few years, so have the number of proposed representations of this structure. Existing structures typically fall into two categories; those that are hashing-based and provide verymore »
Finally, we describe an application of this index to the taxonomic read assignment problem. We show that by adopting, essentially, the approach of Kraken, but replacing k-mer presence with coverage by chains of consistent unique maximal matches, we can improve the space, speed and accuracy of taxonomic read assignment.
Availability and implementation pufferfish is written in C++11, is open source, and is available at https://github.com/COMBINE-lab/pufferfish.
Supplementary information Supplementary data are available at Bioinformatics online.
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Today’s graphics processing unit (GPU) applications produce vast volumes of data, which are challenging to store and transfer efficiently. Thus, data compression is becoming a critical technique to mitigate the storage burden and communication cost. LZSS is the core algorithm in many widely used compressors, such as Deflate. However, existing GPU-based LZSS compressors suffer from low throughput due to the sequential nature of the LZSS algorithm. Moreover, many GPU applications produce multi-byte data (e.g., int16/int32 index, floating-point numbers), while the current LZSS compression only takes single-byte data as input. To this end, in this work, we propose GPULZ, a highly efficient LZSS compression on modern GPUs for multi-byte data. The contribution of our work is fourfold: First, we perform an in-depth analysis of existing LZ compressors for GPUs and investigate their main issues. Then, we propose two main algorithm-level optimizations. Specifically, we (1) change prefix sum from one pass to two passes and fuse multiple kernels to reduce data movement between shared memory and global memory, and (2) optimize existing pattern-matching approach for multi-byte symbols to reduce computation complexity and explore longer repeated patterns. Third, we perform architectural performance optimizations, such as maximizing shared memory utilization by adapting data partitionsmore »
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As the number of weight parameters in deep neural networks (DNNs) continues growing, the demand for ultra-efficient DNN accelerators has motivated research on non-traditional architectures with emerging technologies. Resistive Random-Access Memory (ReRAM) crossbar has been utilized to perform insitu matrix-vector multiplication of DNNs. DNN weight pruning techniques have also been applied to ReRAM-based mixed-signal DNN accelerators, focusing on reducing weight storage and accelerating computation. However, the existing works capture very few peripheral circuits features such as Analog to Digital converters (ADCs) during the neural network design. Unfortunately, ADCs have become the main part of power consumption and area cost of current mixed-signal accelerators, and the large overhead of these peripheral circuits is not solved efficiently. To address this problem, we propose a novel weight pruning framework for ReRAM-based mixed-signal DNN accelerators, named TINYADC, which effectively reduces the required bits for ADC resolution and hence the overall area and power consumption of the accelerator without introducing any computational inaccuracy. Compared to state-of-the-art pruning work on the ImageNet dataset, TINYADC achieves 3.5× and 2.9× power and area reduction, respectively. TINYADC framework optimizes the throughput of state-of-the-art architecture design by 29% and 40% in terms of the throughput per unit of millimeter squaremore »
- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Publisher's Version of Record
- https://doi.org/10.1109/PACT.2019.00030
