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1. EXMA: A Genomics Accelerator for Exact-Matching

   https://doi.org/10.1109/HPCA51647.2021.00041  

   Jiang, Lei ; Zokaee, Farzaneh ( February 2021 , IEEE International Symposium on High-Performance Computer Architecture)

   null (Ed.)

   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 CHAIN compression to reduce the data structure size of EXMA tables. Compared to state-of-the-art FM-Index PIMs, EXMA improves search throughput by 4.9 ×, and enhances search throughput per Watt by 4.8×. 

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2. AlignS: A Processing-In-Memory Accelerator for DNA Short Read Alignment Leveraging SOT-MRAM

   Angizi, Shaahin ; Sun, Jiao ; Zhang, Wei ; Fan, Deliang ( June 2019 , 56th Annual Design Automation Conference)

   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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3. A space and time-efficient index for the compacted colored de Bruijn graph

   https://doi.org/10.1093/bioinformatics/bty292  

   Almodaresi, Fatemeh ; Sarkar, Hirak ; Srivastava, Avi ; Patro, Rob ( June 2018 , Bioinformatics)

   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.

   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 very fast access to the underlying k-mer information, and those that are space-frugal and provide asymptotically efficient but practically slower pattern search. Our representation achieves a compromise between these two extremes. By building upon minimum perfect hashing and making use of succinct representations where applicable, our data structure provides practically fast lookup while greatly reducing the space compared to traditional hashing-based implementations. Further, we describe a sampling scheme for this index, which provides the ability to trade off query speed for a reduction in the index size. We believe this representation strikes a desirable balance between speed and space usage, and allows for fast search on large reference sequences.

   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.

   pufferfish is written in C++11, is open source, and is available at https://github.com/COMBINE-lab/pufferfish.

   Supplementary data are available at Bioinformatics online.

    

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4. TinyADC: Peripheral Circuit-aware Weight Pruning Framework for Mixed-signal DNN Accelerators

   https://doi.org/10.23919/DATE51398.2021.9474235  

   Yuan, Geng ; Behnam, Payman ; Cai, Yuxuan ; Shafiee, Ali ; Fu, Jingyan ; Liao, Zhiheng ; Li, Zhengang ; Ma, Xiaolong ; Deng, Jieren ; Wang, Jinhui ; et al ( February 2021 , Design, Automation & Test in Europe Conference & Exhibition (DATE))

   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 square and watt (GOPs/s×mm 2 and GOPs/w), respectively. 

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5. Exploring DNA Alignment-in-Memory Leveraging Emerging SOT-MRAM

   https://doi.org/10.1145/3386263.3407590  

   Angizi, Shaahin ; Zhang, Wei ; Fan, Deliang ( September 2020 , Proceedings of the 2020 on Great Lakes Symposium on VLSI)

   null (Ed.)

   In this work, we review two alternative Processing-in-Memory (PIM) accelerators based on Spin-Orbit-Torque Magnetic Random Access Memory (SOT-MRAM) to execute DNA short read alignment based on an optimized and hardware-friendly alignment algorithm. We first discuss the reconstruction of the existing sequence alignment algorithm based on BWT and FM-index such that it can be fully implemented leveraging PIM functions. We then transform SOT-MRAM array to a potential computational memory by presenting two different reconfigurable sense amplifiers to accelerate the reconstructed alignment-in-memory algorithm. The cross-layer simulation results show that such PIM platforms are able to achieve a nearly ten-fold and two-fold increases in throughput/power/area measure compared with recent ASIC and processing-in-ReRAM designs, respectively. 

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