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This work seeks to leverage Processing-with-storage-technology (PWST) to accelerate a key bioinformatics kernel calledk-mer counting, which involves processing large files of sequence data on the disk to build a histogram of fixed-size genome sequence substrings and thereby entails prohibitively high I/O overhead. In particular, this work proposes a set of accelerator designs called Abakus that offer varying degrees of tradeoffs in terms of performance, efficiency, and hardware implementation complexity. The key to these designs is a set of domain-specific hardware extensions to accelerate the key operations fork-mer counting at various levels of the SSD hierarchy, with the goal of enhancing the limited computing capabilities of conventional SSDs, while exploiting the parallelism of the multi-channel, multi-way SSDs. Our evaluation suggests that Abakus can achieve 8.42×, 6.91×, and 2.32× speedup over the CPU-, GPU-, and near-data processing solutions. 

Part-of-speech (POS) tagging is the foundation of many natural language processing applications. Rule-based POS tagging is a wellknown solution, which assigns tags to the words using a set of predefined rules. Many researchers favor statistical-based approaches over rule-based methods for better empirical accuracy. However, until now, the computational cost of rule-based POS tagging has made it difficult to study whether more complex rules or larger rulesets could lead to accuracy competitive with statistical approaches. In this paper, we leverage two hardware accelerators, the Automata Processor (AP) and Field Programmable Gate Arrays (FPGA), to accelerate rule-based POS tagging by converting rules to regular expressions and exploiting the highly-parallel regular-expressionmatching ability of these accelerators. We study the relationship between rule set size and accuracy, and observe that adding more rules only poses minimal overhead on the AP and FPGA. This allows a substantial increase in the number and complexity of rules, leading to accuracy improvement. Our experiments on Treebank and Brown corpora achieve up to 2,600X and 1,914X speedups on the AP and on the FPGA respectively over rule-based methods on the CPU in the rule-matching stage, up to 58× speedup over the Perceptron POS tagger on the CPU in total testing time, and up to 253× speedup over the LSTM tagger on the GPU in total testing time, while showing a competitive accuracy compared to neural-network and statistical solutions.