Pub Date : 2024-01-17DOI: 10.1109/LCA.2024.3355109
Caden Corontzos;Eitan Frachtenberg
The cost and time to sequence entire genomes have been on a steady and rapid decline since the early 2000s, leading to an explosion of genomic data. In contrast, the growth rates for digital storage device capacity, CPU clock speed, and networking bandwidth have been much more moderate. This gap means that the need for storing, transmitting, and processing sequenced genomic data is outpacing the capacities of the underlying technologies. Compounding the problem is the fact that traditional data compression techniques used for natural language or images are not optimal for genomic data. To address this challenge, many data-compression techniques have been developed, offering a range of tradeoffs between compression ratio, computation time, memory requirements, and complexity. This paper focuses on a specific technique on one extreme of this tradeoff, namely two-bit coding, wherein every base in a genomic sequence is compressed from its original 8-bit ASCII representation to a unique two-bit binary representation. Even for this simple direct-coding scheme, current implementations leave room for significant performance improvements. Here, we show that this encoding can exploit multiple levels of parallelism in modern computer architectures to maximize encoding and decoding efficiency. Our open-source implementation achieves encoding and decoding rates of billions of bases per second, which are much higher than previously reported results. In fact, our measured throughput is typically limited only by the speed of the underlying storage media.
{"title":"Direct-Coding DNA With Multilevel Parallelism","authors":"Caden Corontzos;Eitan Frachtenberg","doi":"10.1109/LCA.2024.3355109","DOIUrl":"10.1109/LCA.2024.3355109","url":null,"abstract":"The cost and time to sequence entire genomes have been on a steady and rapid decline since the early 2000s, leading to an explosion of genomic data. In contrast, the growth rates for digital storage device capacity, CPU clock speed, and networking bandwidth have been much more moderate. This gap means that the need for storing, transmitting, and processing sequenced genomic data is outpacing the capacities of the underlying technologies. Compounding the problem is the fact that traditional data compression techniques used for natural language or images are not optimal for genomic data. To address this challenge, many data-compression techniques have been developed, offering a range of tradeoffs between compression ratio, computation time, memory requirements, and complexity. This paper focuses on a specific technique on one extreme of this tradeoff, namely two-bit coding, wherein every base in a genomic sequence is compressed from its original 8-bit ASCII representation to a unique two-bit binary representation. Even for this simple direct-coding scheme, current implementations leave room for significant performance improvements. Here, we show that this encoding can exploit multiple levels of parallelism in modern computer architectures to maximize encoding and decoding efficiency. Our open-source implementation achieves encoding and decoding rates of billions of bases per second, which are much higher than previously reported results. In fact, our measured throughput is typically limited only by the speed of the underlying storage media.","PeriodicalId":51248,"journal":{"name":"IEEE Computer Architecture Letters","volume":"23 1","pages":"21-24"},"PeriodicalIF":2.3,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139955521","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"计算机科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-12-13DOI: 10.1109/LCA.2023.3342130
Nikhil Agarwal;Mitchell Fream;Souradip Ghosh;Brian C. Schwedock;Nathan Beckmann
Specialized hardware accelerators have gained traction as a means to improve energy efficiency over inefficient von Neumann cores. However, as specialized hardware is limited to a few applications, there is increasing interest in programmable, non-von Neumann architectures to improve efficiency on a wider range of programs. Reconfigurable dataflow architectures (RDAs) are a promising design, but the design space is fragmented and, in particular, existing compiler and software stacks are ad hoc and hard to use. Without a robust, mature software ecosystem, RDAs lose much of their advantage over specialized hardware. This letter proposes a unifying dataflow intermediate representation (UDIR) for RDA compilers. Popular von Neumann compiler representations are inadequate for dataflow architectures because they do not represent the dataflow control paradigm, which is the target of many common compiler analyses and optimizations. UDIR introduces contexts