{"title":"LEC-Codec: Learning-Based Genome Data Compression.","authors":"Zhenhao Sun, Meng Wang, Shiqi Wang, Sam Kwong","doi":"10.1109/TCBB.2024.3473899","DOIUrl":null,"url":null,"abstract":"<p><p>In this paper, we propose a Learning-based gEnome Codec (LEC), which is designed for high efficiency and enhanced flexibility. The LEC integrates several advanced technologies, including Group of Bases (GoB) compression, multi-stride coding and bidirectional prediction, all of which are aimed at optimizing the balance between coding complexity and performance in lossless compression. The model applied in our proposed codec is data-driven, based on deep neural networks to infer probabilities for each symbol, enabling fully parallel encoding and decoding with configured complexity for diverse applications. Based upon a set of configurations on compression ratios and inference speed, experimental results show that the proposed method is very efficient in terms of compression performance and provides improved flexibility in real-world applications.</p>","PeriodicalId":13344,"journal":{"name":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","volume":null,"pages":null},"PeriodicalIF":3.6000,"publicationDate":"2024-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"IEEE/ACM Transactions on Computational Biology and Bioinformatics","FirstCategoryId":"5","ListUrlMain":"https://doi.org/10.1109/TCBB.2024.3473899","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOCHEMICAL RESEARCH METHODS","Score":null,"Total":0}
引用次数: 0
Abstract
In this paper, we propose a Learning-based gEnome Codec (LEC), which is designed for high efficiency and enhanced flexibility. The LEC integrates several advanced technologies, including Group of Bases (GoB) compression, multi-stride coding and bidirectional prediction, all of which are aimed at optimizing the balance between coding complexity and performance in lossless compression. The model applied in our proposed codec is data-driven, based on deep neural networks to infer probabilities for each symbol, enabling fully parallel encoding and decoding with configured complexity for diverse applications. Based upon a set of configurations on compression ratios and inference speed, experimental results show that the proposed method is very efficient in terms of compression performance and provides improved flexibility in real-world applications.
期刊介绍:
IEEE/ACM Transactions on Computational Biology and Bioinformatics emphasizes the algorithmic, mathematical, statistical and computational methods that are central in bioinformatics and computational biology; the development and testing of effective computer programs in bioinformatics; the development of biological databases; and important biological results that are obtained from the use of these methods, programs and databases; the emerging field of Systems Biology, where many forms of data are used to create a computer-based model of a complex biological system