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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.
Original language | English |
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Pages (from-to) | 2447-2458 |
Number of pages | 12 |
Journal | IEEE/ACM Transactions on Computational Biology and Bioinformatics |
Volume | 21 |
Issue number | 6 |
Early online date | 3 Oct 2024 |
DOIs | |
Publication status | Published - Nov 2024 |
Bibliographical note
Publisher Copyright:© 2024 IEEE.
Funding
This work is supported by Key Project of Science and Technology Innovation 2030 supported by the Ministry of Science and Technology of China (Grant No. 2018AAA0101301), and in part by the Hong Kong GRF-RGC General Research Fund under Grant 11209819 (CityU 9042816) and Grant 11203820 (9042598).
Keywords
- Data compression
- learning-based method
- lossless genome compression
- non-reference method
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Dive into the research topics of 'LEC-Codec: Learning-Based Genome Data Compression'. Together they form a unique fingerprint.Projects
- 2 Finished
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Adaptive Dynamic Range Enhancement Oriented to High Dynamic Display (面向高動態顯示的自適應動態範圍增強)
KWONG, S. T. W. (PI), KUO, C.-C. J. (CoI), WANG, S. (CoI) & ZHANG, X. (CoI)
Research Grants Council (HKSAR)
1/01/21 → 31/12/24
Project: Grant Research
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Intelligent Ultra High Definition Video Encoder Optimization for Future Versatile Video Coding (用于未来多功能视频编码的智能超高清视频编码器优化)
KWONG, S. T. W. (PI), ZHOU, M. (CoI), KUO, C.-C. J. (CoI) & WANG, S. (CoI)
Research Grants Council (HKSAR)
1/01/20 → 30/06/23
Project: Grant Research