Huo Hongwei

Personal Information:

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Female   Xidian University   With Certificate of Graduation for Doctorate Study   Professor  


Hongwei Huo received the B.S. degree in mathematics from Northwest University, China, and the M.S. degree in computer science and the Ph.D. degree in electronic engineering from Xidian University.   She is a Professor of Department of Computer Science at Xidian University. She is the director of Lab of Algorithm Theory and Applications for Big Data (ATA).
        Her research interests involve all aspects of algorithms, spanning from the design and analysis of efficient algorithms and data structures for the storage, compression, indexing, and retrieving information for big data like textual collections, larger-scale graph databases, and genomic sequences to the algorithm engineering. She has published more than 100 papers in peer-reviewed journals and leading conferences.

Research: Compressed Data Structures, Compressed Indexes and Retrieval


  • Design and analysis of algorithm, String algorithms, Graph algorithms 

  • Compressed data structure, Compressed indexes and retrieval

  • Succinct indexing for graph databases, Graph compression and search

  • Pan-genome indexing, Genomic compression and pattern search

  • Parallel and distributed algorithms, External memory algorithms, Algorithm engineering

Featured software

GeCSA: Practical High-order Entropy-compressed Text Self-indexing

(Hongwei Huo, Peng Long & Jeffrey Scott Vitter)

Featured publications

  • H. Huo, P. Long, J. S. Vitter, Practical high-order entropy-compressed text self-indexing, IEEE Transactions on Knowledge and Data Engineering (TKDE), 35(3): 2943–2960, 2023Source code published in Code Ocean. PDF.  

  • X. Chen, H. Huo, J. Huan, J. S. Vitter, W. Zheng, and L. Zou, MSQ-Index: a succinct index for fast graph similarity search, IEEE Transactions on Knowledge and Data Engineering (TKDE), 33(6):2654-2668, 2021. PDF.

  • Z. Li, J. Li, and H. Huo, Optimal in-place suffix sorting, Information and Computation (IandC),  285(Part B):104818, May 2022PDF.

  • H. Huo, P. Liu, C. Wang , H. Jiang and J. S.Vitter, CIndex: compressed indexes for fast retrieval of FASTQ files, Bioinformatics38(2):335-343, 2022PDF

  • X. Chen, H. Huo, J. Huan, and J. S. Vitter, An efficient algorithm for graph edit distance computation, Knowl. Based Syst.,163(2019): 762–775, 2019. PDF

  • H. Huo, X. Chen, X. Guo, J. S. Vitter, Efficient compression and indexing for highly repetitive DNA sequence collections, IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 18(6): 2394-2408, 2021. PDF.

  • Z. Sun, H. Huo, J. Huan, and J. S. Vitter, Feature reduction based on semantic similarity for graph classification, Neurocomputing, 397:114–126, 2020. PDF.

  • H. Huo, X. Chen, Y. Zhao, X. Zhu, and J. S. Vitter, Practical succinct text indexes in external memory, Proceedings of the 2018 IEEE Data Compression Conference (DCC'18), Snowbird, USA, 2018.

  • Z. Li, J. Li and H. Huo, Optimal in-place suffix sorting, Proceedings of the 25th International Symposium on String Processing and Information Retrieval (SPIRE'18), Lima, Peru, 2018.

  • H. Huo, Z. Sun, S. Li, J. S. Vitter, et al., CS2A: a compressed suffix array-based method for short read alignment, Proceedings of the 2016 IEEE Data Compression Conference (DCC'16), Snowbird, USA, 2016.

  • H. Huo, L. Chen, H. Zhao, J. S. Vitter, et al., A data-aware FM-index, ACM-SIAM Proceedings of the 17th Meeting on Algorithm Engineering and Experiments (ALENEX'15), San Diego, California, USA, 2015.

  • H. Huo, L. Chen, J. S. Vitter, and Y. Nekrich, A practical implementation of compressed suffix arrays with applications to self-indexing, Proceedings of the 2014 IEEE Data Compression Conference (DCC'14), Snowbird, USA, 2014.


The software developed by her Lab can be accessed at GitHub


Chinese Academy of Sciences, Universities, Research Institutes, Baidu, Tencent, Ali, Huawei, ZTE, Samsung, Meituan, SPSS, IBM, Intel, ByteDance

Education Background

1997.3 2000.3

  • Xidian University
  • Signal and information processing
  • Doctoral degree

1988.9 1991.7

  • Xidian University
  • Computer Software and Theory
  • Master's Degree in Engineering

1982.9 1986.7

  • Northwestern University
  • Computational Mathematics
  • Bachelor's Degree in Science

Work ExperienceMore>>

2001.7 Now
  • 西安电子科技大学
  • 计算机学院
  • 教授
2013.1 2014.1
  • 堪萨斯大学
  • 电子工程与计算机系
  • 访问教授
  • 合作导师:Jeffrey Scott Vitter
1997.7 2001.6
  • 西安电子科技大学
  • 计算机学院
  • 副教授

Social Affiliations

  • IEEE Senior Member

  • ACM Member

  • CCF Senior Member

Research FocusMore>>

  • Algorithm and its complexity: string algorithms, graph algorithms
  • Compressed data structures, Compressed indexes and retrieval for big data
  • Compressed indexing for graph databases, Graph compression and search, Genomic compression and pattern search