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, Y. Yu, Z. He, J. S. Vitter, Indexing labeled property multidigraphs in entropy space, with applications, Proceedings of the 41st IEEE International Conference on Data Engineering  (ICDE'25), Hong Kong SAR, China, 2025. Source Code. PDF. 
  

• H. Huo, Z. He, P. Liu, J. S. Vitter, FM-Adaptive: A practical data-aware FM-Index, Workshop on Compressed Indexing and Graphs, 23rd Symposium on Experimental Algorithms, July 22-25, Venice, Italy, 2025. Source code. PDF.  

• L. Guo, Z. He, H. Huo, Panaln: Indexing pangenopme for read alignment, Bioinformatics, August 28, Online, 2025. Source Code. PDF. 

• 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, 2023. Source code. 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. Source Code. PDF.

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

• H. Huo, P. Liu, C. Wang , H. Jiang and J. S.Vitter, CIndex: compressed indexes for fast retrieval of FASTQ files, Bioinformatics, 38(2):335-343, 2022. Source Code. PDF. 

• 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. Source Code. 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.

Software

The software developed by her Lab can be accessed at GitHub: 

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