Xiaoli Li's Selected Publications

BOOKS

  1. Xiao-Li Li andSee-Kiong Ng(Eds.) (2008) "Biological Data Mining in Protein Interaction Networks”, IGI Global, USA, in press.

BOOK CHAPTERS

  1. Xiao-Li Li and See-Kiong Ng (2008) “Positive Unlabeled Learning for Document Classification”, in Encyclopedia of Data Warehousing and Mining (2nd Edition), J. Wang (Ed), IGI Global, USA, in press.

PAPERS

  1. H. N. Chua, K.L. Tew, Xiao-Li Li, Seekiong Ng, "A Unified Scoring Scheme for Detecting Essential Proteins in Protein Interaction Networks", accepted in IEEE Intl Conference on Tools with Artificial Intelligence ", Accepted by ICTAI 2008, Australia, Ohio, USA, November 3-5, 2008.

  2. Min Wu, Xiao-Li Li, Chee-Keong Kwoh, "Algorithms for Detecting Protein Complexes in PPI Networks: An Evaluation Study", Accepted by PRIB'08, Australia, Oct, 15-17, 2008.

  3. Xiao-Li Li, Jun-Xiang. Lee, B. Veeravalli, and See-Kiong Ng, “Inferring Transcription Factor Interactions Using a Novel HV-SVM Classifier” accepted by International Journal of Computational Biology and Drug Design, 2008.

  4. Xiao-Li Li, Seekiong Ng. " Mining for domain dependency sets from protein interactions", 12th Annual International Conference Research in Computational Molecular Biology ( POSTER, RECOMB 2008), Singapore, (BEST POSTER AWARD).

  5. Kar Leong Tew, Xiao-Li Li and Soon-Heng Tan. "Functional Centrality: Detecting lethality of proteins in protein interaction networks.", Proceedings of 18th International Conference on Genome Informatics (GIW2007). [PDF]

  6. Xiao-Li Li, Bing Liu, Seekiong Ng. " Learning to Classify Documents with Only a Small Positive Training Set", Proceedings of The 18th European Conference on Machine Learning (ECML/PKDD-2007), [PDF]

  7. Xiao-Li Li, Chuan-Sheng Foo, See-Kiong Ng, "Discovering Protein Complexes in Dense Reliable Neighborhoods of Protein Interaction Networks", LSS 6th Annual International Conference on Computational Systems Bioinformatics, CSB-2007, P157-168. [PDF]

  8. Xiao-Li Li, Bing Liu, Seekiong Ng. "Learning to Identify Unexpected Instances in the Test Set .", Proceedings of Twentieth International Joint Conference on Artificial Intelligence, P2802-2807, India, 2007 (IJCAI-07)), [PDF]

  9. Xiao-Li Li, Jun-Xiang Lee, Bharadwaj Veeravalli, and See-Kiong Ng. "An HV-SVM Classifier to Infer TF-TF Interactions using Protein Domains and GO Annotations", Proceedings of the IEEE 7th International Symposium on Bioinformatics and Bioengineering (BIBE 2007) Boston, USA, October 14-17, 2007. [PDF]

  10. Xiao-Li Li, Yin-Chet Tan, and See-Kiong Ng, "Systematic Gene Function Prediction from Gene Expression Data by Using a Fuzzy Nearest-Cluster Method", BMC Bioinformatics, 7(Suppl 4): S23, 2006. [PDF]

  11. Xiao-Li Li, Soon-Heng Tan, and See-Kiong Ng, “Unraveling Multi-Domain Dependencies in protein-Protein Interactions", The First International
    Conference on Computational Systems Biology, Shanghai, China, July 20-23, 2006. [PDF]

  12. Xiao-Li Li, Soon-Heng Tan, and See-Kiong Ng. "Improving domain-based protein interaction prediction using biologically-significant negative dataset.", International Journal of Data Mining and Bioinformatics (IJDMB), Volume 1, Number 2, P138 - 149, 2006. [PDF]

  13. Xiao-Li Li, Yin-Chet Tan, and See-Kiong Ng, "Systematic Gene Function Prediction Using a Fuzzy Nearest-Cluster Method on Gene Expression Data", in Proceedings of the Symposium of Computations in Bioinformatics and Bioscience", Vol. 1, P 171-178, Hangzhou, China, 20-24 June, 2006.

  14. Xiao-Li Li, Soon-Heng Tan, Chuan-Sheng Foo and See-Kiong Ng. "Interaction Graph Mining for Protein Complexes Using Local Clique Merging." in Genome Informatics, Vol. 16, No.2. 2005. [PDF] (BEST PAPER AWARD)

  15. Xiao-Li Li, Soon-Heng Tan, See-Kiong Ng. "Protein Interaction Prediction Using Inferred Domain Interactions and Biologically-Significant Negative Dataset." ICCSA, 318-326. 2005. [PDF]

  16. Xiao-Li Li, Soon-Heng Tan, See-Kiong Ng. "Exploring Cross-Function Domain Interaction Map." in Proceedings of the 2005 International Joint Conference of InCoB, AASBi and KSBI (BIOINFO), Busan, Korea, P 431-436. 2005.[PDF]

  17. Xiao-Li Li, Bing Liu. "Learning from Positive and Unlabeled Examples with Different Data Distributions." in Proceedings European Conference on Machine Learning (ECML-05), [PDF]

  18. Bing Liu, Xiao-Li Li, Wee Sun Lee and Philip S. Yu. "Text Classification by Labeling Words" in Proceedings of Nineteeth National Conference on Artificial Intellgience (AAAI-2004), San Jose, USA, July 2004. [PDF]

  19. Xiao-Li Li, Rohit Joshi, Sreeram Ramachandaran, Tze-Yun Leong. "Classifying Biomedical Citations without Labeled Training Examples." Proceedings of the Third IEEE International Conference on Data Mining (ICDM'04), 455-458. 2004. [PDF]

  20. Xiao-Li Li, and Bing Liu. "Dealing with Different Distributions in Learning from Positive and Unlabeled Web Data." WWW-2004 poster paper. [PDF]

  21. Xiao-Li Li, Tze-Yun Leong. A Support Vector Machine Approach to Solving the Breast Cancer Diagnosis Problem, MEDINFO 2004.

  22. Rohit Joshi, Xiao-Li Li, Sreeram Ramachandaran, and Tze Yun Leong. "Automatic Model Structuring from Text using BioMedical Ontology." Proceedings of AAAI Workshop Adaptive Text Extraction and Mining , 74-79. 2004. [PDF]

  23. Lan Yi, Bing Liu, and Xiao-Li Li. "Eliminating Noisy Information in Web Pages for Data Mining." Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery & Data Mining (KDD-2003), Washington, DC, USA, August 24 - 27, 2003. [PDF]

  24. Bing Liu, Yang Dai, Xiao-Li Li, Wee Sun Lee and and Philip Yu. "Building Text Classifiers Using Positive and Unlabeled Examples." in Proceedings of the Third IEEE International Conference on Data Mining (ICDM'03), Melbourne, Florida, November 19-22, 2003. [PDF]

  25. Xiao-Li Li and Bing Liu. "Learning to classify text using positive and unlabeled data." Proceedings of Eighteenth International Joint Conference on Artificial Intelligence (IJCAI-03), Aug 9-15, 2003, Acapulco, Mexico, [PDF].

  26. Bing Liu, Wee Sun Lee, Philip S Yu and Xiao-Li Li. "Partially Supervised Classification of Text Documents." Proceedings of the Nineteenth International Conference on Machine Learning (ICML-2002), 8-12, July 2002, Sydney, Australia. [PostScript] [Full Paper]

  27. Xiao-Li Li, Bing Liu, Ton-Heng Phang, Minqing Hu, "Using Micro Information Unit for Internet Search," ACM CIKM-2002, McLean, VA, Nov 5-9, 2002. [PDF]

  28. Haoran Wu, Tong-Heng Pang, Bing Liu, Xiao-Li Li. "A Refinement Approach to Handling Model Misfit in Text Categorization," Proceedings of the ACM SIGKDD International Conference on Knowledge Discovery & Data Mining (KDD-2002, full paper), Edmonton, Canada, July 23-26, 2002. [PDF]

  29. Xiao-Li Li, Bing Liu, Tong-Heng Phang, and Minqing Hu. "Web Search Based on Micro Information Units." WWW-2002 (poster), Honolulu, Hawaii, USA 7-11 May 2002. [PDF]

  30. Xiao-Li Li, Zhongzhi Shi. " Innovating web page classification through reducing noise.", Journal of Computer Science and Technology, Volume 17 , Issue 1, Pages: 9 - 17, 2002. [PDF]

  31. Xiao-Li Li, Liu Jimin, Shi Zhongzhi, A Chinese Web page Classifier Based on Support Vector Machine and Unsupervised Clustering, Chinese Journal of Computers, VOL24, NO1, P. 62-68, 2001.

  32. Ye Shiren, You Xiangtao, Shi Zhongzhi, Xiao-Li Li, Efficient Similarity Computing Methods in High Dimentsional Data, Journal of Computer Research and Development, Vol, 37, No. 10, P. 1166-1172, 2001.

  33. Xiao-Li Li, Jimin Liu, Zhongzhi Shi. "A Document Classifier Based on Word Semantic Association." PRICAI 2000,

  34. Xiao-Li Li, Liu Jimin, Shi Zhongzhi. "Combine support vector machines with unsupervised clustering in text classification." Proceedings of Conference on Intelligent Information Processing 16th World Computer Congress, pp.398-405, Beijing, China, 2000

  35. Xiao-Li Li, Shi Zhongzhi, A data mining method to acquire part of speech rules in Chinese text, Journal of Computer Research and Development, Vol. 27, No. 12, P. 1409-1414, 2000.

  36. Xiao-Li Li, Shi Zhongzhi, The Concept-Reasoning Network and its Application in Text Classification, Journal of Computer Research and Development, Vol. 37, No. 9, P. 1032-1038, 2000.

  37. Lu Song, Xiao-Li Li, Bai Suo, Wangshi, An Improved Approach to Weighting Terms in Text, Jounral of Chinese Information Processing, 14(6): 8-13, 2000.

  38. Zhongzhi Shi, Wei Li, Hu Cao and Xiaoli Li, Distributed Information Retrieval Agent JMAT, First Asia-Pacific Conference on Intelligent Agent Technology (IAT'99), Hongkong.

  39. Xiao-Li Li, Liang Yongquan and Shi Zhongzhi, A Dynamic User Interest Acquiring Algorithm in the Internet Information Retrieval, The Fifth International Conference for Young Computer Scientists, Nanjing, 1999.

  40. Xiao-Li Li, Liang Yongquan, Shi Zhongzhi, Capturing User Interest and High quality pages in Internet Information Retrieval, International Conference on Machine Translation & Computer Language Information Processing, Beijing, 1999.

  41. Liang Yongquan, Xiao-Li Li and Shi Zhongzhi, A Computer Go-Playing Model Based on Agent, The Fifth International Conference for Young Computer Scientists, 1999, Nanjing.

  42. Guo Binyan, Xiao-Li Li, Apply the EBL Model in Chinese Sentence Analysis, Pattern Recognition and Artificial Intelligence, Vol , 9, No. 2, 1996.

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