Conference papers

• Dai, Hong-Jie, Richard Tzong-Han Tsai and Wen-Lian Hsu. 2011. Entity Disambiguation Using a Markov-Logic Network. In: The 5th International Joint Conference on Natural Language Processing (IJCNLP), Chiang Mai, Thailand.
• Chung-Yao Chuang, Yi-Hsun Lee and Wen-Lian Hsu, "Text Patterns and Compression Models for Semantic Class Learning" in Proceedings of the 5th International Joint Conference on Natural Language Processing (IJCNLP), Chiang Mai, Thailand, 2011
• Sheng-Chieh Lu, Chia-Feng Tsai, Chih-Chiang Tsou1, Han-Yin Yang, Lien-Chin Chen, Yu-Ju Chen, Ting-Yi Sung and Wen-Lian Hsu, "Improving phosphorylation site assignment by statistical analysis," in Proceedings of the 8th Taiwan Society for Mass Spectrometry Anaual Conference (TSMS2011), Taipei, Taiwan, July 10-12, 2011.
• Hong-Jie Dai, Wei-Chi Tsai, Richard Tzong-Han Tsai,and Wen-Lian Hsu, "Enhancing search results with semantic annotation using augmented browsing," Proceedings of the Twenty-second International Joint Conference on Artifical Intelligence (IJCAI), Barcelona, Catalonia (Spain), (2011)
• Hsing-Kuo Lee, Chun-Hung Lu, Wen-Lian Hsu, Ching-Ching Lu, Wan-Chun Tang, "Using Adaptive Learning Theory and a Schedule-based Flashcard to Enhance the Quality of Online Self Learning", in Proceedings of the e-Case & e-Tech 2011, Tokyo, Japan1 2011.[slides]
• Chun-Hung Lu, Chorng-Shyong Ong, Wen-Lian Hsu, Hsing-Kuo Lee, "Using Filtered Second Order Co-occurrence Matrix to Improve the Traditional Co-occurrence Model", in Proceedings of the e-Case & e-Tech 2011, Tokyo, Japan1 2011.[slides]
• Chung-Yao Chuang and Wen-Lian Hsu, "Multivariate Multi-Model Approach for Globally Multimodal Problems," ACM SIGEVO Genetic and Evolutionary Computation Conference 2010 (GECCO 2010), Portland, USA,  (2010). [slides]
• Tian-Jian Jiang,Shih-Hung Liu,Cheng-Lung Sung, and Wen-Lian Hsu, "Term Contributed Boundary Feature using Conditional Random Fields for Chinese Word Segmentation Task", in proceeding of the 22nd Coference on Computational and Speech Processing (ROCLING 2010), Pages 143-156, Puli, Nantou, Taiwan, September 2010. [slides]
• Tian-Jian Jiang,Shih-Hung Liu,Cheng-Lung Sung, and Wen-Lian Hsu, "Term Contributed Boundary Tagging by Conditional Random Fields for SIGHAN 2010 Chinese Word Segmentation Bakeoff", in proceeding of the CIPS-SIGHAN Joint Conference on Chinese Language Processing, Pages 266-269 Beijing, China, August 28-29, 2010.
• Hong-Jie Dai1, Po-Ting Lai, Richard Tzong-Han Tsai and Wen-Lian Hsu, "Global Ranking via Data Fusion", in proceeding of the 23rd International Conference on Computational Linguistics (COLING 2010). Beijing, China; 2010.
• Cheng-Wei Lee, Min-Yuh Day, Wen-Lian Hsu, "An Empirical Comparative Study of Manual Rule-Based and Statistical Question Classifiers on Heterogeneous Unseen Data", in Proceedings of the Sixth Asia Information Retrieval Societies Conference (AIRS) (2010). [poster]
• Hsin-Nan Lin, Ting-Yi Sung, Shinn-Ying Ho and Wen-Lian Hsu, "Improving protein secondary structure prediction based on short subsequences with local structure similarity", in Proceedings of the Ninth International Conference on Bioinformatics (InCoB2010) Tokyo, Japan. 26-28 September 2010.  [slides]
• Sheng-Chieh Lu, Chia-Feng Tsai, Chih-Chiang Tsou, Han-Yin Yang, Lien-Chin Chen, Yu-Ju Chen, Ting-Yi Sung, and Wen-Lian Hsu, "Improving phosphorylation site assignment by statistical analysis on CID fragmentation," 58th ASMS Conference on Mass Spectrometry, Salt Lake City, Utah, (2010).[slides]
• Dai, H.-J., Lai, P.-T., Huang, C.-H., Chang, Y.-C., Bow, Y.-Y., Wu, H.-T., Tsai, R.T.-H. and Hsu, W.-L., IASL-IISR Interactor Normalization System:" Using a Multi-stage Gene Normalization Algorithm and SVM-based ranking" , in proceedings of BioCreAtIvE II.5 Challenge Evaluation Workshop. Madrid, Spain, (2009).
• Yu-Lin Chu, Chun-Hung Lu and Wen-Lian Hsu, "LE-Story: An Intelligent Storytelling Environment for Chinese Learning", in Proceedings of the 17th International Conference on Computers in Education(ICCE 2009), Hong Kong, (2009).
• Lai, P.-T., Bow, Y.-Y., Huang, C.-H., Dai, H.-J., Tsai, R.T.-H. and Hsu, W.-L., “Using Contextual Information to Clarify Gene Normalization Ambiguity“, The IEEE International Conference on Information Reuse and Integration (IEEE IRI 2009), Las Vegas, USA, (2009).
• Chih-Chiang Tsou, Ting-Yi Sung, and Wen-Lian Hsu, “MassComp-Q: A comprehensive quantitation software tool for stable isotope labeling and label-free quantitative proteomics”, 57th ASMS Conference on Mass Spectrometry, Philadelphia, Pennsylvania, (2009).[slides]
• Yi-Ting Wang, Chia-feng Tsai, Tzu-Chan Hong, Chih-Chiang Tsou, Pei-Yi Lin, Tse-Ming Hong, Pan-Chyr Yang, Ting-Yi Sung, Wen-Lian Hsu, and Yu-Ju Chen, "A Simple Label-free LC-MS/MS Strategy Towards Comprehensive Phosphoproteomics View that Depict the Mechanisms of Cancer Cell Invasion," 57th ASMS Conference on Mass Spectrometry, Philadelphia, Pennsylvania, (2009).[slides]
• Sheng-Ta Tsai, Chia-Ning Shen, Chih-Chiang Tsou, Wan-Yu Mao, Wei-Chao Chang, Wen-Lian Hsu, and Chung-Hsuan Chen, "Comparative proteomic analysis of liver cancer stem cells," 57th ASMS Conference on Mass Spectrometry, Philadelphia, Pennsylvania, (2009).[slides]
• Min-Yuh Day, Chorng-Shyong Ong, Wen-Lian Hsu, "An Analysis of Research on Information Reuse and Integration", in Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2009), Las Vegas, Nevada, (2009).[slides]
• Yi-Ting Wang, Chia-Feng Tsai, Pei-Yi Lin, Tzu-Chan Hong, Chih-Chiang Tsou, Wen-Lian Hsu, Ting-Yi Sung, Tze Min Hong, Pan-Chyr Yang, and Yu-Ju Chen, "SEMI-quantitation Strategy for Label-free Quantitative Profiling of Phosphoproteome in Lung Cancer of Different Invasive Potential," 56th ASMS Conference on Mass Spectrometry, Denver, Colorado, (2008). [slides]
• Chien-Peng Wu, Pei-Yi Lin, Chih-Wei Chien, Chia-Li Han, Chih-Chiang Tsou, Ting-Yi Sung, Wen-Lian Hsu, and Yu-Ju Chen, "Altered Membrane Proteomic Signature in Human Colorectal Cancer Revealed by Label-free Quantitation Strategy," 56th ASMS Conference on Mass Spectrometry, Denver, Colorado, (2008). [slides]
• Chih-Chiang Tsou, Chia-Feng Tsai, Ethan Yin-Hao Tsui, Paul Chuan-Yih Yu, Yi-Ting Wang, Pei-Yi Lin, Yu-Ju Chen, Ting-Yi Sung and Wen-Lian Hsu, IDEAL-Q: an automated tool for high-performance label-free quantitative analysis, 56th ASMS Conference on Mass Spectrometry, Denver, Colorado, (2008).[slides]
• Pei-Yi Lin, Chia-feng Tsai, Chih-Chiang Tsou, Chien-Peng Wu, Yi-Ting Wang, Ting-Yi Sung, Wen-Lian Hsu, and Yu-Ju Chen, "High-speed Proteomic Signature by Swift LC-MS/MS and Label-free Quantitation," 56th ASMS Conference on Mass Spectrometry, Denver, Colorado, (2008).[slides]
• Ryan T.K. Lin, Justin Liang-Te Chiu, Hong-Jei Dai, Min-Yuh Day, Richard Tzong-Han Tsai, Wen-Lian Hsu (2008), "Biological Question Answering with Syntactic and Semantic Feature Matching and an Improved Mean Reciprocal Ranking Measurement", in Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2008), Las Vegas, Nevada, (2008).
• Ryan T.K. Lin, Hong-Jei Dai, Yue-Yang Bow, Min-Yuh Day, Richard Tzong-Han Tsai, Wen-Lian Hsu (2008), "Result Identification for Biomedical Abstracts Using Conditional Random Fields", in Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2008), Las Vegas, Nevada, (2008).
• Pei-Hsuan Chou, Hong-Jie Dai, Chi-Hsin Huang, Richard Tzong-Han Tsai, Wen-Lian Hsu, "A Web Application for Biomedical Entities and Relations Annotation Using the Unstructured Information Management Architecture," in Proceedings of 2008 International Computer Symposium, Taipei, Taiwan, (2008).
• Yi-Hsun Lee, Cheng-Wei Lee, Cheng-Lung Sung, Mon-Tin Tzou, Chih-Chien Wang, Shih-Hung Liu, Cheng-Wei Shih , Pei-Yin Yang and Wen-Lian Hsu, "Complex Question Answering with ASQA at NTCIR 7 ACLIA" in proceeding of the 7th NTCIR Workshop Meeting , Tokyo, Japan, December 16-19, pp. 70-76, (2008).
• Cheng-Lung Sung, Hsu-Chun Yen, Wen-Lian Hsu, "Compute the Term Contributed Frequency" in Proceedings of Intelligent Systems Design And Applications (ISDA2008), (2008).
• Cheng-Lung Sung, Cheng-Wei Lee, Hsu-Chun Yen, Wen-Lian Hsu, "An Alignment-based Surface Pattern for a Question Answering System", in Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2008), Las Vegas, Nevada, USA, July, 13-15, 2008, pp. 172-177, (2008).
• Chorng-Shyong Ong, Min-Yuh Day, Wen-Lian Hsu, "Development of an Evaluation Model for Question Answering Systems", in Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2008), Las Vegas, Nevada, USA, July, 13-15, 2008, pp. 178-183, (2008).[slides]
• Cheng-Lung Sung, Min-Yuh Day, Hsu-Chun Yen, Wen-Lian Hsu,"A Template Alignment Algorithm for Question Classification", in Proceedings of the IEEE International Conference on Intelligence and Security Informatics (IEEE ISI 2008), Taipei, Taiwan, June 17-20, 2008, pp. 197-199.(2008).
• Chorng-Shyong Ong, Min-Yuh Day, Kuo-Tay Chen, Wen-Lian Hsu,"User-Centered Evaluation of Question Answering Systems", in Proceedings of the IEEE International Conference on Intelligence and Security Informatics (IEEE ISI 2008), Taipei, Taiwan, June 17-20, 2008, pp. 286-287.(2008).
• Chun-Hung Lu, Chih-Chien Wang, Min-Yuh Day, Chorng-Shyong Ong, Wen-Lian Hsu, "Using “Cited by” Information to Find the Context of Research Papers", in Proceedings of the First International Workshop on Social Computing (SOCO 2008), June 17, 2008, Lecture Notes in Computer Science (LNCS), Vol. 5075, pp. 343-354, (2008).
• Chia-Wei Wu, Wen-Lian Hsu, Richard Tzong-Han Tsai, "Semi-joint Labeling for Chinese Named Entity Recognition," Proceedings of AIRS'08, (2008).[slides]
• Yu-Chun Wang, Richard Tzong-Han Tsai and Wen-Lian Hsu, " Learning Patterns from the Web to Translate Named Entities for Cross Language Information Retrieval," Proceedings of IJCNLP, (2008).
• Chang-Chih Tseng, Chun-Hung Lu, Wen-Lian Hsu, "A Mobile Environment for Chinese Language Learning", in Proceedings of HCI International 2007, July 22-27, 2007, Lecture Notes in Computer Science (LNCS), Vol. 4558 pp. 485-489, (2007).
• Richard Tzong-Han Tsai, Hong-Jei Dai, Hsi-Chuan Hung, Ryan T.K. Lin, Wen-Chi Chou, Ying-Shan Su, Min-Yuh Day, Wen-Lian Hsu (2007) ,"BESearch: A Supervised Learning Approach to Search for Molecular Event Participants", in Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2007), Las Vegas, Nevada, USA, August, 13-15, 2007, pp. 412-417. (2007). [slides]
• Hong-Jie Dai, Hsi-Chuan Hung, Richard Tzong-Han Tsai, & Wen-Lian Hsu. IASL Systems in the Gene Mention Tagging Task and Protein Interaction Article Sub-task . Proceedings of Second BioCreAtIvE Challenge Workshop (2007). [slides]
• Hsi-Chuan Hung, Richard Tzong-Han Tsai, & Wen-Lian Hsu, "Identifying Protein Interaction Abstracts with Contextual Bag of Words", Proceedings of the AAAI-07 Student Workshop (2007).[slides]
• Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Wen-Lian Hsu, "On the accuracy of transmembrane helix prediction methods using an updated benchmark," Technical Report TR-IIS-007-010, Institute of Information Science, Academia Sinica, (2007).
• Mon-Tin Tzou, Chun-Hung Lu, Chin-Chien Wang, Cheng-Wei Lee, Wen-Lian Hsu, “Extending knowledge of AIML by using RDF” in proceeding of the 15th International Conference on Computers in Education(ICCE2007) Workshop, Hiroshima, Japan, November, 2007, 5-9, pp 92-94, (2007)
• Chin-Chien Wang, Chun-Hung Lu, Mon-Tin Tzou, Cheng-Wei Lee, Wen-Lian Hsu, “Task-based Learning through Dialogue Management” in proceeding of the 15th International Conference on Computers in Education(ICCE2007) Workshop, Hiroshima, Japan, November, 2007, 5-9, pp 95-97, (2007)
• Wen-Lian Hsu, “ Implications of Web 2.0 on Information Research,” Invited Talk, Workshop on Web 2.0 Technology and Applications, (2007).
• Yu-Chun Wang,Yi-HsunLee, Chu-Cheng Lin,Richard Tzong-Han Tsai, Wen-Lian Hsu," Korean-Chinese Person Name Translation for Cross Language Information Retrieval",Proceedings of ROCLING2007, pp. 37-44.(2007).
• Richard Tzong-Han Tsai, Hsi-Chuan Hung, Hong-Jie Dai, and Wen-Lian Hsu, “ Exploiting Unlabeled Internal Data in Conditional Random Fields to Reduce Word Segmentation Errors for Chinese Texts,” Proceeding of the Interspeech-2007 Conference, 2007.
• Yu-Chun Wang, Cheng-Wei Lee, Richar Tzong-Han Tsai and Wen-Lian Hsu, " IASL System for NTCIR-6 Korean-Chinese Cross-Language Information Retrieval", in Proceedings of NTCIR-6 Workshop Meeting, Tokyo, Japan, May 15-18, 2007, pp. 26-30. (2007)
• Min-Yuh Day, Chorng-Shyong Ong, Wen-Lian Hsu, "Question Classification in English-Chinese Cross-Language Question Answering: An Integrated Genetic Algorithm and Machine Learning Approach", in Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2007), Las Vegas, Nevada, USA, August, 13-15, 2007, pp. 203-208. (2007). [slides]
• Cheng-Wei Lee, Min-Yuh Day, Cheng-Lung Sung, Yi-Hsun Lee, Tian-Jian Jiang, Chia-Wei Wu, Cheng-Wei Shih, Yu-Ren Chen, Wen-Lian Hsu, "Chinese-Chinese and English-Chinese Question Answering with ASQA at NTCIR-6 CLQA", in Proceedings of NTCIR-6 Workshop Meeting, Tokyo, Japan, May 15-18, 2007, pp. 175-181. (2007). [slides]
• Richard Tzong-Han Tsai, Hong-Jie Dai, Hsi-Chuan Hung, & Wen-Lian Hsu. Exploiting Unlabeled Internal Data in Conditional Random Fields to Reduce Word Segmentation Errors for Chinese Texts. Proceedings of the Interspeech-2007 Conference (2007).
• Wen-Chi Chou, Richard Tzong-Han Tsai, Ying-Shan Su,Wei Ku, Ting-Yi Sung and Wen-Lian Hsu, "A Semi-Automatic Method for Annotating a Biomedical Proposition Bank," ACL Workshop on Frontiers in Linguistically Annotated Corpora 2006 (2006).
• Tsai, R. T.-H., Lin, W.-C. C. Y.-C., Ku, W., Su, Y.-S., Sung, T.-Y., & Hsu, W.-L., "BIOSMILE: Adapting Semantic Role Labeling for Biomedical Verbs: An Exponential Model Coupled with Automatically Generated Template Features," Proceedings of BioNLP-2006, (2006). (acceptance rate: 27.5%) [slides]
• Emily Chia-Yu Su, Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, and Wen-Lian Hsu, "Protein subcellular localization prediction based on compartment-specific biological features," Proceedings of IEEE Computational Systems Bioinformatics Conference (CSB'06), Stanford, CA, (2006), Acceptance rate, 19% (30/156).
• Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Wen-Lian Hsu, "Transmembrane Helix and Topology Prediction Using Hierarchical SVM Classifiers and an Alternating Geometric Scoring Function," Proceedings of IEEE Computational Systems Bioinformatics Conference (CSB’06), Stanford, CA, (2006), Acceptance rate, 19% (30/156).[pp]
• Hua-Sheng Chiu,  Hsin-Nan Lin,  Allan Lo,  Ting-Yi Sung,  Wen-Lian Hsu, "A two-stage classifier for protein beta-turn prediction using support vector machines," in Proceedings of IEEE International Conference on Granular Computing (IEEE GrC), (2006).
• Ching-Tai Chen, Hsin-Nan Lin, Ting-Ying Sung and Wen-Lian Hsu, "A Knowledge-based Approach to Protein Local Structure Prediction," Journal of Bioinformatics and Computational Biology, Vol. 4, (2006), 1287-1307, also in Proceedings of Asia Pacific Bioinformatics Conference (APBC).
• Tsai, R. T.H., Dai, H.J., Sung, C.L., Hung, H.C., Day, M.Y., & Hsu, W.L. Chinese Word Segmentation with Minimal Linguistic Knowledge: An Im-proved Conditional Random Fields Coupled with Character Clustering and Auto-matically Discovered Template Matching. Paper presented at the IEEE IRI-06. (2006).
• Min-Yuh Day, Chun-Hung Lu, Chorng-Shyong Ong, Shih-Hung Wu, and Wen-Lian Hsu, "Integrating Genetic Algorithms with Conditional Random Fields to Enhance Question Informer Prediction", Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2006), Waikoloa, Hawaii, USA, Sep 16-18, 2006 (2006). [slides]
• Richard Tzong-Han Tsai, Hsieh-Chuan Hung, Cheng-Lung Sung, Hong-Jie Dai, and Wen-Lian Hsu, "On Closed Task of Chinese Word Segmentation: An Improved CRF Model Coupled with Character Clustering and Automatically Generated Template Matching," Proceedings of SIGHAN Workshop, (2006).[slides]
• Chia-Wei Wu, Shyh-Yi Jan, Richard Tzong-Han Tsai, Wen-Lian Hsu, " On Using Ensemble Methods for Chinese Named Entity Recognition," Proceedings of SIGHAN Workshop, (2006). [slides]
• Tzong-Han Tsai, Chia-Wei Wu, Chun-Nan Chi, Ding He, Ting-Yi Sung, Wen-Lian Hsu "Biomedical Literature Mining: Technologies and IASL’s Experiences", WSA 2005 Workshop invited paper (2005).Tsai, T.-H., Wu, S.-H. and Hsu, W.-L. , "Exploitation of linguistic features using a CRF-based biomedical named entity recognizer",  ACL Workshop on Linking Biological Literature, Ontologies and Databases: Mining Biological Semantics. Detroit (2005). [slides]
• Wu, C.-W., Tsai, T.-H. and Hsu, W.-L. , "Learning to Integrate Web Taxonomies with Fine-Grained Relations: A Case Study Using Maximum Entropy Model", AIRS-2005. Springer, Jeju Island, Korea. (2005) acceptance rate: 23% (32/136) [slides]
• Min-Yuh Day, Tzong-Han Tsai, Cheng-Lung Sung, Cheng-Wei Lee, Shih-Hung Wu, Chorng-Shyong Ong, Wen-Lian Hsu, “ A Knowledge-based Approach to Citation Extraction,” Proceedings of IEEE IRI-2005, (2005).[slides]
• Cheng-Wei Lee, Cheng-Wei Shih, Min-Yuh Day, Tzong-Han Tsai, Tian-Jian Jiang, Chia-Wei Wu, Cheng-Lung Sung, Yu-Ren Chen, Shih-Hung Wu and Wen-Lian Hsu (2005), "ASQA: Academia Sinica Question Answering System for NTCIR-5 CLQA," in Proceedings of NTCIR-5 Workshop, Tokyo, Japan, 202-208, (2005). [slides]
• Cheng-Wei Lee, Cheng-Wei Shih, Min-Yuh Day, Tzong-Han Tsai, Tian-Jian Jiang, Chia-Wei Wu, Cheng-Lung Sung, Yu-Ren Chen, Shih-Hung Wu, and Wen-Lian Hsu (2005), "Perspectives on Chinese Question Answering Systems," in Proceedings of the Workshop on the Sciences of the Artificial (WSA 2005), Hualien, Taiwan, (2005). [slides]
• Min-Yuh Day, Cheng-Wei Lee, Shih-Hung Wu, Chorng-Shyong Ong, Wen-Lian Hsu, "An Integrated Knowledge-based and Machine Learning Approach for Chinese Question Classification", Proceedings of the IEEE International Conference on Natural Language Processing and Knowledge Engineering (IEEE NLP-KE 2005), (2005).[slides]
• Shih-Hung Wu, Cheng-Wei Shih, Chia-Wei Wu, Tzong-Han Tsai, and Wen-Lian Hsu, "Applying Maximum Entropy to Robust Chinese Shallow Parsing", Proceedings of ROCLING2005, (2005).[slides]
• Tsai, T.-H., Wu, C.-W., Lin, Y.-C. and Hsu, W.-L. (2005), "Exploiting full parsing information to label semantic roles using an ensemble of ME and SVM via integer linear programming", CoNLL-2005.
• Min-Yuh Day, Chun-Hung Lu, Jin-Tan David Yang, Guey-Fa Chiou, Chorng-Shyong Ong, Wen-Lian Hsu, " Designing an Ontology-based Intelligent Tutoring Agent with Instant Messaging," Proceedings of ICALT2005,(2005). [slides]
• Hao-Chuan Wang, Chun-Hung Lu, Jun-Yi Yang, Hsin-Wen Hu, Guey-Fa Chiou, Yueh-Tzu Chiang, and Wen-Lian Hsu, “An Empirical Exploration on Using Wiki in an English as Second Language Course,” Proceedings of ICALT2005, (2005).
• Wen-Lian Hsu*, “A Linear Time Algorithm for Finding a Maximal Planar Subgraph Based on PC-Trees,” Lecture Notes in Computer Science 2108, 207-217, (2005).
• W. L. Hsu, J. M. Chang, W. C. Chou, J. B. Chen, K. P. Wu, T. Y. Sung, C. F. Chang, W. J. Wu and T. H. Huang, “An Iterative Relaxation Technique for the NMR Backbone Assignment Problem,”invited talk, in Proceedings of IEEE Fourth Symposium on Bioinformatics and Bioengineering (BIBE2004), (2004).
• Wen-Lian Hsu, “Survey - A Paradigm Shift in Biological Computing,” French-Taiwanese Conference on Information Technology, invited talk, (2004).
• Yi-Feng Lin, Tzong-Han Tsai, Wen-Chi Chou, Kuen-Pin Wu, Ting-Yi Sung, Wen-Lian Hsu, “ A Maximum Entropy Approach to Biomedical Named Entity Recognition,  Proceedings of 4th ACM SIGKDD Workshop on Data Mining in Bioinformatics (BioKDD), (2004).
• Yi-Feng Lin, Wen-Chi Chou, Kuen-Pin Wu, Ting-Yi Sung, Wen-Lian Hsu, “InfoMap: A Framework for Integrated Proteomic Knowledge Base,” Proceedings of 3^rd International Proteomics Conference (IPC’04), invited talk, (2004).
• Cheng-Wei Shih, Tzong-Han Tsai, Shih-Hung Wu, Chiu-Chen Hsieh, and Wen-Lian Hsu, “The Construction of a Chinese Named Entity Tagged Corpus: CNEC1.0,” Proceedings of ROCLING2004, (2004).[slides]
• Jia-Lin Tsai, Tien-Jien Chiang and Wen-Lian Hsu, "Applying Meaningful Word-Pair Identifier to the Chinese Syllable-to-Word Conversion Problem," Proceedings of ROCLING2004, (2004).
• Chun-Hung Lu, Shih-Hung Wu, LiongYu Tu, Wen-Lian Hsu,"The Design of An Intelligent Tutoring System Based on the Ontology of Procedural Knowledge", Proceedings of the IEEE International Conference on Advanced Learning Technologies, ICALT2004,(2004).[slides]
• W. L. Hsu and R. McConnell, "PQ Trees PC Trees and Planar Graphs," Handbook of Data Structures and Applications, Dinesh P Mehta and Sartaj Sahni ed., (2003).
• Wen-Lian Hsu, “A Paradigm Shift in Biological Computing,” Fudan International Bioinformatics Workshop, invited talk, (2003).
• Jia-Lin Tsai, Cheng-Lung Sung and Wen-Lian Hsu, "Chinese Word Auto-Confirmation System using a Hybrid Approach," Proceedings of ROCLING XV, (2003).
• S. H. Wu, T. H. Tsai and W. L. Hsu, “Domain Event Extraction and Representation with Domain Ontology,” Proceedings of IJCAI’03 Workshop on Information Integration on the Web, Menlo Park, CA, (2003).
• S. H. Wu, T. H. Tsai and W. L. Hsu, “Text Categorization Using Automatically Acquired Domain Ontology,” Proceedings of IRAL2003 Workshop on Information Retrieval with Asian Languages, Sapporo, Japan, (2003).
• Wing-Kwong Wong, Sheng-Cheng Hsu, Wen-Lian Hsu, and Chin-Tang Cho, “Computer-assisted Learning Environment with Automated Chinese Word Problem Categorization,” Proceedings of ICCE2003, (2003).
• K. P. Wu, H. N. Lin, T. Y. Sung, and W. L. Hsu, “A New Similarity Measure among Protein Sequences,” Proceedings of IEEE The Computational Systems Bioinformatics Conference (CSB’03), Stanford, CA, (2003), Acceptance rate, 19% (27/138).
• W. L. Hsu, “An Efficient Implementation of the PC-Tree Algorithm of Shih & Hsu's Planarity Test,” Technical Report, Institute of Information Science, Academia Sinica,  (2003).
• W. L. Hsu, “PC-Trees and Maximal Planar Subgraphs,” Keynote speech, ICS’02, Hualien, (2002).
• J. L. Tsai and W. L. Hsu, “Applying an NVEF Word-Pair Identifier to the Chinese Syllable-to-Word Conversion Problem,” COLING’02, Taipei, (2002).
• L.Y., Tu, W. L. Hsu and S. H., Wu, “A Cognitive Student Model – An Ontological Approach,” ICCE’02, Auckland, (2002).
• S. H. Wu and W. L. Hsu, “ AutoMap: A Semi-Automatic Ontology Acquisition Tool for Chinese Corpus,” COLING’02, Taipei, (2002).
• C. C. Hsieh, T. H. Tsai, W. L. Hsu, D. Wible, “Exploiting Knowledge Representation in an Intelligent Tutoring System for English Lexical Errors,” ICCE’02, Auckland, (2002).
• 許聞廉，「智慧型問答搜尋技術」，邀請演講，中文搜尋引擎技術研討會，台北，(2001).
• Shih-Hung Wu, Min-Yuh Day, W. L. Hsu, “FAQ-Centered Organizational Memory,” IJCAI’01 Workshop on Knowledge Management and Organization Memory, Seattle, (2001).
• C. L. Sung, W. L. Hsu, S. H. Wu and W. K. Shih, “The Design and Implementation of Intelligent Desktop Agent,” Proceedings of TAAI’01, Kaoshiung, (2001)
• W. L. Hsu, Y. S. Chen and S. H. Wu, “Event Identification Based on the Information Map - INFOMAP,” NLPKE’01, Tucson, (2001).
• W. L. Hsu, “PC-trees vs. PQ-trees,” invited talk, Workshop on Graph Structures and Algorithms, also, appeared in Lecture Notes in Computer Science 2108, 207-217, (2001).
• W. L. Hsu, “Interactive CAI in Natural Language,” Keynote Speech, International Conference on Computer Assisted Instruction and Internet Computing, Taipei, (2000).
• W. L. Hsu,“Simulating Human Intelligence,” Keynote Speech, Fifth Conference on Artificial Intelligence and Applications, Taipei, (2000).
• W. L. Hsu, Yi-Shiou Chen and Yuan-Kai Wang, “Natural language agents – An agent society on the Internet,” Proceedings of PRIMA’99, (1999).
• W. L. Hsu, 「網際網路的檢索與知識管理」，專題講座，National Computer Symposium, Taipei, (1999).
• H. L. Wang, W. K. Shih, C. N. Hsu, Y. S. Chen, Y. L. Wang and W. L. Hsu, “Personal Navigating Agent,” Proceedings of AGENT’99, (1999).
• C. C. Chen and W. L. Hsu, "A document similarity measurement without dictionaries," Proceedings of the Fourth International Workshop on Information Retrieval with Asian Languages IRAL'99, (1999).
• W. L. Hsu, Yi-Shiou Chen and Yuan-Kai Wang, “A Context sensitive model for concept understanding” Proceedings of ITALLC’98, (1998), 161-169
• Yi-Shiou Chen, Schy Chiou, Yuan-Kai Wang, and Wen-Lian Hsu, “Personal Brower,” Proc. ACM SIGIR’98, (1998).
• Y. K. Wang , Y. S. Chen and W. L. Hsu, “Empirical study of mandarin Chinese discourse analysis,” Proceedings. of the 10^th IEEE International Conference on Tools with AI, (1998).
• Y. K. Wang , Y. S. Chen and W. L. Hsu, “A knowledge-based approach for natural language processing,” Technical Report, (1998).
• Y. K. Wang , W. L. Hsu and Y. S. Chen, “The anaphoric expressions of Chinese algebraic word problem,” Proceedings of the 1998 International Symposium on Multimedia Information Processing, (1998).
• Wing-Kwong Wong, W. L. Hsu, Yi-Shiou Chen, Yuan-Kai Wang, Shun-Tao Pai, “Natural language educational agents in a networked Chinese logo learning environment”, Proceedings of ICCE’98, (1998).
• W. L. Hsu, W. F. Lu, "On clone assembly algorithms - an error tolerant test for interval graph recognition", Proc. IEEE International Joint Symposia on Intelligence and Systems, (1998), 118-125.
• W. L. Hsu, “Fault Tolerant DNA computing,” invited talk, DIMACS Workshop, Hong Kong, (1998).
• W. L. Hsu and W. F. Lu, “From Satellite DNA to HTML table understanding,” invited talk, CTS Workshop on Combinatorics and Algorithms, Taipei, (1998).
• W. L. Hsu, “Elementary school Math. tutoring agent”, Proceedings of Agent Technology Workshop, (1997).
• 許聞廉，『模擬人類理解的新嘗試』，張昭鼎紀念研討會，國立中正大學，(1996).
• W. L. Hsu,, "On-line recognition of interval graphs", Lecture Notes in Computer Science 1120, 27-38, (1996).
• W. L. Hsu, "Finding maximal planar subgraphs in linear time", Lecture Notes in Computer Science 1004, ISAAC ' 95, (1995).
• W. L. Hsu, W. K. Shih and P. H. Yeh, "Object oriented concept representation", Proceeding of ICCPOL'95, (1995).
• W. L. Hsu, “On the design of a computer that speak fluent Chinese,” Proceedings of RAMs’95, (1995).
• 許聞廉、陳克健，「自然智慧型輸入系統的語意分析─脈絡會意法」, Proceedings of the 6th International Symposium on Cognitive Aspects of the Chinese Language, (1993), 527-540.
• Fu Chang, Ying-Chu Chen, Hon-Son Don, W. L. Hsu, and Ching-I Kao, "Stroke segmentation as a basis for structural matching of Chinese characters", Second International Conference on Document Analysis and Recognition, (1993).
• W. K. Shih and W. L. Hsu, " A simple test for planar graphs," Proceedings of the International Workshop on Discrete Math. and Algorithms, University of Hong Kong, 110-122, (1993).
• W. L. Hsu, "A new test for interval graphs", Lecture Notes in Computer Science 657, 11-16, (1992).