Professor Wen-Lian Hsu

	Vita
	Education
	Experience
	Research Interests
	Awards
	Teaching
	Lab
	Publications

	Journal papers
	Conference papers

	IASL won the first place in the International Competition - BioCreAtIvE II.5 Interactor Normalization Task (2009)
	IASL won the first place in NTCIR-6 Cross Language Question Answering System (NTCIR-6 CLQA) competition (2007)
	「IASL team won the first place over 13 teams in the WS CityU closed track of the SIGHAN 2006 Word Segmentation Contest(2006)
	IASL team was ranked 2nd among 10 teams in the WS CKIP closed track of the SIGHAN 2006 Word Segmentation Contest (2006)

	Wen-Lian Hsu Professor, IEEE Fellow Distinguished Research Fellow Institute of Information Science, Academia Sinica Taipei, Taiwan, R. O. C. Phone:886-2-27883799 ext.1804 Fax:886-2-27824814 E-mail:hsu@iis.sinica.edu.tw
Vita Wen-Lian Hsu received a B.S. from the Department of Mathematics, National Taiwan University in 1973. He received an M.S. and a Ph.D. in operations research from Cornell University in 1978 and 1980, respectively. From 1979 to 1980, he worked as a research associate in the Center for Operations Research and Econometrics (CORE) at Universite Catholique de Louvain, Belgium. In 1980, he joined Northwestern University as an assistant professor and was promoted to tenured associate professor in 1986. He joined the Institute of Information Science as a research fellow in 1989. Dr. Hsu's earlier research while in Northwestern University is focused on graph algorithms. His main contribution is on perfect graphs and special classes of intersection graphs. Most of his publications appear in JACM and SIAM J. Computing. Recently, he invented the PC-tree data structure to design very efficient algorithms in planar graphs and intersection graphs. In the meantime, he has applied similar techniques to tackle computational problems in Biology such as error-tolerant algorithms in DNA sequence analysis. Right after joining the institute in 1989, he initiated the project ``intelligent Chinese phonetic input system'' (in cooperation with K. J, Chen), aiming at resolving a major bottleneck in the computerization of Chinese language -- the input method. A software resulted from this project, 自然輸入法(GOING), achieved a hit ratio close to 96% and was selected as one of the ten best Chinese computer products of Taiwan in 1993. This software has been widely used in Taiwan and the number of downloads in PC Home web station is close to 600,000. Later, he moved into the research of Intelligent Agent on the Internet, and produced the Math. Problem Solving Agent in 1997, and a Chinese natural language Q & A system, @skbots, in 1999. He is currently working on DNA sequence analysis, Genome knowledge base and intelligent knowledge management systems. Dr. Hsu has published in various top-notch journals in discrete mathematics, operations research and computer science. He has been invited to deliver lectures in many international conferences. He has been the conference chairs of ISAAC'91 and COCOON'98, ITS’06 and has been involved in the editorship of the following journals: Managing Editor of Journal of Information Science (1995-2001), International Journal of Foundation of Computer Science (1993-2002), Information Processing Letters (2001-), and International Journal of Bioinformatics Research and Applications (2005-). He has been the president of the Artificial Intelligence Society in Taiwan (2001-2002).
Education Ph.D. Cornell University, Operations Research, 1980(Advisor - George L. Nemhauser) M.S.Cornell University, Operations Research, 1978 B.S.National Taiwan University, Mathematics, 1973
Experience 2008-present Professor, Distinguished Research Fellow, Institute of Information Science, Academia Sinica. 1989-2008 Professor, Research Fellow, Institute of Information Science, Academia Sinica. 2001-present Professor (joint appointment), Department of Computer Science, National Tsing-Hua University. 1997-1998 Acting Director, Institute of Information Science, Academia Sinica 1996-1997 Visiting Professor, CSLI center, Stanford University. 1986-1989 Associate Professor (with tenure), Department of IE/MS,Northwestern University. 1980-1986 Assistant Professor, Department of IE/MS,Northwestern University. 1979-1980 Postdoctoral Fellow, Center for Operations Research and Econometrics(CORE), Universite Catholique de Louvain. 1977-1979 Research Assistant, Cornell University. 1975-1977 Teaching Assistant, Cornell University
Research Interests Our main research topic is natural language understanding. Nearly all of the following systems require certain understanding capability to achieve high precision rates: semantic search on the web, Chinese voice input and output, spelling checker and machine translation. Our Chinese input system--GOING, which automatically translates a chu-in sequence into characters with a hit ratio close to 96%, is widely used in Taiwan. It received the Distinguished Chinese Information Product Award（中文傑出資訊產品獎）in 1993. In PC Home software download area, GOING has been downloaded 600,000times. Within the top 10 download software, it is the only one developed domestically. Our model for concept understanding can utilize heterogeneous knowledge representation systems. We have extended our model to that on Internet intelligent agents, especially on the database agents. These software agents will become indispensable in the semantic search engine and the electronic commerce on the Internet. Another direction we are moving into is the development of educational tutoring systems. We have successfully implemented a system that can understand and solve (and explain how so solve) the mathematics word problems of primary school (grade 3). Our major achievement is the development of a knowledge representation kernel, InfoMap, for the semantic analysis of natural language, which can be applied to a wide variety of application systems. We are currently utilizing this kernel to develop an Intelligent Knowledge Management System over the World Wide Web. There are several technology transfer programs currently going on with private companies. In DNA sequence analysis, we have been studying the physical mapping and the clone assembly problem. When the experimental error is within 15%, we have developed an error-tolerant algorithm for the clone assembly problem (as well as the physical mapping problem) that can determine the relative positions of each clone (respectively, each probe) given the clone overlapping relationships. By combining our knowledge management tools, InfoMap, and natural language agent, we are currently constructing a Question Answering system for genomic and proteomic knowledge. We shall further extend this system to help biologist to execute certain natural language scripts automatically in their dry labs. Finally, we shall utilize InfoMap to facilitate the accurate search of various relationships in biological literature.
Teaching 2012 Graphical Algorithm & Applications to bioinfomatics
Awards Research Initiation Award of the National Science Foundation, 1981 Intelligent Chinese Input Software -- Top ten Most Distinguished Chinese computer products（十大傑出中文資訊產品獎）in Taiwan, 1993. Outstanding Research Awards（國科會傑出研究獎） by the National Science Council (NSC) of Taiwan in 1991~1992 Outstanding Research Awards（國科會傑出研究獎）by NSC, 1994~1995 Outstanding Research Awards（國科會傑出研究獎）by NSC, 1996~1997. K.T. Lee Research Breakthrough Award（李國鼎穿石獎）in 1999 NSC Designated Research Fellow（國科會特約研究員獎）in 1999 NSC Appointed Outstanding Research Award（國科會傑出特約研究員獎）in 2005 Academia Sinica Investigator Award（中央研究院深耕計畫獎）in 2005 IEEE Fellow 2006 Teco-Award (東元獎) in 2008 Pan Wen Yuan Distinguished Research Award (潘文淵研究傑出獎) in 2010.
Lab Intelligent Agent Systems Lab

Publications

Journal papers

Hong-Jie Dai, Johnny Chi-Yang Wu, Richard Tzong-Han Tsai, Wen-Harn Pan,Wen-Lian Hsu1*, "T-HOD: A Literature-based Candidate Gene Database for Hypertension, Obesity, and Diabetes", Database-The Journal of Biological Databases and Curation,2013.

Lien-Chin Chen, Mei-Ying Liu, Yung-Chin Hsiao, Wai-Kok Chong, Hsin-Yi Wu, Wen-Lian Hsu, Pao-Chi Liao*, Ting-Yi Sung*, Shih-Feng Tsai*, Jau-Song Yu*, Yu-Ju Chen*, "Decoding the disease-associated proteins encoded in the human Chromosome 4," Journal of Proteome Research, volume 12, number 1, pages 33-44, January 2013.

Emily CY Su, Jia-Ming Chang, Cheng-Wei Cheng, Ting-Yi Sung, Wen-Lian Hsu, "Prediction of nuclear proteins using nuclear translocation signals proposed by probabilistic latent semantic indexing," BMC Bioinformatics, volume 13, number Suppl 17, pages S13, October 2012.

Hong-Jie Dai, Chun-Yu Chen, Chi-Yang Wu, Po-Ting Lai, Richard Tzong-Han Tsai, Wen-Lian Hsu, "Coreference resolution of medical concepts in discharge summaries by exploiting contextual information," JAMIA, 19(5): 888-896, (2012)

Cheng-Wei Shih, Cheng-Wei Lee, Richard Tzong-Han Tsai, Wen-Lian Hsu, "Validating Contradiction in Texts Using Online Co-Mention Pattern Checking" ACM Transactions on Asian Language Information Processing (TALIP), Volume 11 Issue 4, December 2012, pp. 17:1-12:21, (2012).

Ching-Tai Chen, Hung-Pin Peng, Jhih-Wei Jian, Keng-Chang Tsai, Jeng-Yih Chang, Ei-Wen Yang, Jun-Bo Chen, Wen-Lian Hsu*, An-Suei Yang*, "Protein-Protein Interaction Site Predictions with Three-Dimensional Probability Distributions of Interacting Atoms on Protein Surfaces", PLoS ONE, 7(6): e37706, (2012).

Jhih-Siang Lai, Cheng-Wei Cheng, Ting-Yi Sung, Wen-Lian Hsu, "Computational Comparative Study of Tuberculosis Proteomes Using a Model Learned from Signal Peptide Structures," PLoS ONE, Volume 7, Issue 4, e35018, April (2012).

Chung-Ming Yu, Hung-Pin Peng, Ing-Chien Chen, Yu-Ching Lee, Jun-Bo Chen, Keng-Chang Tsai, Ching-Tai Chen, Jeng-Yih Chang, Ei-Wen Yang, Po-Chiang Hsu, Jhih-Wei Jian,Hung-Ju Hsu, Hung-Ju Chang, Wen-Lian Hsu, Kai-Fa Huang, Alex Che Ma and An-Suei Yang, "Rationalization and Design of the Complementarity Determining Region Sequences in an Antibody-Antigen Recognition Interface," PLoS ONE, Volume 7, Issue 3, e33340, March (2012).

Mike Tian-Jian Jiang, Tsung-Hsien Lee,Wen-Lian Hsu, "The Left and Right Context of a Word: Overlapping Chinese Syllable Word Segmentation with Minimal Context," Volume 12 Issue 1, pages 2:1-23, ACM Transactions on Asian Language Information Processing (TALIP), (2013).

Putty-Reddy Sudhir, Chia-Lang Hsu, Mei-Jung Wang, Yi-Ting Wang, Yu-Ju Chen, Ting-Yi Sung, Wen-Lian Hsu, Ueng-Cheng Yang, Jeou-Yuan Chen, “Phosphoproteomics identifies oncogenic Ras signaling targets and their involvement in lung adenocarcinomas,” PLoS ONE, 6(5): e20199, (2011).

Yu-Ching Fang, Po-Ting Lai, Hong-Jie Dai and Wen-Lian Hsu*, “MeInfoText 2.0: gene methylation and cancer relation extraction from biomedical literature,” BMC Bioinformatics 12:471, (2011).

Hsin-Nan Lin, Cédric Notredame, Jia-Ming Chang, Ting-Yi Sung*, Wen-Lian Hsu*, “Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words,” PLoS ONE 6(12): e27872, (2011).

Hong-Jie Dai, Yen-Ching Chang, Richard Tzong-Han Tsai,and Wen-Lian Hsu, "Integration of Gene Normalization Stages and Co-reference Resolution Using a Markov-Logic Network," Bioinformatics first published online June 17, 2011 doi:10.1093/bioinformatics/btr358 (2011)

Allan Lo, Cheng-Wei Cheng, Yi-Yuan Chiu, Ting-Yi Sung, Wen-Lian Hsu, "TMPad: an integrated structural database for helix-packing folds in transmembrane proteins," Nucleic Acid Research 39, D347-D355, (2011).

Hsin-Nan Lin, Ting-Yi Sung and Wen-Lian Hsu,"Identification of Essential Residues from Protein Secondary Structure Prediction and Applications", in Sequence and Genome Analysis: Methods and Applications, Z. Zhao, Editor., iConcept Press.(2010)

Wei-Chao Chang, Chuan-Kai Chou, Chih-Chiang tsou, S.-H. Li, Chein-Hung Chen, Yu-Xing Zhuo, Wen-Lian Hsu and Chung-Hsuan Chen, "Comparative Proteomic Analysis of Proteins Involved in the Tumorigenic Process of Seminal Vesicle Carcinoma in Transgenic Mice," International Journal of Proteomics 2010, Article ID 726968, (2010).

Yi-Ting Wang , Chia-Feng Tsai , Tzu-Chan Hong , Chih-Chiang Tsou , Pei-Yi Lin , Szu-Hua Pan , Tse-Ming Hong , Pan-Chyr Yang , Ting-Yi Sung , Wen-Lian Hsu , and Yu-Ju Chen, "An Informatics-assisted Label-free Quantitation Strategy that Depicts Phosphoproteomic Profiles in Lung Cancer Cell Invasion," Journal of Proteome Research 9, 5582-5597, (2010).

Hsin-Nan Lin, Ting-Yi Sung, Shinn-Ying Ho, Wen-Lian Hsu, "Improving protein secondary structure prediction based on short subsequences with local structure similarity," BMC Genomics 11(Suppl 4):S4, (2010).

Dai, H.-J., Chang, Y.-C., Tsai, R.T.-H. and Hsu, W.-L., "New challenges for biological text-mining in the next decade", Journal of Computer Science and Technology, 25, 169-179, (2010).

Chih-Chiang Tsou, Chia-Feng Tsai, Ying-Hao Tsui, Putty-Reddy Sudhir, Yi-Ting Wang, Yu-Ju Chen, Jeou-Yuan Chen, Ting-Yi Sung*, and Wen-Lian Hsu*, "IDEAL-Q: An automated tool for label-free quantitation analysis using an efficient peptide alignment approach and spectral data validation," Molecular & Cellular Proteomics, 9, 131-144, (2010)

Richard Tzong-Han Tsai, Po-Ting Lai, Hong-Jie Dai, Chi-Hsin Huang, Yue-Yang Bow, Yen-Ching Chang, Wen-Harn Pan, and Wen-Lian Hsu*, "HypertenGene: Extracting key hypertension genes from biomedical literature with position and automatically-generated template features," BMC Bioinformatics, 10(Suppl 15):S9, 3 December (2009).

Hsin-Nan Lin, Ching-Tai Chen, Ting-Yi Sung, Shinn-Ying Ho and WenLian Hsu, "Protein subcellular localization prediction of eukaryotes using a knowledge-based approach," BMC Bioinformatics, 10(Suppl 15):S8, December 3, (2009) .[slides]

Chorng-Shyong Ong, Min-Yuh Day and Wen-Lian Hsu, "The measurement of user satisfaction with question answering systems", Information & Management , Volume 46, Issue 7, pp. 397-403, October, (2009).

Chih-Chiang Tsou, Yin-Hao Tsui, Yi-Hwa Yian, Yi-Ju Chen, Han-Yin Yang, Chuan-Yih Yu, Ke-Shiuan Lynn, Yu-Ju Chen, Ting-Yi Sung, and Wen-Lian Hsu, "MaXIC-Q Web: A Fully Automated Web Service Using Statistical and Computational Methods for Protein Quantitation Based on Stable Isotope Labeling and LC-MS," Nucleic Acids Research Vol. 37, No. suppl_2 W661-W669e, June 15, (2009).

Allan Lo, Yi-Yuan Chiu, Einar Andreas Rødland, Ping-Chiang Lyu, Ting-Yi Sung*, and Wen-Lian Hsu*, "Predicting helix-helix interactions from residue contacts in membrane proteins," Bioinformatics 25(8), 996-1003, February 25, (2009).

Ke-Shiuan Lynn, Li-Lan Li, Yen-Ju Lin, Chiuen-Huei Wang, Shu-Hui Sheng, Ju-Hwa Lin, Wayne Liao, Wen-Lian Hsu*, Wen-Harn Pan*, "A Neural Network Model for Constructing Endophenotypes of Common Complex Diseases - An Application to Male Young-onset Hypertension Microarray Data." Bioinformatics 25(8), 981-988, February 23, (2009).

Ryan T.K. Lin, Justin Liang-Te Chiu, Hong-Jie Dai, Richard Tzong-Han Tsai, Min-Yuh Day, and Wen-Lian Hsu, "A supervised learning approach to biological question answering", Integrated Computer-Aided Engineering 16, 271–281, August, (2009).

Cheng-Lung Sung, Cheng-Wei Lee, Hsu-Chun Yen, and Wen-Lian Hsu, "Alignment-based surface patterns for factoid question answering systems," Integrated Computer-Aided Engineering 16, 259-269, August, (2009).

Yu-Chun Wang, Richard Tzong-Han Tsai & Wen-Lian Hsu, “Web-based pattern learning for named entity translation in Korean–Chinese cross-language information retrieval,” Expert Systems with Applications, 36(2), Part 2, 3990-3995, March, (2009).

Ching-Tai Chen, Ei-Wen Yang, Wen-Lian Hsu*, and An-Suei Yang*, "Protease Substrate Site Predictors Derived from Machine Learning on Multilevel Substrate Phage Display Data," Bioinformatics 24(23):2691-2697, (2008).

Cheng-Wei Cheng, Emily Chia-Yu Su, Ting-Yi Sung and Wen-Lian Hsu, "Predicting RNA-binding sites of proteins using support vector machines and evolutionary information," BMC Bioinformatics 9(Suppl 12):S6, (2008).

Jia-Ming Chang, Emily Chia-Yu Su, Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Wen-Lian Hsu, "PSLDoc: Protein subcellular localization prediction based on gapped-dipeptides and probabilistic latent semantic analysis," PROTEINS: Structure, Function, and Bioinformatics 72, 693-710, (2008).

Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Ping-Chiang Lyu, and Wen-Lian Hsu*, "Enhanced membrane protein topology prediction using a hierarchical classification method and a new scoring function," Journal of Proteome Research 7, 487-496, (2008).

Richard Tzong-Han Tsai, Hong-Jie Dai, Chi-Hsin Huang and Wen-Lian Hsu, "Semi-automatic conversion between biomedical predicate argument structure standards," BMC Bioinformatics 9(Suppl 12):S18, (2008).

Hong-Jie Dai, Chi-Hsin Huang, Ryan T. K. Lin, Richard Tzong-Han Tsai, and Wen-Lian Hsu, "BIOSMILE web search: a web application for annotating biomedical entities and relations," Nucleic Acid Research 36, W390-W398, (2008).

Richard Tzong-Han Tsai, Hsi-Chuan Hung, Hong-Jie Dai, Yi-Wen Lin, and Wen-Lian Hsu*, “Exploiting Likely-Positive and Unlabeled Data to Improve the Identification of Protein-Protein Interaction Articles,” BMC Bioinformatics, 9(Suppl 1):S3, (2008).

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,"Boosting Chinese Question Answering with Two Lightweight Methods: ABSPs and SCO-QAT", ACM Transactions on Asian Language Information Processing ,Volume 7 , Issue 4, November 2008, pp. 12:1-12:29, (2008).

Cheng-Wei Lee, Yi-Hsun Lee, and Wen-Lian Hsu, “ Exploring Shallow Answer Ranking Features in Cross-Lingual and Monolingual Factoid Question Answering,” Computational Linguistics & Chinese Language Processing 13, 1-26, (2008).

Chia-Wei Wu, Richard Tzong-Han Tsai, Cheng-Wei Lee,Wen-Lian Hsu, “ Web Taxonomy Integration System with Hierarchical Shrinkage and Fine-Grained Relations,” Expert Systems With Applications , 35(4), 2123-2131, (2008).

Chuan-Yih Yu, Yin-Hao Tsui, Yi-Hwa Yian, Ting-Yi Sung, and Wen-Lian Hsu, "The Multi-Q Web Server for Multiplexed Protein Quantitation," Nucleic Acids Research.35, W707-712, (2007).

Chun-Nan Hsu, Jin-Mei Lai, Chia-Hung Liu, Huei-Hun Tseng, Chih-Yun Lin, Kuan-Ting Lin, Hsu-Hua Yeh, Ting-Yi Sung, Wen-Lian Hsu, Li-Jen Su, Sheng-An Lee, Chang-Han Chen, Gen-Cher Lee, Der-Tsai Lee, Yow-Ling Shiue, Chang-Wei Yeh, Chao-Hui Chang, Cheng-Yan Kao and Chi-Ying Huang, "Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online)," BMC Bioinformatics 8:66, (2007).

Emily Chia-Yu Su, Hua-Sheng Chiu, Allan Lo, Jenn-Kang Hwang, Ting-Yi Sung, and Wen-Lian Hsu, "Protein subcellular localization prediction based on compartment-specific features and structure conservation," BMC Bioinformatics, 8:330, (2007). [slides]

Min-Yuh Day, Richard Tzong-Han Tsai, Cheng-Lung Sung, Chiu-Chen Hsieh, Cheng-Wei Lee, Shih-Hung Wu, Kun-Pin Wu, Chorng-Shyong Ong, Wen-Lian Hsu, " Reference Metadata Extraction Using a Hierarchical Knowledge Representation Framework", Decision Support Systems, Volume 43, Issue 1, February 2007, pp.152-167. (2007)

Chun-Hung Lu, Chorng-Shyong Ong, Wen-Lian Hsu, "Using an ITS as an Arithmetic Assistant for Teachers-3-year Review," Journal of Internet Technology 8, 289-298, (2007).

Wing-Kwong Wong, Sheng-Cheng Hsu, Shih-Hung Wu, Cheng-Wei Lee, and Wen-Lian Hsu, "LIM-G: Learner-initiating Instruction Model based on Cognitive Knowledge for Geometry Word Problem Comprehension," Computers and Education 48, , 582-601, (2007).

Kuen-Pin Wu, Jia-Ming Chang, Jun-Bo Chen, Chi-Fon Chang, Wen-Jin Wu, Tai-Huang Huang, Ting-Yi Sung and Wen-Lian Hsu, “RIBRA-an Error-Tolerant Algorithm for the NMR Backbone Assignment Problem,” Journal of Computational Biology 13, 229-244 (2006); also, in Proceedings of the International conference on Research in Computational Molecular Biology (RECOMB’05), acceptance rate: 18% (39/217).

Richard Tzong-Han Tsai, Wen-Chi Chou, Yu-Chun Lin, Ying-Shan Su, Cheng-Lung Sung, Hong-Jie Dai, Irene Tzu-Hsuan Yeh, Wei Ku, Ting-Yi Sung and Wen-Lian Hsu, “BIOSMILE: A semantic role labeling system for biomedical verbs using a maximum-entropy model with automatically generated template features,” BMC Bioinformatics, 8:325, (2007).

Wen-Ting Lin, Wei-Neng Hung, Yi-Hwa Yian, Kun-Pin Wu, Chia-Li Han, Yet-Ran Chen, Yu-Ju Chen, Ting-Yi Sung and Wen-Lian Hsu, "Multi-Q: A Fully Automated Tool for Multiplexed Protein Quantitation," Journal of Proteome Research, 2006. 5(9): p.2328-2338

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).

Richard Tzong-Han Tsai, Cheng-Lung Sung, Hong-Jie Dai, Hsieh-Chuan Hung, Ting-Yi Sung and Wen-Lian Hsu, “NERBio: Using Selected Word Conjunction, Term Normalization, and Global Patterns to Improve Biomedical Named Entity Recognition,” BMC Bioinformatics 7(Suppl 5) :S11, (2006).

Tzong-Han Tsai, Shih-Hung Wu, Wen-Chi Chou, Yu-Chun Lin, Ding He, Ting-Yi Sung, Wen-Lian Hsu, “Various Criteria in the Evaluation of Biomedical Named Entity Recognition,” BMC Bioinformatics. 7:92, (2006) (Impact Factor: 4.96).

Tzong-han Tsai, Wen-Chi Chou, Shih-Hung Wu, Ting-Yi Sung, Jieh Hsiang, Wen-Lian Hsu, "Integrating Linguistic Knowledge into a Conditional Random Field Framework to Identify Biomedical Named Entities," Expert Systems with Applications 30 (1), 117-128, (2006).

Chun-Hung Lu, Guey-Fa Chiou, Min-Yuh Day, Chorng-Shyong Ong, Wen-Lian Hsu, "Using Instant Messaging to Provide an Intelligent Learning Environment." Intelligent Tutoring Systems, Lecture Notes in Computer Science 4053, 575-583, (2006).[slides]

Hsin-Nan Lin, Kuen-Pin Wu, Jia-Ming Chang, Ting-Yi Sung and Wen-Lian Hsu, "GANA – A Genetic Algorithm for NMR Backbone Resonance Assignment,"Nucleic Acids Research 33(14), 4593-4601, (2005).

Hsin-Nan Lin, Jia-Ming Chang, Kuen-Pin Wu, Ting-Yi Sung and Wen-Lian Hsu, "HYPROSP II - A knowledge-based hybrid method for protein secondary structure prediction based on local prediction confidence," Bioinformatics 21, 3227-3233, (2005).

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]

Chun-Hung Lu, Shih-Hung Wu, LiongYu Tu, Wen-Lian Hsu, “Ontological Support in Modeling Learners' Problem Solving Process,” Journal of Educational Technology & Society 8(4), 64-74, (2005).

Kuen-Pin Wu, Hsin-Nan Lin, Jia-Ming Chang, Ting-Yi Sung and Wen-Lian Hsu, "HYPROSP: a hybrid protein secondary structure prediction algorithm—a knowledge-based approach," Nucleic Acids Research 32(17):5059-5065, (2004).

Jia-Lin Tsai, Gladys Hsieh and Wen-Lian Hsu, "Auto-Generation of NVEF Knowledge in Chinese," Computational Linguistics & Chinese Language Processing 9, 41-64, (2004)

Tzong-Han Tsai, Shih-Hung Wu, Cheng-Wei Lee, Cheng-Wei Shih and Wen-Lian Hsu, "Mencius: A Chinese Named Entity Recognizer Based on a Maximum Entropy Framework ," Computational Linguistics & Chinese Language Processing 9, 65-82, (2004).

W. F. Lu and W. L. Hsu, “A Test for Interval Graphs on Noisy Data,” Lecture Notes in Computer Science 2647, 195-208, (2003).

W. F. Lu and W. L. Hsu, “A Test for the Consecutive Ones Property on Noisy Data - Application to Physical Mapping and Sequence Assembly,” Journal of Computational Biology 10(5), (2003), 709-735; also appeared in Lecture Notes in Computer Science 1276

W. L. Hsu and R. McConnell, “PC-trees and circular-ones arrangements” Theoretical Computer Science 296(1), 99-116, (2003).

Jia-Lin Tsai, Wen-Lian Hsu and Jeng-Woei Su, “Word Sense Disambiguation and Sense-Based NV Event Frame Identifier”, Computational Linguistics & Chinese Language Processing 7, (2002), 29-46.

W. L. Hsu, "A simple test for the consecutive ones property", Journal of Algorithms 43, 1-16, (2002).

W. L. Hsu and Yi-Shiou Chen, "On Phoneme-to-Character Conversion Systems in Chinese Processing," invited paper, Journal of Chinese Institute of Engineers 5, (1999), 573-579.

W. L. Hsu and T. H. Ma, " Fast and simple algorithms for recognizing chordal comparability graphs and interval gragh," SIAM J. Comput. 28, 1004-1020, (1999).

W. K. Shih and W. L. Hsu, "A new planarity test," Theoretical Computer Science 223, 179-191, (1999).

Y. K. Wang , Y. S. Chen and W. L. Hsu, “A knowledge-based approach for natural language processing,” Technical Report, (1998).

W. L. Hsu, "Perfect graphs," Advances in the Theory of Computation and Computational Mathematics 1, 81-122, (1996).

W. L. Hsu, "O(mn) algorithms for the recognition and isomorphism problems on circular-arc graphs," SIAM J. Comput24, 411-439, (1995).

W. L. Hsu and J. P. Spinrad, "Independent sets in circular-arc graphs," J. Algorithms 19, 145-160, (1995).

W. L. Hsu, "Chinese parsing in a phoneme-to-character conversion system based on semantic pattern matching," International Journal on Computer Processing of Chinese and Oriental Languages 40, (1995), 227-236.

K. H. Tsai and W. L. Hsu, "Fast algorithms for the minimum dominating set problem on permutation graphs," Algorithmica 9, (1993), 601-614.

W. L. Hsu, "A new test for interval graphs", Lecture Notes in Computer Science 657, 11-16, (1992).

W. K. Shih, W. L. Hsu and T. C. Chen, "An O(n2 logn ) algorithm for the Hamiltonian cycle problem on circular-arc graphs," SIAM J. Comput 21, 1026-1046, (1992).

W. L. Hsu and K. H. Tsai, "Linear time algorithms on circular-arc graphs," Information processing Letters 40, 123-129, (1991).

W. K. Shih and W. L. Hsu, "An O(nlogn + mloglogn) algorithm for finding a maximum weight clique in circular-arc graphs," Infor. Process. Letters, 129-134, (1989).

W. K. Shih and W. L. Hsu, "An O(n1.5) algorithm for coloring proper circular-arc graphs," Discrete Applied Math 25, 321-323, (1989).

C. Gabor, W. L. Hsu and K. Supowit, "Recognizing circle graphs in polynomial time," J. Assoc. Comput. Machin., 435-473, (1989).

W. L. Hsu, "The coloring and maximum independent set problems on planar perfect graphs," J. Assoc. Comput. Machin., 535-563, (1988).

W. L. Hsu, "Recognizing planar perfect graphs," J. Assoc. Comput. Machin. 34, 255-288, (1987).

W. L. Hsu, "Decomposition of perfect graphs," J. Combin. Theory (B) 43, 70-94, (1987).

W. L. Hsu, "Coloring planar perfect graphs by decomposition," Combinatorica 6 (4), 381-385, (1986).

W. L. Hsu, "Maximum weight clique algorithms for circle graphs and circular-arc graphs," SIAM J. Computing 14, 224-231, (1985).

W. L. Hsu, "Berge's strong perfect graph conjecture on special graphs: A Survey," Annals of Discrete Math. 21, 107-117, (1984).

W. L. Hsu, "Approximation algorithms for the assembly line crew scheduling problem," Math. of Operations Research 9, 376-383, (1984).

W. L. Hsu and G. L. Nemhauser, "Algorithms for maximum weight cliques, minimum weighted clique covers and cardinality colorings of claw-free perfect graphs," Annals of Discrete Math. 21, 317-329, (1984).

Naamad, W. L. Hsu and D. T. Lee, "On the maximum empty rectangle problem," Discrete Applied Math. 8, 267-277, (1984).

W. L. Hsu, "On the general feasibility test of scheduling lot sizes for several products on one machine,' Management Science 29, 93-105, (1983).

W. L. Hsu, "The distance-domination numbers of trees," Operations Research Letters 1, (3), 96-100, (1982).

W. L. Hsu and G. L. Nemhauser, "A polynomial algorithm for the minimum weighted clique cover problem on claw-free perfect graphs," (with G. L. Nemhauser), Discrete Math. 38, 65-71, (1982).

W. L. Hsu, Y. Ikura and G. L. Nemhauser, "A polynomial algorithm for maximum weighted vertex packing on graphs without long odd cycles," Math. Prog. 20, 225-232, (1981).

W. L. Hsu, "How to color claw-free perfect graphs," Annals of Discrete Math. 11, 189-197, (1981).

W. L. Hsu and G. L. Nemhauser, "Algorithm for minimum covering by cliques and maximum cliques in claw-free perfect graphs," Discrete Math. 37, 181-191, (1981).

W. L. Hsu and G. L. Nemhauser, "Easy and hard bottleneck location problems," Discrete Applied Math. 1, 209-215, (1979).

Conference papers

Yung-Chun Chang, Pi-Hua Chuang, Chien Chin Chen and Wen-Lian Hsu, "FISER: An Effective Method for Detecting Interactions between Topic Persons", Lecture Notes in Computer Science Volume 7675, 2012, pp 275-285, 2012.
Yung-Chun Chang, Jian-Ming Chen, Hong-Jie Dai, Johnny Chi-Yang Wu, Chun-Hung Lu, Richard Tzong-Han Tsai, and Wen-Lian Hsu, "TEMPTING: A TEMPoral relation extracting System for the i2b2 2012 TLINK Track," 2012 i2b2 Shared-Tasks and Workshop on Challenges in Natural Language Processing for Clinical Data, Lecture Notes in Artificial Intelligence, November 2012.

Johnny Chi-Yang Wu, Hong-Jie Dai, Richard Tzong-Han Tsai, Wen-Harn Pan, Wen-Lian Hsu, "T-HOD (Text-mined Hypertension, Obesity, Diabetes Candidate Gene Database)," in Proceedings of BioCreative 2012, (2012).

Hong-Jie Dai, Chi-Yang Wu, Richard Tzong-Han Tsai, Wen-Lian Hsu, "From Entity Recognition to Entity Linking: A Survey of Advanced Entity Linking Techniques," in Proceedings of the 26th Annual Conference of the Japanese Society for Artificial Intelligence (JSAI), (2012).

Tang, Wan-Chun; Lu, Chun-Hung; Lu, Ching-Ching; Hsu, Wen-Lian; Hue, Chih-Wei., "On the Use of Praat：A step toward the Improvement of Hakka Pronunciation Teaching," in Proceedings of the International Conference on e-Commerce, e-Administration, e-Society, e-Education, and e-Technology (e-CASE 2011), Japan, 2011.

Lu, Ching-Ching; Lu, Chun-Hung; Meg M. Lu; Hue, Chih-Wei; Hsu, Wen-Lian., "Poetry Writing with e-Learning," in Proceedings of the International Conference on e-Commerce, e-Administration, e-Society, e-Education, and e-Technology (e-CASE 2011), Japan, 2011.

Lu, hing-Ching , Lu, Chun-Hung , Lu, Meg Ming-Chen, Hue, Chih-Wei, Hsu, Wen-Lian., "Canonical Chinese Syntax Awareness Facilitated by an e-Learning Program," Paper presented at EET, Chengdu, China,

Lu, Ching-Ching , Lu, Chun-Hung , Lu, Meg Ming-Chen, Hue, Chih-Wei, Hsu, Wen-Lian., "Canonical Chinese syntax awareness facilited by an e-leraning program," in Proceedings of Advances in Intelligent and Soft Computing, 109, 472-280. Spinger Press, 2011.

Ting-hao Yang, Tian-Jian Jiang, Chan-hung Kuo, “Unsupervised Overlapping Feature Selection for Conditional Random Fields Learning in Chinese Word Segmentation,“ in Proceedings of the 23rd Conference on Computational Linguistics and Speech Processing (ROCLING 2011), pp109-122, (2011) [Errata] [slides]

Mike Tian-Jian Jiang, Cheng-Wei Shih, Chan-Hung Kuo, Richard Tzong-Han Tsai, and Wen-Lian Hsu, "Evaluation via Negativa of Chinese Word Segmentation for Information Retrieval," in Proceedings of the 25th Pacific Asia Conference on Language, Information and Computation (PACLIC 25), pages 100-109, December 16-18, 2011, Singapore. [slides]

Mike Tian-Jian Jiang, Cheng-Wei Lee, Chad Liu, Yung-Chun Chang, and Wen-Lian Hsu, "Robustness Analysis of Adaptive Chinese Input Methods," in proceedings of the Workshop on Advances in Text Input Methods, 5th International Joint Conference on Natural Language Processing (IJCNLP 2011), November 2011.[slides] [Errata]

Mike Tian-Jian Jiang, Chan-Hung Kuo and Wen-Lian Hsu, "English-to-Chinese Machine Transliteration using Accessor Variety Features of Source Graphemes," in Proceedings of the 2011 Named Entities Workshop, IJCNLP 2011, pages 86–90, Chiang Mai, Thailand, November 12, 2011. [slides]

Mike Tian-Jian Jiang, Chan-Hung Kuo and Wen-Lian Hsu, "Using Accessor Variety Features of Source Graphemes in Machine Transliteration of English to Chinese, " International Conference on Technologies and Applications of Artificial Intelligence (TAAI), 2011. [slides] [Errata]

Yi-Hsun Lee, Chung-Yao Chuang, and Wen-Lian Hsu, "Iteratively Estimating Pattern Reliability and Seed Quality With Extraction Consistency" in Proceedings of the 25th Pacific Asia Conference on Language, Information and Computation (PACLIC), Singapore, 2011.

Dai, Hong-Jie, Richard Tzong-Han Tsai and Wen-Lian Hsu, "Entity Disambiguation Using a Markov-Logic Network" in The 5th International Joint Conference on Natural Language Processing (IJCNLP), Chiang Mai, Thailand, 2011.

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).

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", in 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", in Proceedings of the 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).

W. K. Shih and W. L. Hsu, "An approximation algorithm for coloring circular-arc graphs," SIAM conference on Discrete Mathematics, San Francisco, (1990).

K. H. Tsai and W. L. Hsu, "A linear time algorithm for the maximum two track assignment problem," proc. 27th Allerton Conference on Communication, Control and Computing, 291-300, (1989).

W. L. Hsu, "Efficient algorithms for the maximum weight clique problem on circular-arc graphs and circle graphs," Progress in Graph Theory, J. A. Bondy and U. S. R. Murty ed., 335-345, (1984).

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Intelligent Agent Systems Lab│Institute of Information Science│Academia Sinica│GOING	[中文版] [English Version]