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Distinguished Research Fellow  |  Hsu, Wen-Lian  
 
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Publications
 
Journal Articles
 
1. Yung-Chun Chang, Pi-Hua Chuang, Chien Chin Chen and Wen-Lian Hsu, "FISER: A Feature-based Detection System for Topic Person Interactions," Journal of Intelligent Information Systems, Submitted.
2. Yung-Chun Chang, Yu-Lun Hsieh, Cen-Chieh Chen, and Wen-Lian Hsu, "A Semantic Frame-based Intelligent Agent for Topic Detection," Soft Computing, Submitted.
3. Wei-Chun Chung, Chien-Chih Chen, Jan-Ming Ho, Chung-Yen Lin, Wen-Lian Hsu, Yu-Chun Wang, Der-Tsai Lee, Feipei Lai, Chih-Wei Huang and Yu-Jung Chang, "CloudDOE: A User-Friendly Tool for Deploying Hadoop Clouds and Analyzing High-Throughput Sequencing Data with MapReduce," PLoS One, volume 9, number 6, pages 10.1371/journal.pone.0098146, June 2014, http://clouddoe.iis.sinica.edu.tw/ :::icon
4. Yung-Chun Chang, Yu-Lun Hsieh, Cen-Chieh Chen, Wen-Lian Hsu, "Semantic Frame-based Natural Language Understanding for Intelligent Topic Detection Agent," Lecture Notes in Computer Science, volume 8481, pages 339-348, June 2014.
5. Yung-Chun Chang, Johnny Chi-Yang Wu, Jian-Ming Chen, Hong-Jie Dai, Wen-Lian Hsu, "TEMPTing System: A Hybrid Method of Rule and Machine Learning for Temporal Relation Extraction in Patient Discharge Summaries," Journal of Biomedical Informatics, volume 46, pages 54-62, November 2013.
6. Jia-Ming Chang, Jean-Francois Taly, Ionas Erb, Ting-Yi Sung, Wen-Lian Hsu, Chuan Yi Tang, Cedric Notredame, Emily Chia-Yu Su, "Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations," PLoS ONE, volume 8, number 10, pages e75542, October 2013. :::icon
7. Chia-Ying Cheng, Chia-Feng Tsai, Yu-Ju Chen, Ting-Yi Sung* and Wen-Lian Hsu, "Spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications," Journal of Proteome Research, volume 12, pages 2305-2310, April 2013.
8. 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," Transactions on Asian Language Information Processing (TALIP), volume 12, number Issue 1, pages 2:1-23, March 2013. :::icon
9. Hong-Jie Dai, Johnny Chi-Yang Wu, Richard Tzong-Han Tsai, Wen-Harn Pan,Wen-Lian Hsu, "T-HOD: A Literature-based Candidate Gene Database for Hypertension, Obesity, and Diabetes," Database-The Journal of Biological Databases and Curation, volume 2013, number 10.1093, pages bas061, February 2013.
10. 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. :::icon
11. Cheng-Wei Shih, Cheng-Wei Lee, Richard Tzong-Han Tsai, Wen-Lian Hsu, "Validating Contradiction in Texts Using Online Co-Mention Pattern Checking," Transactions on Asian Language Information Processing (TALIP), volume 11, number Issue 4, pages 17:1-12:21, December 2012.
12. 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.
13. 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, volume 7(6), pages e37706, June 2012.
14. 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," JAMIA(Journal of the American Medical Informatics Association) ), volume 19, number 5, pages 888-896, May 2012.
15. 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, number 3, pages e33340, March 2012. :::icon
16. Ting Lo, Chia-Feng Tsai, Yu-Ru V. Shih, Yi-Ting Wang, Sheng-Chieh Lu, Ting-Yi Sung, Wen-Lian Hsu, Yu-Ju Chen, and Oscar K. Lee, "Phosphoproteomic analysis of human mesenchymal stromal cells during osteogenic differentiation," Journal of Proteome Research, volume 11, number 2, pages 586-598, February 2012.
17. 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, volume 12, pages 471, December 2011.
18. 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, volume 27, number 18, pages 2586-2594, June 2011.
19. 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, volume 6, number 5, pages e20199, May 2011.
20. 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," BMC Genomics, volume 11, number S4, December 2010.
21. Hong-Jie Dai, Yen-Ching Chang, Richard Tzong-Han Tsai, and Wen-Lian Hsu, "New challenges for biological text-mining in the next decade," Journal of Computer Science and Technology, volume 25, pages 169-179, 2010.
22. 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, volume 9, pages 5582--5597, 2010.
23. Wei-Chao Chang, Chuan-Kai Chou, Chih-Chiang Tsou, Sheng-Hsiang Li, Chein-Hung Chen, Yu-Xing Zhuo, Wen-Lian Hsu, and Chung-Hsuan Chen, "Comparative Proteomic Analysis of Proteins Involved in Tumorigenic Process of Seminal Vesicle Carcinoma in Transgenic Mice," International Journal of Proteomics, 2010.
24. Hsin-Nan Lin, Ching-Tai Chen, Ting-Yi Sung, Shinn-Ying Ho and Wen-Lian Hsu, "Protein subcellular localization prediction of eukaryotes using a knowledge-based approach," BMC Bioinformatics, volume 10, number Suppl 15, pages S8, December 2009.
25. Chorng-Shyong Ong, Min-Yuh Day and Wen-Lian Hsu, "The measurement of user satisfaction with question answering systems," Information & Management, volume Volume 46, number Issue 7, pages 397-403, October 2009.
26. 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, volume 36(2), number Part 2, pages 3990-3995, 2009.
27. Ke-Shiuan Lynn, Li-Lan Li, Yen-Ju Lin, Chiuen-Huei Wang, Shu-Hui Sheng, Ju-Hwa Lin, Wayne Liao, Wen-Lian Hsu and Wen-Harn Pan, "A Neural Network Model for Constructing Endophenotypes of Common Complex Diseases - An Application to Male Young-onset Hypertension Microarray Data," Bioinformatics, volume 25(8), pages 981-988,, 2009.
28. Richard Tsai, Po T. Lai, Hong J. Dai, Chi H. Huang, Yue Y. Bow, Yen C. Chang, Wen H. Pan, Wen L. Hsu, "HypertenGene: Extracting key hypertension genes from biomedical literature with position and automatically-generated template features," BMC Bioinformatics, volume 10, number Suppl 15. S9, 2009.
29. 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, volume 9, number (Suppl 12):S18., December 2008.
30. 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, number 9(Suppl 1), pages S3, February 2008.
31. 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, volume 7, number 2, pages 487–496, January 2008. :::icon
32. Chia-Wei Wu, Cheng-Wei Lee, Wen-Lian Hsu, Richard Tzong-Han Tsai, "Web Taxonomy Integration System with Hierarchical Shrinkage and Fine-Grained Relations," Expert Systems with Applications, volume 35(4),, pages 2123-2131, 2008.
33. 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, volume 24(23), pages 2691-2697, 2008.
34. 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, number Issue 4, 2008.
35. Cheng-Wei Lee, Yi-Hsun Lee, and Wen-Lian Hsu, "Exploring Shallow Answer Ranking Features in Cross-Lingual and Monolingual Factoid Question Answering," International Journal of Computational Linguistics and Chinese Language Processing, volume 13,, number 1-26,, 2008.
36. 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, number Issue 1, pages 152-167, February 2007.
37. 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, volume 8, number 330, 2007. :::icon
38. 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, 2007.
39. 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, volume 48, pages 582-601, 2007.
40. 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, Chan-Han Chen, Gen-Cher Lee, D.T. Lee, Yow-Ling Shiue, Chang-Wei Yeh, Chao-Hui Chang, Cheng-Yan Kao, Chi-Ying F. Huang, "Detection of the inferred interaction network in hepatocellular carcinoma from EHCO (Encyclopedia of Hepatocellular Carcinoma genes Online)," BMC Bioinformatics, volume 8, number 66, pages 1471-2105, 2007.
41. 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, volume 5, number 9, pages 2328--2338, September 2006.
42. 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, volume 13, number 2, pages 229-244, March 2006.
43. Richard 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, volume 30, number 1, pages 117-128, 2006. :::icon
44. Ching-Tai Chen, Hsin-Nan Lin, Ting-Ying Sung, Wen-Lian Hsu, "HYPLOSP: A Knowledge-based Approach to Protein Local Structure Prediction," Journal of Bioinformatics and Computational Biology, volume 4, pages 1287-1307, 2006.
45. 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, volume 21, pages 3227--3233, August 2005.
46. 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, volume 33, number 14, pages 4593-4601, August 2005.
47. Chun-Hung Lu, Shih-Hung Wu, LiongYu Tu, Wen-Lian Hsu, "Ontological Support in Modeling Learners' Problem Solving Process," Journal of Educational Technology & Society, volume 8, number 4, pages 64-74, 2005.
48. 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, volume 32, number 17, pages 5059-5065, September 2004.
49. Tsai, Jia-Lin, Gladys Hsieh and Wen-Lian Hsu, "Auto-Generation of NVEF Knowledge in Chinese," International Journal of Computational Linguistics and Chinese Language Processing, volume 9, number 1, pages 41-46, February 2004.
50. Richard Tzong-Han Tsai, Shih-Hung Wu, Cheng-Wei Lee, Cheng-Wei Shih and Wen-Lian Hsu, "Mencius: A Chinese Named Entity Recognizer Using Maximum Entropy-based Hybrid Model," International Journal of Computational Linguistics and Chinese Language Processing, volume 9, number 1, pages 65-82, February 2004.
51. 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, volume 10, number 5, pages 709-735, 2003, also appeared in Lecture Notes in Computer Science 1276
52. W. L. Hsu and R. McConnell, "PC-trees and circular-ones arrangements," Theoretical Computer Science, volume 296, number 1, pages 99-116, 2003.
53. W. F. Lu and W. L. Hsu, "A Test for Interval Graphs on Noisy Data," Lecture Notes in Computer Science, volume 2647, pages 195-208, 2003.
54. W. L. Hsu, "A simple test for the consecutive ones property," J. Algorithms, volume 43, pages 1-16, January 2002.
55. Jia-Lin Tsai, Wen-Lian Hsu and Jeng-Woei Su, "Word Sense Disambiguation and Sense-Based NV Event Frame Identifier," International Journal of Computational Linguistics and Chinese Language Processing, number 29-46, 2002.
56. W. L. Hsu and T. H. Ma, "Fast and simple algorithms for recognizing chordal comparability graphs and interval gragh," SIAM J. Computing, volume 28, pages 1004-1020, 1999.
57. W. L. Hsu and Yi-Shiou Chen, "On Phoneme-to-Character Conversion Systems in Chinese Processing," Chinese Institute of Engineers, volume 5, pages 573-579, 1999.
58. W. K. Shih and W. L. Hsu, "A new planarity test," Theoretical Computer Science, volume 223, pages 179-191, 1999.
59. W. L. Hsu, "Perfect Graphs," Advances in the Theory of Computation and Computational Mathematics, volume 1, pages 81-122, January 1996.
60. W. L. Hsu and J. P. Spinrad, "Independent sets in circular-arc graphs," J. Algorithms, volume 19, pages 145-160, January 1995.
61. W. L. Hsu, "O(mn) algorithms for the recognition and isomorphism problems on circular-arc graphs," volume 24, pages 411-439, 1995.
62. W. L. Hsu, "Chinese parsing in a phoneme-to-character conversion systembased on semantic pattern matching," International Journal on Computer Processing of Chinese and Oriental Languages, volume 40, pages 227-236, 1995.
63. K. H. Tsai and W. L. Hsu, "Fast algorithms for the minimum dominating set problem on permutation graphs," Algorithmica, pages 601-614, 1993.
64. W. K. Shih, W. L. Hsu and T. C. Chen, "An O(n2logn) algorithm for the Hamiltonian cycle problem on circular-arc graphs," volume 21, pages 1026-1046, 1992.
65. W. L. Hsu and K. H. Tsai, "Linear time algorithms on circular-arc graphs," Information processing Letters, volume 40, pages 123-129, 1991.
66. C. Gabor, W. L. Hsu and K. Supowit, "Recognizing circle graphs in polynomial time," volume 36, number 3, pages 435-473, July 1989.
67. 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, pages 129-134, 1989.
68. W. K. Shih and W. L. Hsu, "An O(n1.5) algorithm for coloring proper circular-arc graphs," Discrete Applied Mathematics, volume 25, pages 321-323, 1989.
69. W. L. Hsu, "The coloring and maximum independent set problems on planar perfect graphs," volume 35, number 3, pages 535-563, July 1988.
70. W. L. Hsu, "Recognizing planar perfect graphs," J. Assoc. Comput. Machin., volume 34, number 2, pages 255-288, April 1987.
71. W. L. Hsu, "Decomposition of perfect graphs," J. Combin. Theory, volume 43, pages 70-94, 1987.
72. W. L. Hsu, "Coloring planar perfect graphs by decomposition," Combinatorica, volume 6, number 4, pages 381-385, 1986.
73. W. L. Hsu, "Maximum weight clique algorithms for circle graphs and circular-arc graphs," SIAM J. Computing, volume 14, pages 224-231, 1985.
74. W. L. Hsu, "Berge's strong perfect graph conjecture on special graphs: A Survey," Annals of Discrete Mathematics, volume 21, pages 107-117, 1984.
75. A. Naamad, W. L. Hsu and D. T. Lee, "On the maximum empty rectangle problem," Discrete Applied Mathematics, volume 8, pages 267-277, 1984.
76. 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 Mathematics, volume 21, pages 317-329, 1984.
77. W. L. Hsu, "Approximation algorithms for the assembly line crew scheduling problem," Math. of Operations Research, volume 9, pages 376-383, 1984.
78. W. L. Hsu, "On the general feasibility test of scheduling lot sizes for several products on one machine," Management Science, volume 29, pages 93-105, 1983.
79. W. L. Hsu and G. L. Nemhauser, "A polynomial algorithm for the minimum weighted clique cover problem on claw-free perfect graphs," Discrete Mathematics, volume 38, pages 65-71, 1982.
80. W. L. Hsu, "The distance-domination numbers of trees," Operations Research Letters, volume 1, number 3, pages 96-100, 1982.
81. W. L. Hsu, "How to color claw-free perfect graphs," Annals of Discrete Mathematics, volume 11, pages 189-197, 1981.
82. W. L. Hsu and G. L. Nemhauser, "Algorithm for minimum covering by cliques and maximum cliques in claw-free perfect graphs," Discrete Mathematics, volume 37, pages 181-191, 1981.
83. W. L. Hsu, Y. Ikura and G. L. Nemhauser, "A polynomial algorithm for maximum weighted vertex packing on graphs without long odd cycles," Math., volume 20, pages 225-232, 1981.
84. W. L. Hsu and G. L. Nemhauser, "Easy and hard bottleneck location problems," Discrete Applied Mathematics, volume 1, pages 209-215, 1979.
 
 
Conference Papers
 
1. Yung-Chun Chang, Yu-Lun Hsieh, Chad Liu, Cen-Chieh Chen, Johnny Chi-Yang Wu, Wen-Lian Hsu, "A Frame-based Approach for Detecting Reader's Emotion," The 23rd ACM International Conference on Information and Knowledge Management (CIKM 2014), Submitted.
2. Yung-Chun Chang, Yu-Lun Hsieh, Cen-Chieh Chen, Chad Liu, Chun-Hung Lu, Wen-Lian Hsu, "Semantic Frame-based Statistical Approach for Topic Detection," The 28th Pacific Asia Conference on Language, Information and Computing (PACLIC 28), Submitted.
3. Yung-Chun Chang, Chien Chin Chen, Wen-Lian Hsu, "Discovering the interactions between persons from Chinese Topic Documents," The 26th Conference on Computational Linguistics and Speech Processing (ROCLING 2014), Submitted.
4. Yu-Lun Hsieh, Shih-Hung Liu, Ting-Hao Yang, Yu-Hsuan Chen, Yung-Chun Chang, Chiu-Chen Hsieh, Cheng-Wei Shih, Chun-Hung Lu, Wen-Lian Hsu, "A Frame-based Approach for Reference Metadata Extraction," The 2014 Conference on Technologies and Applications of Artificial Intelligence (TAAI 2014), Submitted.
5. Kuan-Yu Chen, Shih-Hung Liu, Berlin Chen, Ea-Ee Jan, Hsin-Min Wang, Wen-Lian Hsu, and Hsin-Hsi Chen, "Leveraging Effective Query Modeling Techniques for Speech Recognition and Summarization," the Conference on Empirical Methods in Natural Language Processing (EMNLP 2014), Doha, Qatar, October 2014.
6. Kuan-Yu Chen, Shih-Hung Liu, Berlin Chen, Hsin-Min Wang, Wen-Lian Hsu, and Hsin-Hsi Chen, "A Recurrent Neural Network Language Modeling Framework for Extractive Speech Summarization," IEEE International Conference on Multimedia & Expo (ICME 2014), July 2014, (acceptance rate: 29.7%) :::icon
7. Yung-Chun Chang, Yu-Lun Hsieh, Cen-Chieh Chen, Wen-Lian Hsu, "Semantic Frame-based Natural Language Understanding for Intelligent Topic Detection Agent," The 27th International Conference on Industrial, Engineering & Other Applications of Applied Intelligent Systems (IEA-AIE 2014), Lecture Notes in Computer Science, volume 8481, Springer, pages 339-348, June 2014.
8. Shih-Hung Liu, Kuan-Yu Chen, Yu-Lun Hsieh, Berlin Chen, Hsin-Min Wang, Hsu-Chun Yen, Wen-Lian Hsu, "Effective pseudo-relevance feedback for language modeling in extractive speech summarization," IEEE Int. Conf. Acoustics, Speech, and Signal Processing (ICASSP2014), Florence,Italy, May 2014. :::icon
9. Yung-Chun Chang, Chien Chin Chen, and Wen-Lian Hsu, "A Composite Kernel Approach for Detecting Interactive Segments in Chinese Topic Documents," the 9th Asia Information Retrieval Societies Conference (AIRS 2013), Lecture Notes in Computer Science, pages 215-226, December 2013.
10. Shih-Hung Liu, Kuan-Yu Chen, Hsin-Min Wang, Wen-Lian Hsu, and Berlin Chen, "Improved Sentence Modeling Techniques for Extractive Speech Summarization," The 25th ROCLING Conference on Computational Linguistics and Speech Processing, October 2013, (in Chinese) (best paper award) :::icon
11. Chen-Chun Chen, Cheng-Wei Cheng, Ke-Shiuan Lynn, Wan-Chih Su, Chia-Ying Cheng, Wen-Lian Hsu, Chi-Huey Wong, Yu-Ju Chen and Ting-Yi Sung, "GlycoPepDecipher: Automated Identification of Intact N-linked Glycopeptides," 12th HUPO World Congress, September 2013.
12. Hui-Yin Chang, Nai-Yuan Chiang, Chia-Feng Tsai, Ya-Wen Tsai, Yu-Ju Chen, Ting-Yi Sung and Wen-Lian Hsu, "ProtDIA-id: An automatic tool to extract MS/MS spectra for protein identification in proteomic experiments using data-independent acquisition," 61th ASMS Conference on Mass Spectrometry and Allied Topics, June 2013.
13. T. Mamie Lih, Ke-Shiuan Lynn, Hui-Ying Chang, Mei-Ling Cheng, Ming-Shi Shiao, Wen-Harn Pan, Ting-Yi Sung and Wen-Lian Hsu, "Metab-ID: a software for metabolite identification from MS1 data," 61th ASMS Conference on Mass Spectrometry and Allied Topics, June 2013.
14. Yung-Chun Chang, Pi-Hua Chuang, Chien Chin Chen and Wen-Lian Hsu, "FISER : An Effective Method for Detecting Interactions between Topic Persons," the 8th Asia Information Retrieval Societies Conference (AIRS 2012), Lecture Notes in Artificial Intelligence, pages 267-277, December 2012.
15. From Entity Recognition to Entity Linking: A Survey of Advanced Entity Linking Techniques, "Hong-Jie Dai, Chi-Yang Wu, Richard Tzong-Han Tsai, Wen-Lian Hsu," the 26th Annual Conference of the Japanese Society for Artificial Intelligence (JSAI), December 2012.
16. Yung-Chun Chang, Pi-Hua Chuang, Chien Chin Chen, and Wen-Lian Hsu, "FISER: An Effective Method for Detecting Interactions between Topic Persons," the 8th Asia Information Retrieval Societies Conference (AIRS 2012), Lecture Notes in Computer Science, pages 275-285, December 2012.
17. 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.
18. Hui-Yin Chang, Ke-Shiuan Lynn, T. Mamie Lih, Nai-Yuan Chiang, Mei-Ling Cheng, Wen-Harn Pan, Yet-Ran Chen, Ting-Yi Sung, Wen-Lian Hsu, "Metab-Q: An automatic tool for metabolic fingerprinting," 60th ASMS Conference on Mass Spectrometry and Allied Topics, ASMS, May 2012.
19. Chia-Ying Cheng, Chia-Feng Tsai, Han-Yin Yang, Yu-Ju Chen, Ting-Yi Sung, Wen-Lian Hsu, "Improving peptide identification by integrating database searching and spectral library searching," 60th ASMS Conference on Mass Spectrometry and Allied Topics, ASMS, May 2012.
20. Chih-Chiang Tsou, Han-Yin Yang, Ying-Che Chang, Kay-Hooi Khoo, Yu-Ju Chen, Alexey Nesvizhskii, Ting-Yi Sung, Wen-Lian Hsu, "IDEAL-Q+: computational tool for labeling and label-free mass spectrometry-based proteomics," 60th ASMS Conference on Mass Spectrometry and Allied Topics, ASMS, May 2012.
21. 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)," BioCreative 2012, April 2012.
22. 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," 25th Pacific Asia Conference on Language, Information and Computation (PACLIC 25), pages 100-109, Singapore, December 2011.
23. Chung-Yao Chuang, Yi-Hsun Lee, and Wen-Lian Hsu, "Text Patterns and Compression Models for Semantic Class Learning," Proceedings of the 5th International Joint Conference on Natural Language Processing, Chiang Mai, Thailand, November 2011. :::icon :::icon
24. Mike Tian-Jian Jiang, Cheng-Wei Lee, Chad Liu, Yung-Chun Chang, and Wen-Lian Hsu, "Robustness Analysis of Adaptive Chinese Input Methods," Workshop on Advances in Text Input Methods, 5th International Joint Conference on Natural Language Processing (IJCNLP 2011), November 2011.
25. Dai, Hong-Jie, Richard Tzong-Han Tsai and Wen-Lian Hsu, "Entity Disambiguation Using a Markov-Logic Network," The 5th International Joint Conference on Natural Language Processing (IJCNLP), Chiang Mai, Thailand, November 2011.
26. Ting-hao Yang, Tian-Jian Jiang, Chan-hung Kuo, "Unsupervised Overlapping Feature Selection for Conditional Random Fields Learning in Chinese Word Segmentation," 23rd Conference on Computational Linguistics and Speech Processing (ROCLING 2011), pages 109-122, November 2011.
27. 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," the 8th Taiwan Society for Mass Spectrometry Anaual Conference (TSMS2011), Taipei, Taiwan, July 2011.
28. Mike Tian-Jian Jiang, Cheng-Wei Lee, Chad Liu, Yung-Chun Chang and Wen-Lian Hsu, "Robustness Analysis of Adaptive Chinese Input Methods," the Workshop on Advances in Text Input Methods (WTIM 2011), Lecture Notes in Computer Science, pages 53-61, July 2011.
29. Hong-Jie Dai, Wei-Chi Tsai, Richard Tzong-Han Tsai,and Wen-Lian Hsu, "Enhancing search results with semantic annotation using augmented browsing," the Twenty-second International Joint Conference on Artifical Intelligence (IJCAI), Barcelona, Catalonia (Spain), July 2011.
30. Han-Yin Yang, Chih-Chiang Tsou, Yi-Ju Chen, Yen-Yi Lin, Yu-Ju Chen, Ting-Yi Sung, and Wen-Lian Hsu, "An automated tool for detecting modification-specific marker ions to improve the sensitivity of modified peptide identification," 59th ASMS Conference on Mass Spectormetry, June 2011.
31. 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," the International Conference on e-Commerce, e-Administration, e-Society, e-Education, and e-Technology (e-CASE 2011), January 2011.
32. Hsing-Kuo Lee, Chun-Hung Lu, Wen-Lian Hsu, Ching-Ching Lu, "Using Adaptive Learning Theory and a Schedule-based Flashcard to Enhance the Quality of Online Self Learning," the e-Case & e-Tech 2011, Tokyo, Japan, 2011.
33. 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," the e-Case & e-Tech 2011, Tokyo, Japan, 2011.
34. Chih-Chiang Tsou, Han-Yin Yang, Ting-Yi Sung, and Wen-Lian Hsu, "IDEAL-Q Plus: extended version for stable isotope labeling, label-free, and comparative quantitation analysis with assigning reliability to protein quantitation ratio," HUPO2010, September 2010.
35. Sheng-Shieh Lu, Chia-Feng Tsai, Chih-Chiang Tsou, Han-Ying 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, July 2010.
36. Pei-Yi Lin, Chia-Feng Tsai, Chih-Chiang Tsou, Chia-Li Han, Yi-Ting Wang, Ting-Yi Sung, Wen-Lian Hsu, and Yu-Ju Chen, "High-speed proteomic signature by informatics-assisted label-free quantitation," 58th ASMS Conference on Mass Spectrometry, May 2010.
37. Yi-Ting Wang, Chia-Feng Tsai, Tzu-Chan Hong, Chih-Chiang Tsou, Pei-Yi Lin, Sih-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," 58th ASMS Conference on Mass Spectrometry, May 2010.
38. Chung-Yao Chuang and Wen-Lian Hsu, "Multivariate Multi-Model Approach for Globally Multimodal Problems," In Proceedings of ACM SIGEVO Genetic and Evolutionary Computation Conference 2010 (GECCO-2010), pages 311-318, 2010.
39. 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, June 2009.
40. 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, June 2009.
41. 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, June 2009.
42. Dai H-J, Lai P-T, Huang C-H, Chang Y-C, Bow Y-Y, Wu H-T, Tsai RT-H, Hsu W-L, "IASL-IISR Interactor Normalization System: Using a Multi-stage Gene Normalization Algorithm and SVM-based ranking," BioCreAtIvE II5 Challenge Evaluation Workshop, Madrid, Spain, 2009.
43. Emily Chia-Yu Su, Jia-Ming Chang, Ting-Yi Sung, and Wen-Lian Hsu, "Prediction of Protein Nuclear Localization Based on Smoothed Evolutionary Information and Probabilistic Latent Semantic Indexing," The 7th Asia Pacific Bioinformatics Conference, Beijing, China, 2009.
44. Lin RTK, Chiu JL-T, Dai H-J, Tsai RT-H, Day M-Y, Hsu W-L, "A supervised learning approach to biological question answering," Integrated Computer-Aided Engineering 2009, volume 16:271-281, 2009.
45. Lai P-T, Bow Y-Y, Huang C-H, Dai H-J, Tsai RT-H, 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.
46. Tsai RT-H, Lai P-T, Dai H-J, Huang C-H, Chang Y-C, Hsu W-L, "HypertenGene: Extracting key hypertension genes from biomedical literature with position and automatically-generated template features," 8th InCoB - Seventh International Conference on Bioinformatics, 2009.
47. Ryan T.K. Lin, Justin Liang-Te Chiu, Hong-Jei Dai, Min-Yuh Day, Richard Tzong-Han Tsai, Wen-Lian Hsu, "Biological Question Answering with Syntactic and Semantic Feature Matching and an Improved Mean Reciprocal Ranking Measurement," IEEE International Conference on Information Reuse and Integration (IEEE IRI 2008), July 2008.
48. Cheng-Lung Sung, Cheng-Wei Lee, Hsu-Chun Yen, Wen-Lian Hsu, "An Alignment-based Surface Pattern for a Question Answering System," the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2008), pages pp. 172-177., July 2008.
49. Chorng-Shyong Ong, Min-Yuh Day, Wen-Lian Hsu, "Development of an Evaluation Model for Question Answering Systems," IEEE International Conference on Information Reuse and Integration (IEEE IRI 2008), pages pp. 178-183., July 2008.
50. Ryan T.K. Lin, Hong-Jei Dai, Yue-Yang Bow, Min-Yuh Day, Richard Tzong-Han Tsai, Wen-Lian Hsu, "Result Identification for Biomedical Abstracts Using Conditional Random Fields," IEEE International Conference on Information Reuse and Integration (IEEE IRI 2008), July 2008.
51. Chorng-Shyong Ong, Min-Yuh Day, Kuo-Tay Chen, Wen-Lian Hsu, "User-Centered Evaluation of Question Answering Systems," IEEE International Conference on Intelligence and Security Informatics (IEEE ISI 2008), number pp. 286-287, June 2008.
52. 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, June 2008.
53. 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," the First International Workshop on Social Computing (SOCO 2008), Lecture Notes in Computer Science, volume Vol. 5075,, number pp. 343-354., June 2008.
54. 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, June 2008.
55. 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, June 2008.
56. 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, June 2008.
57. Cheng-Lung Sung, Min-Yuh Day, Hsu-Chun Yen, Wen-Lian Hsu, "A Template Alignment Algorithm for Question Classification," IEEE International Conference on Intelligence and Security Informatics (IEEE ISI 2008), pages pp. 197-199, June 2008.
58. 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," IJCNLP, 2008.
59. Ethan Y. H. Tsui, Yi-Hwa Yian, Chih-Chiang Tsou, Paul C. Y. Yu, Ke-Shiuan Lynn, Wen-Chi Chou, Yi-Ju Chen, Yu-Ju Chen, Ting-Yi Sung, Wen-Lian Hsu, "MaXIC-Q: A Fully Automated Generic Tool Using Statistical and Computational Methods for Protein Quantitation Based on Isotope Labeling and LC-MS," 56th ASMS Conference on Mass Spectrometry, Denver, Colorado, 2008.
60. Cheng-Lung Sung, Hsu-Chun Yen, Wen-Lian Hsu, "Compute the Term Contributed Frequency," Intelligent Systems Design And Applications (ISDA2008), 2008.
61. Emily Chia-Yu Su, Jia-Ming Chang, Ting-Yi Sung, Wen-Lian Hsu, "Prediction of Protein Nuclear Localization Based on Smoothed Evolutionary Information and Probabilistic La-tent Semantic Indexing," The 19th International Conference on Genome Informatics, Gold Coast , Australia, 2008.
62. 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, pages pp. 70-76,, Tokyo, Japan, 2008.
63. Chia-Wei Wu, Wen-Lian Hsu, Richard Tzong-Han Tsai, "Semi-joint Labeling for Chinese Named Entity Recognition," AIRS'08, 2008.
64. Chih-Chiang. Tsou, Chuan-Yih Yu, Ethan Yin-Hao Tsui, Ting-Yi Sung, Wen-Lian Hsu, "LaFree-Q: A New Generic Tool for Label-free Quantitative Proteomics," Proteomics Society International Conference 2007, December 2007, Poster
65. Chuan-Yih Yu, Ethan Yin-Hao Tsui, Chih-Chiang Tsou, Ting-Yi Sung, and Wen-Lian Hsu, "MSMRI: A Comprehensive Visualization and Validation Tool for Mass Spectral Analysis," Taiwan Proteomics Society International Conference 2007, December 2007, Poster
66. 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," IEEE International Conference on Information Reuse and Integration (IEEE IRI 2007), pages pp. 203-208, Las Vegas, Nevada, USA, August 2007.
67. Richard Tzong-Han Tsai, Hong-Jei Dai, Hsi-Chuan Hung, Ryan T.K. Lin, Wen-Chi Chou, Ying-Shan Su, Min-Yuh Day, and Wen-Lian Hsu, "BESearch: A Supervised Learning Approach to Search for Molecular Event Participants," Proceedings of the IEEE International Conference on Information Reuse and Integration (IEEE IRI 2007), pages 412-417, August 2007.
68. 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," NTCIR-6 Workshop Meeting, pages pp. 26-30, Tokyo, Japan, May 2007.
69. 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," NTCIR-6 Workshop Meeting, pages pp. 175-181, Tokyo, Japan, May 2007.
70. 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," InterSpeech, 2007.
71. Hsi-Chuan Hung, Richard Tzong-Han Tsai, & Wen-Lian Hsu, "Identifying Protein Interaction Abstracts with Contextual Bag of Words," AAAI-07 Student Workshop, 2007.
72. Hong-Jie Dai, Hsieh-Chuan Hung, Richard Tzong-Han Tsai, and Wen-Lian Hsu, "IASL Systems in the Gene Mention Tagging Task and Protein Interaction Article Sub-task," Proceedings of Second BioCreAtIvE Challenge Evaluation Workshop, pages 69-76, 2007.
73. 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," Proceedings of the Sixth International Conference on Bioinformatics (InCoB 2007), 2007.
74. 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," IEEE International Conference on Information Reuse and Integration (IEEE IRI 2006), Waikoloa, Hawaii, USA, September 2006.
75. Hong-Jie Dai, Hsieh-Chuan Hung, Cheng-Lung Sung, Min-Yuh Day, Wen-Lian Hsu, "Chinese Word Segmentation with Minimal Linguistic Knowledge: An Improved Conditional Random Fields Coupled with Character Clustering and Automatically Discovered Template Matching," Proceedings of the 2006 IEEE International Conference on Information Reuse and Integration (IRI-2006), number Pages 274 - 279, September 2006.
76. 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 the Fifth SIGHAN Workshop on Chinese Language Processing, pages 108--117, July 2006.
77. Ching-Tai Chen, Hsin-Nan Lin, Kun-Pin Wu, Ting-Yi Sung, and Wen-Lian Hsu, "A Knowledge-based Approach to Protein Local Structure Prediction," Asia Pacific Bioinformatics Conference (APBC), 2006, (acceptance rate: 29%) :::icon
78. 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), Stanford, CA, 2006. :::icon
79. Emily Chia-Yu Su, Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, 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. :::icon
80. 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.
81. 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," Proceedings of ACL Workshop on Frontiers in Linguistically Annotated Corpora, 2006. :::icon
82. Chun-Hung Lu, Guey-Fa Chiou, Min-Yuh Day, Chorng-Shyong Ong, and Wen-Lian Hsu, "Using Instant Messaging to Provide an Intelligent Learning Environment," ITS, 4053, pages 575-583, 2006.
83. 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.," IEEE IRI-06., 2006.
84. 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," Proceedings of IEEE International Conference on Granular Computing (IEEE GrC), 2006. :::icon
85. 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," BioNLP-2006, 2006.
86. Shih-Hung Wu, Cheng-Wei Shih, Chia-Wei Wu, Richard Tzong-Han Tsai, and Wen-Lian Hsu, "Applying Maximum Entropy to Robust Chinese Shallow Parsing," Proceedings of ROCLING2005, 2005.
87. Min-Yuh Day, Richard 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.
88. 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," IEEE NLP-KE 2005, 2005.
89. 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, 2005.
90. Cheng-Wei Lee, Cheng-Wei Shih, Min-Yuh Day, Tzorg-Han Tsai, Tian-Jian Jiang, Chia-Wei Wu, Cheng-Lung Sung, Yu-Ren Chen, Shih-Hung Wu, Wen-Lian Hsu, "ASQA: Academia Sinica Question Answering System," Proceedings of NTCIR-5 CLQA Track, 2005.
91. 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," Workshop on the Sciences of Artificial (WSA) 2005, invited paper, 2005.
92. Tsai, T.-H., Wu, C.-W., Lin, Y.-C. and Hsu, W.-L., "Exploiting full parsing information to label semantic roles using an ensemble of ME and SVM via integer linear programming," CoNLL-2005, 2005.
93. 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.
94. Wen-Lian Hsu, "A Linear Time Algorithm for Finding a Maximal Planar Subgraph Based on PC-Trees," COCOON' 05, 2005.
95. 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.
96. 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, 2005.
97. 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, "ASQA: Academia Sinica Question Answering System for NTCIR-5 CLQA," NTCIR-5 Workshop, pages 202-208, Tokyo, Japan, 2005.
98. 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, "Perspectives on Chinese Question Answering Systems," Workshop on the Sciences of the Artificial (WSA 2005), Hualien, Taiwan, 2005.
99. Wen-Lian 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," Proceedings of IEEE Fourth Symposium on Bioinformatics and Bioengineering (BIBE2004), pages 89-90, May 2004.
100. Yi-Feng Lin, Wen-Chi Chou, Kuen-Pin Wu, Ting-Yi Sung, and Wen-Lian Hsu, "InfoMap: A Framework for Integrated Proteomic Knowledge Base," Proceedings of 3rd International Proteomics Conference (IPC' 04), 2004, invited talk
101. Chun-Hung Lu, Shih-Hung Wu, LiongYu Tu, and Wen-Lian Hsu, "The Design of An Intelligent Tutoring System Based on the Ontology of Procedural Knowledge," Proceedings of ICALT2004, 2004.
102. Wen-Lian Hsu, "Survey - A Paradigm Shift in Biological Computing," French-Taiwanese Conference on Information Technology, 2004, invited talk
103. Cheng-Wei Shih, Richard 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.
104. 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.
105. Jia-Lin Tsai, Cheng-Wei Shih, and Wen-Lian Hsu, "Applying Bottom-to-Top Mapping to Chinese Shallow Parsing," Proceedings of AIRS' 04, 2004.
106. W. F. Lu and W. L. Hsu, "A Clustering Algorithm for Interval Graph Test on Noisy Data," Experimental and Efficient Algorithms: Second International Workshop, WEA 2003, Lecture Notes in Computer Science, 2647, pages 195-208, January 2003.
107. 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, 2003.
108. K. P. Wu, H. N. Lin, T. Y. Sung, and W. L. Hsu, "A New Similarity Measure among Protein Sequences," Proceedings of IEEE CSB2003 Computer Society Bioinformatics Conference, 2003.
109. Wen-Lian Hsu, "A Paradigm Shift in Biological Computing," Fudan International Bioinformatics Workshop, 2003, invited talk
110. 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, 2003.
111. Richard Tzong-Han Tsai, Shih-Hung Wu, and Wen-Lian Hsu, "Mencius: A Chinese Named Entity Recognizer Based on a Maximum Entropy Framework," Proceedings of ROCLING2003, 2003.
112. 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.
113. Jia-Lin Tsai, Gladys Hsieh and Wen-Lian Hsu, "Auto-Discovery of NVEF Word-Pairs in Chinese," Proceedings of ROCLING2003, 2003.
114. Jia-Lin Tsai, Cheng-Lung Sung and Wen-Lian Hsu, "Chinese Word Auto-Confirmation Agent," Proceedings of ROCLING2003, 2003.
115. C. W. Hue C. H. Kao, M. Lo, L. Y. Tu and W. L. Hsu, "NTUs: An Intelligent Tutorial System Fosters Number Concepts Through Computational Scaffolding," ICCE' 02, Auckland, 2002.
116. 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.
117. G. 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.
118. W.L. Hsu, "PC-Trees and Maximal Planar Subgraphs," ICS' 02, 2002, Keynote speech
119. S. H. Wu and W. L. Hsu, "AutoMap: A Semi-Automatic Ontology Acquisition Tool for Chinese Corpus," COLING' 02, Taipei, 2002.
120. L.Y., Tu, W. L. Hsu and S. H., Wu, "A Cognitive Student Model - An Ontological Approach," ICCE' 02, Auckland, 2002.
121. Shih-Hung Wu, Min-Yuh Day, Wen-Lian Hsu, "FAQ-Centered Organizational Memory," IJCAI'01 Workshop on Knowledge Management and Organizational Memories, Seattle, August 2001, Seattle
122. Wen-Lian Hsu, "PC-Trees vs. PQ-Trees," Annual Internationall Computing and Combinatorics Conference, Lecture Notes in Computer Science, 2108, pages 207-217, August 2001.
123. W. L. Hsu, Y. S. Chen and S. H. Wu, "Concept Structure Identification Based on the Information Map - INFOMAP," NLPKE'01, International Conference on Natural Language Processing and Knowledge Engineering, Tucson, January 2001.
124. W. L. Hsu, S. H. Wu, L. Y. Tu and M. Shia, "Applying Dialogue Systems to Student Model," GCCCE '01, January 2001.
125. G. Lin, W. K. Wong, W. L. Hsu, S. H. Wu, "Knowledge-Based Understanding of Simple Text about Geometry," GCCCE '01, January 2001.
126. 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.
127. W. L. Hsu, Y. S. Chen and S. H. Wu, "Event Identification Based on the Information Map - INFOMAP," NLPKE' 01, Tucson, 2001.
128. W. L. Hsu, "PC-trees vs. PQ-trees," Workshop on Graph Structures and Algorithms, January 2000, invited talk, University of Toronto
129. H. L. Wang, S. H. Wu, I. C. Wang, C. L. Sung, W. L. Hsu, W. K. Shih, "Semantic Search on Internet Tabular Information Extraction for Answering Queries," Information and Knowledge Management, pages 243-249, Washington DC, January 2000.
130. W. L. Hsu, "Simulating Human Intelligence," Fifth Conference on Artificial Intelligence and Application, Taipei, January 2000, Keynote speech
131. W. L. Hsu, "Interactive CAI in Natural Language," International Conference on Computer Assisted Instruction and Internet Computing, Taipei, January 2000, Keynote Speech
132. H. L. Wang, W. K. Shih, C. N. Hsu, Y. S. Chen, Y. L. Wang and W. L. Hsu, "Personal Navigating Agent," Proceedings of the third annual conference on Autonomous Agents, ACM, pages 432-433, April 1999.
133. W. L. Hsu, Yi-Shiou Chen and Yuan-Kai Wang, "Natural language agents – An agent society on the Internet," PRIMA'99, January 1999.
134. C. C. Chen and W. L. Hsu, "A document similarity measurement without dictionaries," Fourth International Workshop on Information Retrieval with Asian Languages IRAL'99, January 1999.
135. W. L. Hsu, "網際網路的檢索與知識管理," National Computer Symposium, Taipei, January 1999, 專題講座
136. Y. K. Wang , W. L. Hsu and Y. S. Chen, "The anaphoric expressions of Chinese algebraic word problem," International Symposium on Multimedia Information Processing, Chung-Li, Taiwan, R.O.C., December 1998.
137. 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," 26th International Conference on Coastal Engineering, ICCE'98, Copenhagen, Denmark, June 1998.
138. W. L. Hsu, W. F. Lu, "On clone assembly algorithms - an error tolerant test for interval graph recognition," IEEE International Joint Symposia on Intelligence and Systems, pages 118-125, May 1998.
139. W. L. Hsu, "Fault Tolerant DNA computing," DIMACS Workshop, Hong Kong, January 1998, invited talk
140. W. L. Hsu, Yi-Shiou Chen and Yuan-Kai Wang, "A Context sensitive model for concept understanding," International Conference on Information-Theoretic Approaches to Logic, Language, and Computation, ITALLC'98, pages 161-169, January 1998.
141. Y. K. Wang , Y. S. Chen and W. L. Hsu, "Empirical study of mandarin Chinese discourse analysis," 10th IEEE International Conference on Tools with AIName, January 1998.
142. W. L. Hsu and W. F. Lu, "From Satellite DNA to HTML table understanding," CTS Workshop on Combinatorics and Algorithms, Taipei, January 1998, invited talk
143. Yi-Shiou Chen, Schy Chiou, Yuan-Kai Wang, and Wen-Lian Hsu, "Personal Brower," ACM SIGIR Conf on Information Retrieval, 1998.
144. Y. K. Wang , Y. S. Chen and W. L. Hsu, "A knowledge-based approach for natural language processing," Technical Reports, 1998.
145. W. L. Hsu, "Elementary school Math. tutoring agent," Agent Technology Workshop, January 1997.
146. W. L. Hsu, "On physical mapping algorithms - an error tolerant test for the consecutive ones property," Annual International Computing and Combinatorics Conference, Lecture Notes in Computer Science, 1276, pages 242-250, January 1997.
147. W. L. Hsu, W. K. Shih and P. H. Yeh, "Object oriented concept representation," Int'l Conf. on Computer Processing of Oriental Languages, ICCPOL'95, Honolulu, Hawaii, November 1995.
148. W. L. Hsu, "On-line recognition of interval graphs," ACM Conference on Computer and Communication Security, Lecture Notes in Computer Science, 1120, pages 27-38, Brest, France, July 1995.
149. W. L. Hsu, "Finding maximal planar subgraphs in linear time," International Symposium on Algorithms and Computation, Lecture Notes in Computer Science, 1004, volume 1004, Springer, pages 352-361, Cairns, Australia, January 1995.
150. W. L. Hsu, "On the design of a computer that speak fluent Chinese," RAMs'95, January 1995.
151. 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," Intl Conf on Document Analysis and Recognition, IEEE, pages 35-40, October 1993.
152. 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," The 6th International symposium on Cognitive Aspects of the Chinese Language, pages 527-540, January 1993.
153. W. K. Shih and W. L. Hsu, "A simple test for planar graphs," Proceedings of the International Workshop on Discrete Math. and Algorithms, pages 110-122, University of Hong Kong, 1993.
154. W. L. Hsu, "A new test for interval graphs," Workshop on Graph Theory, Lecture Notes in Computer Science, 657, pages 11-16, January 1992.
155. W. K. Shih and W. L. Hsu, "An approximation algorithm for coloring circular-arc graphs," SIAM Conference on Discrete Mathematics, San Francisco, January 1990.
156. K. H. Tsai and W. L. Hsu, "A linear time algorithm for the maximum two track assignment problem," 27th Allerton Conference on Communication, pages 291-300, January 1989, Control and Computing
 
 
Others
 
1.
2. Jhih-Siang Lai, Cheng-Wei Cheng, Allan Lo, Ting-Yi Sung and Wen-Lian Hsu, "Lipid exposure prediction enhances the inference of rotational angles of transmembrane helices," Submitted.
3. Hsin-Nan Lin, Ting-Yi Sung and Wen-Lian Hsu, "Sequence and Genome Analysis: Methods and Applications," Z. Zhao, editor, iConcept Press, 2010.
4. Wen-Lian Hsu and Ting-Yi Sung,, chapter "Automated generic analysis tools for protein quantitation using stable isotope labeling," "Proteome Bioinformatics," Simon J. Hubbard and Andrew R. Jones, editors, Methods in Molecular Biology, volume 604, pages 257-272, Humana Press, 2010.
5. Hsin-Nan Lin, Ting-Yi Sung and Wen-Lian Hsu, "Identification of Essential Residues from Protein Secondary Structure Prediction and Applications," Z. Zhao, editor, Sequence and Genome Analysis: Methods and Applications, 2010.
6. Ethan Yin-Hao Tsui, Yi-Hwa Yian, Chih-Chiang Tsou, Paul Chuan-Yih Yu, Ke-Shiuan Lynn, Wen-Chi Chou, Yi-Ju Chen, Yu-Ju Chen, Ting-Yi Sung, and Wen-Lian Hsu, "MaXIC-Q: A Fully Automated Generic Tool Using Statistical and Computational Methods for Protein Quantitation Based on Stable Isotope Labeling and LC-MS," TR-IIS-08-004, Institute of Information Science, Academia Sinica 2008.
7. Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, Wen-Lian Hsu, TR-IIS-007-010, "On the accuracy of transmembrane helix prediction methods using an updated benchmark," Institute of Information Science, Academia Sinica 2007. :::icon
8. Jia-Ming Chang, Emily Chia-Yu Su, Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, and Wen-Lian Hsu, "PSLDoc: Protein subcellular localization prediction based on document classification," ., 2007. :::icon
9. Jia-Ming Chang, Emily Chia-Yu Su, Allan Lo, Hua-Sheng Chiu, Ting-Yi Sung, and Wen-Lian Hsu, "A document classification strategy to predict protein subcellular localization using sequence motifs and evolutionary information," 2007. :::icon
10. W. L. Hsu, "An Efficient Implementation of the PC-Tree Algorithm of Shih & Hsu's Planarity Test," number TR-IIS-03-015, Institute of Information Science, Academia Sinica 2003.
11. W. L. Hsu,, chapter "Efficient algorithms for the maximum weight clique problem on circular-arc graphs and circle graphs," Progress in graph theory, J. Adrian Bondy and U.S.R. Murty, editors, pages 335-345, Academic Press, January 1984.
 
 
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