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Distinguished Research Fellow/Professor  |  Hsu, Wen-Lian  
 
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Publications
 
Journal Articles
 
1. Chi-Jen Chen, Neha Warikoo, Yung-Chun Chang, Jin-Hua Chen, and Wen-Lian Hsu, "Medical Knowledge Infused Convolutional Neural Networks for Cohort Selection in Clinical Trials," to appear in JAMIA(Journal of the American Medical Informatics Association) ).
2. Ming-Siang Huang, Po-Ting Lai, Pei-Yen Lin, Yu-Ting You, Richard Tzong-Han Tsai and Wen-Lian Hsu, "Biomedical Named Entity Recognition and Linking Datasets: Survey and Our Recent Development," Briefings in Bioinformatics, July 2020.
3. Hsin-Nan Lin ,Wen-Lian Hsu, "GSAlign: an efficient sequence alignment tool for intra-species genomes," BMC Genomics, volume 21, number 182, pages 1-10, February 2020. :::icon
4. Hsi-Yuan Huang, Yang-Chi-Dung Lin, Jing Li, Kai-Yao Huang, Sirjana Shrestha, Hsiao-Chin Hong, Yun Tang, Yi-Gang Chen, Chen-Nan Jin, Yuan Yu, Jia-Tong Xu, Yue-Ming Li, Xiao-Xuan Cai, Zhen-Yu Zhou, Xiao-Hang Chen, Yuan-Yuan Pei, Liang Hu, Jin-Jiang Su, Shi-Dong Cui, Fei Wang, Yue-Yang Xie, Si-Yuan Ding, Meng-Fan Luo, Chih-Hung Chou, Nai-Wen Chang, Kai-Wen Chen, Yu-Hsiang Cheng, Xin-Hong Wan, Wen-Lian Hsu, Tzong-Yi Lee, Feng-Xiang Wei, Hsien-Da Huang, "miRTarBase 2020: updates to the experimentally validated microRNA–target interaction database," Nucleic Acids Research (Oxford), volume 48, number D1, pages D148–D154, October 2019.
5. Hong-Jie Dai, Chen-Kai Wang, Nai-Wen Chang, Ming-Siang Huang, Jitendra Jonnagaddala, Feng-Duo Wang, Wen-Lian Hsu, "Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature," Database (Oxford), volume 2019, pages Appeared, February 2019.
6. Po-Ting Lai, Ming-Siang Huang, Ting-Hao Yang, Richard Tzong-Han Tsai, Wen-Lian Hsu, "Statistical Principle-based Approach for Gene and Protein Related Object Recognition," Journal of Cheminformatics, volume 10, pages 64, December 2018.
7. Cheng-Wei Cheng, Yixuan Zhou, Wen-Harn Pan, Supriya Dey, Chung-Yi Wu, Wen-Lian Hsu and Chi-Huey Wong, "Hierarchical and programmable one-pot synthesis of oligosaccharides," Nature Communications, volume 9, number 5202, pages 1-9, December 2018.
8. Neha Warikoo, Yung-Chun Chang, and Wen-Lian Hsu, "LPTK: A Linguistic Pattern-Aware Dependency Tree Kernel Approach for the BioCreative VI CHEMPROT Task," Database (Oxford), volume 2018, pages bay108, October 2018.
9. Yung-Chun Chang, Cheng-Wei Shih, and Wen-Lian Hsu, "Entailment-based Intelligent Agent for Software Project Monitoring and Control," IEEE Systems Journal, volume 12, number 1, pages 216-227, March 2018, 10.1109/JSYST.2016.2563463
10. Hsin-Nan Lin and Wen-Lian Hsu, "DART: a fast and accurate RNA-seq mapper with a partitioning strategy," Bioinformatics, volume 34, number 2, pages 190-197, January 2018.
11. Hui-Yin Chang, Ching-Tai Chen, Chu-Ling Ko, Yi-Ju Chen, Yu-Ju Chen, Wen-Lian Hsu, Chiun-Gung Juo, Ting-Yi Sung, "iTop-Q: an intelligent tool for top-down proteomics quantita-tion using DYAMOND algorithm," Analytical Chemistry, volume 89, number 24, pages 13128–13136, December 2017, DOI: 10.1021/acs.analchem.7b02343 :::icon
12. Hsin-Nan Lin and Wen-Lian Hsu, "Kart: a divide-and-conquer algorithm for NGS read alignment," Bioinformatics, volume 1;33(15), pages 2281-2287, August 2017.
13. Shih-Hung Liu, Kuan-Yu Chen, Yu-Lun Hsieh, Berlin Chen, Hsin-Min Wang, Hsu-Chun Yen, and Wen-Lian Hsu, "A Position-Aware Language Modeling Framework for Extractive Broadcast News Speech Summarization," ACM Transactions on Asian and Low-Resource Language Information Processing, volume 16, number 4, pages 1-13, Article 27, August 2017.
14. Yung-Chun Chang, Pi-Hua Chuang, Chien Chin Chen and Wen-Lian Hsu, "FISER: A Feature-based Detection System for Topic Person Interactions," Computational Intelligence, volume 2017, pages 5, May 2017.
15. Yung-Chun Chang, Cheng-Wei Shih, Wen-Lian Hsu, "Entailment-based Intelligent Agent for Software Project Monitoring and Control," IEEE Systems Journal, volume 12, pages 216-227, March 2017.
16. Nai-Wen Chang, Hong-Jie Dai, Yung-Yu Shih, Chi-Yang Wu, Mira Anne C Dela Rosa, Rofeamor P Obena, Yu-Ju Chen, Wen-Lian Hsu, Yen-Jen Oyang, "Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy," Database (Oxford), volume 2017, pages bax082, January 2017.
17. Yung-Chun Chang, Chun-Han Chu, Chien Chin Chen, and Wen-Lian Hsu, "Linguistic Template Extraction for Recognizing Reader-Emotion," International Journal of Computational Linguistics and Chinese Language Processing, volume 21, number 1, pages 29-50, September 2016.
18. Yuxiang Jiang, ..., Caster Chen, Wen-Lian Hsu et al., "An expanded evaluation of protein function prediction methods shows an improvement in accuracy," Genome Biology, volume 7;17(1), pages 184, September 2016.
19. Yung-Chun Chang, Chun-Han Chu, Yu-Chen Su, Chien Chin Chen, and Wen-Lian Hsu, "PIPE: A BioC Module for Protein-protein Interaction Passage Extraction," Database (Oxford), volume 2016, pages baw101, August 2016.
20. Yung-Chun Chang, Chien Chin Chen, and Wen-Lian Hsu, "SPIRIT: A Tree Kernel-based Method for Topic Person Interaction Detection," IEEE Transactions on Knowledge and Data Engineering (TKDE), volume 28, number 9, pages 2494-2507, August 2016.
21. T. Mamie Lih, Wai-Kok Choong, Chen-Chun Chen, Cheng-Wei Cheng, Hsin-Nan Lin, Ching-Tai Chen, Hui-Yin Chang, Wen-Lian Hsu and Ting-Yi Sung, "MAGIC-web: a platform for untargeted and targeted N-linked glycoprotein identification," Nucleic Acids Research, volume 44, number Web Server Issue, pages W575-580, July 2016.
22. Hong-Jie Dai, Chu-Hsien Su, Po-Ting Lai, Ming-Siang Huang, Jitendra Jonnagaddala, Toni Rose Jue, Shruti Rao, Hui-Jou Chou, Marija Milacic, Onkar Singh, Syed Abdul Shabbir, Wen-Lian Hsu, "MET network in PubMed: a text-mined network visualization and curation system," Database (Oxford), volume ., number ., pages ., May 2016.
23. Hui-Yin Chang, Ching-Tai Chen, T. Mamie Lih, Ke-Shiuan Lynn, Chiun-Gung Juo, Wen-Lian Hsu, Ting-Yi Sung, "iMet-Q: a user-friendly tool for metabolomics quantitation using dynamic peak-width determination," PLoS ONE, volume 11, number 1, pages e0146112, January 2016.
24. Yung-Chun Chang, Zhong-Yong Chen, Chien Chin Chen, and Wen-Lian Hsu, "Constructing Topic Person Interaction Networks Using a Tree Kernel-based Method," International Journal of Languages, Literature and Linguistics, volume 1, number 4, pages 238-245, December 2015.
25. Wai-Kok Choong, Hui-Yin Chang, Ching-Tai Chen, Chia-Feng Tsai, Wen-Lian Hsu, Yu-Ju Chen, and Ting-Yi Sung, "Informatics View on the Challenges of Identifying Missing Proteins from Shotgun Proteomics," Journal of Proteome Research, volume 14, number 12, pages 5396-5407, December 2015.
26. Nai-Wen Chang, Hong-Jie Dai, Jitendra Jonnagaddala, Chih-Wei Chen, Richard Tzong-Han Tsai, Wen-Lian Hsu, "A Context-Aware Approach for Progression Tracking of Medical Concepts in Electronic Medical Records," Journal of Biomedical Informatics, volume S150-7, pages ., December 2015.
27. Chih-Hung Chou, Nai-Wen Chang, Sirjana Shrestha, Sheng-Da Hsu, Yu-Ling Lin, Wei-Hsiang Lee, Chi-Dung Yang, Hsiao-Chin Hong, Ting-Yen Wei, Siang-Jyun Tu, Tzi-Ren Tsai, Shu-Yi Ho, Ting-Yan Jian, Hsin-Yi Wu, Pin-Rong Chen, Nai-Chieh Lin, Hsin-Tzu Huang, Tzu-Ling Yang, Chung-Yuan Pai, Chun-San Tai, Wen-Liang Chen, Chia-Yen Huang, Chun-Chi Liu, Shun-Long Weng, Kuang-Wen Liao, Wen-Lian Hsu,* and Hsien-Da Huang*, "miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database," Nucleic Acids Research, volume doi: 10.1093/nar/gkv1258, pages ., November 2015.
28. Kuan-Yu Chen, Shih-Hung Liu, Berlin Chen, Hsin-Min Wang, Ea-Ee Jan, Wen-Lian Hsu, Hsin-Hsi Chen, "Extractive broadcast news summarization leveraging recurrent neural network language modeling techniques," IEEE/ACM Transactions on Audio, Speech, and Language Processing, volume 23, number 8, pages 1322-1334, August 2015. :::icon
29. Yung-Chun Chang, Yu-Lun Hsieh, Cen-Chieh Chen, and Wen-Lian Hsu, "A Semantic Frame-based Intelligent Agent for Topic Detection," Soft Computing, volume 2015, pages 1-11, July 2015.
30. Shih-Hung Liu, Kuan-Yu Chen, Berlin Chen, Hsin-Min Wang, Hsu-Chun Yen, and Wen-Lian Hsu, "Combining Relevance Language Modeling and Clarity Measure for Extractive Speech Summarization," IEEE/ACM Transactions on Audio, Speech, and Language Processing, volume 23, number 6, pages 957 - 969, June 2015. :::icon
31. Ke-Shiuan Lynn, Mei-Ling Cheng, Yet-Ran Chen, Chin Hsu, Ann Chen, T. Mamie Lih, Hui-Yin Chang, Ching-jang Huang, Ming-Shi Shiao, Wen-Harn Pan*, Ting-Yi Sung*, and Wen-Lian Hsu*, "Metabolite Identification for Mass Spectrometry-Based Metabolomics Using Multiple Types of Correlated Ion Information," Analytical Chemistry, volume 87, number 4, pages 2143–2151, February 2015.
32. Ke-Shiuan Lynn, Chen-Chun Chen, T. Mamie Lih, Cheng-Wei Cheng, Wan-Chih Su, Chun-Hao Chang, Chia-Ying Cheng, Wen-Lian Hsu, Yu-Ju Chen, and Ting-Yi Sung, "MAGIC: An Automated N-Linked Glycoprotein Identification Tool Using a Y1-Ion Pattern Matching Algorithm and in Silico MS2 Approach," Analytical Chemistry, volume 87, number 4, pages 2466-2473, February 2015. :::icon
33. Hong-Jie Dai, Johnny Chi-Yang Wu , Wei-San Lin, Aaron James F. Reyes, Mira Anne C. dela Rosa, Shabbir Syed-Abdul, Richard Tzong-Han Tsai and Wen-Lian Hsu, "LiverCancerMarkerRIF: a liver cancer biomarker interactive curation system combining text mining and expert annotations," Database-The Journal of Biological Databases and Curation, volume ., number ., pages pii: bau085, August 2014.
34. 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/ (IF: 3.730,Journal ranking: Multidisciplinary Sciences/Q1: 7/56, 12.5%) :::icon
35. 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.
36. 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.
37. 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
38. Ke-Shiuan Lynn, Chen-Hua Lu, Han-Ying Yang, Wen-Lian Hsu and Wen-Harn Pan, "Construction of Gene Clusters Resembling Genetic Causal Mechanisms for Common Complex Disease with an Application to Young-Onset Hypertension," BMC Genomics, volume 14, number 497, pages ., July 2013.
39. 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, number 5, pages 2305-2310, May 2013.
40. Chia-Ying Cheng, Chia-Feng Tsai, Yu-Ju Chen, Ting-Yi Sung, and Wen-Lian Hsu, "A spectrum-based method to generate good decoy libraries for spectral library searching in peptide identifications," Journal of Proteome Research, volume 3, number 12(5), pages 2305-10, April 2013.
41. 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
42. 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.
43. 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
44. 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.
45. 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.
46. 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.
47. 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.
48. 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, number 4, pages e35018, April 2012.
49. 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
50. 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.
51. 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, volume 6, number 12, pages e27872, December 2011.
52. 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.
53. 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.
54. 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.
55. 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 Acids Research, volume 39, number Database issue (Suppl. 1 ), pages D347--355, January 2011.
56. 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.
57. 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.
58. 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.
59. 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.
60. 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., pages S9, December 2009.
61. 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.
62. 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.
63. 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, volume 16, number 3, pages 259-269, June 2009.
64. Chih-Chiang Tsou, Yin-Hao Tsui, Yi-Hwa Yian, Yi-Ju Chen, Chuan-Yih Yu, Han-Yin Yang, 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, volume 37, pages W661-W669, June 2009.
65. 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, volume 25, number 8, pages 996-1003, April 2009.
66. 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, April 2009.
67. 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.
68. 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.
69. Cheng-Wei Cheng, Emily Chia-Yu Su, Jenn-Kang Hwang, Ting-Yi Sung and Wen-Lian Hsu, "Predicting RNA-binding sites of proteins using support vector machines and evolutionary information," BMC Bioinformatics, volume 9, number (Suppl 12), pages S6, December 2008.
70. Chia-Wei Wu, Cheng-Wei Lee, Wen-Lian Hsu, Richard Tzong-Han Tsai, "Web taxonomy integration with hierarchical shrinkage algorithm and fine-grained relations," Expert Systems with Applications, volume 35, number 4, pages 2123-2131, November 2008.
71. 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, November 2008.
72. 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 Acids Research, volume 36, pages W390-W398, July 2008.
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," BMC Bioinformatics, number 9(Suppl 1), pages S3, February 2008.
74. 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
75. 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.
76. 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.
77. 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.
78. 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, volume 8, number 325, pages ., September 2007.
79. 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, volume W707-712, pages 35, June 2007.
80. 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, May 2007.
81. 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, February 2007.
82. 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.
83. 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, volume ., pages ., January 2007.
84. 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
85. 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, volume 7, number S11, pages ., December 2006.
86. 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.
87. 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.
88. Richard 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, volume 7, number 92, pages ., February 2006.
89. 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, February 2006.
90. 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
91. 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.
92. 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.
93. 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.
94. 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.
95. 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.
96. 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.
97. 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
98. W. L. Hsu and R. McConnell, "PC-trees and circular-ones arrangements," Theoretical Computer Science, volume 296, number 1, pages 99-116, 2003.
99. 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.
100. W. L. Hsu, "A simple test for the consecutive ones property," J. Algorithms, volume 43, pages 1-16, January 2002.
101. 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.
102. 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.
103. 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.
104. W. K. Shih and W. L. Hsu, "A new planarity test," Theoretical Computer Science, volume 223, pages 179-191, 1999.
105. W. L. Hsu, "Perfect Graphs," Advances in the Theory of Computation and Computational Mathematics, volume 1, pages 81-122, January 1996.
106. W. L. Hsu and J. P. Spinrad, "Independent sets in circular-arc graphs," J. Algorithms, volume 19, pages 145-160, January 1995.
107. W. L. Hsu, "O(mn) algorithms for the recognition and isomorphism problems on circular-arc graphs," volume 24, pages 411-439, 1995.
108. 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.
109. K. H. Tsai and W. L. Hsu, "Fast algorithms for the minimum dominating set problem on permutation graphs," Algorithmica, pages 601-614, 1993.
110. 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.
111. W. L. Hsu and K. H. Tsai, "Linear time algorithms on circular-arc graphs," Information processing Letters, volume 40, pages 123-129, 1991.
112. C. Gabor, W. L. Hsu and K. Supowit, "Recognizing circle graphs in polynomial time," volume 36, number 3, pages 435-473, July 1989.
113. 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.
114. 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.
115. W. L. Hsu, "The coloring and maximum independent set problems on planar perfect graphs," volume 35, number 3, pages 535-563, July 1988.
116. W. L. Hsu, "Recognizing planar perfect graphs," J. Assoc. Comput. Machin., volume 34, number 2, pages 255-288, April 1987.
117. W. L. Hsu, "Decomposition of perfect graphs," J. Combin. Theory, volume 43, pages 70-94, 1987.
118. W. L. Hsu, "Coloring planar perfect graphs by decomposition," Combinatorica, volume 6, number 4, pages 381-385, 1986.
119. W. L. Hsu, "Maximum weight clique algorithms for circle graphs and circular-arc graphs," SIAM J. Computing, volume 14, pages 224-231, 1985.
120. 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.
121. W. L. Hsu, "Approximation algorithms for the assembly line crew scheduling problem," Math. of Operations Research, volume 9, pages 376-383, 1984.
122. A. Naamad, W. L. Hsu and D. T. Lee, "On the maximum empty rectangle problem," Discrete Applied Mathematics, volume 8, pages 267-277, 1984.
123. W. L. Hsu, "Berge's strong perfect graph conjecture on special graphs: A Survey," Annals of Discrete Mathematics, volume 21, pages 107-117, 1984.
124. 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.
125. 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.
126. W. L. Hsu, "The distance-domination numbers of trees," Operations Research Letters, volume 1, number 3, pages 96-100, 1982.
127. 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.
128. 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.
129. W. L. Hsu, "How to color claw-free perfect graphs," Annals of Discrete Mathematics, volume 11, pages 189-197, 1981.
130. W. L. Hsu and G. L. Nemhauser, "Easy and hard bottleneck location problems," Discrete Applied Mathematics, volume 1, pages 209-215, 1979.
 
 
 
 
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