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研
人 Distinguished Research Fellow
員 許聞廉 Wen-Lian Hsu
Faculty Ph.D., Operations Research, Cornell University, United States
T +886-2-2788-3799 ext. 2211 E hsu@iis.sinica.edu.tw
F +886-2-2782-4814 W iasl.iis.sinica.edu.tw/hsu/en/about/
・ Associate Professor (with tenure), Department of IE/MS, Northwestern University (1986-
1989)
・ K.T. Lee Research Breakthrough Award（李國鼎穿石獎）(1999)
・ President, Taiwanese Association for Arti cial Intelligence (TAAI) (2001-2002)
・ NSC Appointed Outstanding Re-search Award（國科會傑出特約研究員獎）(2005)
・ IEEE Fellow (2006)
・ President, Association for Computational Linguistics and Chinese Language Processing
(ACLCLP) (2011-2012)
・ Distinguished Research Fellow, Institute of Information Science, Academia Sinica,
(2008-present)
・ Director, Institute of Information Science, Academia Sinica (2012-2018)
Research Description
My main research interests include the following: graph algorithms, natural language understanding; and bioinformatics. In graph
algorithms, we have done extensive and ground-breaking work on two fundamental classes of special graphs, namely interval graphs and
planar graphs, in which a new data structure PC-tree was introduced as a natural representation for planar graph embedding. In natural
language understanding, we have developed the following: a) A Chinese input system, GOING ( 自然輸入法 ), which is being used by more
than a million people in Taiwan; b) A knowledge annotation and inference kernel, InfoMap, which supports the implementation of our
NLU modules and has helped us win numerous awards in international contests, such as Chinese question answering, word segmentation,
recognizing Inference in Text Tasks. In biological literature mining, we also won the 1st place in BioCreative gene normalization task in 2009
and 2017; c) A statistical principle-based approach (SPBA) as well as a reduction algorithm (together called RPBA), which is a conceptual
pattern-based machine learning (ML) approach that garners the bene ts of both rule-based and traditional statistical ML approaches. RPBA
can be simultaneously used for speech recognition, parsing, natural language generation, and machine translation, which is perfect for
NLU. We have been awarded by MOST a 4-year AI innovation grant of US$ 400,000 a year on NLU and Dialogue system. In bioinformatics,
we have developed the following: a) A suite of software for protein quantitation (Multi-Q, Maxi-Q, and Ideal-Q); b) An ultra-e cient divide-
and-conquer algorithm, called Kart, for NGS read mapping, which divides a read into small fragments that can be aligned independently in
parallel. Superb results were obtained applying this to RNA-seq, and whole genome comparison; c) An automated method, Auto-CHO, for
the programmable one-pot oligosaccharide synthesis, drastically reducing the complexity of intermediate separation and protecting group
manipulation.
Publications
1. C. Gabor, W. L. Hsu and K. Supowit, "Recognizing circle graphs Chin Chen, Wen-Lian Hsu, "Linguistic Template Extraction for
in polynomial time," J. Assoc. Comput. Machin., 435-473, (1989). Recognizing Reader-Emotion and Emotional Resonance Writing
Assistance," ACL-IJCNLP 2015, 775-780, (2015).
2. W. K. Shih and W. L. Hsu, "A new planarity test," Theoretical
Computer Science 223, 179-191, (1999). 7. Chih-Hung Chou, Nai-Wen Chang, …, Wen-Lian Hsu,*
and Hsien-Da Huang,* "miRTarBase 2016: updates to the
3. K. P. Wu, H. N. Lin, J. M. Chang, T. Y. Sung, and W. L. Hsu, experimentally validated miRNA-target interactions database,"
"HYPROSP: A Hybrid Protein Secondary Structure Prediction Nucleic Acids Research, doi: 10.1093/nar/gkv1258, November
Algorithm - a Knowledge-Based Approach," Nucleic Acids 20, (2015).
Research 32(17), 5059-5065, (2004).
8. Hsin-Nan Lin and Wen-Lian Hsu, "Kart: a divide-and-conquer
4. Hong-Jie Dai, Chi-Hsin Huang, Ryan T. K. Lin, Richard Tzong- algorithm for NGS read alignment," Bioinformatics 33, 2281-
Han Tsai, and Wen-Lian Hsu, "BIOSMILE web search: a web 2287, (2017).
application for annotating biomedical entities and relations,"
Nucleic Acids Research 36, W390-W398, (2008). 9. Cheng-Wei Cheng, Yixuan Zhou, Wen-Harn Pan, Supriya Dey,
Chung-Yi Wu, Wen-Lian Hsu, Chi-Huey Wong, "Hierarchical
5. Chih-Chiang Tsou, Chia-Feng Tasi, Ying-Hao Tsui, Putty-Reddy and programmable one-pot synthesis of oligosaccharides," Nature
Sudhir, Yi-Ting Wang, Yu-Ju Chen, Jeou-Yuan Chen, Ting- Communications 9, Article number:5202, (2018).
Yi Sung, and Wen-Lian Hsu, "IDEAL-Q: An automated tool
for label-free quantitation analysis using an efficient peptide 10. Ming-Siang Huang, Po-Ting Lai, Pei-Yen Lin, Yu-Ting You,
alignment approach and spectral data validation," Molecular & Richard Tzong-Han Tsai and Wen-Lian Hsu, Biomedical Named
Cellular Proteomics 9, 131-144, (2010). Entity Recognition and Linking Datasets: Survey and Our Recent
Development, Briefings in Bioinformatics (Oxford), March
6. Yung-Chun Chang, Cen-Chieh Chen, Yu-Lun Hsieh, Chien (2020).
146
人 Distinguished Research Fellow
員 許聞廉 Wen-Lian Hsu
Faculty Ph.D., Operations Research, Cornell University, United States
T +886-2-2788-3799 ext. 2211 E hsu@iis.sinica.edu.tw
F +886-2-2782-4814 W iasl.iis.sinica.edu.tw/hsu/en/about/
・ Associate Professor (with tenure), Department of IE/MS, Northwestern University (1986-
1989)
・ K.T. Lee Research Breakthrough Award（李國鼎穿石獎）(1999)
・ President, Taiwanese Association for Arti cial Intelligence (TAAI) (2001-2002)
・ NSC Appointed Outstanding Re-search Award（國科會傑出特約研究員獎）(2005)
・ IEEE Fellow (2006)
・ President, Association for Computational Linguistics and Chinese Language Processing
(ACLCLP) (2011-2012)
・ Distinguished Research Fellow, Institute of Information Science, Academia Sinica,
(2008-present)
・ Director, Institute of Information Science, Academia Sinica (2012-2018)
Research Description
My main research interests include the following: graph algorithms, natural language understanding; and bioinformatics. In graph
algorithms, we have done extensive and ground-breaking work on two fundamental classes of special graphs, namely interval graphs and
planar graphs, in which a new data structure PC-tree was introduced as a natural representation for planar graph embedding. In natural
language understanding, we have developed the following: a) A Chinese input system, GOING ( 自然輸入法 ), which is being used by more
than a million people in Taiwan; b) A knowledge annotation and inference kernel, InfoMap, which supports the implementation of our
NLU modules and has helped us win numerous awards in international contests, such as Chinese question answering, word segmentation,
recognizing Inference in Text Tasks. In biological literature mining, we also won the 1st place in BioCreative gene normalization task in 2009
and 2017; c) A statistical principle-based approach (SPBA) as well as a reduction algorithm (together called RPBA), which is a conceptual
pattern-based machine learning (ML) approach that garners the bene ts of both rule-based and traditional statistical ML approaches. RPBA
can be simultaneously used for speech recognition, parsing, natural language generation, and machine translation, which is perfect for
NLU. We have been awarded by MOST a 4-year AI innovation grant of US$ 400,000 a year on NLU and Dialogue system. In bioinformatics,
we have developed the following: a) A suite of software for protein quantitation (Multi-Q, Maxi-Q, and Ideal-Q); b) An ultra-e cient divide-
and-conquer algorithm, called Kart, for NGS read mapping, which divides a read into small fragments that can be aligned independently in
parallel. Superb results were obtained applying this to RNA-seq, and whole genome comparison; c) An automated method, Auto-CHO, for
the programmable one-pot oligosaccharide synthesis, drastically reducing the complexity of intermediate separation and protecting group
manipulation.
Publications
1. C. Gabor, W. L. Hsu and K. Supowit, "Recognizing circle graphs Chin Chen, Wen-Lian Hsu, "Linguistic Template Extraction for
in polynomial time," J. Assoc. Comput. Machin., 435-473, (1989). Recognizing Reader-Emotion and Emotional Resonance Writing
Assistance," ACL-IJCNLP 2015, 775-780, (2015).
2. W. K. Shih and W. L. Hsu, "A new planarity test," Theoretical
Computer Science 223, 179-191, (1999). 7. Chih-Hung Chou, Nai-Wen Chang, …, Wen-Lian Hsu,*
and Hsien-Da Huang,* "miRTarBase 2016: updates to the
3. K. P. Wu, H. N. Lin, J. M. Chang, T. Y. Sung, and W. L. Hsu, experimentally validated miRNA-target interactions database,"
"HYPROSP: A Hybrid Protein Secondary Structure Prediction Nucleic Acids Research, doi: 10.1093/nar/gkv1258, November
Algorithm - a Knowledge-Based Approach," Nucleic Acids 20, (2015).
Research 32(17), 5059-5065, (2004).
8. Hsin-Nan Lin and Wen-Lian Hsu, "Kart: a divide-and-conquer
4. Hong-Jie Dai, Chi-Hsin Huang, Ryan T. K. Lin, Richard Tzong- algorithm for NGS read alignment," Bioinformatics 33, 2281-
Han Tsai, and Wen-Lian Hsu, "BIOSMILE web search: a web 2287, (2017).
application for annotating biomedical entities and relations,"
Nucleic Acids Research 36, W390-W398, (2008). 9. Cheng-Wei Cheng, Yixuan Zhou, Wen-Harn Pan, Supriya Dey,
Chung-Yi Wu, Wen-Lian Hsu, Chi-Huey Wong, "Hierarchical
5. Chih-Chiang Tsou, Chia-Feng Tasi, Ying-Hao Tsui, Putty-Reddy and programmable one-pot synthesis of oligosaccharides," Nature
Sudhir, Yi-Ting Wang, Yu-Ju Chen, Jeou-Yuan Chen, Ting- Communications 9, Article number:5202, (2018).
Yi Sung, and Wen-Lian Hsu, "IDEAL-Q: An automated tool
for label-free quantitation analysis using an efficient peptide 10. Ming-Siang Huang, Po-Ting Lai, Pei-Yen Lin, Yu-Ting You,
alignment approach and spectral data validation," Molecular & Richard Tzong-Han Tsai and Wen-Lian Hsu, Biomedical Named
Cellular Proteomics 9, 131-144, (2010). Entity Recognition and Linking Datasets: Survey and Our Recent
Development, Briefings in Bioinformatics (Oxford), March
6. Yung-Chun Chang, Cen-Chieh Chen, Yu-Lun Hsieh, Chien (2020).
146
