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685 results on '"Hsu, Wen-Lian"'

1. Natural Adversarial Sentence Generation with Gradient-based Perturbation

Author

Hsieh, Yu-Lun, Cheng, Minhao, Juan, Da-Cheng, Wei, Wei, Hsu, Wen-Lian, and Hsieh, Cho-Jui

Subjects
Computer Science - Information Retrieval, Computer Science - Computation and Language, Computer Science - Cryptography and Security, Computer Science - Machine Learning
Abstract

This work proposes a novel algorithm to generate natural language adversarial input for text classification models, in order to investigate the robustness of these models. It involves applying gradient-based perturbation on the sentence embeddings that are used as the features for the classifier, and learning a decoder for generation. We employ this method to a sentiment analysis model and verify its effectiveness in inducing incorrect predictions by the model. We also conduct quantitative and qualitative analysis on these examples and demonstrate that our approach can generate more natural adversaries. In addition, it can be used to successfully perform black-box attacks, which involves attacking other existing models whose parameters are not known. On a public sentiment analysis API, the proposed method introduces a 20% relative decrease in average accuracy and 74% relative increase in absolute error.

Published
2019

2. Revised JNLPBA Corpus: A Revised Version of Biomedical NER Corpus for Relation Extraction Task

Author

Huang, Ming-Siang, Lai, Po-Ting, Tsai, Richard Tzong-Han, and Hsu, Wen-Lian

Subjects
Computer Science - Information Retrieval, Computer Science - Computation and Language
Abstract

The advancement of biomedical named entity recognition (BNER) and biomedical relation extraction (BRE) researches promotes the development of text mining in biological domains. As a cornerstone of BRE, robust BNER system is required to identify the mentioned NEs in plain texts for further relation extraction stage. However, the current BNER corpora, which play important roles in these tasks, paid less attention to achieve the criteria for BRE task. In this study, we present Revised JNLPBA corpus, the revision of JNLPBA corpus, to broaden the applicability of a NER corpus from BNER to BRE task. We preserve the original entity types including protein, DNA, RNA, cell line and cell type while all the abstracts in JNLPBA corpus are manually curated by domain experts again basis on the new annotation guideline focusing on the specific NEs instead of general terms. Simultaneously, several imperfection issues in JNLPBA are pointed out and made up in the new corpus. To compare the adaptability of different NER systems in Revised JNLPBA and JNLPBA corpora, the F1-measure was measured in three open sources NER systems including BANNER, Gimli and NERSuite. In the same circumstance, all the systems perform average 10% better in Revised JNLPBA than in JNLPBA. Moreover, the cross-validation test is carried out which we train the NER systems on JNLPBA/Revised JNLPBA corpora and access the performance in both protein-protein interaction extraction (PPIE) and biomedical event extraction (BEE) corpora to confirm that the newly refined Revised JNLPBA is a competent NER corpus in biomedical relation application. The revised JNLPBA corpus is freely available at iasl-btm.iis.sinica.edu.tw/BNER/Content/Revised_JNLPBA.zip., Comment: 17 pages

Published
2019
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3. An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Author

Jiang, Yuxiang, Oron, Tal Ronnen, Clark, Wyatt T, Bankapur, Asma R, D'Andrea, Daniel, Lepore, Rosalba, Funk, Christopher S, Kahanda, Indika, Verspoor, Karin M, Ben-Hur, Asa, Koo, Emily, Penfold-Brown, Duncan, Shasha, Dennis, Youngs, Noah, Bonneau, Richard, Lin, Alexandra, Sahraeian, Sayed ME, Martelli, Pier Luigi, Profiti, Giuseppe, Casadio, Rita, Cao, Renzhi, Zhong, Zhaolong, Cheng, Jianlin, Altenhoff, Adrian, Skunca, Nives, Dessimoz, Christophe, Dogan, Tunca, Hakala, Kai, Kaewphan, Suwisa, Mehryary, Farrokh, Salakoski, Tapio, Ginter, Filip, Fang, Hai, Smithers, Ben, Oates, Matt, Gough, Julian, Törönen, Petri, Koskinen, Patrik, Holm, Liisa, Chen, Ching-Tai, Hsu, Wen-Lian, Bryson, Kevin, Cozzetto, Domenico, Minneci, Federico, Jones, David T, Chapman, Samuel, C., Dukka B K., Khan, Ishita K, Kihara, Daisuke, Ofer, Dan, Rappoport, Nadav, Stern, Amos, Cibrian-Uhalte, Elena, Denny, Paul, Foulger, Rebecca E, Hieta, Reija, Legge, Duncan, Lovering, Ruth C, Magrane, Michele, Melidoni, Anna N, Mutowo-Meullenet, Prudence, Pichler, Klemens, Shypitsyna, Aleksandra, Li, Biao, Zakeri, Pooya, ElShal, Sarah, Tranchevent, Léon-Charles, Das, Sayoni, Dawson, Natalie L, Lee, David, Lees, Jonathan G, Sillitoe, Ian, Bhat, Prajwal, Nepusz, Tamás, Romero, Alfonso E, Sasidharan, Rajkumar, Yang, Haixuan, Paccanaro, Alberto, Gillis, Jesse, Sedeño-Cortés, Adriana E, Pavlidis, Paul, Feng, Shou, Cejuela, Juan M, Goldberg, Tatyana, Hamp, Tobias, Richter, Lothar, Salamov, Asaf, Gabaldon, Toni, Marcet-Houben, Marina, Supek, Fran, Gong, Qingtian, Ning, Wei, Zhou, Yuanpeng, Tian, Weidong, Falda, Marco, Fontana, Paolo, Lavezzo, Enrico, Toppo, Stefano, Ferrari, Carlo, Giollo, Manuel, Piovesan, Damiano, Tosatto, Silvio, del Pozo, Angela, Fernández, José M, Maietta, Paolo, Valencia, Alfonso, Tress, Michael L, Benso, Alfredo, Di Carlo, Stefano, Politano, Gianfranco, Savino, Alessandro, Rehman, Hafeez Ur, Re, Matteo, Mesiti, Marco, Valentini, Giorgio, Bargsten, Joachim W, van Dijk, Aalt DJ, Gemovic, Branislava, Glisic, Sanja, Perovic, Vladmir, Veljkovic, Veljko, Veljkovic, Nevena, Almeida-e-Silva, Danillo C, Vencio, Ricardo ZN, Sharan, Malvika, Vogel, Jörg, Kansakar, Lakesh, Zhang, Shanshan, Vucetic, Slobodan, Wang, Zheng, Sternberg, Michael JE, Wass, Mark N, Huntley, Rachael P, Martin, Maria J, O'Donovan, Claire, Robinson, Peter N, Moreau, Yves, Tramontano, Anna, Babbitt, Patricia C, Brenner, Steven E, Linial, Michal, Orengo, Christine A, Rost, Burkhard, Greene, Casey S, Mooney, Sean D, Friedberg, Iddo, and Radivojac, Predrag

Subjects
Quantitative Biology - Quantitative Methods
Abstract

Background: The increasing volume and variety of genotypic and phenotypic data is a major defining characteristic of modern biomedical sciences. At the same time, the limitations in technology for generating data and the inherently stochastic nature of biomolecular events have led to the discrepancy between the volume of data and the amount of knowledge gleaned from it. A major bottleneck in our ability to understand the molecular underpinnings of life is the assignment of function to biological macromolecules, especially proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, accurately assessing methods for protein function prediction and tracking progress in the field remain challenging. Methodology: We have conducted the second Critical Assessment of Functional Annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. One hundred twenty-six methods from 56 research groups were evaluated for their ability to predict biological functions using the Gene Ontology and gene-disease associations using the Human Phenotype Ontology on a set of 3,681 proteins from 18 species. CAFA2 featured significantly expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis also compared the best methods participating in CAFA1 to those of CAFA2. Conclusions: The top performing methods in CAFA2 outperformed the best methods from CAFA1, demonstrating that computational function prediction is improving. This increased accuracy can be attributed to the combined effect of the growing number of experimental annotations and improved methods for function prediction., Comment: Submitted to Genome Biology

Published
2016
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4. KIDER: Knowledge-Infused Document Embedding Representation for Text Categorization

Author

Chen, Yu-Ting, Lin, Zheng-Wen, Chang, Yung-Chun, Hsu, Wen-Lian, Goos, Gerhard, Founding Editor, Hartmanis, Juris, Founding Editor, Bertino, Elisa, Editorial Board Member, Gao, Wen, Editorial Board Member, Steffen, Bernhard, Editorial Board Member, Woeginger, Gerhard, Editorial Board Member, Yung, Moti, Editorial Board Member, Fujita, Hamido, editor, Fournier-Viger, Philippe, editor, Ali, Moonis, editor, and Sasaki, Jun, editor

Published
2020
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7. An Ensemble Neural Network Model for Benefiting Pregnancy Health Stats from Mining Social Media

Author

Warikoo, Neha, Chang, Yung-Chun, Dai, Hong-Jie, Hsu, Wen-Lian, Hutchison, David, Series Editor, Kanade, Takeo, Series Editor, Kittler, Josef, Series Editor, Kleinberg, Jon M., Series Editor, Mattern, Friedemann, Series Editor, Mitchell, John C., Series Editor, Naor, Moni, Series Editor, Pandu Rangan, C., Series Editor, Steffen, Bernhard, Series Editor, Terzopoulos, Demetri, Series Editor, Tygar, Doug, Series Editor, Weikum, Gerhard, Series Editor, Tseng, Yuen-Hsien, editor, Sakai, Tetsuya, editor, Jiang, Jing, editor, Ku, Lun-Wei, editor, Park, Dae Hoon, editor, Yeh, Jui-Feng, editor, Yu, Liang-Chih, editor, Lee, Lung-Hao, editor, and Chen, Zhi-Hong, editor

Published
2018
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13. An Interaction Pattern Kernel Approach for Protein-Protein Interaction Extraction from Biomedical Literature

Author

Chang, Yung-Chun, Su, Yu-Chen, Chang, Nai-Wen, Hsu, Wen-Lian, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Goebel, Randy, Series editor, Tanaka, Yuzuru, Series editor, Wahlster, Wolfgang, Series editor, Siekmann, Jörg, Series editor, Cheng, Shin-Ming, editor, and Day, Min-Yuh, editor

Published
2014
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14. A Frame-Based Approach for Reference Metadata Extraction

Author

Hsieh, Yu-Lun, Liu, Shih-Hung, Yang, Ting-Hao, Chen, Yu-Hsuan, Chang, Yung-Chun, Hsieh, Gladys, Shih, Cheng-Wei, Lu, Chun-Hung, Hsu, Wen-Lian, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Goebel, Randy, Series editor, Tanaka, Yuzuru, Series editor, Wahlster, Wolfgang, Series editor, Siekmann, Jörg, Series editor, Cheng, Shin-Ming, editor, and Day, Min-Yuh, editor

Published
2014
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15. Semantic Frame-Based Natural Language Understanding for Intelligent Topic Detection Agent

Author

Chang, Yung-Chun, Hsieh, Yu-Lun, Chen, Cen-Chieh, Hsu, Wen-Lian, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Kobsa, Alfred, editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Weikum, Gerhard, editor, Goebel, Randy, editor, Tanaka, Yuzuru, editor, Wahlster, Wolfgang, editor, Siekmann, Jörg, editor, Ali, Moonis, editor, Pan, Jeng-Shyang, editor, Chen, Shyi-Ming, editor, and Horng, Mong-Fong, editor

Published
2014
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16. A Composite Kernel Approach for Detecting Interactive Segments in Chinese Topic Documents

Author

Chang, Yung-Chun, Chen, Chien Chin, Hsu, Wen-Lian, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Banchs, Rafael E., editor, Silvestri, Fabrizio, editor, Liu, Tie-Yan, editor, Zhang, Min, editor, Gao, Sheng, editor, and Lang, Jun, editor

Published
2013
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17. FISER: An Effective Method for Detecting Interactions between Topic Persons

Author

Chang, Yung-Chun, Chuang, Pi-Hua, Chen, Chien Chin, Hsu, Wen-Lian, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Hou, Yuexian, editor, Nie, Jian-Yun, editor, Sun, Le, editor, Wang, Bo, editor, and Zhang, Peng, editor

Published
2012
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18. An Empirical Comparative Study of Manual Rule-Based and Statistical Question Classifiers on Heterogeneous Unseen Data

Author

Lee, Cheng-Wei, Day, Min-Yuh, Hsu, Wen-Lian, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Sudan, Madhu, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Vardi, Moshe Y., Series editor, Weikum, Gerhard, Series editor, Cheng, Pu-Jen, editor, Kan, Min-Yen, editor, Lam, Wai, editor, and Nakov, Preslav, editor

Published
2010
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20. Using 'Cited by' Information to Find the Context of Research Papers

Author

Lu, Chun-Hung, Wang, Chih-Chien, Day, Min-Yuh, Ong, Chorng-Shyong, Hsu, Wen-Lian, Hutchison, David, Series editor, Kanade, Takeo, Series editor, Kittler, Josef, Series editor, Kleinberg, Jon M., Series editor, Kobsa, Alfred, Series editor, Mattern, Friedemann, Series editor, Mitchell, John C., Series editor, Naor, Moni, Series editor, Nierstrasz, Oscar, Series editor, Pandu Rangan, C., Series editor, Steffen, Bernhard, Series editor, Terzopoulos, Demetri, Series editor, Tygar, Doug, Series editor, Weikum, Gerhard, Series editor, Yang, Christopher C., editor, Chen, Hsinchun, editor, Chau, Michael, editor, Chang, Kuiyu, editor, Lang, Sheau-Dong, editor, Chen, Patrick S., editor, Hsieh, Raymond, editor, Zeng, Daniel, editor, Wang, Fei-Yue, editor, Carley, Kathleen, editor, Mao, Wenji, editor, and Zhan, Justin, editor

Published
2008
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21. Semi-joint Labeling for Chinese Named Entity Recognition

Author

Wu, Chia-Wei, Tsai, Richard Tzong-Han, Hsu, Wen-Lian, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Li, Hang, editor, Liu, Ting, editor, Ma, Wei-Ying, editor, Sakai, Tetsuya, editor, Wong, Kam-Fai, editor, and Zhou, Guodong, editor

Published
2008
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22. A Mobile Environment for Chinese Language Learning

Author

Tseng, Chang-Chih, Lu, Chun-Hung, Hsu, Wen-Lian, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Doug, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Smith, Michael J., editor, and Salvendy, Gavriel, editor

Published
2007
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26. Using Instant Messaging to Provide an Intelligent Learning Environment

Author

Lu, Chun-Hung, Chiou, Guey-Fa, Day, Min-Yuh, Ong, Chorng-Shyong, Hsu, Wen-Lian, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Ikeda, Mitsuru, editor, Ashley, Kevin D., editor, and Chan, Tak-Wai, editor

Published
2006
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27. Learning to Integrate Web Taxonomies with Fine-Grained Relations: A Case Study Using Maximum Entropy Model

Author

Wu, Chia-Wei, Tsai, Tzong-Han, Hsu, Wen-Lian, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Lee, Gary Geunbae, editor, Yamada, Akio, editor, Meng, Helen, editor, and Myaeng, Sung Hyon, editor

Published
2005
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28. RIBRA–An Error-Tolerant Algorithm for the NMR Backbone Assignment Problem

Author

Wu, Kuen-Pin, Chang, Jia-Ming, Chen, Jun-Bo, Chang, Chi-Fon, Wu, Wen-Jin, Huang, Tai-Huang, Sung, Ting-Yi, Hsu, Wen-Lian, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Istrail, Sorin, editor, Pevzner, Pavel, editor, Waterman, Michael, editor, Miyano, Satoru, editor, Mesirov, Jill, editor, Kasif, Simon, editor, and Pevzner, Pavel A., editor

Published
2005
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35. Ontological Support in Modeling Learners' Problem Solving Process

Author

Lu, Chun-Hung, Wu, Chia-Wei, Wu, Shih-Hung, Chiou, Guey-Fa, and Hsu, Wen-Lian

Abstract

This paper presents a new model for simulating procedural knowledge in the problem solving process with our ontological system, InfoMap. The method divides procedural knowledge into two parts: process control and action performer. By adopting InfoMap, we hope to help teachers construct curricula (declarative knowledge) and teaching strategies by capturing students' problem-solving processes (procedural knowledge) dynamically. Using the concept of declarative and procedural knowledge in intelligent tutoring systems, we can accumulate and duplicate the knowledge of the curriculum manager and student. (Contains 12 figures.)

Published
2005

36. Designing a Tutoring Agent for Facilitating Collaborative Learning with Instant Messaging

Author

Hsu, Sheng-Cheng, Day, Min-Yuh, Wu, Shih-Hung, Wong, Wing-Kwong, Hsu, Wen-Lian, Hutchison, David, editor, Kanade, Takeo, editor, Kittler, Josef, editor, Kleinberg, Jon M., editor, Mattern, Friedemann, editor, Mitchell, John C., editor, Naor, Moni, editor, Nierstrasz, Oscar, editor, Pandu Rangan, C., editor, Steffen, Bernhard, editor, Sudan, Madhu, editor, Terzopoulos, Demetri, editor, Tygar, Dough, editor, Vardi, Moshe Y., editor, Weikum, Gerhard, editor, Ikeda, Mitsuru, editor, Ashley, Kevin D., editor, and Chan, Tak-Wai, editor

Published
2006
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44. Fast algorithms for the dominating set problem on permutation graphs

Author

Tsai, Kuo-Hui, Hsu, Wen-Lian, Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Asano, Tetsuo, editor, Ibaraki, Toshihide, editor, Imai, Hiroshi, editor, and Nishizeki, Takao, editor

Published
1990
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