ÿþ<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN"> <HTML> <HEAD> <META HTTP-EQUIV="CONTENT-TYPE" CONTENT="text/html; charset=utf-8"> <TITLE>Arzucan Ozgur</TITLE> <META NAME="GENERATOR" CONTENT="NeoOffice 2.1 (Unix)"> <META NAME="CREATED" CONTENT="20090414;16005700"> <META NAME="CHANGED" CONTENT="20090414;16072800"> <STYLE TYPE="text/css"> <!-- TD P.style12 { font-family: "Arial", "Helvetica", sans-serif; font-size: 10pt } H2.style13 { font-family: "Arial", "Helvetica", sans-serif; font-size: 16pt } H3.style15 { font-family: "Arial", "Helvetica", sans-serif; font-size: 12pt } P.style8 { font-family: "Arial"; font-size: 10pt } --> </STYLE> </HEAD> <BODY LANG="en-US" DIR="LTR"> <H1 align="left"><font face="Arial" style="font-size: 22pt">Arzucan Özgür</font></H1> <TABLE WIDTH=92% BORDER=0 CELLPADDING=2 CELLSPACING=2 STYLE="page-break-before: always"> <TR> <TD> <IMG SRC="arzucan.jpg" NAME="graphics1" ALIGN=LEFT WIDTH=260 HEIGHT=210 BORDER=0></TD> <TD WIDTH=67%> <P CLASS="style12" ALIGN=LEFT><FONT SIZE=2 STYLE="font-size: 9pt"><FONT FACE="Arial">Assistant Professor <BR><A HREF="http://www.cmpe.boun.edu.tr/" TARGET="_blank">Department of Computer Engineering</A> <BR><A HREF="http://www.boun.edu.tr/" TARGET="_blank">Bogazici University</A> <BR>34342 Bebek, Istanbul, Turkey</FONT></FONT> </P> <P CLASS="style12" ALIGN=LEFT><BR><FONT SIZE=2 STYLE="font-size: 9pt"><FONT FACE="Arial"><STRONG>Office:</STRONG> ETA 18</FONT></FONT> <BR><FONT SIZE=2 STYLE="font-size: 9pt"><FONT FACE="Arial"><STRONG>Phone:</STRONG> +90 212 359 7226 </FONT></FONT> <BR><FONT SIZE=2 STYLE="font-size: 9pt"><FONT FACE="Arial"><STRONG>E-Mail:</STRONG> arzucan.ozgur<IMG SRC="at.gif" NAME="graphics2" ALT="at" ALIGN=BOTTOM WIDTH=15 HEIGHT=15 BORDER=0>boun.edu.tr</FONT></FONT></P> </TD> </TR> </TABLE> <P>&nbsp;</P> <HR SIZE=1> <H2 CLASS="style13">Education</H2> <P CLASS="style11"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif"><STRONG>University of Michigan, Ann Arbor, Michigan, USA</STRONG><BR>&nbsp;&nbsp;&nbsp;&nbsp;Ph.D., Computer Science and Engineering&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2006 - 2010<BR><BR><STRONG>Bogazici University, Istanbul, Turkey </STRONG><BR>&nbsp;&nbsp;&nbsp;&nbsp;M.S., Computer Engineering&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;2002 - 2004 <BR>&nbsp;&nbsp;&nbsp;&nbsp;B.S., Computer Engineering&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;1998 - 2002</FONT></FONT></P> <HR SIZE=1> <H2 CLASS="style13">Research Interests</H2> <P CLASS="style12">Text Mining, Information Retrieval, Information Extraction, Natural Language Processing, and Bioinformatics. </P> <H3 CLASS="style15">Publications</H3> <UL TYPE=DISC> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif"> Yoshinobu Kano, Jari Björne, Filip Ginter, Ekaterina Buyko, Udo Hahn, Kevin Bretonnel Cohen, Karin Verspoor, Christophe Roeder, Lawrence E Hunter, Halil Kilicoglu, Sabine Bergler, Sofie Van Landeghem, Thomas Van Parys, Yves Van de Peer, Makoto Miwa, Sophia Ananiadou, Mariana Neves, Alberto Pascual-Montano, Arzucan Özgür, Dragomir R Radev, Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Jin-Dong Kim, Sampo Pyysalo, Tomoko Ohta and Jun'ichi Tsujii. <A HREF="http://www.biomedcentral.com/1471-2105/12/481/abstract" TARGET="_blank"> U-Compare bio-event meta-service: compatible BioNLP event extraction services</A>. <EM>BMC Bioinformatics</EM>, 12:481, 2011. </FONT></FONT></P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Arzucan Ozgur, Zuoshuang Xiang, Dragomir R. Radev, and Yongqun He. <A HREF="papers/JBS11.pdf" TARGET="_blank"> Mining of vaccine-associated IFN-gamma gene interaction networks using the Vaccine Ontology</A>. <EM>Journal of Biomedical Semantics</EM>, 2(Suppl 2):S8, 2011. </FONT></FONT></P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Vahed Qazvinian, Dragomir R. Radev, and Arzucan Ozgur. <A HREF="papers/C10-1101.pdf" TARGET="_blank">Citation Summarization Through Keyphrase Extraction.</A> <EM> Proceedings of the 23rd International Conference on Computational Linguistics (COLING 2010)</EM>, pages 895-903, Beijing, China, August 23-27, 2010. </FONT></FONT></P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Arzucan Ozgur, Dragomir R. Radev, and Yongqun He. <A HREF="papers/Bio-Ontologies2010.pdf" TARGET="_blank">Mining of vaccine-associated IFN-gamma gene interaction networks using the Vaccine Ontology.</A> <EM>Proceedings of Bio-Ontologies 2010: Semantic Applications in Life Sciences, ISMB</EM>, Boston, MA, USA, July 9-10, 2010. </FONT></FONT></P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Arzucan Ozgur, Zuoshuang Xiang, Dragomir R. Radev, and Yongqun He. <A HREF="papers/JBB10.pdf" TARGET="_blank">Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks.</A> <EM>Journal of Biomedicine and Biotechnology</EM>, vol. 2010, Article ID 426479, 2010. </FONT></FONT></P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Arzucan Ozgur and Dragomir R. Radev. <A HREF="papers/EMNLP145.pdf" TARGET="_blank">Detecting Speculations and their Scopes in Scientific Text.</A> In <EM>Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP'09)</EM>, pages 1398-1407, Singapore, August 2009.</FONT></FONT></P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Arzucan Ozgur and Dragomir R. Radev. <A HREF="papers/W09-1416.pdf" TARGET="_blank">Supervised classification for extracting biomedical events</A>. <I>Proceedings of the BioNLP'09 Workshop Shared Task on Event Extraction at NAACL-HLT</I>, Boulder, Colorado, USA, pages 111-114, June 2009.</FONT></FONT></P> <LI><P STYLE="margin-bottom: 0in"><FONT FACE="Arial, Helvetica, sans-serif"><FONT SIZE=2>V. Glenn Tarcea, Terry Weymouth, Alex Ade, Jing Gao, Vasudeva Mahavisno, Zach Wright, Adriane Chapman, Magesh Jayapandian, Arzucan Ozgur, Yuanyuan Tian, Jim Cavalcoli, Barbara Mirel, Jignesh Patel, Dragomir Radev, Brian Athey, David States, and H.V. Jagadish. <A HREF="http://nar.oxfordjournals.org/cgi/content/full/gkn722" TARGET="_blank">Michigan Molecular Interactions (MiMI) R2: From Interacting Proteins to Pathways</A>. <I>Nucleic Acids Research</I>, 37 (Database Issue), D642-D646, 2009. </FONT></FONT> </P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Arzucan Ozgur, Thuy Vu, Gunes Erkan, and Dragomir R. Radev. <A HREF="papers/bioinformatics08.pdf" TARGET="_blank">Identifying gene-disease associations using centrality on a literature mined gene interaction network</A>. <EM>Bioinformatics</EM>, Volume 24, Number 13, pp. i277-i285, 2008. </FONT></FONT> </P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Florian Leitner, Martin Krallinger, Carlos Rodriguez-Penagos, Joerg Hakenberg, Conrad Plake, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tasi, Hsi-Chuan Hung, William W. Lau, Calvin A. Johnson, Rune Saetre, Kazuhiro Yoshida, Yan Hua Chen, Sun Kim, Soo-Yong Shin, Byoung-Tak Zhang, William A. Baumgartner, Jr., Lawrence Hunter, Barry Haddow, Michael Matthew, Xinglong Wang, Patrick Ruch, Frederic Ehrler, Arzucan Ozgur, Gunes Erkan, Dragomir R. Radev, Michael Krauthammer, ThaiBinh Luong, Robert Hoffmann, Chris Sander, and Alfonso Valencia. <A HREF="papers/gb-2008-9-s2-s6.pdf" TARGET="_blank">Introducing meta-services for biomedical information extraction</A>. <EM>Genome Biology</EM>, 9(S2):S6, 2008. </FONT></FONT> </P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Arzucan Ozgur, Burak Cetin, and Haluk Bingol. <A HREF="http://www.worldscinet.com/cgi-bin/details.cgi?id=voliss:ijmpc_1905&amp;type=toc" TARGET="_blank">Co-occurrence Network of Reuters News</A>. <EM>International Journal of Modern Physics C </EM>(<EM>IJMPC)</EM>, Volume 19, Issue 5, pp. 689-702, 2008. </FONT></FONT> </P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Gunes Erkan, Arzucan Ozgur, and Dragomir R. Radev. <A HREF="papers/D07-1024.pdf" TARGET="_blank">Semi-supervised classification for extracting protein interaction sentences using dependency parsing</A>. In <EM>Proceedings of the Conference of Empirical Methods in Natural Language Processing (EMNLP '07)</EM>, Prague, Czech Republic, June 28-30 2007. </FONT></FONT> </P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Gunes Erkan, Arzucan Ozgur, and Dragomir R. Radev. <A HREF="papers/biocreative07.pdf" TARGET="_blank">Extracting interacting protein pairs and evidence sentences by using dependency parsing and machine learning techniques </A>. In <EM>Proceedings of the Second BioCreAtIvE Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology</EM>, Madrid, Spain, ISBN 84-933255-6-2, April 23-25 2007. </FONT></FONT> </P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Arzucan Ozgur and Tunga Gungor. <A HREF="papers/KI06.pdf" TARGET="_blank">Classification of Skewed and Homogenous Document Corpora with Class-Based and Corpus-Based Keywords</A>. <EM>29th German Conference on Artificial Intelligence (KI 2006)</EM>, <EM>Eds. C.Freksa, M.Kohlhase and K.Schill, June 2006, Bremen - LNAI (Lecture Notes in Artificial Intelligence),</EM> Vol.4314, 2006, p.91-101, Springer-Verlag, Berlin Heidelberg. </FONT></FONT> </P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Arzucan Ozgur and Taflan I. Gundem. <A HREF="papers/science.pdf" TARGET="_blank">Efficient Indexing Technique for XML-Based Electronic Product Catalogs</A>. <EM>Electronic Commerce Research and Applications</EM>, Volume 5, Issue 1, pp. 66-77, Elsevier Science, 2006. </FONT></FONT> </P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Arzucan Ozgur, Levent Ozgur, and Tunga Gungor. <A HREF="papers/ozgur-gungor05.pdf" TARGET="_blank">Text Categorization with Class-Based and Corpus-Based Keyword Selection</A>. <EM>Lecture Notes in Computer Science</EM>, Vol.3733, (<EM>Proc. of the 20th International Symposium on Computer and Information Sciences</EM>), pp.607-616, Springer-Verlag, 2005. </FONT></FONT> </P> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Arzucan Ozgur and Haluk Bingol. <A HREF="papers/ozgur-bingol.pdf" TARGET="_blank">Social Network of Co-occurrence in News Articles</A><STRONG>.</STRONG> <EM>Lecture Notes in Computer Science, </EM>Vol. 3280, (<EM>Proc. of the 19th International Symposium on Computer and Information Sciences</EM>), pp. 688-697, Springer Verlag, 2004. (You can download the dataset used in this study from <A HREF="papers/CoOccurrenceData.zip">here</A>.) </FONT></FONT> </P> </UL> <H3 CLASS="style15">Thesis</H3> <UL TYPE=DISC> <LI><P><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Arzucan Ozgur. <A HREF="papers/thesis-arzucan.pdf" TARGET="_blank">Text and Network Mining for Literature-Based Scientific Discovery in Biomedicine</A>, <EM>Ph.D. Thesis</EM>, Computer Science and Engineering, University of Michigan, Ann Arbor, MI, USA, September 2010. Advisor: <A HREF="http://clair.si.umich.edu/~radev/" TARGET="_blank">Dragomir R. Radev</A>.</FONT></FONT> </P> <LI><P><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif">Arzucan Ozgur. <A HREF="papers/ms-thesis-arzucan.pdf" TARGET="_blank">Supervised and Unsupervised Machine Learning Techniques for Text Document Categorization</A>, <EM>M.S. Thesis</EM>, Computer Engineering, Bogazici University, Istanbul, Turkey, July 2004. Advisor: <A HREF="http://www.cmpe.boun.edu.tr/~ethem/" TARGET="_blank">Ethem Alpaydin</A>. (You can download the pre-processed datasets used in this study from <A HREF="papers/datasets.zip">here</A>.) </FONT></FONT> </P> </UL> <H3 CLASS="style15">Patents</H3> <UL TYPE=DISC> <LI> A System and Method for Generating Queries, US Patent Pending. Filed by Avaya Labs in 2009. </UL> <P>&nbsp;</P> <HR SIZE=1> <H2 CLASS="style13">Teaching</H2> <P CLASS="style12"><STRONG>Spring 2012</STRONG> <UL TYPE=DISC> <LI><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif"><A HREF="http://www.cmpe.boun.edu.tr/courses/cmpe150/spring2012/java/" TARGET="_blank">CMPE 150 - Introduction to Computing (Java)</A></FONT></FONT> </UL> </P> <P CLASS="style12"><STRONG>Fall 2011</STRONG> <UL TYPE=DISC> <LI><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif"><A HREF="http://www.cmpe.boun.edu.tr/courses/cmpe150/fall2011/java/" TARGET="_blank">CMPE 150 - Introduction to Computing (Java)</A></FONT></FONT> <LI><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif"><A HREF="http://www.cmpe.boun.edu.tr/courses/cmpe59H/fall2011/" TARGET="_blank">CMPE 59H - Bioinformatics</A></FONT></FONT> </UL> </P> <P CLASS="style12"><STRONG>Summer 2011</STRONG> <UL TYPE=DISC> <LI><P STYLE="margin-bottom: 0in"><FONT SIZE=2><FONT FACE="Arial, Helvetica, sans-serif"><A HREF="http://www.cmpe.boun.edu.tr/courses/cmpe493/summer2011/" TARGET="_blank">CMPE 493 - Introduction to Information Retrieval</A></FONT></FONT></P> </UL> </P> <HR SIZE=1> <P CLASS="style8">&nbsp;</P> </BODY> </HTML>