Arzucan Özgür

Publications

Google Scholar Profile       DBLP Profile

• Gokce Uludogan, Elif Ozkirimli, Kutlu Ulgen, Nilgun Karali, Arzucan Ozgur. Exploiting pretrained biochemical language models for targeted drug design. Bioinformatics, Volume 38, Issue Supplement_2, Pages ii155–ii161, 2022.

• Arda Celebi and Arzucan Ozgur. Cluster-based mention typing for named entity disambiguation. Natural Language Engineering, 28(1), 1-37, 2022.

• Utku Turk, Furkan Atmaca, Saziye Betul Ozates, Gozde Berk, Seyyit Talha Bedir, Abdullatif Koksal, Balkiz Ozturk Basaran, Tunga Gungor, Arzucan Ozgur. Resources for Turkish dependency parsing: Introducing the BOUN treebank and the BoAT annotation tool. Language Resources and Evaluation, 56 (1), pp. 259-307, 2022.

• Saziye Betul Ozates, Arzucan Ozgur, Tunga Gungor, Balkiz Ozturk Basaran. A Hybrid Deep Dependency Parsing Approach Enhanced With Rules and Morphology: A Case Study for Turkish. IEEE Access, vol. 10, pp. 93867-93886, 2022.

• Saziye Betul Ozates, Arzucan Ozgur, Tunga Gungor, Ozlem Cetinoglu. Improving Code-Switching Dependency Parsing with Semi-Supervised Auxiliary Tasks. Findings of the Association for Computational Linguistics: NAACL 2022, pp. 1159-1171, 2022.

• Mustafa Melih Mutlu and Arzucan Ozgur. A Dataset and BERT-based Models for Targeted Sentiment Analysis on Turkish Texts. In Proceedings of the 60th Annual Meeting of the Association for Computational Linguistics: Student Research Workshop, pages 467–472, Dublin, Ireland, 2022. Association for Computational Linguistics.

• Gonul Ayci, Murat Sensoy, Arzucan Ozgur, and Pinar Yolum. Uncertainty-aware Personal Assistant for Making Personalized Privacy Decisions. ACM Trans. Internet Technol., 2022.

• Zehra Melce Husunbeyi, Didar Akar, and Arzucan Ozgur. Identifying Hate Speech Using Neural Networks and Discourse Analysis Techniques. In Proceedings of the First Workshop on Language Technology and Resources for a Fair, Inclusive, and Safe Society (LATERAISSE) within the 13th Language Resources and Evaluation Conference, pages 32–41, Marseille, France, 2022. European Language Resources Association.

• Artur Yakimovich, Arzucan Ozgur, Tunca Dogan, and Elif Ozkirimli. Editorial: Machine Learning Methodologies to Study Molecular Interactions. Front Mol Biosci, 8:806474, 2021.

• Riza Ozcelik, Hakime Ozturk, Arzucan Ozgur, and Elif Ozkirimli. ChemBoost: A Chemical Language Based Approach for Protein - Ligand Binding Affinity Prediction. Molecular Informatics, 40, 2000212, 2021.

• N. Ozlem Ozcan Simsek, Arzucan Ozgur, Fikret Gurgen. A novel gene selection method for gene expression data for the task of cancer type classification. Biol Direct, 16, 7, 2021.

• Yi Huang, Buse Giledereli, Abdullatif Koksal, Arzucan Ozgur, and Elif Ozkirimli. Balancing Methods for Multi-label Text Classification with Long-Tailed Class Distribution. In Proceedings of the 2021 Conference on Empirical Methods in Natural Language Processing (EMNLP), pages 8153–8161, Online and Punta Cana, Dominican Republic, 2021. Association for Computational Linguistics.

• Yi Huang, Buse Giledereli, Abdullatif Koksal, Arzucan Ozgur, and Elif Ozkirimli. PIDNA at BioASQ MESINESP: Hybrid Semantic Indexing for Biomedical Articles in Spanish. CLEF (Working Notes), 241-246, 2021.

• Abdullatif Koksal, Yusuf Yuksel, Bekir Yildirim, and Arzucan Ozgur. BOUN at SemEval-2021 Task 9: Text Augmentation Techniques for Fact Verification in Tabular Data. In Proceedings of the 15th International Workshop on Semantic Evaluation (SemEval-2021), pages 431–437, Online, 2021. Association for Computational Linguistics.

• Abdullatif Koksal and Arzucan Ozgur. Twitter Dataset and Evaluation of Transformers for Turkish Sentiment Analysis. 29th Signal Processing and Communications Applications Conference (SIU), pp. 1-4, 2021. IEEE.

• Melik Masarifoglu, Umit Tigrak, Sefa Hakyemez, Guven Gul, Erdal Bozan, Ali Hakan Buyuklu, and Arzucan Ozgur. Sentiment Analysis of Customer Comments in Banking using BERT-based Approaches. 29th Signal Processing and Communications Applications Conference (SIU), pp. 1-4, 2021. IEEE.

• Talha Bedir, Karahan Sahin, Onur Gungor, Suzan Uskudarli, Arzucan Ozgur, Tunga Gungor, and Balkiz Ozturk Basaran. Overcoming the challenges in morphological annotation of Turkish in universal dependencies framework. In Proceedings of the Joint 15th Linguistic Annotation Workshop (LAW) and 3rd Designing Meaning Representations (DMR) Workshop, pages 112–122, Punta Cana, Dominican Republic, 2021. Association for Computational Linguistics.

• Hakime Ozturk, Arzucan Ozgur, Philippe Schwaller, Teodoro Laino, and Elif Ozkirimli. Exploring chemical space using natural language processing methodologies for drug discovery. Drug Discovery Today, Volume 25, Issue 4, ages 689-705, 2020.

• Abdullatif Koksal, Hilal Donmez, Riza Ozcelik, Elif Ozkirimli, and Arzucan Ozgur. Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature. In Proceedings of the 1st Workshop on NLP for COVID-19 (Part 2) at EMNLP 2020, Online, 2020. Association for Computational Linguistics.

• Abdullatif Koksal and Arzucan Ozgur. The RELX Dataset and Matching the Multilingual Blanks for Cross-Lingual Relation Classification. In Findings of the Association for Computational Linguistics: EMNLP 2020, pages 340–350, 2020. Association for Computational Linguistics.

• Berfu Buyukoz, Ali Hurriyetoglu, and Arzucan Ozgur. Analyzing ELMo and DistilBERT on Socio-political News Classification. In Proceedings of the Workshop on Automated Extraction of Socio-political Events from News, pages 9–18, Marseille, France, 2020. European Language Resources Association (ELRA).

• Jiayuan He, Dat Quoc Nguyen, Saber A Akhondi, Christian Druckenbrodt, Camilo Thorne, Ralph Hoessel, Zubair Afzal, Zenan Zhai, Biaoyan Fang, Hiyori Yoshikawa, Ameer Albahem, Jingqi Wang, Yuankai Ren, Zhi Zhang, Yaoyun Zhang, Mai Hoang Dao, Pedro Ruas, Andre Lamurias, Francisco M Couto, Copara Zea, Jenny Linet, Nona Naderi, Julien David Marc Knafou, Patrick Ruch, Douglas Teodoro, Daniel M Lowe, John Mayfield, Abdullatif Koksal, Hilal Donmez, Elif Özkirimli, Arzucan Ozgur, Darshini Mahendran, Gabrielle Gurdin, Nastassja Lewinski, Christina Tang, Bridget T McInnes, CS Malarkodi, Pattabhi Rk Rao, Sobha Lalitha Devi, Lawrence Cavedon, Trevor Cohn, Timothy Baldwin, Karin Verspoor. An extended overview of the CLEF 2020 ChEMU lab: information extraction of chemical reactions from patents. In Proceedings of CLEF (Conference and Labs of the Evaluation Forum) 2020 Working Notes, Thessaloniki, Greece, September 22-25, 2020.

• Hilal Donmez, Abdullatif Koksal, Elif Özkirimli, Arzucan Ozgur. BOUN-REX at CLEF-2020 ChEMU Task 2: Evaluating Pretrained Transformers for Event Extraction. In Proceedings of CLEF (Conference and Labs of the Evaluation Forum) 2020 Working Notes, Thessaloniki, Greece, September 22-25, 2020.

• Mert Tiftikci, Arzucan Ozgur, Yongqun He, Junguk Hur. Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels. BMC Bioinformatics, 20 (Suppl 21), 707, 2019.

• N. Ozlem Ozcan Simsek, Arzucan Ozgur, Fikret Gurgen. Statistical representation models for mutation information within genomic data. BMC Bioinformatics, 20:324, 2019.

• Ilknur Karadeniz and Arzucan Ozgur. Linking entities through an ontology using word embeddings and syntactic re-ranking. BMC Bioinformatics, 20:156, 2019.

• Rezarta Islamaj Dogan,Sun Kim,Andrew Chatr-Aryamontri, Chih-Hsuan Wei,Donald Comeau, Rui Antunes, Sergio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Husunbeyi, Arzucan Ozgur, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu. Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database, Volume 2019, bay147, 2019.

• Ilknur Karadeniz, Omer Faruk Tuna, Arzucan Ozgur. BOUN-ISIK Participation: An Unsupervised Approach for the Named Entity Normalization and Relation Extraction of Bacteria Biotopes. Proceedings of The 5th Workshop on BioNLP Open Shared Tasks, pages 150-157, Hong Kong, China, November 4, 2019.

• Utku Turk, Furkan Atmaca, Saziye Betul Ozates, Balkiz Ozturk Basaran, Tunga Gungor, Arzucan Ozgur. Improving the Annotations in the Turkish Universal Dependency Treebank. Proceedings of the Third Workshop on Universal Dependencies (UDW, SyntaxFest 2019), Paris, France, 26 August, 2019.

• Utku Turk, Furkan Atmaca, Saziye Betul Ozates, Abdullatif Koksal, Balkiz Ozturk Basaran, Tunga Gungor, Arzucan Ozgur. Turkish Treebanking: Unifying and Constructing Efforts. Proceedings of the 13th Linguistic Annotation Workshop (LAW), pages 166-177, Florence, Italy, 1 August, 2019.

• Atif Emre Yuksel, Yasar Alim Turkmen, Arzucan Ozgur, and Berna Altinel Turkish Tweet Classification with Transformer Encoder. In Proceedings of the International Conference on Recent Advances in Natural Language Processing (RANLP 2019), pages 1380–1387, Varna, Bulgaria. 2019.

• Atif Hakime Ozturk, Elif Ozkirimli, and Arzucan Ozgur.WideDTA: prediction of drug-target binding affinity. ArXiv preprint, arXiv:1902.04166, 2019.

• Hakime Ozturk, Arzucan Ozgur, and Elif Ozkirimli. DeepDTA: deep drug-target binding affinity prediction. Bioinformatics, Volume 34, Issue 17, Pages i821-i829, 2018.

• Hakime Ozturk, Elif Ozkirimli, and Arzucan Ozgur. A novel methodology on distributed representations of proteins using their interacting ligands. Bioinformatics, Volume 34, Issue 13, Pages i295-i303, 2018.

• Arda Celebi and Arzucan Ozgur. Segmenting hashtags and analyzing their grammatical structure. Journal of the Association for Information Science and Technology (JASIST), doi: 10.1002/asi.23989, 69(5):675-686, 2018.

• Caner Derici, Yigit Aydin, Cigdem Yenialaca, Nihal Yagmur Aydin, Gunizi Kartal, Arzucan Ozgur, Tunga Gungor. A closed-domain question answering framework using reliable resources to assist students. Natural Language Engineering, Volume 24, Issue 5, pp. 725-762, 2018.

• Junguk Hur, Arzucan Ozgur, and Yongqun He. Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs. Journal of Biomedical Semantics, 9:17, 2018.

• Saziye Betul Ozates, Arzucan Ozgur, Tunga Gungor, Balkiz Ozturk. A Morphology-Based Representation Model for LSTM-Based Dependency Parsing of Agglutinative Languages. Proceedings of the CoNLL 2018 Shared Task: Multilingual Parsing from Raw Text to Universal Dependencies, pages 238-247, Brussels, Belgium, October 31 - November 1, 2018.

• Gizem Sogancioglu, Hakime Ozturk, and Arzucan Ozgur. BIOSSES: a semantic sentence similarity estimation system for the biomedical domain. Bioinformatics, 33 (14): i49-i58, 2017.

• Ferhat Aydin, Zehra Melce Husunbeyi, and Arzucan Ozgur. Automatic query generation using word embeddings for retrieving passages describing experimental methods. Database, 2017: baw166, doi: 10.1093/database/baw166, 2017.

• Junguk Hur, Arzucan Ozgur, and Yongqun He. Ontology-based literature mining of E. coli vaccine-associated gene interaction networks. Journal of Biomedical Semantics, 8:12, 2017.

• Atakan Yuksel, Hakime Ozturk, Elif Ozkirimli, Arzucan Ozgur. CNN-based Chemical-Protein Interactions Classification. Proceedings of the BioCreative VI Workshop, pages 184-186, Bethesda, MD, 2017.

• Arzucan Ozgur, Junguk Hur, Yongqun He. The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature. BioData Mining, 9:41, doi: 10.1186/s13040-016-0118-0, 2016.

• Erinc Gokdeniz, Arzucan Ozgur, Resit Canbeyli. Automated Neuroanatomical Relation Extraction: A Linguistically Motivated Approach with a PVT Connectivity Graph Case Study. Frontiers in Neuroinformatics, 10:39. doi: 10.3389/fninf.2016.00039, 2016.

• Sun Kim, Rezarta Islamaj Dogan, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer M. Rust, Riza Batista-Navarro, Jacob Carter, Sophia Ananiadou, Sérgio Matos, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen, Wen-Lian Hsu, Yifan Peng, Cecilia N. Arighi, Cathy H. Wu, K. Vijay-Shanker, Ferhat Aydin, Zehra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski, Mike Tyers, W. John Wilbur, Donald C. Comeau. BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database, 2016 : baw121. doi: 10.1093/database/baw121, 2016.

• Mert Tiftikci, Hakan Sahin, Berfu Buyukoz, Alper Yayıkcı, Arzucan Ozgur. Ontology-based Categorization of Bacteria and Habitat Entities using Information Retrieval Techniques. Proceedings of the 4th BioNLP Shared Task Workshop, pages 56–63, Berlin, Germany, August 13, 2016. Association for Computational Linguistics.

• Cagil Sonmez, Arzucan Ozgur, Erdem Yoruk. Towards Building a Political Protest Database to Explain Changes in the Welfare State. Proceedings of the 10th SIGHUM Workshop on Language Technology for Cultural Heritage, Social Sciences, and Humanities (LaTeCH), pages 106–110, Berlin, Germany, August 11, 2016. Association for Computational Linguistics.

• Hakime Ozturk, Elif Ozkirimli, Arzucan Ozgur. A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction. BMC Bioinformatics, 17:128, 2016.

• Ahmet Yildirim, Suzan Uskudarli, Arzucan Ozgur. Identifying Topics in Microblogs Using Wikipedia. PLoS ONE, 11(3): e0151885, 2016.

• Arda Celebi and Arzucan Ozgur. Segmenting Hashtags using Automatically Created Training Data. In Proceedings of the 10th Language Resources and Evaluation Conference (LREC 2016), 23-28 May, 2016. (Data sets and tools)

• Saziye Betül Ozates, Arzucan Ozgur and Dragomir Radev. Sentence Similarity based on Dependency Tree Kernels for Multi-document Summarization. In Proceedings of the 10th Language Resources and Evaluation Conference (LREC 2016), 23-28 May, 2016.

• Eda Okur, Hakan Demir, and Arzucan Ozgur. Named Entity Recognition on Twitter for Turkish using Semi-supervised Learning with Word Embeddings. In Proceedings of the 10th Language Resources and Evaluation Conference (LREC 2016), 23-28 May, 2016.

• Ilknur Karadeniz, Junguk Hur, Yongqun He, and Arzucan Ozgur. Literature Mining and Ontology based Analysis of Host-Brucella Gene-Gene Interaction Network. Frontiers in Microbiology, 6:1386, 2015.

• Arzucan Ozgur, Junguk Hur, and Yongqun He. Extension of the Interaction Network Ontology for literature mining of gene-gene interaction networks from sentences with multiple interaction keywords. Proceedings of International Workshop on Biomedical Data Mining, Modeling, and Semantic Integration: A Promising Approach to Solving Unmet Medical Needs (BDM2I 2015), The International Semantic Web Conference (ISWC 2015), Bethlehem, PA, USA, October 11-15, 2015.

• Ferhat Aydın, Zehra Melce Hüsünbeyi, and Arzucan Ozgur. Retrieving Passages Describing Experimental Methods using Ontology and Term Relevance based Query Matching. Proceedings of the Fifth BioCreative Challenge Evaluation Workshop, pp. 42-50, Sevilla, Spain, September 9-11, 2015.

• Ilknur Karadeniz and Arzucan Ozgur. Detection and Categorization of Bacteria Habitats using Shallow Linguistic Analysis. BMC Bioinformatics, 16 (Suppl 10):S5, 2015.

• Wallace K. B. Chan, Hongjiu Zhang, Jianyi Yang, Jeffrey R. Brender, Junguk Hur, Arzucan Özgür, and Yang Zhang. GLASS: a comprehensive database for experimentally-validated GPCR-ligand associations. Bioinformatics, Volume 31, Issue 18, Pp. 3035-3042, 2015.

• Caner Derici, Kerem Çelik, Ekrem Kutbay, Yigit Aydin, Tunga Güngör, Arzucan Özgür, Günizi Kartal. Question Analysis for a Closed Domain Question Answering System. Proceedings of the Conference on Intelligent Text Processing and Computational Linguistics (CICLing), LNCS 9042, pp. 468–482, Springer, 2015.

• Saliha Durmus, Tunahan Cakir, Arzucan Ozgur, Reinhard Guthke. A Review on Computational Systems Biology of Pathogen-Host Interactions. Frontiers in Microbiology, 6:235, 2015.

• Hakime Ozturk, Elif Ozkirimli, Arzucan Ozgur. Classification of Beta-Lactamases and Penicillin Binding Proteins Using Ligand-Centric Network Models. PLoS ONE, 10(2): e0117874, 2015.

• Junguk Hur, Arzucan Ozgur, Zuoshuang Xiang, and Yongqun He. Development and Application of an Interaction Network Ontology for Literature Mining of Vaccine-associated Gene-Gene Interactions. Journal of Biomedical Semantics, 6:2, 2015.

• Hakan Demir and Arzucan Ozgur. Improving Named Entity Recognition for Morphologically Rich Languages using Word Embeddings. The 13th International Conference on Machine Learning and Applications (ICMLA'14), Detroit, Michigan, USA, December, 2014.

• Cagil Sonmez and Arzucan Ozgur. A Graph-based Approach for Contextual Text Normalization. Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing (EMNLP), pages 313-324, Doha, Qatar, October, 2014. Association for Computational Linguistics.

• Muhammed Yavuz Nuzumlali and Arzucan Ozgur. Analyzing Stemming Approaches for Turkish Multi-Document Summarization. Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing (EMNLP), pages 702-706, Doha, Qatar, October, 2014. Association for Computational Linguistics.

• Burak Aydın and Arzucan Ozgur. Expanding Machine Translation Training Data with an Out-of-Domain Corpus using Language Modeling based Vocabulary Saturation. Conference of the Association for Machine Translation in the Americas (AMTA), Vancouver, Canada, October, 2014.

• Melike Korucuoglu, Senol Isci, Arzucan Ozgur, Hasan H. Otu. Bayesian Pathway Analysis of Cancer Microarray Data. PLoS ONE, 9(7): e102803, 2014.

• Arda Celebi and Arzucan Ozgur. Self-training a Constituency Parser using N-gram Trees. In Proceedings of the 9th Language Resources and Evaluation Conference (LREC 2014), Reykjavik, Iceland, May, 2014.

• İlknur Karadeniz and Arzucan Özgür. Bacteria Biotope Detection, Ontology-based Normalization, and Relation Extraction using Syntactic Rules. In Proceedings of BioNLP Shared Task 2013 Workshop, Sofia, Bulgaria, August, 2013. Association for Computational Linguistics.

• Nadin Kökciyan, Arda Çelebi, Arzucan Özgür, and Suzan Üsküdarlı. BOUNCE: Sentiment Classification in Twitter using Rich Feature Sets. In Proceedings of the Second Joint Conference on Lexical and Computational Semantics (*SEM), Volume 2: Seventh International Workshop on Semantic Evaluation (SemEval 2013), Atlanta, Georgia, June, 2013.

• Saliha Durmuş Tekir, Tunahan Çakır, Emre Ardıç, Ali Semih Sayılırbaş, Gökhan Konuk, Mithat Konuk, Hasret Sarıyer, Azat Uğurlu, İlknur Karadeniz, Arzucan Özgür, F. Erdoğan Sevilgen, and Kutlu Ö. Ülgen. PHISTO: Pathogen-Host Interaction Search Tool. Bioinformatics, Vol. 29 no. 10, pages 1357-1358, 2013.

• Cuneyd Murad Ozsert and Arzucan Ozgur. Word Polarity Detection using a Multilingual Approach. Proceedings of the Conference on Intelligent Text Processing and Computational Linguistics (CICLing), Samos, Greece, LNCS 7817, pp. 75–82, Springer, 2013. (You can download the Turkish positive/negative seed words from here.)

• Arda Celebi and Arzucan Ozgur. N-gram Parsing for Jointly Training a Discriminative Constituency Parser. Proceedings of the Conference on Intelligent Text Processing and Computational Linguistics (CICLing), Samos, Greece, 2013.

• Junguk Hur, Arzucan Ozgur, Zuoshuang Xiang, and Yongqun He. Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. Journal of Biomedical Semantics, 3:18, 2012.

• 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. U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinformatics, 12:481, 2011.

• Arzucan Ozgur, Zuoshuang Xiang, Dragomir R. Radev, and Yongqun He. Mining of vaccine-associated IFN-gamma gene interaction networks using the Vaccine Ontology. Journal of Biomedical Semantics, 2(Suppl 2):S8, 2011.

• Vahed Qazvinian, Dragomir R. Radev, and Arzucan Ozgur. Citation Summarization Through Keyphrase Extraction. Proceedings of the 23rd International Conference on Computational Linguistics (COLING 2010), pages 895-903, Beijing, China, August 23-27, 2010.

• Arzucan Ozgur, Zuoshuang Xiang, Dragomir R. Radev, and Yongqun He. Literature-based discovery of IFN-gamma and vaccine-mediated gene interaction networks. Journal of Biomedicine and Biotechnology, vol. 2010, Article ID 426479, 2010.

• Arzucan Ozgur and Dragomir R. Radev. Detecting Speculations and their Scopes in Scientific Text. In Proceedings of the Conference on Empirical Methods in Natural Language Processing (EMNLP'09), pages 1398-1407, Singapore, August 2009.

• Arzucan Ozgur and Dragomir R. Radev. Supervised classification for extracting biomedical events. Proceedings of the BioNLP'09 Workshop Shared Task on Event Extraction at NAACL-HLT, Boulder, Colorado, USA, pages 111-114, June 2009.

• 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. Michigan Molecular Interactions (MiMI) R2: From Interacting Proteins to Pathways. Nucleic Acids Research, 37 (Database Issue), D642-D646, 2009.

• Arzucan Ozgur, Thuy Vu, Gunes Erkan, and Dragomir R. Radev. Identifying gene-disease associations using centrality on a literature mined gene interaction network. Bioinformatics, Volume 24, Number 13, pp. i277-i285, 2008.

• 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. Introducing meta-services for biomedical information extraction. Genome Biology, 9(S2):S6, 2008.

• Arzucan Ozgur, Burak Cetin, and Haluk Bingol. Co-occurrence Network of Reuters News. International Journal of Modern Physics C (IJMPC), Volume 19, Issue 5, pp. 689-702, 2008.

• Gunes Erkan, Arzucan Ozgur, and Dragomir R. Radev. Semi-supervised classification for extracting protein interaction sentences using dependency parsing. In Proceedings of the Conference of Empirical Methods in Natural Language Processing (EMNLP '07), Prague, Czech Republic, June 28-30 2007.

• Gunes Erkan, Arzucan Ozgur, and Dragomir R. Radev. Extracting interacting protein pairs and evidence sentences by using dependency parsing and machine learning techniques . In Proceedings of the Second BioCreAtIvE Challenge Workshop - Critical Assessment of Information Extraction in Molecular Biology, Madrid, Spain, ISBN 84-933255-6-2, April 23-25 2007.

• Arzucan Ozgur and Tunga Gungor. Classification of Skewed and Homogenous Document Corpora with Class-Based and Corpus-Based Keywords. 29th German Conference on Artificial Intelligence (KI 2006), Eds. C.Freksa, M.Kohlhase and K.Schill, June 2006, Bremen - LNAI (Lecture Notes in Artificial Intelligence), Vol.4314, 2006, p.91-101, Springer-Verlag, Berlin Heidelberg.

• Arzucan Ozgur and Taflan I. Gundem. Efficient Indexing Technique for XML-Based Electronic Product Catalogs. Electronic Commerce Research and Applications, Volume 5, Issue 1, pp. 66-77, Elsevier Science, 2006.

• Arzucan Ozgur, Levent Ozgur, and Tunga Gungor. Text Categorization with Class-Based and Corpus-Based Keyword Selection. Lecture Notes in Computer Science, Vol.3733, (Proc. of the 20th International Symposium on Computer and Information Sciences), pp.607-616, Springer-Verlag, 2005.

• Arzucan Ozgur and Haluk Bingol. Social Network of Co-occurrence in News Articles. Lecture Notes in Computer Science, Vol. 3280, (Proc. of the 19th International Symposium on Computer and Information Sciences), pp. 688-697, Springer Verlag, 2004. (You can download the dataset used in this study from here.)

Thesis

• Arzucan Ozgur. Text and Network Mining for Literature-Based Scientific Discovery in Biomedicine, Ph.D. Thesis, Computer Science and Engineering, University of Michigan, Ann Arbor, MI, USA, September 2010. Advisor: Dragomir R. Radev.

• Arzucan Ozgur. Supervised and Unsupervised Machine Learning Techniques for Text Document Categorization, M.S. Thesis, Computer Engineering, Bogazici University, Istanbul, Turkey, July 2004. Advisor: Ethem Alpaydin. (You can download the pre-processed datasets used in this study from here.)

Patents

• George Erhart, Valentine Matula, Arzucan Ozgur, and David Skiba. System and Method for Generating Queries, United States Patent and Trademark Office (USPTO), US 8301619. Assigned to Avaya Inc., Basking Ridge, N.J. (US), October 2012.