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Arzucan Özgür
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- affiliation: Bogaziçi University, Department of Computer Engineering, Istanbul, Turkey
- affiliation: University of Michigan, Department of EECS, Ann Arbor, MI, USA
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2020 – today
- 2024
- [c56]Gökçe Uludogan
, Atif Emre Yüksel, Ümit Tunçer, Burak Isik, Yasemin Korkmaz, Didar Akar, Arzucan Özgür:
Detecting Hate Speech in Turkish Print Media: A Corpus and A Hybrid Approach with Target-oriented Linguistic Knowledge. CASE 2024: 205-214 - [c55]Gökçe Uludogan
Overview of the Hate Speech Detection in Turkish and Arabic Tweets (HSD-2Lang) Shared Task at CASE 2024. CASE 2024: 229-233 - [c54]Hasin Rehana, Benu Bansal, Nur Bengisu Çam, Jie Zheng, Yongqun He, Arzucan Özgür, Junguk Hur:
Nested Named Entity Recognition using Multilayer BERT-based Model. CLEF (Working Notes) 2024: 197-206 - [c53]Merve Ünlü Menevse, Yusufcan Manav, Ebru Arisoy, Arzucan Özgür:
Dealing with Data Scarcity in Spoken Question Answering. LREC/COLING 2024: 4449-4455 - [c52]Salih Furkan Akkurt
Evaluating the Quality of a Corpus Annotation Scheme Using Pretrained Language Models. LREC/COLING 2024: 6504-6514 - 2023
- [j34]Kazim Kivanç Eren
Improving the filtering of false positive single nucleotide variations by combining genomic features with quality metrics. Bioinform. 39(12) (2023) - [j33]Inci M. Baytas
Editorial: Pattern recognition for healthcare analytics. Frontiers Digit. Health 5 (2023) - [j32]Gönül Ayci
Can We Explain Privacy? IEEE Internet Comput. 27(4): 75-80 (2023) - [j31]Riza Özçelik, Alperen Bag, Berk Atil, Melih Barsbey
A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models. J. Comput. Biol. 30(11): 1226-1239 (2023) - [j30]Melih Barsbey
A Computational Software for Training Robust Drug-Target Affinity Prediction Models: pydebiaseddta. J. Comput. Biol. 30(11): 1240-1245 (2023) - [j29]Gonul Ayci
Uncertainty-Aware Personal Assistant for Making Personalized Privacy Decisions. ACM Trans. Internet Techn. 23(1): 13:1-13:24 (2023) - [c51]Gonul Ayci, Arzucan Özgür, Murat Sensoy, Pinar Yolum:
Explain to Me: Towards Understanding Privacy Decisions. AAMAS 2023: 2790-2791 - [c50]Suzan Uskudarli
TULAP - An Accessible and Sustainable Platform for Turkish Natural Language Processing Resources. EACL (System Demonstrations) 2023: 219-227 - [c49]Musa Ihtiyar, Ömer Özdemir, Mustafa Erengül, Arzucan Özgür:
A Dataset for Investigating the Impact of Context for Offensive Language Detection in Tweets. EMNLP (Findings) 2023: 1543-1549 - [c48]Inanç Arin, Zeynep Isik, Seçilay Kutal
SIU2023-NST - Hate Speech Detection Contest. SIU 2023: 1-4 - [i21]Gonul Ayci, Pinar Yolum, Arzucan Özgür, Murat Sensoy:
Explain to Me: Towards Understanding Privacy Decisions. CoRR abs/2301.02079 (2023) - [i20]Hasin Rehana, Nur Bengisu Çam, Mert Basmaci, Yongqun He, Arzucan Özgür
Evaluation of GPT and BERT-based models on identifying protein-protein interactions in biomedical text. CoRR abs/2303.17728 (2023) - [i19]Musa Nuri Ihtiyar, Arzucan Özgür:
Generative Language Models on Nucleotide Sequences of Human Genes. CoRR abs/2307.10634 (2023) - 2022
- [j28]Saziye Betül Özates
A Hybrid Deep Dependency Parsing Approach Enhanced With Rules and Morphology: A Case Study for Turkish. IEEE Access 10: 93867-93886 (2022) - [j27]Utku Türk
Resources for Turkish dependency parsing: introducing the BOUN Treebank and the BoAT annotation tool. Lang. Resour. Evaluation 56(1): 259-307 (2022) - [j26]Arda Çelebi, Arzucan Özgür
Cluster-based mention typing for named entity disambiguation. Nat. Lang. Eng. 28(1): 1-37 (2022) - [c47]Mustafa Melih Mutlu, Arzucan Özgür:
A Dataset and BERT-based Models for Targeted Sentiment Analysis on Turkish Texts. ACL (student) 2022: 467-472 - [c46]Büsra Marsan, Salih Furkan Akkurt, Muhammet Sen, Merve Gürbüz, Onur Güngör, Saziye Betül Özates, Suzan Üsküdarli, Arzucan Özgür, Tunga Güngör, Balkiz Öztürk:
Enhancements to the BOUN Treebank Reflecting the Agglutinative Nature of Turkish. ALTNLP 2022: 71-80 - [c45]Nailcan Kara, Yagiz Levent Gume, Umit Tigrak, Gokce Ezeroglu, Serdar Mola, Omer Burak Akgun, Arzucan Özgür
A SHAP-based Active Learning Approach for Creating High-Quality Training Data. IEEE Big Data 2022: 4002-4008 - [c44]Merve Ünlü Menevse
A Framework for Automatic Generation of Spoken Question-Answering Data. EMNLP (Findings) 2022: 4659-4666 - [c43]Saziye Betül Özates
Improving Code-Switching Dependency Parsing with Semi-Supervised Auxiliary Tasks. NAACL-HLT (Findings) 2022: 1159-1171 - [i18]M. Melih Mutlu, Arzucan Özgür:
A Dataset and BERT-based Models for Targeted Sentiment Analysis on Turkish Texts. CoRR abs/2205.04185 (2022) - [i17]Gonul Ayci, Murat Sensoy
A Self-aware Personal Assistant for Making Personalized Privacy Decisions. CoRR abs/2205.06544 (2022) - [i16]Büsra Marsan, Salih Furkan Akkurt, Muhammet Sen, Merve Gürbüz, Onur Güngör, Saziye Betül Özates, Suzan Üsküdarli, Arzucan Özgür, Tunga Güngör, Balkiz Öztürk:
Enhancements to the BOUN Treebank Reflecting the Agglutinative Nature of Turkish. CoRR abs/2207.11782 (2022) - [i15]Gökçe Uludogan, Elif Özkirimli, Kutlu Ö. Ülgen, Nilgün Karali, Arzucan Özgür:
Exploiting Pretrained Biochemical Language Models for Targeted Drug Design. CoRR abs/2209.00981 (2022) - 2021
- [c42]Yi Huang, Buse Giledereli, Abdullatif Köksal, Arzucan Özgür, Elif Ozkirimli:
PIDNA at BioASQ MESINESP: Hybrid Semantic Indexing for Biomedical Articles in Spanish. CLEF (Working Notes) 2021: 241-246 - [c41]Yi Huang, Buse Giledereli, Abdullatif Köksal, Arzucan Özgür, Elif Ozkirimli:
Balancing Methods for Multi-label Text Classification with Long-Tailed Class Distribution. EMNLP (1) 2021: 8153-8161 - [c40]Abdullatif Köksal, Yusuf Yüksel, Bekir Yildirim, Arzucan Özgür:
BOUN at SemEval-2021 Task 9: Text Augmentation Techniques for Fact Verification in Tabular Data. SemEval@ACL/IJCNLP 2021: 431-437 - [c39]Abdullatif Köksal, Arzucan Özgür
Twitter Dataset and Evaluation of Transformers for Turkish Sentiment Analysis. SIU 2021: 1-4 - [c38]Melik Masarifoglu, Umit Tigrak, Sefa Hakyemez, Guven Gul, Erdal Bozan, Ali Hakan Buyuklu, Arzucan Özgür
Sentiment Analysis of Customer Comments in Banking using BERT-based Approaches. SIU 2021: 1-4 - [i14]Riza Özçelik, Alperen Bag, Berk Atil, Arzucan Özgür, Elif Özkirimli:
DebiasedDTA: Model Debiasing to Boost Drug-Target Affinity Prediction. CoRR abs/2107.05556 (2021) - [i13]Yi Huang, Buse Giledereli, Abdullatif Köksal, Arzucan Özgür, Elif Ozkirimli:
Balancing Methods for Multi-label Text Classification with Long-Tailed Class Distribution. CoRR abs/2109.04712 (2021) - [i12]Arda Çelebi, Arzucan Özgür:
Cluster-based Mention Typing for Named Entity Disambiguation. CoRR abs/2109.11389 (2021) - 2020
- [c37]Hilal Dönmez, Abdullatif Köksal, Elif Özkirimli, Arzucan Özgür:
BOUN-REX at CLEF-2020 ChEMU Task 2: Evaluating Pretrained Transformers for Event Extraction. CLEF (Working Notes) 2020 - [c36]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
An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents. CLEF (Working Notes) 2020 - [c35]Abdullatif Köksal, Hilal Dönmez, Riza Özçelik, Elif Ozkirimli, Arzucan Özgür:
Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature. NLP4COVID@EMNLP 2020 - [c34]Abdullatif Köksal, Arzucan Özgür:
The RELX Dataset and Matching the Multilingual Blanks for Cross-lingual Relation Classification. EMNLP (Findings) 2020: 340-350 - [i11]Hakime Öztürk, Arzucan Özgür, Philippe Schwaller, Teodoro Laino, Elif Özkirimli Ölmez:
Exploring Chemical Space using Natural Language Processing Methodologies for Drug Discovery. CoRR abs/2002.06053 (2020) - [i10]Saziye Betül Özates, Arzucan Özgür, Tunga Güngör, Balkiz Öztürk:
A Hybrid Approach to Dependency Parsing: Combining Rules and Morphology with Deep Learning. CoRR abs/2002.10116 (2020) - [i9]Utku Türk, Furkan Atmaca, Saziye Betül Özates
Resources for Turkish Dependency Parsing: Introducing the BOUN Treebank and the BoAT Annotation Tool. CoRR abs/2002.10416 (2020) - [i8]Abdullatif Köksal, Hilal Dönmez, Riza Özçelik, Elif Ozkirimli, Arzucan Özgür:
Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature. CoRR abs/2009.02526 (2020) - [i7]Abdullatif Köksal, Arzucan Özgür:
The RELX Dataset and Matching the Multilingual Blanks for Cross-Lingual Relation Classification. CoRR abs/2010.09381 (2020)
2010 – 2019
- 2019
- [j25]Rezarta Islamaj Dogan
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database J. Biol. Databases Curation 2019: bay147 (2019) - [j24]Ilknur Karadeniz
Linking entities through an ontology using word embeddings and syntactic re-ranking. BMC Bioinform. 20(1): 156:1-156:12 (2019) - [j23]N. Ozlem Ozcan, Arzucan Özgür
Statistical representation models for mutation information within genomic data. BMC Bioinform. 20(1): 324:1-324:13 (2019) - [j22]Mert Tiftikci, Arzucan Özgür
Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels. BMC Bioinform. 20-S(21): 707 (2019) - [c33]Utku Türk
Turkish Treebanking: Unifying and Constructing Efforts. LAW@ACL 2019: 166-177 - [c32]Ilknur Karadeniz, Ömer Faruk Tuna, Arzucan Özgür:
BOUN-ISIK Participation: An Unsupervised Approach for the Named Entity Normalization and Relation Extraction of Bacteria Biotopes. BioNLP-OST@EMNLP-IJNCLP 2019: 150-157 - [c31]Atif Emre Yüksel, Yacsar Alim Türkmen, Arzucan Özgür, Berna Altinel
Turkish Tweet Classification with Transformer Encoder. RANLP 2019: 1380-1387 - [c30]Melike Esma Ilter, Lale Akarun
Identifying Image Related Sentences in News Articles. SIU 2019: 1-4 - [i6]Hakime Öztürk
WideDTA: prediction of drug-target binding affinity. CoRR abs/1902.04166 (2019) - 2018
- [j21]Hakime Öztürk
A novel methodology on distributed representations of proteins using their interacting ligands. Bioinform. 34(13): i295-i303 (2018) - [j20]Hakime Öztürk
DeepDTA: deep drug-target binding affinity prediction. Bioinform. 34(17): i821-i829 (2018) - [j19]Junguk Hur
Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs. J. Biomed. Semant. 9(1): 17:1-17:10 (2018) - [j18]Arda Çelebi, Arzucan Özgür:
Segmenting hashtags and analyzing their grammatical structure. J. Assoc. Inf. Sci. Technol. 69(5): 675-686 (2018) - [c29]Saziye Betül Özates, Arzucan Özgür, Tunga Gungor, Balkiz Öztürk:
A Morphology-Based Representation Model for LSTM-Based Dependency Parsing of Agglutinative Languages. CoNLL Shared Task (2) 2018: 238-247 - [i5]Hakime Öztürk, Elif Özkirimli Ölmez, Arzucan Özgür:
DeepDTA: Deep Drug-Target Binding Affinity Prediction. CoRR abs/1801.10193 (2018) - [i4]Eda Okur, Hakan Demir, Arzucan Özgür:
Named Entity Recognition on Twitter for Turkish using Semi-supervised Learning with Word Embeddings. CoRR abs/1810.08732 (2018) - [i3]Hakime Öztürk
A chemical language based approach for protein - ligand interaction prediction. CoRR abs/1811.00761 (2018) - 2017
- [j17]Ferhat Aydin, Zehra Melce Hüsünbeyi
Automatic query generation using word embeddings for retrieving passages describing experimental methods. Database J. Biol. Databases Curation 2017: baw166 (2017) - [j16]Gizem Sogancioglu, Hakime Öztürk
BIOSSES: a semantic sentence similarity estimation system for the biomedical domain. Bioinform. 33(14): i49-i58 (2017) - [j15]Junguk Hur
Ontology-based literature mining of E. coli vaccine-associated gene interaction networks. J. Biomed. Semant. 8(1): 12:1-12:10 (2017) - [c28]Deger Ayata, Murat Saraclar, Arzucan Özgür:
BUSEM at SemEval-2017 Task 4A Sentiment Analysis with Word Embedding and Long Short Term Memory RNN Approaches. SemEval@ACL 2017: 777-783 - [c27]Deger Ayata, Murat Saraclar, Arzucan Özgür:
Turkish tweet sentiment analysis with word embedding and machine learning. SIU 2017: 1-4 - [c26]Deger Ayata, Murat Saraclar, Arzucan Özgür:
Political opinion/sentiment prediction via long short term memory recurrent neural networks on Twitter. SIU 2017: 1-4 - [i2]Arda Çelebi, Arzucan Özgür:
Description of the BOUN System for the Trilingual Entity Detection and Linking Tasks at TAC KBP 2017. TAC 2017 - [i1]Mert Tiftikci, Arzucan Özgür, Yongqun He, Junguk Hur:
Extracting Adverse Drug Reactions using Deep Learning and Dictionary Based Approaches. TAC 2017 - 2016
- [j14]Arzucan Özgür, Junguk Hur
The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature. BioData Min. 9: 41:1-41:17 (2016) - [j13]Sun Kim, Rezarta Islamaj Dogan
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. Database J. Biol. Databases Curation 2016 (2016) - [j12]Hakime Öztürk
A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction. BMC Bioinform. 17: 128 (2016) - [j11]Erinç Gökdeniz, Arzucan Özgür, Resit Canbeyli:
Automated Neuroanatomical Relation Extraction: A Linguistically Motivated Approach with a PVT Connectivity Graph Case Study. Frontiers Neuroinformatics 10: 39 (2016) - [c25]Mert Tiftikci, Hakan Sahin, Berfu Büyüköz, Alper Yayikçi, Arzucan Özgür:
Ontology-Based Categorization of Bacteria and Habitat Entities using Information Retrieval Techniques. BioNLP (Shared Task) 2016: 56-63 - [c24]Arzucan Özgür, Junguk Hur, Zuoshuang Xiang, Edison Ong, Dragomir R. Radev, Yongqun He:
Ignet: A Centrality and INO-based Web System for Analyzing and Visualizing Literature-mined Networks. ICBO/BioCreative 2016 - [c23]Çagil Sönmez, Arzucan Özgür, Erdem Yörük:
Towards Building a Political Protest Database to Explain Changes in the Welfare State. LaTeCH@ACL 2016 - [c22]Arda Çelebi, Arzucan Özgür:
Segmenting Hashtags using Automatically Created Training Data. LREC 2016 - [c21]Eda Okur, Hakan Demir, Arzucan Özgür:
Named Entity Recognition on Twitter for Turkish using Semi-supervised Learning with Word Embeddings. LREC 2016 - [c20]Saziye Betül Özates, Arzucan Özgür, Dragomir R. Radev:
Sentence Similarity based on Dependency Tree Kernels for Multi-document Summarization. LREC 2016 - 2015
- [j10]Wallace K. B. Chan, Hongjiu Zhang
GLASS: a comprehensive database for experimentally validated GPCR-ligand associations. Bioinform. 31(18): 3035-3042 (2015) - [j9]Junguk Hur
Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. J. Biomed. Semant. 6: 2 (2015) - [j8]Ilknur Karadeniz, Arzucan Özgür:
Detection and categorization of bacteria habitats using shallow linguistic analysis. BMC Bioinform. 16(S10): S5 (2015) - [c19]Caner Derici, Kerem Çelik, Ekrem Kutbay, Yigit Aydin, Tunga Güngör
Question Analysis for a Closed Domain Question Answering System. CICLing (2) 2015: 468-482 - [c18]Arzucan Özgür, Junguk Hur, Yongqun He:
Extension of the Interaction Network Ontology for Literature Mining of Gene-gene Interaction Networks from Sentences with Multiple Interaction Keywords. BDM2I@ISWC 2015 - 2014
- [c17]Burak Aydin, Arzucan Özgür:
Expanding machine translation training data with an out-of-domain corpus using language modeling based vocabulary saturation. AMTA 2014: 180-192 - [c16]Cagil Sonmez, Arzucan Özgür:
A Graph-based Approach for Contextual Text Normalization. EMNLP 2014: 313-324 - [c15]Muhammed Yavuz Nuzumlali, Arzucan Özgür:
Analyzing Stemming Approaches for Turkish Multi-Document Summarization. EMNLP 2014: 702-706 - [c14]Hakan Demir, Arzucan Özgür:
Improving Named Entity Recognition for Morphologically Rich Languages Using Word Embeddings. ICMLA 2014: 117-122 - [c13]Arda Çelebi, Arzucan Özgür:
Self-training a Constituency Parser using n-gram Trees. LREC 2014: 2893-2896 - [c12]Caner Derici, Kerem Çelik, Arzucan Özgür, Tunga Gungor
Rule-based focus extraction in Turkish question answering systems. SIU 2014: 1604-1607 - 2013
- [j7]Saliha Durmus Tekir, Tunahan Çakir
PHISTO: pathogen-host interaction search tool. Bioinform. 29(10): 1357-1358 (2013) - [j6]Arda Çelebi, Arzucan Özgür:
N-gram Parsing for Jointly Training a Discriminative Constituency Parser. Polibits 47: 5-12 (2013) - [c11]Ilknur Karadeniz, Arzucan Özgür:
Bacteria Biotope Detection, Ontology-based Normalization, and Relation Extraction using Syntactic Rules. BioNLP@ACL (Shared Task) 2013: 170-177 - [c10]Cüneyd Murad Özsert, Arzucan Özgür:
Word Polarity Detection Using a Multilingual Approach. CICLing (2) 2013: 75-82 - [c9]Nadin Kökciyan, Arda Çelebi, Arzucan Özgür, Suzan Üsküdarli:
BOUNCE: Sentiment Classification in Twitter using Rich Feature Sets. SemEval@NAACL-HLT 2013: 554-561 - 2012
- [j5]Junguk Hur
Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. J. Biomed. Semant. 3: 18 (2012) - 2011
- [j4]Arzucan Özgür, Zuoshuang Xiang, Dragomir R. Radev, Yongqun He:
Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. J. Biomed. Semant. 2(S-2): S8 (2011) - [j3]Yoshinobu Kano, Jari Björne, Filip Ginter, Tapio Salakoski, Ekaterina Buyko, Udo Hahn, K. Bretonnel Cohen, Karin Verspoor
U-Compare bio-event meta-service: compatible BioNLP event extraction services. BMC Bioinform. 12: 481 (2011) - 2010
- [b1]Arzucan Özgür:
Text and Network Mining for Literature-Based Scientific Discovery in Biomedicine. University of Michigan, USA, 2010 - [c8]Vahed Qazvinian, Dragomir R. Radev, Arzucan Özgür:
Citation Summarization Through Keyphrase Extraction. COLING 2010: 895-903
2000 – 2009
- 2009
- [j2]V. Glenn Tarcea, Terry E. Weymouth, Alexander S. Ade, Aaron V. Bookvich, Jing Gao, Vasudeva Mahavisno, Zach Wright, Adriane Chapman, Magesh Jayapandian, Arzucan Özgür
Michigan molecular interactions r2: from interacting proteins to pathways. Nucleic Acids Res. 37(Database-Issue): 642-646 (2009) - [c7]Arzucan Özgür, Dragomir R. Radev:
Supervised Classification for Extracting Biomedical Events. BioNLP@HLT-NAACL (Shared Task) 2009: 111-114 - [c6]Arzucan Özgür, Dragomir R. Radev:
Detecting Speculations and their Scopes in Scientific Text. EMNLP 2009: 1398-1407 - 2008
- [c5]Arzucan Özgür
Identifying gene-disease associations using centrality on a literature mined gene-interaction network. ISMB 2008: 277-285 - 2007
- [c4]Günes Erkan, Arzucan Özgür, Dragomir R. Radev:
Semi-Supervised Classification for Extracting Protein Interaction Sentences using Dependency Parsing. EMNLP-CoNLL 2007: 228-237 - 2006
- [j1]Arzucan Özgür
Efficient indexing technique for XML-based electronic product catalogs. Electron. Commer. Res. Appl. 5(1): 66-77 (2006) - [c3]Arzucan Özgür, Tunga Güngör:
Classification of Skewed and Homogenous Document Corpora with Class-Based and Corpus-Based Keywords. KI 2006: 91-101 - 2005
- [c2]Arzucan Özgür, Levent Özgür, Tunga Güngör:
Text Categorization with Class-Based and Corpus-Based Keyword Selection. ISCIS 2005: 606-615 - 2004
- [c1]Arzucan Özgür, Haluk Bingöl:
Social Network of Co-occurrence in News Articles. ISCIS 2004: 688-695
Coauthor Index
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