Social Network of Co-occurrence in News Articles. - Arzucan Özgür; Haluk Bingöl (ISCIS, 2004)

Text Categorization with Class-Based and Corpus-Based Keyword Selection. - Arzucan Özgür; Levent Özgür; Tunga Güngör (ISCIS, 2005)

Classification of Skewed and Homogenous Document Corpora with Class-Based and Corpus-Based Keywords. - Arzucan Özgür; Tunga Güngör (KI, 2006)

Efficient indexing technique for XML-based electronic product catalogs. - Arzucan Özgür; Taflan Imre Gündem (Electron. Commer. Res. Appl., 2006)

Semi-Supervised Classification for Extracting Protein Interaction Sentences using Dependency Parsing. - Günes Erkan; Arzucan Özgür; Dragomir R. Radev (EMNLP-CoNLL, 2007)

Identifying gene-disease associations using centrality on a literature mined gene-interaction network. - Arzucan Özgür; Thuy Vu; Günes Erkan; Dragomir R. Radev (ISMB, 2008)

Supervised Classification for Extracting Biomedical Events. - Arzucan Özgür; Dragomir R. Radev (BioNLP@HLT-NAACL (Shared Task), 2009)

Detecting Speculations and their Scopes in Scientific Text. - Arzucan Özgür; Dragomir R. Radev (EMNLP, 2009)

Michigan molecular interactions r2: from interacting proteins to pathways. - V. Glenn Tarcea; Terry E. Weymouth; Alexander S. Ade; Aaron V. Bookvich; Jing Gao; Vasudeva Mahavisno; Zach Wright; Adriane Chapman; Magesh Jayapandian; Arzucan Özgür; Yuanyuan Tian 001; James D. Cavalcoli; et al. (Nucleic Acids Res., 2009)

Citation Summarization Through Keyphrase Extraction. - Vahed Qazvinian; Dragomir R. Radev; Arzucan Özgür (COLING, 2010)

Text and Network Mining for Literature-Based Scientific Discovery in Biomedicine. - Arzucan Özgür (2010)

Mining of vaccine-associated IFN-γ gene interaction networks using the Vaccine Ontology. - Arzucan Özgür; Zuoshuang Xiang; Dragomir R. Radev; Yongqun He (J. Biomed. Semant., 2011)

U-Compare bio-event meta-service: compatible BioNLP event extraction services. - Yoshinobu Kano; Jari Björne; Filip Ginter; Tapio Salakoski; Ekaterina Buyko; Udo Hahn; K. Bretonnel Cohen; Karin Verspoor; Christophe Roeder; Lawrence E. Hunter; Halil Kilicoglu; Sabine Bergler; et al. (BMC Bioinform., 2011)

Identification of fever and vaccine-associated gene interaction networks using ontology-based literature mining. - Junguk Hur; Arzucan Özgür; Zuoshuang Xiang; Yongqun He (J. Biomed. Semant., 2012)

Bacteria Biotope Detection, Ontology-based Normalization, and Relation Extraction using Syntactic Rules. - Ilknur Karadeniz; Arzucan Özgür (BioNLP@ACL (Shared Task), 2013)

Word Polarity Detection Using a Multilingual Approach. - Cüneyd Murad Özsert; Arzucan Özgür (CICLing (2), 2013)

BOUNCE: Sentiment Classification in Twitter using Rich Feature Sets. - Nadin Kökciyan; Arda Çelebi; Arzucan Özgür; Suzan Üsküdarli (SemEval@NAACL-HLT, 2013)

PHISTO: pathogen-host interaction search tool. - Saliha Durmus Tekir; Tunahan Çakir; Emre Ardiç; Ali Semih Sayilirbas; Gökhan Konuk; Mithat Konuk; Hasret Sariyer; Azat Ugurlu; Ilknur Karadeniz; Arzucan Özgür; Fatih Erdogan Sevilgen; Kutlu Ö. Ülgen (Bioinform., 2013)

N-gram Parsing for Jointly Training a Discriminative Constituency Parser. - Arda Çelebi; Arzucan Özgür (Polibits, 2013)

Expanding machine translation training data with an out-of-domain corpus using language modeling based vocabulary saturation. - Burak Aydin; Arzucan Özgür (AMTA, 2014)

Analyzing Stemming Approaches for Turkish Multi-Document Summarization. - Muhammed Yavuz Nuzumlali; Arzucan Özgür (EMNLP, 2014)

A Graph-based Approach for Contextual Text Normalization. - Cagil Sonmez; Arzucan Özgür (EMNLP, 2014)

Improving Named Entity Recognition for Morphologically Rich Languages Using Word Embeddings. - Hakan Demir; Arzucan Özgür (ICMLA, 2014)

Self-training a Constituency Parser using n-gram Trees. - Arda Çelebi; Arzucan Özgür (LREC, 2014)

Rule-based focus extraction in Turkish question answering systems. - Caner Derici; Kerem Çelik; Arzucan Özgür; Tunga Gungor; Ekrem Kutbay; Yigit Aydin; Günizi Kartal (SIU, 2014)

Question Analysis for a Closed Domain Question Answering System. - Caner Derici; Kerem Çelik; Ekrem Kutbay; Yigit Aydin; Tunga Güngör; Arzucan Özgür; Günizi Kartal (CICLing (2), 2015)

Extension of the Interaction Network Ontology for Literature Mining of Gene-gene Interaction Networks from Sentences with Multiple Interaction Keywords. - Arzucan Özgür; Junguk Hur; Yongqun He (BDM2I@ISWC, 2015)

GLASS: a comprehensive database for experimentally validated GPCR-ligand associations. - Wallace K. B. Chan; Hongjiu Zhang; Jianyi Yang 002; Jeffrey R. Brender; Junguk Hur; Arzucan Özgür; Yang Zhang 040 (Bioinform., 2015)

Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions. - Junguk Hur; Arzucan Özgür; Zuoshuang Xiang; Yongqun He (J. Biomed. Semant., 2015)

Detection and categorization of bacteria habitats using shallow linguistic analysis. - Ilknur Karadeniz; Arzucan Özgür (BMC Bioinform., 2015)

Ontology-Based Categorization of Bacteria and Habitat Entities using Information Retrieval Techniques. - Mert Tiftikci; Hakan Sahin; Berfu Büyüköz; Alper Yayikçi; Arzucan Özgür (BioNLP (Shared Task), 2016)

Ignet: A Centrality and INO-based Web System for Analyzing and Visualizing Literature-mined Networks. - Arzucan Özgür; Junguk Hur; Zuoshuang Xiang; Edison Ong; Dragomir R. Radev; Yongqun He (ICBO/BioCreative, 2016)

Towards Building a Political Protest Database to Explain Changes in the Welfare State. - Çagil Sönmez; Arzucan Özgür; Erdem Yörük (LaTeCH@ACL, 2016)

Segmenting Hashtags using Automatically Created Training Data. - Arda Çelebi; Arzucan Özgür (LREC, 2016)

Named Entity Recognition on Twitter for Turkish using Semi-supervised Learning with Word Embeddings. - Eda Okur; Hakan Demir; Arzucan Özgür (LREC, 2016)

Sentence Similarity based on Dependency Tree Kernels for Multi-document Summarization. - Saziye Betül Özates; Arzucan Özgür; Dragomir R. Radev (LREC, 2016)

The Interaction Network Ontology-supported modeling and mining of complex interactions represented with multiple keywords in biomedical literature. - Arzucan Özgür; Junguk Hur; Yongqun He (BioData Min., 2016)

BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. - 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 001; et al. (Database J. Biol. Databases Curation, 2016)

A comparative study of SMILES-based compound similarity functions for drug-target interaction prediction. - Hakime Öztürk; Elif Özkirimli Ölmez; Arzucan Özgür (BMC Bioinform., 2016)

Automated Neuroanatomical Relation Extraction: A Linguistically Motivated Approach with a PVT Connectivity Graph Case Study. - Erinç Gökdeniz; Arzucan Özgür; Resit Canbeyli (Frontiers Neuroinformatics, 2016)

BUSEM at SemEval-2017 Task 4A Sentiment Analysis with Word Embedding and Long Short Term Memory RNN Approaches. - Deger Ayata; Murat Saraclar; Arzucan Özgür (SemEval@ACL, 2017)

Turkish tweet sentiment analysis with word embedding and machine learning. - Deger Ayata; Murat Saraclar; Arzucan Özgür (SIU, 2017)

Political opinion/sentiment prediction via long short term memory recurrent neural networks on Twitter. - Deger Ayata; Murat Saraclar; Arzucan Özgür (SIU, 2017)

Description of the BOUN System for the Trilingual Entity Detection and Linking Tasks at TAC KBP 2017. - Arda Çelebi; Arzucan Özgür (TAC, 2017)

Extracting Adverse Drug Reactions using Deep Learning and Dictionary Based Approaches. - Mert Tiftikci; Arzucan Özgür; Yongqun He; Junguk Hur (TAC, 2017)

Automatic query generation using word embeddings for retrieving passages describing experimental methods. - Ferhat Aydin; Zehra Melce Hüsünbeyi; Arzucan Özgür (Database J. Biol. Databases Curation, 2017)

BIOSSES: a semantic sentence similarity estimation system for the biomedical domain. - Gizem Sogancioglu; Hakime Öztürk; Arzucan Özgür (Bioinform., 2017)

Ontology-based literature mining of E. coli vaccine-associated gene interaction networks. - Junguk Hur; Arzucan Özgür; Yongqun He (J. Biomed. Semant., 2017)

A Morphology-Based Representation Model for LSTM-Based Dependency Parsing of Agglutinative Languages. - Saziye Betül Özates; Arzucan Özgür; Tunga Gungor; Balkiz Öztürk (CoNLL Shared Task (2), 2018)

A novel methodology on distributed representations of proteins using their interacting ligands. - Hakime Öztürk; Elif Özkirimli Ölmez; Arzucan Özgür (Bioinform., 2018)

DeepDTA: deep drug-target binding affinity prediction. - Hakime Öztürk; Arzucan Özgür; Elif Özkirimli Ölmez (Bioinform., 2018)

Ontology-based literature mining and class effect analysis of adverse drug reactions associated with neuropathy-inducing drugs. - Junguk Hur; Arzucan Özgür; Yongqun He (J. Biomed. Semant., 2018)

A chemical language based approach for protein - ligand interaction prediction. - Hakime Öztürk; Arzucan Özgür; Elif Özkirimli Ölmez (CoRR, 2018)

Segmenting hashtags and analyzing their grammatical structure. - Arda Çelebi; Arzucan Özgür (J. Assoc. Inf. Sci. Technol., 2018)

Turkish Treebanking: Unifying and Constructing Efforts. - Utku Türk; Furkan Atmaca; Saziye Betül Özates; Abdullatif Köksal; Balkiz Öztürk Basaran; Tunga Gungor; Arzucan Özgür (LAW@ACL, 2019)

BOUN-ISIK Participation: An Unsupervised Approach for the Named Entity Normalization and Relation Extraction of Bacteria Biotopes. - Ilknur Karadeniz; Ömer Faruk Tuna; Arzucan Özgür (BioNLP-OST@EMNLP-IJNCLP, 2019)

Turkish Tweet Classification with Transformer Encoder. - Atif Emre Yüksel; Yacsar Alim Türkmen; Arzucan Özgür; Berna Altinel (RANLP, 2019)

Identifying Image Related Sentences in News Articles. - Melike Esma Ilter; Lale Akarun; Arzucan Özgür (SIU, 2019)

Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. - Rezarta Islamaj Dogan; Sun Kim; Andrew Chatr-aryamontri; Chih-Hsuan Wei; Donald C. Comeau; Rui Antunes 002; Sérgio Matos; Qingyu Chen 001; Aparna Elangovan; Nagesh C. Panyam; Karin Verspoor; Hongfang Liu; et al. (Database J. Biol. Databases Curation, 2019)

Linking entities through an ontology using word embeddings and syntactic re-ranking. - Ilknur Karadeniz; Arzucan Özgür (BMC Bioinform., 2019)

Statistical representation models for mutation information within genomic data. - N. Ozlem Ozcan; Arzucan Özgür; Fikret Gürgen (BMC Bioinform., 2019)

Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels. - Mert Tiftikci; Arzucan Özgür; Yongqun He; Junguk Hur (BMC Bioinform., 2019)

WideDTA: prediction of drug-target binding affinity. - Hakime Öztürk; Elif Özkirimli Ölmez; Arzucan Özgür (CoRR, 2019)

BOUN-REX at CLEF-2020 ChEMU Task 2: Evaluating Pretrained Transformers for Event Extraction. - Hilal Dönmez; Abdullatif Köksal; Elif Özkirimli 001; Arzucan Özgür (CLEF (Working Notes), 2020)

An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents. - Jiayuan He 002; Dat Quoc Nguyen; Saber A. Akhondi; Christian Druckenbrodt; Camilo Thorne; Ralph Hoessel; Zubair Afzal; Zenan Zhai; Biaoyan Fang; Hiyori Yoshikawa; Ameer Albahem; Jingqi Wang; et al. (CLEF (Working Notes), 2020)

Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature. - Abdullatif Köksal; Hilal Dönmez; Riza Özçelik; Elif Ozkirimli 001; Arzucan Özgür (NLP4COVID@EMNLP, 2020)

The RELX Dataset and Matching the Multilingual Blanks for Cross-lingual Relation Classification. - Abdullatif Köksal; Arzucan Özgür (EMNLP (Findings), 2020)

Exploring Chemical Space using Natural Language Processing Methodologies for Drug Discovery. - Hakime Öztürk; Arzucan Özgür; Philippe Schwaller; Teodoro Laino; Elif Özkirimli Ölmez (CoRR, 2020)

A Hybrid Approach to Dependency Parsing: Combining Rules and Morphology with Deep Learning. - Saziye Betül Özates; Arzucan Özgür; Tunga Güngör; Balkiz Öztürk (CoRR, 2020)

PIDNA at BioASQ MESINESP: Hybrid Semantic Indexing for Biomedical Articles in Spanish. - Yi Huang; Buse Giledereli; Abdullatif Köksal; Arzucan Özgür; Elif Ozkirimli 001 (CLEF (Working Notes), 2021)

Balancing Methods for Multi-label Text Classification with Long-Tailed Class Distribution. - Yi Huang; Buse Giledereli; Abdullatif Köksal; Arzucan Özgür; Elif Ozkirimli 001 (EMNLP (1), 2021)

BOUN at SemEval-2021 Task 9: Text Augmentation Techniques for Fact Verification in Tabular Data. - Abdullatif Köksal; Yusuf Yüksel; Bekir Yildirim; Arzucan Özgür (SemEval@ACL/IJCNLP, 2021)

Twitter Dataset and Evaluation of Transformers for Turkish Sentiment Analysis. - Abdullatif Köksal; Arzucan Özgür (SIU, 2021)

Sentiment Analysis of Customer Comments in Banking using BERT-based Approaches. - Melik Masarifoglu; Umit Tigrak; Sefa Hakyemez; Guven Gul; Erdal Bozan; Ali Hakan Buyuklu; Arzucan Özgür (SIU, 2021)

DebiasedDTA: Model Debiasing to Boost Drug-Target Affinity Prediction. - Riza Özçelik; Alperen Bag; Berk Atil; Arzucan Özgür; Elif Özkirimli 001 (CoRR, 2021)

A Dataset and BERT-based Models for Targeted Sentiment Analysis on Turkish Texts. - Mustafa Melih Mutlu; Arzucan Özgür (ACL (student), 2022)

Enhancements to the BOUN Treebank Reflecting the Agglutinative Nature of Turkish. - Büsra Marsan; Salih Furkan Akkurt; Muhammet Sen; Merve Gürbüz; Onur Güngör 001; Saziye Betül Özates; Suzan Üsküdarli; Arzucan Özgür; Tunga Güngör; Balkiz Öztürk (ALTNLP, 2022)

A SHAP-based Active Learning Approach for Creating High-Quality Training Data. - Nailcan Kara; Yagiz Levent Gume; Umit Tigrak; Gokce Ezeroglu; Serdar Mola; Omer Burak Akgun; Arzucan Özgür (IEEE Big Data, 2022)

A Framework for Automatic Generation of Spoken Question-Answering Data. - Merve Ünlü Menevse; Yusufcan Manav; Ebru Arisoy; Arzucan Özgür (EMNLP (Findings), 2022)

Improving Code-Switching Dependency Parsing with Semi-Supervised Auxiliary Tasks. - Saziye Betül Özates; Arzucan Özgür; Tunga Gungor; Özlem Çetinoglu (NAACL-HLT (Findings), 2022)

A Hybrid Deep Dependency Parsing Approach Enhanced With Rules and Morphology: A Case Study for Turkish. - Saziye Betül Özates; Arzucan Özgür; Tunga Güngör; Balkiz Öztürk Basaran (IEEE Access, 2022)

Exploiting pretrained biochemical language models for targeted drug design. - Gökçe Uludogan; Elif Özkirimli 001; Kutlu Ö. Ülgen; Nilgün Karali; Arzucan Özgür (Bioinform., 2022)

A Self-aware Personal Assistant for Making Personalized Privacy Decisions. - Gonul Ayci; Murat Sensoy; Arzucan Özgür; Pinar Yolum (CoRR, 2022)

Resources for Turkish dependency parsing: introducing the BOUN Treebank and the BoAT annotation tool. - Utku Türk; Furkan Atmaca; Saziye Betül Özates; Gözde Berk; Seyyit Talha Bedir; Abdullatif Köksal; Balkiz Öztürk Basaran; Tunga Güngör; Arzucan Özgür (Lang. Resour. Evaluation, 2022)

Cluster-based mention typing for named entity disambiguation. - Arda Çelebi; Arzucan Özgür (Nat. Lang. Eng., 2022)

Explain to Me: Towards Understanding Privacy Decisions. - Gonul Ayci; Arzucan Özgür; Murat Sensoy; Pinar Yolum (AAMAS, 2023)

TULAP - An Accessible and Sustainable Platform for Turkish Natural Language Processing Resources. - Suzan Uskudarli; Muhammet Sen; Salih Furkan Akkurt; Merve Gürbüz; Onur Güngör 001; Arzucan Özgür; Tunga Güngör (EACL (System Demonstrations), 2023)

A Dataset for Investigating the Impact of Context for Offensive Language Detection in Tweets. - Musa Ihtiyar; Ömer Özdemir; Mustafa Erengül; Arzucan Özgür (EMNLP (Findings), 2023)

SIU2023-NST - Hate Speech Detection Contest. - Inanç Arin; Zeynep Isik; Seçilay Kutal; Somaiyeh Dehghan; Arzucan Özgür; Berrin Yanikoglu (SIU, 2023)

Evaluation of GPT and BERT-based models on identifying protein-protein interactions in biomedical text. - Hasin Rehana; Nur Bengisu Çam; Mert Basmaci; Yongqun He; Arzucan Özgür; Junguk Hur (CoRR, 2023)

Generative Language Models on Nucleotide Sequences of Human Genes. - Musa Nuri Ihtiyar; Arzucan Özgür (CoRR, 2023)

Can We Explain Privacy? - Gönül Ayci; Arzucan Özgür; Murat Sensoy; Pinar Yolum (IEEE Internet Comput., 2023)

Uncertainty-Aware Personal Assistant for Making Personalized Privacy Decisions. - Gonul Ayci; Murat Sensoy; Arzucan Özgür; Pinar Yolum (ACM Trans. Internet Techn., 2023)

Editorial: Pattern recognition for healthcare analytics. - Inci M. Baytas; Yifan Peng 002; Arzucan Özgür (Frontiers Digit. Health, 2023)

A Computational Software for Training Robust Drug-Target Affinity Prediction Models: pydebiaseddta. - Melih Barsbey; Riza Özçelik; Alperen Bag; Berk Atil; Arzucan Özgür; Elif Ozkirimli 001 (J. Comput. Biol., 2023)

A Framework for Improving the Generalizability of Drug-Target Affinity Prediction Models. - Riza Özçelik; Alperen Bag; Berk Atil; Melih Barsbey; Arzucan Özgür; Elif Ozkirimli 001 (J. Comput. Biol., 2023)

Improving the filtering of false positive single nucleotide variations by combining genomic features with quality metrics. - Kazim Kivanç Eren; Esra Çinar; Hamza Umut Karakurt; Arzucan Özgür (Bioinform., 2023)

Linguistic Laws Meet Protein Sequences: A Comparative Analysis of Subword Tokenization Methods. - Burak Suyunu; Enes Taylan; Arzucan Özgür (BIBM, 2024)

Overview of the Hate Speech Detection in Turkish and Arabic Tweets (HSD-2Lang) Shared Task at CASE 2024. - Gökçe Uludogan; Somaiyeh Dehghan; Inanç Arin; Elif Erol; Berrin Yanikoglu; Arzucan Özgür (CASE, 2024)

Detecting Hate Speech in Turkish Print Media: A Corpus and A Hybrid Approach with Target-oriented Linguistic Knowledge. - Gökçe Uludogan; Atif Emre Yüksel; Ümit Tunçer; Burak Isik; Yasemin Korkmaz; Didar Akar; Arzucan Özgür (CASE, 2024)

Nested Named Entity Recognition using Multilayer BERT-based Model. - Hasin Rehana; Benu Bansal; Nur Bengisu Çam; Jie Zheng 001; Yongqun He; Arzucan Özgür; Junguk Hur (CLEF (Working Notes), 2024)

Evaluating the Quality of a Corpus Annotation Scheme Using Pretrained Language Models. - Salih Furkan Akkurt; Onur Güngör 001; Büsra Marsan; Tunga Gungor; Balkiz Öztürk Basaran; Arzucan Özgür; Susan Üsküdarli (LREC/COLING, 2024)

Dealing with Data Scarcity in Spoken Question Answering. - Merve Ünlü Menevse; Yusufcan Manav; Ebru Arisoy; Arzucan Özgür (LREC/COLING, 2024)

Cancer Vaccine Adjuvant Name Recognition from Biomedical Literature using Large Language Models. - Hasin Rehana; Jie Zheng 001; Leo Yeh; Benu Bansal; Nur Bengisu Çam; Christianah Jemiyo; Brett A. McGregor; Arzucan Özgür; Yongqun He; Junguk Hur (CoRR, 2025)

evoBPE: Evolutionary Protein Sequence Tokenization. - Burak Suyunu; Özdeniz Dolu; Arzucan Özgür (CoRR, 2025)

GNNMutation: a heterogeneous graph-based framework for cancer detection. - Nuriye Özlem Özcan Simsek; Arzucan Özgür; Fikret Gürgen (BMC Bioinform., 2025)