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<!DOCTYPE html>
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<title>Home | Boğaziçi University Text Analytics and BIoInformatics Lab</title>
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<h1 class="lab-section-title"></h1>
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<div class="lab-section-title"><strong>Text Analytics and BIoInformatics Lab</strong></div>
<div>TABI</div>
</div>
</div>
<h1 class="lab-section-title">Research Areas</h1>
<div class="panel panel-default lab-panel">
<div class="panel-body text-left">
<div class="lab-panel col-xs-12">
<div class="small-title">Natural Language Processing and Bioinformatics</div>
<ul class="color-with-marker">
<li>Word and sentence processing and analysis
<ul class="color-with-marker">
<li>Morphological analysis</li>
<li>Multi-word expressions</li>
<li>Dependency parsing</li>
</ul>
</li>
<li>Information retrieval and information extraction
<ul class="color-with-marker">
<li>Named entity recognition</li>
<li>Normalisation</li>
<li>Relation extraction</li>
<li>Text summarisation</li>
<li>Sentiment analysis</li>
</ul>
</li>
<li>Machine translation</li>
<li>Text mining for biological and natural languages</li>
<li>Protein-protein and protein-compound interaction prediction</li>
<li>Chemical language processing for drug discovery</li>
<li>Disease diagnosis support using genomic data</li>
</ul>
</div>
</div>
</div>
<h1 class="lab-section-title">Recent Publications</h1>
<div class="row-fluid">
<h2 class="lab-subsection-title">2020</h2>
</div>
<div id="bibtex_display">
<div class="row bibtexentry" style="">
<div class="col-xs-12">
<div class="panel panel-default lab-panel">
<div class="panel-body">
<a class="url"
href="https://www.aclweb.org/anthology/2020.findings-emnlp.32">
<div class="small-title"><span class="title">The RELX Dataset and Matching the Multilingual Blanks for Cross-Lingual Relation Classification</span>
</div>
</a>
<div>by <span class="author">
<span class="Abdullatif Koksal">
<span class="first">Abdullatif</span> <span
class="last">Köksal</span>
</span>
<span class="bibtex_js_conjunction"> and</span>
<span class="Arzucan Ozgur">
<span class="first">Arzucan</span><span
class="last"> Ozgur</span>
</span>
</span>
</div>
<div>in
<span class="">
<span class="journal">Findings of the Association for Computational Linguistics at EMNLP</span>
</span>
, <span class="year">2020</span></div>
</div>
</div>
</div>
</div>
<div class="row bibtexentry" style="">
<div class="col-xs-12">
<div class="panel panel-default lab-panel">
<div class="panel-body">
<a class="url"
href="https://www.aclweb.org/anthology/2020.nlpcovid19-2.21">
<div class="small-title"><span class="title">Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature</span>
</div>
</a>
<div>by <span class="author">
<span class="Abdullatif Koksal">
<span class="first">Abdullatif</span> <span
class="last">Koksal</span>
</span>,
<span class="Hilal Donmez">
<span class="first">Hilal</span> <span class="last">Donmez</span>
</span>,
<span class="Riza Ozcelik">
<span class="first">Riza</span> <span class="last">Ozcelik</span>
</span>,
<span class="Elif Ozkirimli">
<span class="first">Elif</span> <span class="last">Ozkirimli</span>
</span>
<span class="bibtex_js_conjunction"> and</span>
<span class="Arzucan Ozgur">
<span class="first">Arzucan</span><span
class="last"> Ozgur</span>
</span>
</span>
</div>
<div>in
<span class="">
<span class="journal">Proceedings of the 1st Workshop on NLP for COVID-19 (Part 2) at EMNLP</span>
</span>
, <span class="year">2020</span></div>
</div>
</div>
</div>
</div>
<div class="row bibtexentry" style="">
<div class="col-xs-12">
<div class="panel panel-default lab-panel">
<div class="panel-body">
<a class="url"
href="https://www.aclweb.org/anthology/2020.aespen-1.4">
<div class="small-title"><span class="title">Analyzing ELMo and DistilBERT on Socio-political News Classification</span>
</div>
</a>
<div>by <span class="author">
<span class="Berfu Buyukoz">
<span class="first">Berfu</span> <span class="last">Buyukoz</span>
</span>,
<span class="Ali Hurriyetoglu">
<span class="first">Ali</span> <span
class="last">Hurriyetoglu</span>
</span>
<span class="bibtex_js_conjunction"> and</span>
<span class="Arzucan Ozgur">
<span class="first">Arzucan</span><span
class="last"> Ozgur</span>
</span>
</span>
</div>
<div>in
<span class="">
<span class="journal">Proceedings of the Workshop on Automated Extraction of Socio-political Events from News at ELRA</span>
</span>
, <span class="year">2020</span></div>
</div>
</div>
</div>
</div>
<div class="row bibtexentry" style="">
<div class="col-xs-12">
<div class="panel panel-default lab-panel">
<div class="panel-body">
<a class="url"
href="https://doi.org/10.1016/j.drudis.2020.01.020">
<div class="small-title"><span class="title">Exploring chemical space using natural language processing methodologies for drug discovery</span>
</div>
</a>
<div>by <span class="author">
<span class="Hakime Ozturk">
<span class="first">Hakime</span> <span class="last">Ozturk</span>
</span>,
<span class="Arzucan Ozgur">
<span class="first">Arzucan</span> <span class="last">Ozgur</span>
</span>,
<span class="Philippe Schwaller">
<span class="first">Philippe</span> <span
class="last">Schwaller</span>
</span>,
<span class="Teodoro Laino">
<span class="first">Teodoro</span> <span class="last">Laino</span>
</span>
<span class="bibtex_js_conjunction"> and</span>
<span class="Elif Ozkirimli">
<span class="first">Elif</span><span
class="last"> Ozkirimli</span>
</span>
</span>
</div>
<div>in
<span class="">
<span class="journal">Drug Discovery Today</span>
</span>
, <span class="year">2020</span></div>
</div>
</div>
</div>
</div>
<div class="row bibtexentry" style="">
<div class="col-xs-12">
<div class="panel panel-default lab-panel">
<div class="panel-body">
<a class="url"
href="https://arxiv.org/abs/2002.10116">
<div class="small-title"><span class="title">A Hybrid Approach to Dependency Parsing: Combining Rules and Morphology with Deep Learning</span>
</div>
</a>
<div>by <span class="author">
<span class="Saziye Betul Ozates">
<span class="first">Saziye Betul</span> <span
class="last"> Ozates</span>
</span>,
<span class="Arzucan Ozgur">
<span class="first">Arzucan</span> <span class="last">Ozgur</span>
</span>,
<span class="Tunga Gungor">
<span class="first">Tunga</span> <span class="last">Gungor</span>
</span>
<span class="bibtex_js_conjunction"> and</span>
<span class="Balkiz Ozturk">
<span class="first">Balkız</span> <span class="last">Ozturk</span>
</span>
</span>
</div>
<div>in
<span class="">
<span class="journal">arXiv preprint</span>
</span>
, <span class="year">2020</span></div>
</div>
</div>
</div>
</div>
<div class="row bibtexentry" style="">
<div class="col-xs-12">
<div class="panel panel-default lab-panel">
<div class="panel-body">
<a class="url"
href="https://arxiv.org/abs/2002.10416">
<div class="small-title"><span class="title">Resources for Turkish Dependency Parsing: Introducing the BOUN Treebank and the BoAT Annotation Tool</span>
</div>
</a>
<div>by <span class="author">
<span class="Utku Turk">
<span class="first">Utku</span> <span class="last"> Turk</span>
</span>,
<span class="Furkan Atmaca">
<span class="first">Furkan</span> <span class="last"> Atmaca</span>
</span>,
<span class="Saziye Betul Ozates">
<span class="first">Saziye Betul</span> <span
class="last"> Ozates</span>
</span>,
<span class="Gozde Berk">
<span class="first">Gozde</span> <span class="last"> Berk</span>
</span>,
<span class="Seyyit Talha">
<span class="first">Seyyit Talha</span> <span
class="last"> Bedir</span>
</span>,
<span class="Balkiz Ozturk Basaran">
<span class="first">Balkız</span> <span
class="last"> Ozturk Basaran</span>
</span>,
<span class="Tunga Gungor">
<span class="first">Tunga</span> <span class="last">Gungor</span>
</span>
<span class="bibtex_js_conjunction"> and</span>
<span class="Arzucan Ozgur">
<span class="first">Arzucan</span> <span class="last">Ozgur</span>
</span>
</span>
</div>
<div>in
<span class="">
<span class="journal">arXiv preprint</span>
</span>
, <span class="year">2020</span></div>
</div>
</div>
</div>
</div>
<div class="row bibtexentry" style="">
<div class="col-xs-12">
<div class="panel panel-default lab-panel">
<div class="panel-body">
<a class="url"
href="https://www.aclweb.org/anthology/2020.emnlp-main.662/">
<div class="small-title"><span class="title">Data and Representation for Turkish Natural Language Inference</span>
</div>
</a>
<div>by <span class="author">
<span class="Emrah Budur">
<span class="first">Emrah</span> <span class="last">Budur</span>
</span>,
<span class="Riza Ozcelik">
<span class="first">Riza</span> <span class="last">Ozcelik</span>
</span>,
<span class="Tunga Gungor">
<span class="first">Tunga</span><span
class="last"> Gungor</span>
</span>
<span class="bibtex_js_conjunction"> and</span>
<span class="Christopher Potts">
<span class="first">Christopher</span><span
class="last"> Potts</span>
</span>
</span>
</div>
<div>in
<span class="">
<span class="journal">Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP)</span>
</span>
, <span class="year">2020</span></div>
</div>
</div>
</div>
</div>
<div class="row bibtexentry" style="">
<div class="col-xs-12">
<div class="panel panel-default lab-panel">
<div class="panel-body">
<a class="url"
href="https://arxiv.org/abs/2011.04451">
<div class="small-title"><span class="title">Hierarchical Multitask Learning Approach for BERT</span>
</div>
</a>
<div>by <span class="author">
<span>
<span class="first">Çağla</span> <span class="last">Aksoy</span>
</span>,
<span>
<span class="first">Alper</span> <span class="last">Ahmetoğlu</span>
</span>
<span class="bibtex_js_conjunction"> and</span>
<span>
<span class="first">Tunga</span><span
class="last"> Gungor</span>
</span>
</span>
</div>
<div>in
<span class="">
<span class="journal">arXiv preprint</span>
</span>
, <span class="year">2020</span></div>
</div>
</div>
</div>
</div>
<div class="row bibtexentry" style="">
<div class="col-xs-12">
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<div class="small-title"><span class="title">Intrinsic and Extrinsic Evaluation of Word Embedding Models</span>
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<div>by <span class="author">
<span>
<span class="first">Gökçe</span> <span class="last">Yeşiltaş</span>
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<span>
<span class="first">Tunga</span><span
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<div>in
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<span class="journal">Innovations in Intelligent Systems and Applications Conference (ASYU)</span>
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<div class="small-title"><span class="title">Generating a Concept Relation Network for Turkish Based on ConceptNet Using Translational Methods</span>
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<div>by <span class="author">
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<span class="first">Arif Sırrı</span> <span
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<span class="bibtex_js_conjunction"> and</span>
<span>
<span class="first">Tunga</span><span
class="last"> Gungor</span>
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<div>in
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<span class="journal">International Conference on Speech and Computer (SPECOM)</span>
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, <span class="year">2020</span></div>
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<div class="small-title"><span class="title">Combination of Recursive and Recurrent Neural Networks for Aspect-Based Sentiment Analysis Using Inter-Aspect Relations</span>
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<div>by <span class="author">
<span>
<span class="first">Cem Rıfkı</span> <span
class="last"> Aydın</span>
</span>
<span class="bibtex_js_conjunction"> and</span>
<span>
<span class="first">Tunga</span><span
class="last"> Gungor</span>
</span>
</span>
</div>
<div>in
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<span class="journal">IEEE Access</span>
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, <span class="year">2020</span></div>
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<a class="url"
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<div class="small-title"><span class="title">Hierarchical Multi Task Learning with Subword Contextual Embeddings for Languages with Rich Morphology</span>
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<div>by <span class="author">
<span>
<span class="first">Arda</span> <span class="last"> Akdemir</span>
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<span>
<span class="first">Tetsuo</span> <span class="last"> Shibuya</span>
</span>
<span class="bibtex_js_conjunction"> and</span>
<span>
<span class="first">Tunga</span><span
class="last"> Gungor</span>
</span>
</span>
</div>
<div>in
<span class="">
<span class="journal">arXiv preprint</span>
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, <span class="year">2020</span></div>
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href="https://doi.org/10.1371/journal.pone.0236863">
<div class="small-title"><span class="title">Microblog topic identification using Linked Open Data</span>
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<div>by <span class="author">
<span>
<span class="first">Ahmet </span> <span class="last">Yıldırım</span>
</span>,
<span class="bibtex_js_conjunction"> and</span>
<span>
<span class="first">Suzan</span><span
class="last"> Üsküdarlı</span>
</span>
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<div>in
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<span class="journal">PLOS ONE</span>
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, <span class="year">2020</span></div>
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<div class="small-title"><span class="title">NeuroBoun: An inquiry-based approach for exploring scientific literature -- a use case in neuroscience</span>
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<div>by <span class="author">
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<span class="first">Suzan </span> <span
class="last">Üsküdarlı</span>
</span>,
<span>
<span class="first">Erinç </span> <span class="last">Gökdeniz</span>
</span>,
<span class="bibtex_js_conjunction"> and</span>
<span>
<span class="first">Reşit</span><span
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</span>
</span>
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<div>in
<span class="">
<span class="journal">arXiv preprint</span>
</span>
, <span class="year">2020</span></div>
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<h2 class="lab-subsection-title">2019</h2>
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<a class="url"
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<div class="small-title"><span class="title">Turkish Tweet Classification with Transformer Encoder</span>
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</a>
<div>by <span class="author">
<span> <span
class="first">Atıf Emre</span><span
class="last"> Yüksel</span> </span>,
<span> <span
class="first">Yaşar Alim</span><span
class="last"> Türkmen</span> </span>
<span
class="Arzucan Ozgur"> <span class="first">Arzucan</span><span
class="last"> Ozgur</span> </span></span>
<span
class="bibtex_js_conjunction"> and
<span> <span
class="first">Berna</span><span
class="last"> Altınel</span> </span>
</span>
</div>
<div>in
<span class="">
<span class="journal">Proceedings of the International Conference on Recent Advances in Natural Language Processing (RANLP)</span>
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, <span class="year">2019</span></div>
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<a class="url"
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<div class="small-title"><span class="title">BOUN-ISIK Participation: An Unsupervised Approach for the Named Entity Normalization and Relation Extraction of Bacteria Biotopes</span>
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</a>
<div>by <span class="author">
<span class="Ilknur Karadeniz"> <span
class="first">Ilknur</span><span
class="last"> Karadeniz</span> </span>,
<span> <span
class="first">Ömer Faruk</span><span
class="last"> Tuna</span> </span>
<span
class="bibtex_js_conjunction"> and</span> <span
class="Arzucan Ozgur"> <span class="first">Arzucan</span><span
class="last"> Ozgur</span> </span></span></div>
<div>in
<span class="">
<span class="journal">Proceedings of The 5th Workshop on BioNLP Open Shared Tasks at EMNLP</span>
</span>
, <span class="year">2019</span></div>
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<a class="url"
href="https://doi.org/10.1186/s12859-019-3195-5">
<div class="small-title"><span class="title">Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels</span>
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<div>by <span class="author">
<span> <span class="first">Mert</span><span
class="last"> Tiftikçi</span> </span>,
<span> <span class="first">Arzucan</span><span
class="last"> Ozgur</span> </span>,
<span> <span class="first">Yongqun</span><span class="last"> He </span> </span>
<span class="bibtex_js_conjunction"> and</span>
<span> <span class="first">Junguk</span><span class="last"> Hur</span> </span></span>
</div>
<div>in
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<span class="journal">BMC Bioinformatics</span>
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, <span class="year">2019</span></div>
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<a class="url"
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<div class="small-title"><span class="title">Statistical representation models for mutation information within genomic data</span>
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<div>by <span class="author"><span class="N. Ozlem Ozcan Simsek"> <span
class="first">N. Ozlem</span><span
class="last"> Ozcan Simsek</span> </span>,
<span class="Arzucan Ozgur"> <span
class="first">Arzucan</span><span
class="last"> Ozgur</span> </span><span
class="bibtex_js_conjunction"> and</span> <span
class="Fikret Gurgen"> <span class="first">Fikret</span><span
class="last"> Gurgen</span> </span></span></div>
<div>in
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<span class="journal">BMC Bioinformatics</span>
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, <span class="year">2019</span></div>
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<div class="small-title"><span class="title">Generating Word and Document Embeddings for Sentiment Analysis</span>
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<div>by <span class="author"><span class="Cem Rifki Aydin"> <span class="first">Cem</span><span
class="last"> Rifki Aydin</span> </span>, <span
class="Tunga Gungor"> <span class="first">Tunga</span><span
class="last"> Gungor</span> </span><span class="bibtex_js_conjunction"> and</span> <span
class="Ali Erkan"> <span class="first">Ali</span><span class="last"> Erkan</span> </span></span>
</div>
<div>in <span class="">
<span class="booktitle">16th International Conference on Intelligent Text Processing and Computational Linguistics (CICLing 2019)</span>
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, <span class="year">2019</span></div>
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<div class="small-title"><span class="title">Developing a Statistical Turkish Sign Language Translation System for Primary School Students</span>
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</a>
<div>by <span class="author"><span class="Buse Buz"> <span
class="first">Buse</span><span class="last"> Buz</span> </span><span
class="bibtex_js_conjunction"> and</span> <span
class="Tunga Gungor"> <span class="first">Tunga</span><span
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<div>in <span class="">
<span class="booktitle">International Symposium on Innovations in Intelligent Systems and Applications (INISTA 2019)</span>
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<div class="small-title"><span class="title">A Detailed Analysis and Improvement of Feature-Based Named Entity Recognition for Turkish</span>
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<div>by <span class="author"><span class="Arda Akdemir"> <span class="first">Arda</span><span
class="last"> Akdemir</span> </span><span class="bibtex_js_conjunction"> and</span> <span
class="Tunga Gungor"> <span class="first">Tunga</span><span
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<div>in <span class="">
<span class="booktitle">21st International Conference on Speech and Computer (SPECOM 2019)</span>
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<div class="small-title"><span class="title">Turkish Treebanking: Unifying and Constructing Efforts</span>
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<div>by <span class="author"><span class="Utku Turk"> <span
class="first">Utku</span><span class="last"> Turk</span> </span>, <span
class="Furkan Atmaca"> <span class="first">Furkan</span><span
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class="first">Saziye Betul</span><span
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class="Abdullatif Koksal"> <span class="first">Abdullatif</span><span
class="last"> Koksal</span> </span>, <span
class="Balkiz Ozturk Basaran"> <span class="first">Balkiz</span><span
class="last"> Ozturk Basaran</span> </span>, <span class="Tunga Gungor"> <span
class="first">Tunga</span><span class="last"> Gungor</span> </span><span
class="bibtex_js_conjunction"> and</span> <span
class="Arzucan Ozgur"> <span class="first">Arzucan</span><span
class="last"> Ozgur</span> </span></span></div>
<div>in <span class="">
<span class="booktitle">Proceedings of the 13th Linguistic Annotation Workshop</span>
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, <span class="year">2019</span></div>
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<div class="small-title"><span class="title">WideDTA: prediction of drug-target binding affinity</span>
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<div>by <span class="author"><span class="Hakime Ozturk"> <span class="first">Hakime</span><span
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class="first">Elif</span><span
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class="Arzucan Ozgur"> <span class="first">Arzucan</span><span
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<div>in <span class="">
<span class="booktitle">arXiv preprint</span>
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, <span class="year">2019</span></div>
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<div class="small-title"><span class="title">Linking entities through an ontology using word embeddings and syntactic re-ranking</span>
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<div>by <span class="author"><span class="Ilknur Karadeniz"> <span
class="first">Ilknur</span><span
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class="bibtex_js_conjunction"> and</span> <span
class="Arzucan Ozgur"> <span class="first">Arzucan</span><span
class="last"> Ozgur</span> </span></span></div>
<div>in
<span class="">
<span class="journal">BMC Bioinformatics</span>
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, <span class="year">2019</span></div>
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