Text Analytics and BIoInformatics Lab
TABI

Research Areas

Natural Language Processing and Bioinformatics
  • Word and sentence processing and analysis
    • Morphological analysis
    • Multi-word expressions
    • Dependency parsing
  • Information retrieval and information extraction
    • Named entity recognition
    • Normalisation
    • Relation extraction
    • Text summarisation
    • Sentiment analysis
  • Machine translation
  • Text mining for biological and natural languages
  • Protein-protein and protein-compound interaction prediction
  • Chemical language processing for drug discovery
  • Disease diagnosis support using genomic data

Recent Publications

2020

The RELX Dataset and Matching the Multilingual Blanks for Cross-Lingual Relation Classification
by Abdullatif Köksal and Arzucan Ozgur
in Findings of the Association for Computational Linguistics at EMNLP , 2020
Vapur: A Search Engine to Find Related Protein - Compound Pairs in COVID-19 Literature
by Abdullatif Koksal , Hilal Donmez , Riza Ozcelik , Elif Ozkirimli and Arzucan Ozgur
in Proceedings of the 1st Workshop on NLP for COVID-19 (Part 2) at EMNLP , 2020
Analyzing ELMo and DistilBERT on Socio-political News Classification
by Berfu Buyukoz , Ali Hurriyetoglu and Arzucan Ozgur
in Proceedings of the Workshop on Automated Extraction of Socio-political Events from News at ELRA , 2020
Exploring chemical space using natural language processing methodologies for drug discovery
by Hakime Ozturk , Arzucan Ozgur , Philippe Schwaller , Teodoro Laino and Elif Ozkirimli
in Drug Discovery Today , 2020
A Hybrid Approach to Dependency Parsing: Combining Rules and Morphology with Deep Learning
by Saziye Betul Ozates , Arzucan Ozgur , Tunga Gungor and Balkız Ozturk
in arXiv preprint , 2020
Resources for Turkish Dependency Parsing: Introducing the BOUN Treebank and the BoAT Annotation Tool
by Utku Turk , Furkan Atmaca , Saziye Betul Ozates , Gozde Berk , Seyyit Talha Bedir , Balkız Ozturk Basaran , Tunga Gungor and Arzucan Ozgur
in arXiv preprint , 2020
Data and Representation for Turkish Natural Language Inference
by Emrah Budur , Riza Ozcelik , Tunga Gungor and Christopher Potts
in Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP) , 2020
Hierarchical Multitask Learning Approach for BERT
by Çağla Aksoy , Alper Ahmetoğlu and Tunga Gungor
in arXiv preprint , 2020
Intrinsic and Extrinsic Evaluation of Word Embedding Models
by Gökçe Yeşiltaş and Tunga Gungor
in Innovations in Intelligent Systems and Applications Conference (ASYU) , 2020
Generating a Concept Relation Network for Turkish Based on ConceptNet Using Translational Methods
by Arif Sırrı Özçelik and Tunga Gungor
in International Conference on Speech and Computer (SPECOM) , 2020
Combination of Recursive and Recurrent Neural Networks for Aspect-Based Sentiment Analysis Using Inter-Aspect Relations
by Cem Rıfkı Aydın and Tunga Gungor
in IEEE Access , 2020
Hierarchical Multi Task Learning with Subword Contextual Embeddings for Languages with Rich Morphology
by Arda Akdemir Tetsuo Shibuya and Tunga Gungor
in arXiv preprint , 2020
Microblog topic identification using Linked Open Data
by Ahmet Yıldırım , and Suzan Üsküdarlı
in PLOS ONE , 2020
NeuroBoun: An inquiry-based approach for exploring scientific literature -- a use case in neuroscience
by Suzan Üsküdarlı , Erinç Gökdeniz , and Reşit Canbeyli
in arXiv preprint , 2020

2019

Turkish Tweet Classification with Transformer Encoder
by Atıf Emre Yüksel , Yaşar Alim Türkmen Arzucan Ozgur and Berna Altınel
in Proceedings of the International Conference on Recent Advances in Natural Language Processing (RANLP) , 2019
BOUN-ISIK Participation: An Unsupervised Approach for the Named Entity Normalization and Relation Extraction of Bacteria Biotopes
by Ilknur Karadeniz , Ömer Faruk Tuna and Arzucan Ozgur
in Proceedings of The 5th Workshop on BioNLP Open Shared Tasks at EMNLP , 2019
Machine learning-based identification and rule-based normalization of adverse drug reactions in drug labels
by Mert Tiftikçi , Arzucan Ozgur , Yongqun He and Junguk Hur
in BMC Bioinformatics , 2019
Statistical representation models for mutation information within genomic data
by N. Ozlem Ozcan Simsek , Arzucan Ozgur and Fikret Gurgen
in BMC Bioinformatics , 2019
Generating Word and Document Embeddings for Sentiment Analysis
by Cem Rifki Aydin , Tunga Gungor and Ali Erkan
in 16th International Conference on Intelligent Text Processing and Computational Linguistics (CICLing 2019) , 2019
Developing a Statistical Turkish Sign Language Translation System for Primary School Students
by Buse Buz and Tunga Gungor
in International Symposium on Innovations in Intelligent Systems and Applications (INISTA 2019) , 2019
A Detailed Analysis and Improvement of Feature-Based Named Entity Recognition for Turkish
by Arda Akdemir and Tunga Gungor
in 21st International Conference on Speech and Computer (SPECOM 2019) , 2019
Turkish Treebanking: Unifying and Constructing Efforts
by Utku Turk , Furkan Atmaca , Saziye Betul Ozates , Abdullatif Koksal , Balkiz Ozturk Basaran , Tunga Gungor and Arzucan Ozgur
in Proceedings of the 13th Linguistic Annotation Workshop , 2019
WideDTA: prediction of drug-target binding affinity
by Hakime Ozturk , Elif Ozkirimli and Arzucan Ozgur
in arXiv preprint , 2019
Linking entities through an ontology using word embeddings and syntactic re-ranking
by Ilknur Karadeniz and Arzucan Ozgur
in BMC Bioinformatics , 2019
A Hybrid Translation System from Turkish Spoken Language to Turkish Sign Language
by Dilek Kayahan and Tunga Gungor
in International Symposium on Innovations in Intelligent Systems and Applications (INISTA 2019) , 2019
Joint Learning of Named Entity Recognition and Dependency Parsing using Separate Datasets
by Arda Akdemir and Tunga Gungor
in Computacion y Sistemas , 2019
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine
by Rezarta Islamaj Dogan , Sun Kim , Andrew Chatr-Aryamontri , Chih-Hsuan Wei , Donald C 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 and Zhiyong Lu
in Database , 2019
Representing Overlaps in Sequence Labeling Tasks with a Novel Tagging Scheme: bigappy-unicrossy
by Gozde Berk , Berna Erden and Tunga Gungor
in 16th International Conference on Intelligent Text Processing and Computational Linguistics (CICLing 2019) , 2019
The effect of morphology in named entity recognition with sequence tagging
by Onur Gungor , Tunga Gungor and Suzan Uskudarli
in Natural Language Engineering , 2019
Identifying Image Related Sentences in News Articles
by Melike Esma Ilter , Lale Akarun and Arzucan Ozgur
in 27th Signal Processing and Communications Applications Conference (SIU) , 2019
Improving the Annotations in the Turkish Universal Dependency Treebank
by Utku Turk , Furkan Atmaca , Saziye Betul Ozates , Balkiz Ozturk , Tunga Gungor and Arzucan Ozgur
in Proceedings of the Third Workshop on Universal Dependencies (UDW, SyntaxFest) , 2019
Supervised Learning Methods in Classifying Organized Behavior in Tweet Collections
by Erdem Beğenilmiş , and Susan Uskudarli
in International Journal on Artificial Intelligence Tools , 2019
Detecting Clitics Related Orthographic Errors in Turkish
by Uğurcan Arıkan , Onur Güngör , and Suzan Üsküdarlı
in Proceedings of the International Conference on Recent Advances in Natural Language Processing (RANLP 2019) , 2019

Recent Theses

2019

Text-based Machine Learning for Modelling Drug-Target Interactions
by Hakime Öztürk in 2019 under the supervision of Arzucan Özgür and co-advised by Elif Özkırımlı
Ontology-based Entity Tagging and Normalization in the Biomedical Domain
by İlknur Karadeniz in 2019 under the supervision of Arzucan Özgür
Hit Song Prediction using Feature-Based Machine Learning
by Anıl Çalışkol in 2019 under the supervision of Arzucan Özgür
Generating a Concept Relation Network for Turkish Based on ConceptNet Using Translational Methods
by Arif Sırrı in 2019 under the supervision of Tunga Güngör
Extracting Protein-Ligand Interactions from the Biomedical Literature using Deep Learning Approaches
by Atakan Yüksel in 2019 under the supervision of Arzucan Özgür and co-advised by Elif Özkırımlı
Identification of Verbal Multiword Expressions using Deep Learning Architectures and Representation Learning Methods
by Berna Erden in 2019 under the supervision of Tunga Güngör
Using Reviews on the Web to Predict Box Office Success with Machine Learning Methods
by Burak Sivrikaya in 2019 under the supervision of Arzucan Özgür
Developing a Statistical Turkish Sign Language Translation System for Primary School Students
by Buse Buz in 2019 under the supervision of Tunga Güngör
Hybrid Translation System from Turkish Spoken Language to Turkish Sign Language
by Dilek Kayahan in 2019 under the supervision of Tunga Güngör
Intrinsic and Extrinsic Evaluation of Word Embedding Models
by Gökçe Yeşiltaş in 2019 under the supervision of Tunga Güngör
Multilingual Identification of Verbal Multiword Expressions using Bidirectional Long Short-term Memory based Architectures
by Gözde Berk in 2019 under the supervision of Tunga Güngör
Identifying Event Nuggets in Turkish News Texts using Natural Language Processing and Machine Learning Methods
by Mehmet Durna in 2019 under the supervision of Arzucan Özgür
Mention Extraction and Normalization using Ontologies in the Biomedical Domain
by Mert Tiftikçi in 2019 under the supervision of Arzucan Özgür

2018

Named Entity Recognition in Turkish Using Deep Learning Models and Joint Learning
by Arda Akdemir in 2018 under the supervision of Tunga Güngör
A Framework For Understanding And Detecting Harassment In Social VR
by Lance Powell in 2018 under the supervision of Arzucan Özgür and Didar Akar
Developing a Turkish Language Recommendation System based on User Conversations
by Murat Elifoğlu in 2018 under the supervision of Tunga Güngör

2017

Developing New Approaches for Multi-platform and Multi-Individual Genomic Sequence Assembly
by Pınar Kavak in 2017 under the supervision of Tunga Güngör and co-advised by Can Alkan