Current Students

PhD Students

  • Gonul Ayci, Co-advise with Pinar Yolum
  • Melih Barsbey, Co-advise with Taylan Cemgil
  • Nuriye Özlem Özcan Şimşek, Co-advise with Fikret Gürgen
  • Burak Suyunu
  • Gokce Uludogan
  • Merve Unlu Menevse, Co-advise with Ebru Arisoy
  • Enes Taylan

MS Students

  • Omer Ak
  • Nur Bengisu Cam
  • Omer Faruk Cavas
  • Sadullah Gultekin, Co-advise with Pinar Yanardag
  • Musa Nuri İhtiyar
  • Berke Kavak
  • Burak Can Koban
  • Yusufcan Manav, Co-advise with Ebru Arisoy
  • Busra Oguzoglu
  • Bugrahan Sahin
  • Cansu Damla Yilmaz

PhD Alumni

  • Ilknur Karadeniz, (PhD, 2019), Thesis: Ontology-based Entity Tagging and Normalization in the Biomedical Domain.
    Next Position: Assistant Professor at Isik University, Computer Engineering Department, Istanbul.
  • Hakime Ozturk, (PhD, 2019, Co-advise with Elif Ozkirimli), Thesis: Text-based Machine Learning for Modelling Drug-Target Interactions.
    Next Position: Researcher at DKFZ (German Cancer Research Center), Heidelberg.
  • Arda Celebi, (PhD, 2020), Thesis: Utilizing Weakly-Supervised Learning for Hashtag Segmentation and Named Entity Disambiguation.
    Next Position: CTO and Co-Founder of VireUp.
  • Saziye Betul Ozates, (PhD, 2022, Co-advise with Tunga Gungor), Thesis: Deep Learning-based Dependency Parsing for Turkish.
    Next Position: Post-doctoral researcher at Koc University, Istanbul.

MS Alumni

  • Bedirhan Caldir, (MS, 2022), Predicting intracellular functions of proteins from amino acid sequences using language processing methods.
  • Atif Emre Yuksel, (MS, 2022), Hate Speech Detection in Turkish News using a Transformer-based Model Enhanced with Linguistic Features.
  • Riza Ozcelik, (MS, 2022, Co-advised with Elif Ozkirimli), Biomolecular language processing for drug-target affinity prediction.
  • Selen Parlar, (MS, 2022, Co-advised with Elif Ozkirimli), Empowering heterogeneous networks for drug-target affinity prediction.
  • Mustafa Melih Mutlu, (MS, 2022), Targeted sentiment analysis on Turkish texts.
  • Abdullatif Koksal, (MS, 2021), Datasets and transformer models for cross-lingual relation classification.
  • Gokce Uludogan, (MS, 2021, Co-advised with Elif Ozkirimli), Targeted drug design with warm start.
  • Hilal Donmez, (MS, 2021, Co-advised with Elif Ozkirimli), Relation extraction for chemical and protein interactions from biomedical documents.
  • Mert Basmaci, (MS, 2021), A hybrid BERT-GAN system for protein-protein interaction extraction from biomedical text.
  • Berfu Buyukoz, (MS, 2020, Co-advised with Ali Hurriyetoglu), Analyzing the generalizability of deep contextualized language representations for text classification.
  • Gamze Ege Kahya, (MS, 2020, Co-advised with Kutlu Ulgen), Prediction of druggability properties of chemicals using machine learning techniques.
  • Zehra Melce Husunbeyi, (MS, 2020), Detecting hate speech in Turkish texts.
  • Mert Tiftikci, (MS, 2019), Mention Extraction and Normalization using Ontologies in the Biomedical Domain.
  • Burak Sivrikaya, (MS, 2019), Using Reviews on the Web to Predict Box Office Success with Machine Learning Methods.
  • Atakan Yuksel, (MS, 2019, Co-advised with Elif Ozkirimli), Extracting Protein-Ligand Interactions from the Biomedical Literature using Deep Learning Approaches.
  • Hamdi Erkut, (MS, 2019, Co-advised with Elif Ozkirimli), Detection of antibiotic resistance in bacteria via machine learning approaches.
  • Mehmet Durna, (MS, 2019), Identifying Event Nuggets in Turkish News Texts using Natural Language Processing and Machine Learning Methods.
  • Anil Caliskol, (MS, 2019), Hit Song Prediction using Feature-Based Machine Learning.
  • Mirac Goksu Ozturk, (MS, 2018, Co-adivsed with Cenk Demiroglu), Speaker Adapted Speech Synthesis with Deep Neural Networks.
  • Gizem Soğancıoğlu, (MS, 2016), A Semantic Sentence Similarity Estimation Approach For The Biomedical Domain.
  • Ferhat Aydın, (MS, 2016), Identifying Passages Describing Protein-Protein Interaction Detection Methods in Biomedical Full Text Articles using Information Retrieval Methods.
  • Erinç Gökdeniz, (MS, 2016, Co-advised with Reşit Canbeyli), Natural Language Processing For Mining Neuroanatomical Relations Among Brain Regions.
  • Muhammed Yavuz Nuzumlalı, (MS, 2015), Analyzing Stemming and Sentence Simplification Methodologies for Turkish Multi-document Text Summarization.
  • Eda Okur, (MS, 2015), Named Entity Recognition for Turkish Microblog Texts using Semi-supervised Learning with Word Embeddings.
  • Hakime Öztürk, (MS, 2014, Co-advised with Elif Özkırımlı), Analyzing Drug Targets using Ligand Similarity.
  • Hakan Demir, (MS, 2014), Semi-Supervised Learning based Named Entity Recognition for Morphologically Rich Languages.
  • Şaziye Betül Özateş, (MS, 2014), Multi-document Summarization using Dependency Grammars.
  • Burak Aydın, (MS, 2014), Utilizing Out-of-domain Data through Language Modeling based Vocabulary Saturation for Turkish-English Machine Translation.
  • Melis Özgür Çetinkaya Demir, (MS, 2014, Co-advised with Ethem Alpaydın), Semi-supervised Learning with Softly Labeled Data for Bioinformatics Applications.
  • Çağıl Uluşahin Sönmez, (MS, 2014), Text Normalization using Lexical and Contextual Features.
  • Gözde Kaymaz, (MS, 2013), Detection of Topic-Based Opinion Leaders in Microblogging Environments.
  • Melike Korucuoğlu, (MS, 2013, Co-advised with Hasan Otu), Bayesian Network Based Pathway Analysis of High Throughput Biological Data.
  • Haluk Doğan, (MS, 2013, Co-advised with Hasan Otu), Discovering a Gene Interaction Atlas using Bayesian Networks and External Biological Knowledge.
  • Arda Çelebi, (MS, 2012), Self-Trained Discriminative Constituency Parser With Hierarchical Joint Learning Approach.
  • Cüneyd Murad Özsert, (MS, 2012), Word Polarity Detection using a Multilingual Approach.