I am a professor of Computer Engineering at the Middle East Technical University (METU), Ankara, Turkey.
My research interests lie in the areas of
 – machine learning for bioinformatics,
 – data stream analysis and clustering, and
 – machine learning applications.

RECENT SELECTED PUBLICATIONS

  • MDeePred: novel multi-channel protein featurization for deep learning-based binding affinity prediction in drug discovery 
    Bioinformatics
    btaa858   [article] [GitHub]
  • CROssBAR: Comprehensive Resource of Biomedical Relations with Deep Learning Applications and Knowledge Graph Representations 
    bioRxiv 2020.09.14.296889   [preprint] [WebPage][WebService]
  • Data stream clustering: a review 
    Artificial Intelligence Review 54:1201–1236   [article]
  • iBioProVis: interactive visualization and analysis of compound bioactivity space 
    Bioinformatics 36:4227–4230   [article] [WebService]
  • DEEPScreen: high performance drug–target interaction prediction with convolutional neural networks using 2-D structural compound representations 
    Chemical Science 11:2531-2557 [article][GitHub]

list of all publications
Google Scholar

SOFTWARE

MDeePred [GitHub] pairwise input deep neural network regressor for drug-target affinity prediction for virtual screening
CROssBAR [Web] Comprehensive Resource of Biomedical Relations with Deep Learning and Knowledge Graph Representations
iBioProVis [Web] visualization of compounds on 2D space in the context of their cognate targets
DEEPScreen [GitHub] virtual screening with deep convolutional neural networks using compound images
DEEPred  [GitHub] automated function prediction
ECPred  [Web][GitHub] Enzyme Commission (EC) number prediction

Other tools and services

PROJECTS

CROssBAR    [WebPage]   
we developed a comprehensive computational resource by linking various biomedical resources, generating relation predictions using machine/deep learning, and developing information-rich knowledge graphs that incorporate available and predicted biomedical relationships with the aim of providing aid to biomedical researchers to further understand disease mechanisms and to discover/develop new drugs

SmartHome Consortium
A consortium of 18 companies and 5 universities lead by Arcelik/BEKO to develop and implement a platform for smart homes. We are interested in data stream analytics and data stream clustering. We have developed a data stream clustering algorithm using UMAP to detect and adopt concept drifts that are changes in data.

More about research

CURRENT GRADUATE STUDENTS

  • Alaettin Zubaroğlu, Ph.D. candidate
  • Alperen Dalkıran, Ph.D. candidate
  • Serkan Özen, Ph.D. candidate
  • Gökhan Özsarı, PhD candidate
  • Ahmet Atakan, PhD candidate
  • Özlem Poyraz, MSc candidate
  • Mehmet Dinç, MSc candidate
  • Ataberk Dönmez, MSc candidate
  • Samet Özdilek, MSc candidate
  • Ali İlker Sığırcı, MSc candidate

Alumni

EDUCATION

Diplôme de Docteur dans la spécialité Informatique (Ph.D. in Computer Science), 1993, Université Paris Descartes (Paris V), Paris, France
Diplôme d’Etudes Approfondies en Informatique, 1991, Université Paris Descartes (Paris V), Paris, France
Master of Science in Electrical and Electronics Engineering, 1990, METU, Ankara, Turkey
Bachelor of Science in Electrical and Electronics Engineering, 1987, METU, Ankara, Turkey

PROFESSIONAL POSITIONS

Professor, METU, Ankara, Turkey, 2005-present
Associate Professor, METU, Ankara, Turkey, 1998-2005
Visiting Research Associate Professor, Virginia Bioinformatics Institute, Virginia Tech, VA, USA, Jan. 2004-Jan. 2005
Assistant Professor, METU, Ankara, Turkey, 1993-1998
Instructor, Université Paris Descartes (Paris V), Paris, France, 1993
Visiting Scholar, New Jersey Institute of Technology, NJ, USA, 1991-1992
Development Engineer, Aselsan Electronics Company, Ankara, Turkey, 1987-1988

MAJOR ADMINISTRATIONAL POSITIONS

Vice President for research, METU, 2010-2016
Chairman of Board, ODTÜ TEKNOKENT (METU Technopolis), 2010-2016
Member of University Senate, METU, 2010-2016
Assistant to President, METU, 2008-2010
Board Member, Informatics Association of Turkey, 2009-2011
Department Chairperson, METU Dep. of Computer Eng., 2007-2008

TEACHING

CONSULTANCY

  • Member, International Technical Advisory Board of Arcelik (Research and Development Directorate), 2011-present
  • Member, Board of Directors of Izmir Biomedicine and Genome Institute (iBG-izmir), 2018-2020
  • Member, Technology Advisory Board of Turkish Aerospace Industries (TAI), 2011-2018

 

CONTACT vatalay AT metu.edu.tr