Publications

2019

2018

2017

  • A.S. Rıfaioğlu, T. Dogan, M.J. Martin, R. Cetin Atalay, V. Atalay, “Multi-task Deep Neural Networks in Automated Protein Function Prediction“, preprint, arXiv:1705.04802.
  • A.S. Rıfaioğlu, M.J. Martin, R. Cetin Atalay, V. Atalay, T. Dogan, “Investigation of Multi-task Deep Neural Networks in Automated Protein Function Prediction”, Oral Presentation at Function COSI ISMB/ECCB 2017: 25th Annual International Conference on Intelligent Systems for Molecular Biology, Prague, Czech Republic, July 2017.
  • A. Dalkıran, A.S. Rıfaioğlu, T. Dogan, V. Atalay, M.J. Martin, R. Cetin Atalay, “Prediction of Enzymatic Properties of Protein Sequences Based on the EC Nomenclature”, Poster Presentation at ISMB/ECCB 2017: 25th Annual International Conference on Intelligent Systems for Molecular Biology, Prague, Czech Republic, July 2017.
  • A.S. Rıfaioğlu, M.J. Martin, R. Cetin Atalay, V. Atalay, T. Dogan “Investigation of Multi-task Deep Neural Networks in Automated Protein Function Prediction”, Oral Presentation at HIBIT 2017: The International Symposium on Health Informatics and Bioinformatics,  METU Northern Cyprus Campus, June 28 – 30, 2017.
  • A. Dalkıran, A.S. Rıfaioğlu, T. Dogan, V. Atalay, M.J. Martin, R. Cetin Atalay, “Prediction of Enzymatic Properties of Protein Sequences Based on the EC Nomenclature”, Poster Presentation at HIBIT 2017: The International Symposium on Health Informatics and Bioinformatics, METU Northern Cyprus Campus, June 28 – 30, 2017.
  • H.F. Danacı, R. Cetin Atalay, V. Atalay, “EClerize: A Customized Force-Directed Layout Algorithm for Biological Networks with EC Attributes”, Oral Presentation at GLBIO 2017: Great Lakes Bioinformatics Conference, Chicago, USA, May 15-17, 2017.
  • A.S. Rıfaioğlu, T. Dogan, Ö.S. Sarac, R. Saidi, V. Atalay, M.J. Martin, R. Cetin Atalay, “UniGOPred: A Large Scale Automated GO Term Annotation System for UniProtKB”, Poster presentation at GLBIO 2017: Great Lakes Bioinformatics Conference, Chicago, USA, May 15-17, 2017  (Best Poster Award).

2015

2014

  • T. Ersahin, L. Carkacioglu, T. Can, O. Konu, V. Atalay, R. Cetin-Atalay, “Identification of novel reference genes based on MeSH categories”, PLoS ONE, Public Library of Science (PLoS), 9(3): e93341, 2014, doi:10.1371/journal.pone.0093341.
  • A.G. Yaman, A.C. Acar, V. Atalay, R. Çetin-Atalay, “Discriminative Modeling of Cell Signaling as Bayesian Networks”, 2nd International Work-Conference on Bioinformatics and Biomedical Engineering (IWBBE 2014), Granada, Spain, April 7-9, 2014.

2012

2010

  • O.S. Sarac, V. Atalay, R. Çetin-Atalay, “GOPred: GO Molecular Function Prediction by Combined Classifiers”, PLoS ONE, Public Library of Science (PLoS), 5(8): e12382, 2010, doi:10.1371/journal.pone.0012382.
  • L. Çarkacıoğlu, R. Çetin-Atalay, Ö. Konu, V. Atalay, T. Can, “Bi-k-Bi Clustering: Mining Large Scale Gene Expression Data Using Two-Level Biclustering”, International Journal of Data Mining and Bioinformatics, Inderscience, Vol. 4, No.6 pp.701-721, 2010, doi:10.1504/IJDMB.2010.037548.
  • Z. Işık, V. Atalay, R. Çetin-Atalay, “Evaluation of Signaling Cascades Based on the Weights from Microarray and ChIP-seq Data”, Journal of Machine Learning Research W&C ProceedingsMIT Press, Vol.8, pp.44-54, 2010.
  • Z. Işık, V. Atalay, C. Aykanat, R. Çetin-Atalay, “Data and Model Driven Hybrid Approach to Activity Scoring of Cyclic Pathways”, 25th International Symposium on Computer and Information Sciences (ISCIS 2010), London, UK, September 22-24, 2010, Lecture Notes in Electrical Engineering, Springer, Vol. 62 pp.91-94.

2009

  • S. Genç, V. Atalay, “Which Shape Representation is the best for Real-Time Hand Interface System?”, 5th International Symposium on Visual Computing, Las Vegas, Nevada, USA, November 30-December 2, 2009.
  • Z. Isik, V. Atalay, R. Cetin-Atalay, “Evaluation of Signaling Cascades Based on the Weights from Microarray and ChIP-seq Data”, Third International Workshop on Machine Learning in Systems Biology (MLSB 2009), Ljubljana, Slovenia, September 5-6, 2009.

2008

  • O.S. Sarac, R. Cetin-Atalay, V. Atalay, “GOPred: Combining classifiers on the GO”, Second International Workshop on Machine Learning in Systems Biology(MLSB08), Brussels, September 13-14, 2008.
  • O.S. Sarac, Ö. Gürsoy-Yüzügüllü, R. Cetin-Atalay, V. Atalay, “Subsequence based feature map for protein function classification”, Journal of Computational Biology and Chemistry, Elsevier, Vol.32, pp.122-130, 2008.

2007

  • O.S. Sarac, Ö. Gürsoy-Yüzügüllü,, R. Cetin-Atalay and V. Atalay, “Protein Function Annotation by Subsequence based Feature Map”, Automated Function Prediction (AFP) and Biosapiens Special Interest Group (SIG) meeting at ISMB/ECCB 2007, Vienna, Austria, July 19-20, 2007.
  • Z.Sokmen, M.Ozturk, V.Atalay, R.Cetin Atalay, “A Hybrid Method For The Identification of Expression Patterns From Microarray Data”, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) and 6th European Conference on Computational Biology (ECCB), Vienna, Austria, July 21-25, 2007.
  • O.Sinan Sarac, O.Gursoy-Yuzugullu, R.Cetin-Atalay and V. Atalay, “Function Annotation via a Discriminative Classifier Database on GO hierarchy”, 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) and 6th European Conference on Computational Biology (ECCB), Vienna, Austria, July 21-25, 2007.
  • O.Sinan Sarac, P.Bezek, R.Cetin-Atalay, V.Atalay, “Spectral Clustering based Subsequence Feature Map for Protein Classification”, 11th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2007), Oakland, California, USA, April 21-25, 2007.

2006

  • A. Teke and V. Atalay, “Texture Classification and Retrieval Using the Random Neural Network Model”, Computational Management Science, Springer, Vol.3, No.3, pp.193-205, 2006.
  • R. Hassanpour and V. Atalay, “An Experimental Study on the Sensitivity of Auto-Calibration to Projective Camera Models Parameters”, Optical Engineering, Vol. 45, 047002, 2006.
  • B. Otlu, V. Atalay, R. Hassanpour, “Relative Consistency of Projective Reconstructions Obtained from the Same Image Pair”, International Journal of Pattern Recognition and Artificial Intelligence, World Scientific, Vol.20, No.5, pp.649-664, 2006.
  • O.S. Sarac, V. Atalay, R. Cetin-Atalay, “Subsequence Feature Map for Protein Classification and Remote Homology Detection”, 5th European Conference on Computational Biology (ECCB), Eliat, Israel, September 10-13, 2006.
  • L. Carkacioglu, T. Can, O. Konu, V. Atalay, R. Cetin-Atalay, “Expression Pattern Analysis of Housekeeping Genes Across Large Number of Microarray Experiments”, 5th European Conference on Computational Biology (ECCB), Eliat, Israel, September 10-13, 2006.
  • O.S. Sarac, V. Atalay, R. Cetin-Atalay, “HMM-based subsequence feature map for Protein Classification and Remote Homology Detection”, 14th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2006), Forteleza, Brazil, August 6-10, 2006.

2005

  • V. Atalay, R. Cetin-Atalay, “Implicit Motif Distribution based Hybrid Computational Kernel for Sequence Classification”, Bioinformatics Journal, Oxford University Press, vol.21, No.8, pp.1429-1436, 2005.
  • O. Dalay and V. Atalay, “Interactive classification of satellite image content based on query by example”, ISPRS Spatial Data Mining Workshop, Ankara, Turkey, 24-25 November, 2005.
  • S. Genc and V. Atalay, “ITouch: Vision-based Intelligent Touch Screen in a Distributed Environment”, doctoral spotlight paper at Seventh International Conference on Multimodal Interfaces (ICMI), Trento, Italy, October 4-6, 2005.

2004

  • M. Musa, D. de Ridder, R. Duin and V. Atalay, “Almost Autonomous Training of Mixtures of Principal Component Analyzers”, Pattern Recognition Letters, vol.25, No.9, pp.1085-1095, 2004.
  • R. Hassanpour and V. Atalay, “Camera auto-calibration using a sequence of 2D images with small rotations”, Pattern Recognition Letters, vol.25, No.9, pp.989-997, 2004.
  • I.A. Erdem, M.E. Erdem, V. Atalay, A.E. Çetin, “Vision-based Continuous Graffiti-like Text Entry System”, Optical Engineering, vol.43, pp.553-558, 2004.
  • R. Hassanpour and V. Atalay, “Delaunay Triangulation based 3D human face modeling from uncalibrated images”, The First IEEE Workshop on Face Processing in Video, Washington, D.C., USA, June 28, 2004.
  • A. Teke and V. Atalay, “Texture Classification and Retrieval Using Random Neural Network Model”, IEEE 6th Southwest Symposium on Image Analysis and Interpretation, Lake Tahoe, Nevada, USA, March 28-30, 2004, IEEE Press, pp.109-113.

2003

  • A.Y. Mulayim, Y. Ulas, V. Atalay, “Silhouette-based 3D Model Reconstruction from Multiple Images”, IEEE Trans. On Systems, Man, and Cybernetics-Part B, Special Issue on 3D Image Analysis and Modeling, Vol.33, No.4, pp.582-591, 2003.
  • U. Yilmaz, A.Y. Mulayim, V. Atalay, “An Image based Inexpensive 3D Scanner”, Int. Journal of Image and Graphics, Special Issue on Virtual Reality and Virtual Environment, World Scientific, Vol.3, No.2, pp.235-264, 2003.
  • C. Guray, N. Celebi, V. Atalay, A.Gunhan, “Ore-Age: An Hybrid system for Assisting and Teaching Mining Method Selection”, Expert Systems with Applications Journal, Pergamon-Elsevier Science, Vol.24, pp.261-271, 2003.
  • M. Ozarar, V. Atalay, R. Cetin-Atalay, “Prediction of protein subcellular localization based on primary sequence data”, 18th International Symposium on Computer and Information Sciences (ISCIS XVII), Antalya, Turkey, 3-5 November, 2003, LNCS 2869, pp.611-618, Springer.
  • M.Musa, R.Duin, D. deRidder, V.Atalay, “Texture Segmentation Using the Mixtures of Principal Component Analyzers”, 18th International Symposium on Computer and Information Sciences (ISCIS XVII), Antalya, Turkey, 3-5 November, 2003, LNCS 2869, pp.505-512, Springer.
  • M.E. Erdem, I.A. Erdem, V. Atalay, “Image based extraction of material reflectance properties of a 3D rigid object”, Eurographics 2003 Annual Conference of the European Association for Computer Graphics, Granada, Spain, 1-6 September 2003.
  • I.S. Sen, V. Atalay, “Occlusion culling for image based rendering with warping”, Eurographics 2003 Annual Conference of the European Association for Computer Graphics, Granada, Spain, 1-6 September 2003.
  • G.K. Akinci, S.U. Korkmaz, V. Atalay, “A character recognizer for Turkish language”, 7th Int. Conf. on Document Analysis and Recognition, Edinburgh, Scotland, 3-6 August 2003.
  • A. Erdem, E. Erdem, V. Atalay, E. Cetin, “Computer vision based unistroke keyboard system and mouse for the handicapped”, Int. Conf. on Multimedia and Expo-ICME 03, Baltimore, Maryland, USA, 6-9 July 2003.

2002

  • S. Baskan, M.M. Bulut and V. Atalay, “Projection based Method for Segmentation of Human Faces and its Evaluation”, Pattern Recognition Letters, Vol.23, No.14, pp.1623-1629, Elsevier Science, December 2002.
  • P. Duygulu and V. Atalay, “A Hierarchical Representation of Form Documents for Identification and Retrieval”, Int. Journal of Document Analysis and Recognition, Vol.5, No.1, pp.17-27, Elsevier Science, 2002.
  • R. Hassanpour and V. Atalay, “Head Modeling with Camera Auto-calibration and Deformation”, 7th Int. Fall Workshop on Vision, Modeling and Visualization-VMV 2002, Erlangen, Germany, 20-22 November 2002.
  • B. Otlu, R. Hassanpour, V. Atalay, “Consistency of projective reconstructions from an image pair”, 9th International Workshop on Systems, Signals and Image Processing, Manchester Town Hall, UK, 7-8 November 2002.
  • A. Erdem, E. Erdem, V. Atalay, E. Cetin, “Vision based gesture-based text entry” demonstration at the 6th Int. Symposium on Wearable Computers, Seattle, Washington, USA, October 7-10, 2002.
  • M. Yaman, V. Atalay, M. Turker, O.N. Gerek, A.E. Cetin, “Texture Segmentation by Using Adaptive Polyphase Subband Decomposition”, 17th International Symposium on Computer and Information Sciences (ISCIS XVII), Orlando, Florida, USA, 28-30 October, 2002.
  • K.Balci and V.Atalay, “PCA for Gender Estimation: Which Eigenvectors Contribute?”, 16th Int. Conference on Pattern Recognition, Quebec City, Canada, August 11-15, 2002, IEEE Press, Vol.3, 363-366.
  • U.Yilmaz, A.Mulayim, and V.Atalay, “Reconstruction of Three Dimensional Models from Real Images”, 3D Data Processing, Visualization, Transmission (3DPVT), Padova, Italy, June 19-21, 2002, IEEE press, eds. G.M.Cortelazzo, C.Guerra, pp.554-557.

2001

  • G. Ongun, U. Halıcı, K. Leblebicioğlu, V. Atalay, S. Beksaç, M. Beksaç, “Automated Contour Detection in Blood Cell Images by an Efficient Snake Algorithm”, Nonlinear Analysis, Vol.47, pp.5839-5847, Pergamon-Elsevier Science, 2001.
  • Ö.F. Özer, O. Özün, C.Ö. Tüzel, V. Atalay, A.E. Çetin, “Vision-based Single-stroke Character Recognition for Wearable Computing”, IEEE Intelligent Systems, Vol.16, pp.33-37, 2001.
  • A.Y. Mulayim and V. Atalay, “Stereo correction on the silhouette-based 3D model reconstruction from multiple images”, SPIE’s 13th International Symposium on Three-Dimensional Image Capture and Applications IV, 24-25 January 2001, Proceedings of SPIE Vol. 4298.
  • S. Baskan, M.M. Bulut, V. Atalay, “Segmentation of facial features using gradient-based approach”, SPIE’s 13th International Symposium on Machine Vision Applications in Industrial Inspection IX, 22-23 January 2001, Proceedings of SPIE Vol. 4301.

Selected Publications prior to 2001

  • A.Y. Mülayim, V. Atalay, O. Özün, F. Schmitt, “On the Silhouette Based 3D Reconstruction and Initial Bounding Cube Estimation”, 5th Int. Fall Workshop on Vision, Modeling and isualization-VMV 2000, Max-Planck-Institut für Informatik, Saarbrucken, Germany, 22-24 November 2000.
  • N. Dicle and V. Atalay, “Image matching using singular value decompositionand Godel coding scheme”, SPIE’s 12th International Symposium on Electronic Imaging-Image and Video Communications and Processing, 26-28 January, Proceedings of SPIE Vol. 3974, 2000.
  • O.N. Gerek , A.E. Cetin , A. Tewfik, and V. Atalay, “Subband Domain Coding of Binary Textual Images for Document Archiving”, IEEE Transactions on Image Processing, Vol.8, No.10, pp.1438-1446, October 1999.
  • E. Oztop, A.Y. Mulayim, V. Atalay, and F. Yarman-Vural, “Repulsive Attractive Network for Baseline Extraction on Document Images”, Signal Processing, Vol.75, No.1, pp.1-10, 1999.
  • Sinan Beksac, Aydan J. Erkmen, Sezer Aksel, Ugur Halici, Kemal Leblebicioglu, Meral Beksac, Volkan Atalay, Lakhmi C. Jain, Intelligent diagnostic systems in maternal and fetal medicine, pp.137-199, in Soft-Computing in Human-Related Sciences, editors: Jain, L. C., Kandel, Abraham, Teodorescu, Horia-Nicolai, CRC press, Singapore, 1999.
  • A.Y. Mulayim, Y. Yener, F. Schmitt, and V. Atalay, “Rotation Axis Extraction of a Turn Table Viewed by a Fixed Camera”, Workshop on Vision, Modelling, and Visualization – VMV’99, Erlangen, Germany, November 17-19, 1999.
  • S. Genc, and V. Atalay, “Texture Extraction from Photographs and Rendering with Dynamic Texture Mapping”, International Conference on Image Analysis and Processing (ICIAP99), Venice, Italy, September 27-29, 1999.
  • V. Atalay, and E. Arslan, ”An SGML Based Viewer for Form Documents”, Fouth International Conference on Document Analysis and Recognition, Bangalore, India, September 20-22, 1999.
  • V. Atalay, and U. Yilmaz, “A Matching Algorithm Based on Linear Features”, Pattern Recognition Letters, Vol.19, No.9, pp.857-867, Elsevier Science,1998.
  • M. Goktepe, V. Atalay, N. Yalabik, and C. Yalabik, “Unsupervised Texture Based Image Segmentation by Simulated Annealing with Markov Random Field and Potts Models”, Proceedings of the Fourteenth International Conference on Pattern Recognition (ICPR), Brisbane, Australia, 16-20 August, pp.820-822, IEEE Computer Society Press, 1998.
  • P. Duygulu, V. Atalay, and E. Dincel, “A Heuristic Algorithm for Hierarchical Representation of Form Documents”, Proceedings of the Fourteenth International Conference on Pattern Recognition (ICPR), Brisbane, Australia, 16-20 August, pp.929-931, IEEE Computer Society Press, 1998.
  • M. Borchani, V. Atalay, and G. Stamon, “Classification d’Images par des Attributs de Texture”, Colloque de Recherche Doctorale Automatique, Genie Informatique et Image, Angers, France, December, 1997.
  • M. Borchani, V. Atalay, and G. Stamon, “Classification d’Images par des Statistiques d’Ordres Differents”, Cinquiemes Rencontres de la Societe Francophone de Classification, Lyon, France, September 1997.
  • E. Oztop, A.Y. Mulayim, F.T. Yarman-Vural, and V. Atalay, “Baseline Extraction on Document Images by Repulsive/ Attractive Network”, IEEE Int. Conf. on Acustics, Signal, and Speech Processing (ICASSP), Munich, Germany, April 1997.
  • M. Goktepe, V. Atalay and N. Yalabik, “Unsupervised Segmentation of Gray Level Markov Model Textures with Hierarchical Self Organizing Maps”, Proceedings of the Thirteenth International Conference on Pattern Recognition (ICPR), Wien, Austria, August 25-29 , vol.4, pp.90-94, IEEE Computer Society Press,1996.
  • M. Koksal, H. Vural, and V. Atalay, “The Investigation of Hydrodynamics of a 2-D Fluidized Bed with Moving Double Plate Distributors Using Image Analysis”, 5th World Congress of Chemical Engineers, San Diego, USA, July 1996.
  • V. Atalay, and E. Gelenbe, “Parallel algorithm for color texture generation using the random neural network model”, International Journal of Pattern Recognition and Artificial Intelligence, Vol.6, No.2-3, pp. 437-446, World Scientific, 1992.
  • V. Atalay, E. Gelenbe, and N. Yalabik, “Texture generation with the random neural network model”, International Journal of Pattern Recognition and Artificial Intelligence, Vol-6, No.1, pp. 131-142, World Scientific,1992.
  • V. Atalay, E. Gelenbe, and N. Yalabik, “Texture generation with the random neural network model”, Proc. International Conference on Artificial Neural Networks (ICANN 91), Helsinki, Finland, July 1991.
  • V. Atalay, and E. Gelenbe, “Parallel algorithm for color texture generation using the random neural network model”, Proc. International Colloqium on Parallel Image Processing, Paris, France, June 1991.
  • V. Atalay, M. Ozcilingir, N. Yalabik, “Computer recognition of Ottoman text”, Proc. International Symposium on Computer and Information Sciences-V (ISCIS), Capadoccia, Turkey, November 1990.