WoS İndeksli Yayınlar Koleksiyonu
Permanent URI for this collectionhttps://hdl.handle.net/20.500.12573/394
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Article Developing a Label Propagation Approach for Cancer Subtype Classification Problem(Tubitak Scientific & Technological Research Council Turkey, 2022-01-01) Guner, Pinar; Bakir-Gungor, Burcu; Coskun, MustafaCancer is a disease in which abnormal cells grow uncontrollably and invade other tissues. Several types of cancer have various subtypes with different clinical and biological implications. Based on these differences, treatment methods need to be customized. The identification of distinct cancer subtypes is an important problem in bioinformatics, since it can guide future precision medicine applications. In order to design targeted treatments, bioinformatics methods attempt to discover common molecular pathology of different cancer subtypes. Along this line, several computational methods have been proposed to discover cancer subtypes or to stratify cancer into informative subtypes. However, existing works do not consider the sparseness of data (genes having low degrees) and result in an ill-conditioned solution. To address this shortcoming, in this paper, we propose an alternative unsupervised method to stratify cancer patients into subtypes using applied numerical algebra techniques. More specifically, we applied a label propagation based approach to stratify somatic mutation profiles of colon, head and neck, uterine, bladder, and breast tumors. We evaluated the performance of our method by comparing it to the baseline methods. Extensive experiments demonstrate that our approach highly renders tumor classification tasks by largely outperforming the state-of-the-art unsupervised and supervised approaches.Conference Object Offer Referees Suggester for the Journal Editors(Institute of Electrical and Electronics Engineers Inc., 2019-06) Cos¸kun, Mustafa; Hacilar, Hilal; Gezer, Cengiz; Güngör, Vehbi Çağrı; Coskun, MustafaAssigning appropriate referees to a journal or conference paper is a vital task for many reasons, including enhancing the journal venue quality and reliance, fair judgement of the papers, and among many others. While assigning the referees to the papers, the editors of a journal venue need to find suitable referees who are both related to field of the given paper and have no conflict of interest with the authors of the paper. Editorial-wise this referee assignment process is implemented in a hand-crafted manner, i.e., the editor needs to find the most suitable referees to the paper via a search engine and manually refines the all unrelated and having conflict of interest authors to the paper authors. Clearly, such a manual referee searching process is tedious and time consuming for the editors.In this paper, we present an alternate automated approach for assigning referees problem using intrinsic random walk with restart proximity measure. In our experiments based on a comprehensive DBLP networks, we show that our approach, called OFFER, significantly outperforms state-of-the-art the random walk with restart based method. © 2021 Elsevier B.V., All rights reserved.Conference Object Offer : Referees Suggester for the Journal Editors(IEEE, 2019) Coskun, Mustafa; Hacilar, Hilal; Gezer, Cengiz; Gungor, Vehbi CagriAssigning appropriate referees to a journal or conference paper is a vital task for many reasons, including enhancing the journal venue quality and reliance, fair judgement of the papers, and among many others. While assigning the referees to the papers, the editors of a journal venue need to find suitable referees who are both related to field of the given paper and have no conflict of interest with the authors of the paper. Editorial-wise this referee assignment process is implemented in a hand-crafted manner, i.e., the editor needs to find the most suitable referees to the paper via a search engine and manually refines the all unrelated and having conflict of interest authors to the paper authors. Clearly, such a manual referee searching process is tedious and time consuming for the editors. In this paper, we present an alternate automated approach for assigning referees problem using intrinsic random walk with restart proximity measure. In our experiments based on a comprehensive DBLP networks, we show that our approach, called OFFER, significantly outperforms state-of-the-art the random walk with restart based method.