[9 Sep 2022 | No comments | 16 views ]
SUPREME: A cancer subtype prediction methodology

SUPREME: A cancer subtype prediction methodology integrating multiomics data using Graph Convolutional Neural Network

To pave the road towards precision medicine in cancer, patients with highly similar biology ought to be grouped into the same cancer subtypes. Utilizing high-dimensional multiomics datasets, several integrative computational approaches have been developed to uncover cancer subtypes. Recently, Graph Neural Networks (GNNs) was discovered to learn node embeddings while utilizing node features and node associations at the same time on graph-structured data. Although there are some …

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Projects »

[9 Sep 2022 | No comments | 16 views ]
SUPREME: A cancer subtype prediction methodology

SUPREME: A cancer subtype prediction methodology integrating multiomics data using Graph Convolutional Neural Network

To pave the road towards precision medicine in cancer, patients with highly similar biology ought to be grouped into the same cancer subtypes. Utilizing high-dimensional multiomics datasets, several integrative computational approaches have been developed to uncover cancer subtypes. Recently, Graph Neural Networks (GNNs) was discovered to learn node embeddings while utilizing node features and node associations at the same time on graph-structured data. Although there are some …

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Projects »

[27 Jun 2022 | No comments | 43 views ]
CRINET: Competing endogenous RNA (ceRNA) interactions inference

CRINET: A computational tool to infer genome-wide competing endogenous RNA (ceRNA) interactions

To understand driving biological factors for complex diseases like cancer, regulatory circuity of genes needs to be discovered. Recently, a new gene regulation mechanism called competing endogenous RNA (ceRNA) interactions has been discovered. Certain genes targeted by common microRNAs (miRNAs) “compete” for these miRNAs, thereby regulate each other by making others free from miRNA regulation. Several computational tools have been published to infer ceRNA networks. In most existing tools, …

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Bioinformatics »

[29 Mar 2018 | No comments | 2,135 views ]

GISTIC is one of the important tools in order to get the amplified or deleted regions in copy number variation data. You are giving the required information, and specifying the parameters (I generally preferred the default values), then it gives you the results. Installation is easy, you need to just follow the instructions in Install.txt in this folder.
If you cannot reach this ftp, and don’t have permission for copying files, then most probably you are using Safari; so try another …

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Projects »

[4 Feb 2013 | 12 Comments | 20,867 views ]
Natural Language Processing – Author Prediction

Üniversitede yüksek lisans dersi olarak almış olduğum NLP (Natural Language Processing) dersi yani Doğal Dil İşleme dersi için proje yapmam gerekiyordu. Bu konuyla ilgilenenler hocalardan fikir almak istedim ve asistanımız olan Harun Reşit Zafer hocaya gittim. Harun hoca da yüksek lisans yıllarında aynı derste yapmış olduğu Yazar Tahmin Sistemi ile ilgili olan projesini geliştirmeyi önerdi, ben de kabul ettim. Yapacağımız konu Author Categorization, yani Yazar Sınıflandırma. Author Categorization’a Author Prediction da denilmektedir. NLP computer science, artificial intelligence, ve linguistics’in çalışma alanına girmektedir. Author …

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Projects »

[27 Dec 2012 | No comments | 3,503 views ]
Image Colorization by using LBP

 “Introduction to Pattern Recognition” dersinde yaptigim bir projeydi. Ancak geliştirilebilir bir proje olduğu için ilgilenenlerle paylaşmak istedim: Projenin amacı machine learning algoritmaları kullanarak renkli training data’ları kullanarak elde edilen kriterleri, renksiz datalar da kullanarak sonuçları görmek. Training datalarım renkli resimler, testing datalarımise renksiz resimler. Sonuçta görmek istediğim ise renksiz olarak verdiğim test datasının renkli versiyonu. Projeye dataları belirleyerek başladım. vision.caltech.edu ve SUN Database linkleri data bulmak için güzel kaynaklar. Buradan 4 tane uçak resmini indirdim. Bunlar jpg uzantılı resimler. Training olarak kullanacağım 3 uçak …

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