GCRIS

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Planar Geometry Estimation With Deep Learning
(Izmir Institute of Technology, 2022) Uzyıldırım, Furkan Eren; Özuysal, Mustafa
Understanding the geometric structure of any scene is one of the oldest problems in Computer Vision. Most scenes include planar regions that provide information about the geometric structure and their automatic detection and segmentation plays an important role in many computer vision applications. In recent years, convolutional neural network architectures have been introduced for piece-wise planar segmentation. They outperform the traditional approaches that generate plane candidates with 3D segmentation methods from the explicitly reconstructed 3D point cloud. However, most of the convolutional neural network architectures are not designed and trained for outdoor scenes, because they require manual annotation, which is a time-consuming task that results in a lack of training data. In this thesis,we propose and develop a deep learning based framework for piece-wise plane detection and segmentation of outdoor scenes without requiring manually annotated training data. We exploit a network trained on imagery with annotated targets and an automatically reconstructed point cloud from either Structure from Motion-Multi View Stereo pipeline or monocular depth estimation network to estimate the training ground truth on the outdoor images in an iterative energy minimization framework. We show that the resulting ground truth estimate of various sets of images in the outdoor domain is good enough to improve network weights of different architectures trained on ground truth annotated images. Moreover, we demonstrate that this transfer learning scheme can be repeated multiple times iteratively to further improve the accuracy of plane detection and segmentation on monocular images of outdoor scenes.
Computational Establishment of Microrna Metabolic Networks
(Izmir Institute of Technology, 2017) Saçar Demirci, Müşerref Duygu; Allmer, Jens
MicroRNAs (miRNAs) are single-stranded, small, non-coding RNAs, that control gene expression at the post transcriptional level through various mechanisms such as translational inhibition, degradation and destabilisation of their target mRNAs. Despite the fact that thousands of miRNAs have been reported in various species, most still remain unknown. Due to this, the identification of new miRNAs is an essential process for analysing miRNA mediated post transcriptional regulation mechanisms. Moreover, many biological approaches suffer from limitations in their capacity to reveal rare miRNAs, and are further restricted to the state of the organism under examination. Such limitations have resulted in the construction of sophisticated computational tools for identification of possible miRNAs in silico. However, these programs suffer from low sensitivity and/or accuracy and as a result they do not provide enough confidence for validating all their predictions experimentally. In this study, the aim is overcoming these challenges by creating a new and adaptable machine learning based method to predict potential miRNAs in any given sequence. The efficiency of proposed method is shown by comparison with available tools on various data sets. By using this approach, miRNAs from the genomes of various organisms like human (Homo sapiens), fly (Drosophila melanogaster) and tomato (Solanum lycopersicum) are identified. Moreover, networks between the possible miRNAs of virus and human genes as well as the communications among nuclear and organelle genomes of Solanum lycopersicum through miRNAs are investigated.

Phd Degree / Doktora

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