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Though deep learning (DL) algorithms are very powerful for image processing tasks, they generally require a lot of data to reach their full potential. Furthermore, there is no straightforward way to impose various properties, given by the prior knowledge about the target task, on the features extracted by a DL model. Therefore, in this thesis we propose several techniques that rely on the power of graph representations to embed prior knowledge inside the learning process. This allows to reduce the solution space and leads to faster optimization convergence and higher accuracy in the representation learning. In our first work, inspired by the ability of a human to correctly classify rotated, shifted or flipped objects, we propose an algorithm that permits to inherently encode invariance to isometric transformations of objects in an image. Our DL architecture is based on graph representations and consists of three novel layers, which we refer to as graph convolutional, dynamic pooling and statistical layers. Our experiments on the image classification tasks show that our network correctly recognizes isometrically transformed objects even though such types of transformation are not seen by the network at training time. Standard DL techniques are typically not able to succeed in solving such a problem without extensive data augmentation. Then, we propose to exploit the properties of graph-based approaches to efficiently process images with various types of projective geometry. In particular, we are interested in increasingly popular omnidirectional cameras, which have a 360 degree field of view. Despite their effectiveness, such cameras create images with specific geometric properties, which require special techniques for efficient processing. We propose an efficient way of adjusting the weights of the graph edges to adapt the filter responses to the geometric image properties introduced by omnidirectional cameras. Our experiments prove that using the proposed graph with properly adjusted edge weights permits to reach better performance as compared to using regular grid graph with equal weights. Finally, the approach described above relies on the isotropic filters, which work well within our transformation invariant architecture for image classification. However, for other problems (e.g. image compression) or even when used without dynamic pooling and statistical layers that are defined within the proposed architecture, these filters are unable to efficiently encode the information about the object. Thus, we introduce a different technique based on anisotropic filters that adapt their shape and size according to the omnidirectional image geometry. The main advantage of this approach compared to the previous one is the ability to encode the orientation of an image pattern, which is important for various tasks such as image compression. Our experiments show that our approach adapts to different image projective geometries and achieves state-of-the-art performance on image classification and compression tasks. Overall we propose several methods, which combine the power of DL and graph signal processing towards incorporating prior information about the target task inside the optimization procedure. We hope that the research efforts presented in this thesis will help the development of efficient DL algorithms that can use various types of prior knowledge to make them efficient even when the available training data is scarce.