Tato magisterská práce se zabývá využitím konvolučních neuronových sítí pro segmentační účely v oblasti transmisní elektronové mikroskopie. Také popisuje zvolenou topologii neuronové sítě - U-NET, použíté augmentační techniky a programové prostředí. Firma Thermo Fisher Scientific (dříve FEI Czech Republic s.r.o) poskytla obrazová data pro účely této práce. Získané segmentační výsledky jsou prezentovány ve formě křivek (ROC, PRC) a ve formě numerických hodnot (ARI, DSC, Chybová matice). Zvolená UNET topologie dosáhla excelentních výsledků v oblasti pixelové segmentace. S největší pravděpodobností, budou tyto výsledky sloužit jako odrazový můstek pro interní firemní výzkum.

This diploma thesis deals with the detection of fire and smoke from the image signal. The approach of this work uses a combination of convolutional and recurrent neural network. Machine learning models created in this work contain inception modules and blocks of long short-term memory. The research part describes selected models of machine learning used in solving the problem of fire detection in static and dynamic image data. As part of the solution, a data set containing videos and still images used to train the designed neural networks was created. The results of this approach are evaluated in conclusion.

This diploma thesis describes and implements the design of a graph neural network usedfor 2D segmentation of neural structure. The first chapter of the thesis briefly introduces the problem of segmentation. In this chapter, segmentation techniques are divided according to the principles of the methods they use. Each type of technique contains the essence of this category as well as a description of one representative. The second chapter of the diploma thesis explains graph neural networks (GNN for short). Here, the thesis divides graph neural networks in general and describes recurrent graph neural networks(RGNN for short) and graph autoencoders, that can be used for image segmentation, in more detail. The specific image segmentation solution is based on the message passing method in RGNN, which can replace convolution masks in convolutional neural networks.RGNN also provides a simpler multilayer perceptron topology. The second type of graph neural networks characterised in the thesis are graph autoencoders, which use various methods for better encoding of graph vertices into Euclidean space. The last part ofthe diploma thesis deals with the analysis of the problem, the proposal of its specific solution and the evaluation of results. The purpose of the practical part of the work was the implementation of GNN for image data segmentation. The advantage of using neural networks is the ability to solve different types of segmentation by changing training data. RGNN with messaging passing and node2vec were used as implementation GNNf or segmentation problem. RGNN training was performed on graphics cards provided bythe school and Google Colaboratory. Learning RGNN using node2vec was very memory intensive and therefore it was necessary to train on a processor with an operating memory larger than 12GB. As part of the RGNN optimization, learning was tested using various loss functions, changing topology and learning parameters. A tree structure method was developed to use node2vec to improve segmentation, but the results did not confirman improvement for a small number of iterations. The best outcomes of the practical implementation were evaluated by comparing the tested data with the convolutional neural network U-Net. It is possible to state comparable results to the U-Net network, but further testing is needed to compare these neural networks. The result of the thesisis the use of RGNN as a modern solution to the problem of image segmentation and providing a foundation for further research.

In recent years, there has been a significant push to implement Deep Neural Networks (DNNs) on edge devices, which requires power and hardware efficient circuits to carry out the intensive matrix-vector multiplication (MVM) operations. This work presents hardware efficient MVM implementation techniques using bit-serial arithmetic and a novel MSB first computation circuit. The proposed designs take advantage of the pre-trained network weight parameters, which are already known in the design stage. Thus, the partial computation results can be pre-computed and stored into look-up tables. Then the MVM results can be computed in a bit-serial manner without using multipliers. The proposed novel circuit implementation for convolution filters and rectified linear activation function used in deep neural networks conducts computation in an MSB-first bit-serial manner. It can predict earlier if the outcomes of filter computations will be negative and subsequently terminate the remaining computations to save power. The benefits of using the proposed MVM implementations techniques are demonstrated by comparing the proposed design with conventional implementation. The proposed circuit is implemented on an FPGA. It shows significant power and performance improvements compared to the conventional designs implemented on the same FPGA.

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Colony Collapse Disorder (CCD) has been a major threat to bee colonies around the world which affects vital human food crop pollination. The decline in bee population can have tragic consequences, for humans as well as the bees and the ecosystem. Bee health has been a cause of urgent concern for farmers and scientists around the world for at least a decade but a specific cause for the phenomenon has yet to be conclusively identified. This work uses Artificial Intelligence and Computer Vision approaches to develop and analyze techniques to help in continuous monitoring of bee traffic which will further help in monitoring forager traffic. Bee traffic is the number of bees moving in a given area in front of the hive over a given period of time. And, forager traffic is the number of bees entering and/or exiting the hive over a given period of time. Forager traffic is an important variable to monitor food availability, food demand, colony age structure, impact of pesticides, etc. on bee hives. This will lead to improved remote monitoring and general hive status and improved real time detection of the impact of pests, diseases, pesticide exposure and other hive management problems.

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Glioblastoma Multiforme (GBM) is a very aggressive brain tumour. Previous studies have suggested that the morphological distribution of single GBM cells may hold information about the severity. This study aims to find if there is a potential for automated morphological qualification and clustering of GBM cells and what it shows. In this context, phase-contrast images from 10 different GBMcell cultures were analyzed. To test the hypothesis that morphological differences exist between the cell cultures, images of single GBM cells images were created from an image over the well using CellProfiler and Python. Singlecellimages were passed through multiple different feature extraction models to identify the model showing the most promise for this dataset. The features were then clustered and quantified to see if any differentiation exists between the cell cultures. The results suggest morphological feature differences exist between GBM cell cultures when using automated models. The siamese network managed to construct clusters of cells having very similar morphology. I conclude that the 10 cell cultures seem to have cells with morphological differences. This highlights the importance of future studies to find what these morphological differences imply for the patients' survivability and choice of treatment.

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Machine learning algorithms based on neural networks have achieved remarkable results and are being extensively used in different domains. However, the machine learning algorithms requires access to raw data which is often privacy sensitive. To address this issue, we develop new techniques to provide solutions for running deep neural networks over encrypted data. In this paper, we develop new techniques to adopt deep neural networks within the practical limitation of current homomorphic encryption schemes. We focus on training and classification of the well-known neural networks and convolutional neural networks. First, we design methods for approximation of the activation functions commonly used in CNNs (i.e. ReLU, Sigmoid, and Tanh) with low degree polynomials which is essential for efficient homomorphic encryption schemes. Then, we train neural networks with the approximation polynomials instead of original activation functions and analyze the performance of the models. Finally, we implement neural networks and convolutional neural networks over encrypted data and measure performance of the models.