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Automatic 3D segmentation of brain images
Bafrnec, Matúš ; Dorazil, Jan (referee) ; Kolařík, Martin (advisor)
This bachelor thesis describes the design and implementation of the system for automatic 3D segmentation of a brain based on convolutional neural networks. The first part is dedicated to a brief history of neural networks and a theoretical description of the functionality of convolutional neural networks. It represents a fast introduction to the problematics and provides theoretical basics needed for the understanding and creation of the system. Individual layers of the neural network and principles of their functionality and mutual relations are also described in this part. The second part of the thesis is about problem analysis, designing of a solution and a comparison between neural networks and other solutions. The result of a magnetic resonance imaging of the head is a series of black-and-white images representing a 3D scan. The task is to tag a brain and to remove unnecessary information in the form of surrounding tissues. The final image of the brain can be utilized in a volumetry or during a diagnostic of neurodegenerative diseases. The advantage of neural networks in comparison with deterministic systems is their flexibility. They allow an adaptation to other segmentation problems just by changing the training dataset, without a need of changes in the architecture. One of the systems performing fully automatic 3D segmentation is called U-Net – its name comes from the similarity of the architecture with the letter U. Three real solutions, the first implementation of U-Net, extended U-Net and recurrent U-Net were presented. The first version of U-Net has been very memory-demanding, it required a training on a processor instead of a graphic card and has not allowed data processing in full resolution. The extended U-Net has resolved these problems by loading data in overlaying series of three images. In addition to the possibility of a training on a graphic card with related decrease in learning time, the accuracy was increased by adding interconnections to the internal architecture of the network. The last version, recurrent U-Net, aims for the optimization of extended U-Net based on the reusage of existing levels. This brings a decrease in a time and resource difficulty. The number of parameters of the network was lowered to less than 20%, without any increase in case of further level addition. This network is one of first recurrent networks used on the problem of 3D segmentation and provides a foundation to further research. The last part focuses on the evaluation of results and the comparison of accuracy, speed and requirements between particular networks. The accuracy of human and machine segmentation is also compared. The extended and recurrent U-Net have surpassed their human opponent, which in real case could save a lot of doctors time and prevent human mistakes. The result of this work is a theoretical basis providing an introduction to the problematics of convolutional neural networks and segmentation, fully working systems for automatic 3D segmentation and the foundation for further research in the field of recurrent networks.
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STATISTICAL LANGUAGE MODELS BASED ON NEURAL NETWORKS
Mikolov, Tomáš ; Zweig, Geoffrey (referee) ; Hajič,, Jan (referee) ; Černocký, Jan (advisor)
Statistické jazykové modely jsou důležitou součástí mnoha úspěšných aplikací, mezi něž patří například automatické rozpoznávání řeči a strojový překlad (příkladem je známá aplikace Google Translate). Tradiční techniky pro odhad těchto modelů jsou založeny na tzv. N-gramech. Navzdory známým nedostatkům těchto technik a obrovskému úsilí výzkumných skupin napříč mnoha oblastmi (rozpoznávání řeči, automatický překlad, neuroscience, umělá inteligence, zpracování přirozeného jazyka, komprese dat, psychologie atd.), N-gramy v podstatě zůstaly nejúspěšnější technikou. Cílem této práce je prezentace několika architektur jazykových modelůzaložených na neuronových sítích. Ačkoliv jsou tyto modely výpočetně náročnější než N-gramové modely, s technikami vyvinutými v této práci je možné jejich efektivní použití v reálných aplikacích. Dosažené snížení počtu chyb při rozpoznávání řeči oproti nejlepším N-gramovým modelům dosahuje 20%. Model založený na rekurentní neurovové síti dosahuje nejlepších publikovaných výsledků na velmi známé datové sadě (Penn Treebank).
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Automatic 3D segmentation of brain images
Bafrnec, Matúš ; Dorazil, Jan (referee) ; Kolařík, Martin (advisor)
This bachelor thesis describes the design and implementation of the system for automatic 3D segmentation of a brain based on convolutional neural networks. The first part is dedicated to a brief history of neural networks and a theoretical description of the functionality of convolutional neural networks. It represents a fast introduction to the problematics and provides theoretical basics needed for the understanding and creation of the system. Individual layers of the neural network and principles of their functionality and mutual relations are also described in this part. The second part of the thesis is about problem analysis, designing of a solution and a comparison between neural networks and other solutions. The result of a magnetic resonance imaging of the head is a series of black-and-white images representing a 3D scan. The task is to tag a brain and to remove unnecessary information in the form of surrounding tissues. The final image of the brain can be utilized in a volumetry or during a diagnostic of neurodegenerative diseases. The advantage of neural networks in comparison with deterministic systems is their flexibility. They allow an adaptation to other segmentation problems just by changing the training dataset, without a need of changes in the architecture. One of the systems performing fully automatic 3D segmentation is called U-Net – its name comes from the similarity of the architecture with the letter U. Three real solutions, the first implementation of U-Net, extended U-Net and recurrent U-Net were presented. The first version of U-Net has been very memory-demanding, it required a training on a processor instead of a graphic card and has not allowed data processing in full resolution. The extended U-Net has resolved these problems by loading data in overlaying series of three images. In addition to the possibility of a training on a graphic card with related decrease in learning time, the accuracy was increased by adding interconnections to the internal architecture of the network. The last version, recurrent U-Net, aims for the optimization of extended U-Net based on the reusage of existing levels. This brings a decrease in a time and resource difficulty. The number of parameters of the network was lowered to less than 20%, without any increase in case of further level addition. This network is one of first recurrent networks used on the problem of 3D segmentation and provides a foundation to further research. The last part focuses on the evaluation of results and the comparison of accuracy, speed and requirements between particular networks. The accuracy of human and machine segmentation is also compared. The extended and recurrent U-Net have surpassed their human opponent, which in real case could save a lot of doctors time and prevent human mistakes. The result of this work is a theoretical basis providing an introduction to the problematics of convolutional neural networks and segmentation, fully working systems for automatic 3D segmentation and the foundation for further research in the field of recurrent networks.
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STATISTICAL LANGUAGE MODELS BASED ON NEURAL NETWORKS
Mikolov, Tomáš ; Zweig, Geoffrey (referee) ; Hajič,, Jan (referee) ; Černocký, Jan (advisor)
Statistické jazykové modely jsou důležitou součástí mnoha úspěšných aplikací, mezi něž patří například automatické rozpoznávání řeči a strojový překlad (příkladem je známá aplikace Google Translate). Tradiční techniky pro odhad těchto modelů jsou založeny na tzv. N-gramech. Navzdory známým nedostatkům těchto technik a obrovskému úsilí výzkumných skupin napříč mnoha oblastmi (rozpoznávání řeči, automatický překlad, neuroscience, umělá inteligence, zpracování přirozeného jazyka, komprese dat, psychologie atd.), N-gramy v podstatě zůstaly nejúspěšnější technikou. Cílem této práce je prezentace několika architektur jazykových modelůzaložených na neuronových sítích. Ačkoliv jsou tyto modely výpočetně náročnější než N-gramové modely, s technikami vyvinutými v této práci je možné jejich efektivní použití v reálných aplikacích. Dosažené snížení počtu chyb při rozpoznávání řeči oproti nejlepším N-gramovým modelům dosahuje 20%. Model založený na rekurentní neurovové síti dosahuje nejlepších publikovaných výsledků na velmi známé datové sadě (Penn Treebank).
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