Master's Thesis
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- Institut für Computervisualistik (16) (remove)
Artificial neural networks is a popular field of research in artificial intelli-
gence. The increasing size and complexity of huge models entail certain
problems. The lack of transparency of the inner workings of a neural net-
work makes it difficult to choose efficient architectures for different tasks.
It proves to be challenging to solve these problems, and with a lack of in-
sightful representations of neural networks, this state of affairs becomes
entrenched. With these difficulties in mind a novel 3D visualization tech-
nique is introduced. Attributes for trained neural networks are estimated
by utilizing established methods from the area of neural network optimiza-
tion. Batch normalization is used with fine-tuning and feature extraction to
estimate the importance of different parts of the neural network. A combi-
nation of the importance values with various methods like edge bundling,
ray tracing, 3D impostor and a special transparency technique results in a
3D model representing a neural network. The validity of the extracted im-
portance estimations is demonstrated and the potential of the developed
visualization is explored.
In this thesis, the performance of the IceCube projects photon propagation
code (clsim) is optimized. The process of GPU code analysis and perfor-
mance optimization is described in detail. When run on the same hard-
ware, the new version achieves a speedup of about 3x over the original
implementation. Comparing the unmodified code on hardware currently
used by IceCube (NVIDIA GTX 1080) against the optimized version run on
a recent GPU (NVIDIA A100) a speedup of about 9.23x is observed. All
changes made to the code are shown and their performance impact as well
as the implications for simulation accuracy are discussed individually.
The approach taken for optimization is then generalized into a recipe.
Programmers can use it as a guide, when approaching large and complex
GPU programs. In addition, the per warp job-queue, a design pattern used
for load balancing among threads in a CUDA thread block, is discussed in
detail.
Constituent parsing attempts to extract syntactic structure from a sentence. These parsing systems are helpful in many NLP applications such as grammar checking, question answering, and information extraction. This thesis work is about implementing a constituent parser for German language using neural networks. Over the past, recurrent neural networks have been used in building a parser and also many NLP applications. In this, self-attention neural network modules are used intensively to understand sentences effectively. With multilayered self-attention networks, constituent parsing achieves 93.68% F1 score. This is improved even further by using both character and word embeddings as a representation of the input. An F1 score of 94.10% was the best achieved by constituent parser using only the dataset provided. With the help of external datasets such as German Wikipedia, pre-trained ELMo models are used along with self-attention networks achieving 95.87% F1 score.
Since the invention of U-net architecture in 2015, convolutional networks based on its encoder-decoder approach significantly improved results in image analysis challenges. It has been proven that such architectures can also be successfully applied in different domains by winning numerous championships in recent years. Also, the transfer learning technique created an opportunity to push state-of-the-art benchmarks to a higher level. Using this approach is beneficial for the medical domain, as collecting datasets is generally a difficult and expensive process.
In this thesis, we address the task of semantic segmentation with Deep Learning and make three main contributions and release experimental results that have practical value for medical imaging.
First, we evaluate the performance of four neural network architectures on the dataset of the cervical spine MRI scans. Second, we use transfer learning from models trained on the Imagenet dataset and compare it to randomly initialized networks. Third, we evaluate models trained on the bias field corrected and raw MRI data. All code to reproduce results is publicly available online.
The Material Point Method (MPM) has proven to be a very capable simulation method in computer graphics that is able to model materials that were previously very challenging to animate [1, 2]. Apart from simulating singular materials, the simulation of multiple materials that interact with each other introduces new challenges. This is the focus of this thesis. It will be shown that the self-collision capabilities of the MPM can naturally handle multiple materials interacting in the same scene on a collision basis, even if the materials use distinct constitutive models. This is then extended by porous interaction of materials as in[3], which also integrates easily with MPM.It will furthermore be shown that regular single-grid MPM can be viewed as a subset of this multi-grid approach, meaning that its behavior can also be achieved if multiple grids are used. The porous interaction is generalized to arbitrary materials and freely changeable material interaction terms, yielding a flexible, user-controllable framework that is independent of specific constitutive models. The framework is implemented on the GPU in a straightforward and simple way and takes advantage of the rasterization pipeline to resolve write-conflicts, resulting in a portable implementation with wide hardware support, unlike other approaches such as [4].
Tracking is an integral part of many modern applications, especially in areas like autonomous systems and Augmented Reality. For performing tracking there are a wide array of approaches. One that has become a subject of research just recently is the utilization of Neural Networks. In the scope of this master thesis an application will be developed which uses such a Neural Network for the tracking process. This also requires the creation of training data as well as the creation and training of a Neural Network. Subsequently the usage of Neural Networks for tracking will be analyzed and evaluated. This includes several aspects. The quality of the tracking for different degrees of freedom will be checked as well as the the impact of the Neural Network on the applications performance. Additionally the amount of required training data is investigated, the influence of the network architecture and the importance of providing depth data as part of the networks input. This should provide an insight into how relevant this approach could be for its adoption in future products.
With the appearance of modern virtual reality (VR) headsets on the consumer market, there has been the biggest boom in the history of VR technology. Naturally, this was accompanied by an increasing focus on the problems of current VR hardware. Especially the control in VR has always been a complex topic.
One possible solution is the Leap Motion, a hand tracking device that was initially developed for desktop use, but with the last major software update it can be attached to standard VR headsets. This device allows very precise tracking of the user’s hands and fingers and their replication in the virtual world.
The aim of this work is to design virtual user interfaces that can be operated with the Leap Motion to provide a natural method of interaction between the user and the VR environment. After that, subject tests are performed to evaluate their performance and compare them to traditional VR controllers.
In scientific data visualization huge amounts of data are generated, which implies the task of analyzing these in an efficient way. This includes the reliable detection of important parts and a low expenditure of time and effort. This is especially important for the big-sized seismic volume datasets, that are required for the exploration of oil and gas deposits. Since the generated data is complex and a manual analysis is very time-intensive, a semi-automatic approach could on one hand reduce the time required for the analysis and on the other hand offer more flexibility, than a fully automatic approach.
This master's thesis introduces an algorithm, which is capable of locating regions of interest in seismic volume data automatically by detecting anomalies in local histograms. Furthermore the results are visualized and a variety of tools for the exploration and interpretation of the detected regions are developed. The approach is evaluated by experiments with synthetic data and in interviews with domain experts on the basis of real-world data. Conclusively further improvements to integrate the algorithm into the seismic interpretation workflow are suggested.
With the emergence of current generation head-mounted displays (HMDs), virtual reality (VR) is regaining much interest in the field of medical imaging and diagnosis. Room-scale exploration of CT or MRI data in virtual reality feels like an intuitive application. However in VR retaining a high frame rate is more critical than for conventional user interaction seated in front of a screen. There is strong scientific evidence suggesting that low frame rates and high latency have a strong influence on the appearance of cybersickness. This thesis explores two practical approaches to overcome the high computational cost of volume rendering for virtual reality. One lies within the exploitation of coherency properties of the especially costly stereoscopic rendering setup. The main contribution is the development and evaluation of a novel acceleration technique for stereoscopic GPU ray casting. Additionally, an asynchronous rendering approach is pursued to minimize the amount of latency in the system. A selection of image warping techniques has been implemented and evaluated methodically, assessing the applicability for VR volume rendering.
Statistical Shape Models (SSMs) are one of the most successful tools in 3Dimage analysis and especially medical image segmentation. By modeling the variability of a population of training shapes, the statistical information inherent in such data are used for automatic interpretation of new images. However, building a high-quality SSM requires manually generated ground truth data from clinical experts. Unfortunately, the acquisition of such data is a time-consuming, error-prone and subjective process. Due to this effort, the majority of SSMs is often based on a limited set of this ground truth training data, which makes the models less statistically meaningful. On the other hand, image data itself is abundant in clinics from daily routine. In this work, methods for automatically constructing a reliable SSM without the need of manual image interpretation from experts are proposed. Thus, the training data is assumed to be the result of any segmentation algorithm or may originate from other sources, e.g. non-expert manual delineations. Depending on the algorithm, the output segmentations will contain errors to a higher or lower degree. In order to account for these errors, areas of low probability of being a boundary should be excluded from the training of the SSM. Therefore, the probabilities are estimated with the help of image-based approaches. By including many shape variations, the corrupted parts can be statistically reconstructed. Two approaches for reconstruction are proposed - an Imputation method and Weighted Robust Principal Component Analysis (WRPCA). This allows the inclusion of many data sets from clinical routine, covering a lot more variations of shape examples. To assess the quality of the models, which are robust against erroneous training shapes, an evaluation compares the generalization and specificity ability to a model build from ground truth data. The results show, that especially WRPCA is a powerful tool to handle corrupted parts and yields to reasonable models, which have a higher quality than the initial segmentations.
While Virtual Reality has been around for decades it gained new life in recent years. The release of the first consumer hardware devices allows fully immersive and affordable VR for the user at home. This availability lead to a new focus of research on technical problems as well as psychological effects. The concepts of presence, describing the feeling of being in the virtual place, body ownership and their impact are central topics in research for a long time and still not fully understood.
To enable further research in the area of Mixed Reality, we want to introduce a framework that integrates the users body and surroundings inside a visual coherent virtual environment. As one of two main aspects we want to merge real and virtual objects to a shared environment in a way such that they are no longer visually distinguishable. To achieve this the main focus is not supposed to be on a high graphical fidelity but on a simplified representation of reality. The essential question is, what level of visual realism is necessary to create a believable mixed reality environment that induces a sense of presence in the user? The second aspect considers the integration of virtual persons. Can characters be recorded and replayed in a way such that they are perceived as believable entities of the world and therefore act as a part of the users environment?
The purpose of this thesis was the development of a framework called Mixed Reality Embodiment Platform. This inital system implements fundamental functionalities to be used as a basis for future extensions to the framework. We also provide a first application that enables user studies to evaluate the framework and contribute to aforementioned research questions.
In recent years head mounted displays (HMD) and their abilities to create virtual realities comparable with the real world moved more into the focus of press coverage and consumers. The reason for this lies in constant improvements in available computing power, miniaturisation of components as well as the constantly shrinking power consumption. These trends originate in the general technical progress driven by advancements made in smartphone sector. This gives more people than ever access to the required components to create these virtual realities. However at the same time there is only limited research which uses the current generation of HMDs especially when comparing the virtual and real world against each other. The approach of this thesis is to look into the process of navigating both real and virtual spaces while using modern hardware and software. One of the key areas are the spatial and peripheral perception without which it would be difficult to navigate a given space. The influence of prior real and virtual experiences on these will be another key aspect. The final area of focus is the influence on the emotional state and how it compares to the real world. To research these influences a experiment using the Oculus Rift DK2 HMD will be held in which subjects will be guided through a real space as well as a virtual model of it. Data will be gather in a quantitative manner by using surveys. Finally, the findings will be discussed based on a statistical evaluation. During these tests the different perception of distances and room size will the compared and how they change based on the current reality. Furthermore, the influence of prior spatial activities both in the real and the virtual world will looked into. Lastly, it will be checked how real these virtual worlds are and if they are sufficiently sophisticated to trigger the same emotional responses as the real world.
This work covers techniques for interactive and physically - based rendering of hair for computer generated imagery (CGI). To this end techniques
for the simulation and approximation of the interaction of light with hair are derived and presented. Furthermore it is described how hair, despite such computationally expensive algorithms, can be rendered interactively.
Techniques for computing the shadowing in hair as well as approaches to render hair as transparent geometry are also presented. A main focus of
this work is the DBK-Buffer, which was conceived, implemented and evaluated. Using the DBK-Buffer, it is possible to render thousands of hairs as
transparent geometry without being dependent on either the newest GPU hardware generation or a great amount of video memory. Moreover, a comprehensive evaluation of all the techniques described was conducted with respect to the visual quality, performance and memory requirements. This
revealed that hair can be rendered physically - based at interactive or even at real - time frame rates.
The mitral valve is one of the four valves in the human heart. It is located in the left heart chamber and its function is to control the blood flow from the left atrium to the left ventricle. Pathologies can lead to malfunctions of the valve so that blood can flow back to the atrium. Patients with a faulty mitral valve function may suffer from fatigue and chest pain. The functionality can be surgically restored, which is often a long and exhaustive intervention. Thorough planning is necessary to ensure a safe and effective surgery. This can be supported by creating pre-operative segmentations of the mitral valve. A post-operative analysis can determine the success of an intervention. This work will combine existing and new ideas to propose a new approach to (semi-)automatically create such valve models. The manual part can guarantee a high quality model and reliability, whereas the automatic part contributes to saving valuable labour time.
The main contributions of the automatic algorithm are an estimated semantic separation of the two leaflets of the mitral valve and an optimization process that is capable of finding a coaptation-line and -area between the leaflets. The segmentation method can perform a fully automatic segmentation of the mitral leaflets if the annulus ring is already given. The intermediate steps of this process will be integrated into a manual segmentation method so a user can guide the whole procedure. The quality of the valve models generated by the method proposed in this work will be measured by comparing them to completely manually segmented models. This will show that commonly used methods to measure the quality of a segmentation are too general and do not suffice to reflect the real quality of a model. Consequently the work at hand will introduce a set of measurements that can qualify a mitral valve segmentation in more detail and with respect to anatomical landmarks. Besides the intra-operative support for a surgeon, a segmented mitral valve provides additional benefits. The ability to patient-specifically obtain and objectively describe the valve anatomy may be the base for future medical research in this field and automation allows to process large data sets with reduced expert dependency. Further, simulation methods that use the segmented models as input may predict the outcome of a surgery.
Object recognition is a well-investigated area in image-based computer vision and several methods have been developed. Approaches based on Implicit Shape Models have recently become popular for recognizing objects in 2D images, which separate objects into fundamental visual object parts and spatial relationships between the individual parts. This knowledge is then used to identify unknown object instances. However, since the emergence of aσordable depth cameras like Microsoft Kinect, recognizing unknown objects in 3D point clouds has become an increasingly important task. In the context of indoor robot vision, an algorithm is developed that extends existing methods based on Implicit Shape Model approaches to the task of 3D object recognition.
Tractography on HARDI data
(2011)
Diffusion weighted imaging is an important modality in clinical imaging and the only possibility to gain insight into the human brain noninvasively and in-vivo. The applications of this imaging technique are diversified. It is used to study the brain, its structure, development and the functionality of the different areas. Further, important fields of application are neurosurgical planning, examinations of pathologies, investigation of Alzheimer-, strokes, and multiple sclerosis. This thesis gives a brief introduction to MRI and diffusion MRI. Based on this, the mostly used data representation in diffusion MRI in clinical imaging, the diffusion tensor, is introduced. As the diffusion tensor suffers from severe limitations new techniques subsumed under the term HARDI (high angular resolution diffusion imaging) are introduced and discussed in detail. Further, an extensive introduction to tractography, approaches that aim at reconstructing neuronal fibers, is given. Based on the knowledge fromthe theoretical part established tractography algorithms are redesigned to handle HARDI data and, thus, improve the reconstruction of neuronal fibers. Among these algorithms, a novel approach is presented that successfully reconstructs fibers on phantom data as well as on human brain data. Further, a novel global classification approach is presented to cluster voxels according to their diffusion properties.