Structural Surface Mapping for Shape Analysis

Natural surfaces are usually associated with feature graphs, such as the cortical surface with anatomical atlas structure. Such a feature graph subdivides the whole surface into meaningful sub-regions. Existing brain mapping and registration methods did not integrate anatomical atlas structures. As a result, with existing brain mappings, it is difficult to visualize and compare the atlas structures. And also existing brain registration methods can not guarantee the best possible alignment of the cortical regions which can help computing more accurate shape similarity metrics for neurodegenerative disease analysis, e.g., Alzheimer’s disease (AD) classification. Also, not much attention has been paid to tackle surface parameterization and registration with graph constraints in a rigorous way which have many applications in graphics, e.g., surface and image morphing. This dissertation explores structural mappings for shape analysis of surfaces using the feature graphs as constraints. (1) First, we propose structural brain mapping which maps the brain cortical surface onto a planar convex domain using Tutte embedding of a novel atlas graph and harmonic map with atlas graph constraints to facilitate visualization and comparison between the atlas structures. (2) Next, we propose a novel brain registration technique based on an intrinsic atlas-constrained harmonic map which provides the best possible alignment of the cortical regions. (3) After that, the proposed brain registration technique has been applied to compute shape similarity metrics for AD classification. (4) Finally, we propose techniques to compute intrinsic graph-constrained parameterization and registration for general genus-0 surfaces which have been used in surface and image morphing applications

An Exploration of Controlling the Content Learned by Deep Neural Networks

With the great success of the Deep Neural Network (DNN), how to get a trustworthy model attracts more and more attention. Generally, people intend to provide the raw data to the DNN directly in training. However, the entire training process is in a black box, in which the knowledge learned by the DNN is out of control. There are many risks inside. The most common one is overfitting. With the deepening of research on neural networks, additional and probably greater risks were discovered recently. The related research shows that unknown clues can hide in the training data because of the randomization of the data and the finite scale of the training data. Some of the clues build meaningless but explicit links between input data the output data called ``shortcuts\u27\u27. The DNN makes the decision based on these ``shortcuts\u27\u27. This phenomenon is also called ``network cheating\u27\u27. The knowledge of such shortcuts learned by DNN ruins all the training and makes the performance of the DNN unreliable. Therefore, we need to control the raw data using in training. Here, we name the explicit raw data as ``content\u27\u27 and the implicit logic learned by the DNN as ``knowledge\u27\u27 in this dissertation. By quantifying the information in DNN\u27s training, we find that the information learned by the network is much less than the information contained in the dataset. It indicates that it is unnecessary to train the neural network with all of the information, which means using partial information for training can also achieve a similar effect of using full information. In other words, it is possible to control the content fed into the DNN, and this strategy shown in this study can reduce the risks (e.g., overfitting and shortcuts) mentioned above. Moreover, use reconstructed data (with partial information) to train the network can reduce the complexity of the network and accelerate the training. In this dissertation, we provide a pipeline to implement content control in DNN\u27s training. We use a series of experiments to prove its feasibility in two applications. One is human brain anatomy structure analysis, and the other is human pose detection and classification

Proceedings of the Third International Workshop on Mathematical Foundations of Computational Anatomy - Geometrical and Statistical Methods for Modelling Biological Shape Variability

International audienceComputational anatomy is an emerging discipline at the interface of geometry, statistics and image analysis which aims at modeling and analyzing the biological shape of tissues and organs. The goal is to estimate representative organ anatomies across diseases, populations, species or ages, to model the organ development across time (growth or aging), to establish their variability, and to correlate this variability information with other functional, genetic or structural information. The Mathematical Foundations of Computational Anatomy (MFCA) workshop aims at fostering the interactions between the mathematical community around shapes and the MICCAI community in view of computational anatomy applications. It targets more particularly researchers investigating the combination of statistical and geometrical aspects in the modeling of the variability of biological shapes. The workshop is a forum for the exchange of the theoretical ideas and aims at being a source of inspiration for new methodological developments in computational anatomy. A special emphasis is put on theoretical developments, applications and results being welcomed as illustrations. Following the successful rst edition of this workshop in 20061 and second edition in New-York in 20082, the third edition was held in Toronto on September 22 20113. Contributions were solicited in Riemannian and group theoretical methods, geometric measurements of the anatomy, advanced statistics on deformations and shapes, metrics for computational anatomy, statistics of surfaces, modeling of growth and longitudinal shape changes. 22 submissions were reviewed by three members of the program committee. To guaranty a high level program, 11 papers only were selected for oral presentation in 4 sessions. Two of these sessions regroups classical themes of the workshop: statistics on manifolds and diff eomorphisms for surface or longitudinal registration. One session gathers papers exploring new mathematical structures beyond Riemannian geometry while the last oral session deals with the emerging theme of statistics on graphs and trees. Finally, a poster session of 5 papers addresses more application oriented works on computational anatomy