40 research outputs found
Quicksilver: Fast Predictive Image Registration - a Deep Learning Approach
This paper introduces Quicksilver, a fast deformable image registration
method. Quicksilver registration for image-pairs works by patch-wise prediction
of a deformation model based directly on image appearance. A deep
encoder-decoder network is used as the prediction model. While the prediction
strategy is general, we focus on predictions for the Large Deformation
Diffeomorphic Metric Mapping (LDDMM) model. Specifically, we predict the
momentum-parameterization of LDDMM, which facilitates a patch-wise prediction
strategy while maintaining the theoretical properties of LDDMM, such as
guaranteed diffeomorphic mappings for sufficiently strong regularization. We
also provide a probabilistic version of our prediction network which can be
sampled during the testing time to calculate uncertainties in the predicted
deformations. Finally, we introduce a new correction network which greatly
increases the prediction accuracy of an already existing prediction network. We
show experimental results for uni-modal atlas-to-image as well as uni- / multi-
modal image-to-image registrations. These experiments demonstrate that our
method accurately predicts registrations obtained by numerical optimization, is
very fast, achieves state-of-the-art registration results on four standard
validation datasets, and can jointly learn an image similarity measure.
Quicksilver is freely available as an open-source software.Comment: Add new discussion
Fast Predictive Multimodal Image Registration
We introduce a deep encoder-decoder architecture for image deformation
prediction from multimodal images. Specifically, we design an image-patch-based
deep network that jointly (i) learns an image similarity measure and (ii) the
relationship between image patches and deformation parameters. While our method
can be applied to general image registration formulations, we focus on the
Large Deformation Diffeomorphic Metric Mapping (LDDMM) registration model. By
predicting the initial momentum of the shooting formulation of LDDMM, we
preserve its mathematical properties and drastically reduce the computation
time, compared to optimization-based approaches. Furthermore, we create a
Bayesian probabilistic version of the network that allows evaluation of
registration uncertainty via sampling of the network at test time. We evaluate
our method on a 3D brain MRI dataset using both T1- and T2-weighted images. Our
experiments show that our method generates accurate predictions and that
learning the similarity measure leads to more consistent registrations than
relying on generic multimodal image similarity measures, such as mutual
information. Our approach is an order of magnitude faster than
optimization-based LDDMM.Comment: Accepted as a conference paper for ISBI 201
A Stable Multi-Scale Kernel for Topological Machine Learning
Topological data analysis offers a rich source of valuable information to
study vision problems. Yet, so far we lack a theoretically sound connection to
popular kernel-based learning techniques, such as kernel SVMs or kernel PCA. In
this work, we establish such a connection by designing a multi-scale kernel for
persistence diagrams, a stable summary representation of topological features
in data. We show that this kernel is positive definite and prove its stability
with respect to the 1-Wasserstein distance. Experiments on two benchmark
datasets for 3D shape classification/retrieval and texture recognition show
considerable performance gains of the proposed method compared to an
alternative approach that is based on the recently introduced persistence
landscapes
Compressing networks with super nodes
Community detection is a commonly used technique for identifying groups in a
network based on similarities in connectivity patterns. To facilitate community
detection in large networks, we recast the network to be partitioned into a
smaller network of 'super nodes', each super node comprising one or more nodes
in the original network. To define the seeds of our super nodes, we apply the
'CoreHD' ranking from dismantling and decycling. We test our approach through
the analysis of two common methods for community detection: modularity
maximization with the Louvain algorithm and maximum likelihood optimization for
fitting a stochastic block model. Our results highlight that applying community
detection to the compressed network of super nodes is significantly faster
while successfully producing partitions that are more aligned with the local
network connectivity, more stable across multiple (stochastic) runs within and
between community detection algorithms, and overlap well with the results
obtained using the full network
Efficient Registration of Pathological Images: A Joint PCA/Image-Reconstruction Approach
Registration involving one or more images containing pathologies is
challenging, as standard image similarity measures and spatial transforms
cannot account for common changes due to pathologies. Low-rank/Sparse (LRS)
decomposition removes pathologies prior to registration; however, LRS is
memory-demanding and slow, which limits its use on larger data sets.
Additionally, LRS blurs normal tissue regions, which may degrade registration
performance. This paper proposes an efficient alternative to LRS: (1) normal
tissue appearance is captured by principal component analysis (PCA) and (2)
blurring is avoided by an integrated model for pathology removal and image
reconstruction. Results on synthetic and BRATS 2015 data demonstrate its
utility.Comment: Accepted as a conference paper for ISBI 201
Parametric Regression on the Grassmannian
We address the problem of fitting parametric curves on the Grassmann manifold
for the purpose of intrinsic parametric regression. As customary in the
literature, we start from the energy minimization formulation of linear
least-squares in Euclidean spaces and generalize this concept to general
nonflat Riemannian manifolds, following an optimal-control point of view. We
then specialize this idea to the Grassmann manifold and demonstrate that it
yields a simple, extensible and easy-to-implement solution to the parametric
regression problem. In fact, it allows us to extend the basic geodesic model to
(1) a time-warped variant and (2) cubic splines. We demonstrate the utility of
the proposed solution on different vision problems, such as shape regression as
a function of age, traffic-speed estimation and crowd-counting from
surveillance video clips. Most notably, these problems can be conveniently
solved within the same framework without any specifically-tailored steps along
the processing pipeline.Comment: 14 pages, 11 figure