195 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
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
Unsupervised Discovery of 3D Hierarchical Structure with Generative Diffusion Features
Inspired by recent findings that generative diffusion models learn
semantically meaningful representations, we use them to discover the intrinsic
hierarchical structure in biomedical 3D images using unsupervised segmentation.
We show that features of diffusion models from different stages of a
U-Net-based ladder-like architecture capture different hierarchy levels in 3D
biomedical images. We design three losses to train a predictive unsupervised
segmentation network that encourages the decomposition of 3D volumes into
meaningful nested subvolumes that represent a hierarchy. First, we pretrain 3D
diffusion models and use the consistency of their features across subvolumes.
Second, we use the visual consistency between subvolumes. Third, we use the
invariance to photometric augmentations as a regularizer. Our models achieve
better performance than prior unsupervised structure discovery approaches on
challenging biologically-inspired synthetic datasets and on a real-world brain
tumor MRI dataset.Comment: MICCAI 202
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
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