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Fast algorithms for biophysically-constrained inverse problems in medical imaging
We present algorithms and software for parameter estimation for forward and inverse tumor growth problems and diffeomorphic image registration. Our methods target the following scenarios: automatic image registration of healthy images to tumor bearing medical images and parameter estimation/calibration of tumor models. This thesis focuses on robust and scalable algorithms for these problems.
Although the proposed framework applies to many problems in oncology, we focus on primary brain tumors and in particular low and high-grade gliomas. For the tumor model, the main quantity of interest is the extent of tumor infiltration into the brain, beyond what is visible in imaging.
The inverse tumor problem assumes that we have patient images at two (or more) well-separated times so that we can observe the tumor growth. Also, the inverse problem requires that the two images are segmented. But in a clinical setting such information is usually not available. In a typical case, we just have multimodal magnetic resonance images with no segmentation. We address this lack of information by solving a coupled inverse registration and tumor problem. The role of image registration is to find a plausible mapping between the patient's
tumor-bearing image and a normal brain (atlas), with known segmentation. Solving this coupled inverse problem has a prohibitive computational cost, especially in 3D. To address this challenge we have developed novel schemes, scaled up to 200K cores.
Our main contributions is the design and implementation of fast solvers for these problems. We also study the performance for the tumor parameter estimation and registration solvers and their algorithmic scalability. In particular, we introduce the following novel algorithms: An adjoint formulation for tumor-growth problems with/without mass-effect; The first parallel 3D Newton-Krylov method for large diffeomorphic image registration; A novel parallel semi-Lagrangian algorithm for solving advection equations in image registration and its parallel implementation on shared and distributed memory architectures; and Accelerated FFT (AccFFT), an open-source parallel FFT library for CPU and GPUs scaled up to 131,000 cores with optimized kernels for computing spectral operators.
The scientific outcomes of this thesis, has appeared in the proceedings of three ACM/IEEE SCxy conferences (two best student paper finalist, and one ACM SRC gold medal), two journal papers, two papers in review, four papers in preparation (coupling, mass effect, segmentation, and multi-species tumor model), and seven conference presentations.Computational Science, Engineering, and Mathematic
Estimating the granularity coefficient of a Potts-Markov random field within an MCMC algorithm
This paper addresses the problem of estimating the Potts parameter B jointly
with the unknown parameters of a Bayesian model within a Markov chain Monte
Carlo (MCMC) algorithm. Standard MCMC methods cannot be applied to this problem
because performing inference on B requires computing the intractable
normalizing constant of the Potts model. In the proposed MCMC method the
estimation of B is conducted using a likelihood-free Metropolis-Hastings
algorithm. Experimental results obtained for synthetic data show that
estimating B jointly with the other unknown parameters leads to estimation
results that are as good as those obtained with the actual value of B. On the
other hand, assuming that the value of B is known can degrade estimation
performance significantly if this value is incorrect. To illustrate the
interest of this method, the proposed algorithm is successfully applied to real
bidimensional SAR and tridimensional ultrasound images
DPP-PMRF: Rethinking Optimization for a Probabilistic Graphical Model Using Data-Parallel Primitives
We present a new parallel algorithm for probabilistic graphical model
optimization. The algorithm relies on data-parallel primitives (DPPs), which
provide portable performance over hardware architecture. We evaluate results on
CPUs and GPUs for an image segmentation problem. Compared to a serial baseline,
we observe runtime speedups of up to 13X (CPU) and 44X (GPU). We also compare
our performance to a reference, OpenMP-based algorithm, and find speedups of up
to 7X (CPU).Comment: LDAV 2018, October 201
Stable Camera Motion Estimation Using Convex Programming
We study the inverse problem of estimating n locations (up to
global scale, translation and negation) in from noisy measurements of a
subset of the (unsigned) pairwise lines that connect them, that is, from noisy
measurements of for some pairs (i,j) (where the
signs are unknown). This problem is at the core of the structure from motion
(SfM) problem in computer vision, where the 's represent camera locations
in . The noiseless version of the problem, with exact line measurements,
has been considered previously under the general title of parallel rigidity
theory, mainly in order to characterize the conditions for unique realization
of locations. For noisy pairwise line measurements, current methods tend to
produce spurious solutions that are clustered around a few locations. This
sensitivity of the location estimates is a well-known problem in SfM,
especially for large, irregular collections of images.
In this paper we introduce a semidefinite programming (SDP) formulation,
specially tailored to overcome the clustering phenomenon. We further identify
the implications of parallel rigidity theory for the location estimation
problem to be well-posed, and prove exact (in the noiseless case) and stable
location recovery results. We also formulate an alternating direction method to
solve the resulting semidefinite program, and provide a distributed version of
our formulation for large numbers of locations. Specifically for the camera
location estimation problem, we formulate a pairwise line estimation method
based on robust camera orientation and subspace estimation. Lastly, we
demonstrate the utility of our algorithm through experiments on real images.Comment: 40 pages, 12 figures, 6 tables; notation and some unclear parts
updated, some typos correcte
The LifeV library: engineering mathematics beyond the proof of concept
LifeV is a library for the finite element (FE) solution of partial
differential equations in one, two, and three dimensions. It is written in C++
and designed to run on diverse parallel architectures, including cloud and high
performance computing facilities. In spite of its academic research nature,
meaning a library for the development and testing of new methods, one
distinguishing feature of LifeV is its use on real world problems and it is
intended to provide a tool for many engineering applications. It has been
actually used in computational hemodynamics, including cardiac mechanics and
fluid-structure interaction problems, in porous media, ice sheets dynamics for
both forward and inverse problems. In this paper we give a short overview of
the features of LifeV and its coding paradigms on simple problems. The main
focus is on the parallel environment which is mainly driven by domain
decomposition methods and based on external libraries such as MPI, the Trilinos
project, HDF5 and ParMetis.
Dedicated to the memory of Fausto Saleri.Comment: Review of the LifeV Finite Element librar
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