Learning to sample in Cartesian MRI

Magnetic Resonance Imaging (MRI) is a non-invasive, non-ionizing imaging modality with unmatched soft tissue contrast. However, compared to imaging methods like X-ray radiography, MRI suffers from long scanning times, due to its inherently sequential acquisition procedure. Shortening scanning times is crucial in clinical setting, as it increases patient comfort, decreases examination costs and improves throughput.Recent developments thanks to compressed sensing (CS) and lately deep learning allow to reconstruct high quality images from undersampled images, and have the potential to greatly accelerate MRI. Many algorithms have been proposed in the context of reconstruction, but comparatively little work has been done to find acquisition trajectories that optimize the quality of the reconstructed image downstream.Although in recent years, this problem has gained attention, it is still unclear what is the best approach to design acquisition trajectories in Cartesian MRI. In this thesis, we aim at contributing to this problem along two complementary directions. First, we provide novel methodological contributions to this problem. We first propose two algorithms that improve drastically the greedy learning-based compressed sensing (LBCS) approach of Gözcü et al. (2018). These two algorithms, called lazy LBCS and stochastic LBCS scale to large, clinically relevant problems such as multi-coil 3D MR and dynamic MRI that were inaccessible to LBCS. We also show that generative adversarial networks (GANs), used to model the posterior distribution in inverse problems, provide a natural criterion for adaptive sampling by leveraging their variance in the measurement domain to guide the acquisition procedure.Secondly, we aim at deepening the understanding of the kind of structures or assumptions that enable mask design algorithms to perform well in practice. In particular, our experiments show that state-of-the-art approaches based on deep reinforcement learning (RL), which have the ability to adapt trajectories on the fly to patient and perform long-horizon planning, bring at best a marginal improvement over stochastic LBCS, which is neither adaptive nor does long-term planning.Overall, our results suggest that methods like stochastic LBCS offer promising alternatives to deep RL. They shine in particular by their scalability and computational efficiency and could be key in the deployment of optimized acquisition trajectories in Cartesian MRI

Mean-Field methods for Structured Deep-Learning in Computer Vision

Pierre Bruno Baqué

In recent years, Machine Learning based Computer Vision techniques made impressive progress. These algorithms proved particularly efficient for image classification or detection of isolated objects. From a probabilistic perspective, these methods can predict marginals, over single or multiple variables, independently, with high accuracy. However, in many tasks of practical interest, we need to predict jointly several correlated variables. Practical applications include people detection in crowded scenes, image segmentation, surface reconstruction, 3D pose estimation and others. A large part of the research effort in today's computer-vision community aims at finding task-specific solutions to these problems, while leveraging the power of Deep-Learning based classifiers. In this thesis, we present our journey towards a generic and practical solution based on mean-field (MF) inference. Mean-field is a Statistical Physics-inspired method which has long been used in Computer-Vision as a variational approximation to posterior distributions over complex Conditional Random Fields. Standard mean-field optimization is based on coordinate descent and in many situations can be impractical. We therefore propose a novel proximal gradient-based approach to optimizing the variational objective. It is naturally parallelizable and easy to implement. We prove its convergence, and then demonstrate that, in practice, it yields faster convergence and often finds better optima than more traditional mean-field optimization techniques. Then, we show that we can replace the fully factorized distribution of mean-field by a weighted mixture of such distributions, that similarly minimizes the KL-Divergence to the true posterior. Our extension of the clamping method proposed in previous works allows us to both produce a more descriptive approximation of the true posterior and, inspired by the diverse MAP paradigms, fit a mixture of mean-field approximations. We demonstrate that this positively impacts real-world algorithms that initially relied on mean-fields. One of the important properties of the mean-field inference algorithms is that the closed-form updates are fully differentiable operations. This naturally allows to do parameter learning by simply unrolling multiple iterations of the updates, the so-called back-mean-field algorithm. We derive a novel and efficient structured learning method for multi-modal posterior distribution based on the Multi-Modal Mean-Field approximation, which can be seamlessly combined to modern gradient-based learning methods such as CNNs. Finally, we explore in more details the specific problem of structured learning and prediction for multiple-people detection in crowded scenes. We then present a mean-field based structured deep-learning detection algorithm that provides state of the art results on this dataset.

EPFL2018

Deep Generative Models and Applications

Tatjana Chavdarova

Over the past few years, there have been fundamental breakthroughs in core problems in machine learning, largely driven by advances in deep neural networks. The amount of annotated data drastically increased and supervised deep discriminative models exceeded human-level performances in certain object detection tasks. The increasing availability in quantity and complexity of unlabelled data also opens up exciting possibilities for the development of unsupervised learning methods. Among the family of unsupervised methods, deep generative models find numerous applications. Moreover, as real-world applications include high dimensional data, the ability of generative models to automatically learn semantically meaningful subspaces makes their advancement an essential step toward developing more efficient algorithms. Generative Adversarial Networks (GANs) are a family of unsupervised generative algorithms that have demonstrated impressive performance for data synthesis and are now used in a wide range of computer vision tasks. Despite this success, they gained a reputation for being difficult to train, which results in a time-consuming and human-involved development process to use them. In the first part of this thesis, we focus on improving the stability and the performances of GANs. Foremost, we consider an alternative training process to the standard one, named SGAN, in which several adversarial âlocalâ pairs of networks are trained independently so that a âglobalâ supervising pair of networks can be trained against them. Experimental results on both toy and real-world problems demonstrate that this approach outperforms standard training in terms of better mitigating mode collapse, stability while converging and that it surprisingly, increases the convergence speed as well. To further reduce the computational footprint while maintaining the stability and performance advantages of SGAN, we focus on training a single pair of adversarial networks using variance reduced gradient. More precisely, we study the effect of the stochastic gradient noise on the training of generative adversarial networks (GANs) and show that it can prevent the convergence of standard game optimization methods, while the batch version converges. We address this issue with two stochastic variance-reduced gradient and extragradient optimization algorithms for GANs, named SVRG-GAN and SVRE, respectively. We observe empirically that SVRE performs similarly to a batch method on the MNIST dataset, while being computationally cheaper, and that SVRE yields more stable GAN training on standard datasets. In the second part of the thesis we present our work on people detection. People detection methods are highly sensitive to occlusions between pedestrians, and using joint visual information from multiple synchronized cameras gives the opportunity to improve detection performance. We address the problem of multi-view people occupancy map estimation using an endâtoâend deep learning algorithm called DeepMCD that jointly utilizes the correlated streams of visual information. DeepMCD empirically outperformed the classical approaches by a large margin. Finally, we present a new large-scale and high-resolution dataset, named WILDTRACK. We provide an accurate joint calibration, as well as a series of benchmark results using baseline algorithms published over the recent months for multi-view detection with deep neural networks, and trajectory estimation using a non-Markovian model.

EPFL2020

From Classical to Unsupervised-Deep-Learning Methods for Solving Inverse Problems in Imaging.

Harshit Gupta

In this thesis, we propose new algorithms to solve inverse problems in the context of biomedical images. Due to ill-posedness, solving these problems require some prior knowledge of the statistics of the underlying images. The traditional algorithms, in the field, assume prior knowledge related to smoothness or sparsity of these images. Recently, they have been outperformed by the second generation algorithms which harness the power of neural networks to learn required statistics from training data. Even more recently, last generation deep-learning-based methods have emerged which require neither training nor training data. This thesis devises algorithms which progress through these generations. It extends these generations to novel formulations and applications while bringing more robustness. In parallel, it also progresses in terms of complexity, from proposing algorithms for problems with 1D data and an exact known forward model to the ones with 4D data and an unknown parametric forward model. We introduce five main contributions. The last three of them propose deep-learning-based latest-generation algorithms that require no prior training. 1) We develop algorithms to solve the continuous-domain formulation of inverse problems with both classical Tikhonov and total-variation regularizations. We formalize the problems, characterize the solution set, and devise numerical approaches to find the solutions. 2) We propose an algorithm that improves upon end-to-end neural-network-based second generation algorithms. In our method, a neural network is first trained as a projector on a training set, and is then plugged in as a projector inside the projected gradient descent (PGD). Since the problem is nonconvex, we relax the PGD to ensure convergence to a local minimum under some constraints. This method outperforms all the previous generation algorithms for Computed Tomography (CT). 3) We develop a novel time-dependent deep-image-prior algorithm for modalities that involve a temporal sequence of images. We parameterize them as the output of an untrained neural network fed with a sequence of latent variables. To impose temporal directionality, the latent variables are assumed to lie on a 1D manifold. The network is then tuned to minimize the data fidelity. We obtain state-of-the-art results in dynamic magnetic resonance imaging (MRI) and even recover intra-frame images. 4) We propose a novel reconstruction paradigm for cryo-electron-microscopy (CryoEM) called CryoGAN. Motivated by generative adversarial networks (GANs), we reconstruct a biomolecule's 3D structure such that its CryoEM measurements resemble the acquired data in a distributional sense. The algorithm is pose-or-likelihood-estimation-free, needs no ab initio, and is proven to have a theoretical guarantee of recovery of the true structure. 5) We extend CryoGAN to reconstruct continuously varying conformations of a structure from heterogeneous data. We parameterize the conformations as the output of a neural network fed with latent variables on a low-dimensional manifold. The method is shown to recover continuous protein conformations and their energy landscape.

EPFL2020

Deep Generative Models and Applications

Tatjana Chavdarova

EPFL2020

Mean-Field methods for Structured Deep-Learning in Computer Vision

Pierre Bruno Baqué

EPFL2018

From Classical to Unsupervised-Deep-Learning Methods for Solving Inverse Problems in Imaging.

Harshit Gupta

EPFL2020