Compressive MRI with deep convolutional and attentive models

Since its advent in the last century, Magnetic Resonance Imaging (MRI) has demonstrated a significant impact on modern medicine and spectroscopy and witnessed widespread use in medical imaging and clinical practice, owing to the flexibility and excellent ability in viewing anatomical structures. Although it provides a non-invasive and ionizing radiation-free tool to create images of the anatomy of the human body being inspected, the long data acquisition process hinders its growth and development in time-critical applications. To shorten the scanning time and reduce the discomfort of patients, the sampling process can be accelerated by leaving out an amount of sampling steps and performing image reconstruction from a subset of measurements. However, the images created with under-sampled signals can suffer from strong aliasing artifacts which unfavorably affect the quality of diagnosis and treatment. Compressed sensing (CS) methods were introduced to alleviate the aliasing artifacts by reconstructing an image from the observed measurements via model-based optimization algorithms. Despite achieved success, the sparsity prior assumed by CS methods can be difficult to hold in real-world practice and challenging to capture complex anatomical structures. The iterative optimization algorithms are often computationally expensive and time-consuming, against the speed demand of modern MRI. Those factors limit the quality of reconstructed images and put restrictions on the achievable acceleration rates. This thesis mainly focuses on developing deep learning-based methods, specifically using modern over-parametrized models, for MRI reconstruction, by leveraging the powerful learning ability and representation capacity of such models. Firstly, we introduce an attentive selection generative adversarial network to achieve fine-grained reconstruction by performing large-field contextual information integration and attention selection mechanism. To incorporate domain-specific knowledge into the reconstruction procedure, an optimization-inspired deep cascaded framework is proposed with a novel deep data consistency block to leverage domain-specific knowledge and an adaptive spatial attention selection module to capture the correlations among high-resolution features, aiming to enhance the quality of recovered images. To efficiently utilize the contextual information hidden in the spatial dimensions, a novel region-guided channel-wise attention network is introduced to incorporate the spatial semantics into a channel-based attention mechanism, demonstrating a light-weight and flexible design to attain improved reconstruction performance. Secondly, a coil-agnostic reconstruction framework is introduced to solve the unknown forward process problem in parallel MRI reconstruction. To avoid the estimation of sensitivity maps, a novel data aggregation consistency block is proposed to approximately perform the data consistency enforcement without resorting to coil sensitivity information. A locality-aware spatial attention module is devised and embedded into the reconstruction pipeline to enhance the model performance by capturing spatial contextual information via data-adaptive kernel prediction. It is demonstrated by experiments that the proposed coil-agnostic method is robust and resilient to different machine configurations and outperforms other sensitivity estimation-based methods. Finally, the research work focusing on dynamic MRI reconstruction is presented. We introduce an optimization-inspired deep cascaded framework to recover a sequence of MRI images, which utilizes a novel mask-guided motion feature incorporation method to explicitly extract and incorporate the motion information into the reconstruction iterations, showing to better preserve the dynamic content. A spatio-temporal Fourier neural block is proposed and embedded into the network to improve the model performance by efficiently retrieving useful information in both spatial and temporal domains. It is demonstrated that the devised framework surpasses other competing methods and can generalize well on other reconstruction models and unseen data, validating its transferability and generalization capacity

Uncertainty quantification in medical image synthesis

Machine learning approaches to medical image synthesis have shown outstanding performance, but often do not convey uncertainty information. In this chapter, we survey uncertainty quantification methods in medical image synthesis and advocate the use of uncertainty for improving clinicians’ trust in machine learning solutions. First, we describe basic concepts in uncertainty quantification and discuss its potential benefits in downstream applications. We then review computational strategies that facilitate inference, and identify the main technical and clinical challenges. We provide a first comprehensive review to inform how to quantify, communicate and use uncertainty in medical synthesis applications

Integrating Physics Modelling with Machine Learning for Remote Sensing

L’observació de la Terra a partir de les dades proporcionades per sensors abord de satèl·lits, així com les proporcionades per models de transferència radiativa o climàtics, juntament amb les mesures in situ proporcionen una manera sense precedents de monitorar el nostre planeta amb millors resolucions espacials i temporals. La riquesa, quantitat i diversitat de les dades adquirides i posades a disposició també augmenta molt ràpidament. Aquestes dades ens permeten predir el rendiment dels cultius, fer un seguiment del canvi d’ús del sòl com ara la desforestació, supervisar i respondre als desastres naturals, i predir i mitigar el canvi climàtic. Per tal de fer front a tots aquests reptes, les dues darreres dècades han evidenciat un gran augment en l'aplicació d'algorismes d'aprenentatge automàtic en l'observació de la Terra. Amb l'anomenat `machine learning' es pot fer un ús eficient del flux de dades creixent en quantitat i diversitat. Els algorismes d'aprenentatge màquina, però, solen ser models agnòstics i massa flexibles i, per tant, acaben per no respectar les lleis fonamentals de la física. D’altra banda, en els darrers anys s’ha produït un augment de la investigació que intenta integrar el coneixement de física en algorismes d’aprenentatge, amb la finalitat d’obtenir solucions interpretables i que tinguin sentit físic. L’objectiu principal d’aquesta tesi és dissenyar diferents maneres de codificar el coneixement físic per proporcionar mètodes d’aprenentatge automàtic adaptats a problemes específics en teledetecció. Introduïm nous mètodes que poden fusionar de manera òptima fonts de dades heterogènies, explotar les regularitats de dades, incorporar equacions diferencials, obtenir models precisos que emulen, i per tant són coherents amb models físics, i models que aprenen parametrizacions del sistema combinant models i simulacions.Earth observation through satellite sensors, models and in situ measurements provides a way to monitor our planet with unprecedented spatial and temporal resolution. The amount and diversity of the data which is recorded and made available is ever-increasing. This data allows us to perform crop yield prediction, track land-use change such as deforestation, monitor and respond to natural disasters and predict and mitigate climate change. The last two decades have seen a large increase in the application of machine learning algorithms in Earth observation in order to make efficient use of the growing data-stream. Machine learning algorithms, however, are typically model agnostic and too flexible and so end up not respecting fundamental laws of physics. On the other hand there has, in recent years, been an increase in research attempting to embed physics knowledge in machine learning algorithms in order to obtain interpretable and physically meaningful solutions. The main objective of this thesis is to explore different ways of encoding physical knowledge to provide machine learning methods tailored for specific problems in remote sensing. Ways of expressing expert knowledge about the relevant physical systems in remote sensing abound, ranging from simple relations between reflectance indices and biophysical parameters to complex models that compute the radiative transfer of electromagnetic radiation through our atmosphere, and differential equations that explain the dynamics of key parameters. This thesis focuses on inversion problems, emulation of radiative transfer models, and incorporation of the abovementioned domain knowledge in machine learning algorithms for remote sensing applications. We explore new methods that can optimally model simulated and in-situ data jointly, incorporate differential equations in machine learning algorithms, handle more complex inversion problems and large-scale data, obtain accurate and computationally efficient emulators that are consistent with physical models, and that efficiently perform approximate Bayesian inversion over radiative transfer models

Artificial Intelligence for Science in Quantum, Atomistic, and Continuum Systems

Advances in artificial intelligence (AI) are fueling a new paradigm of discoveries in natural sciences. Today, AI has started to advance natural sciences by improving, accelerating, and enabling our understanding of natural phenomena at a wide range of spatial and temporal scales, giving rise to a new area of research known as AI for science (AI4Science). Being an emerging research paradigm, AI4Science is unique in that it is an enormous and highly interdisciplinary area. Thus, a unified and technical treatment of this field is needed yet challenging. This work aims to provide a technically thorough account of a subarea of AI4Science; namely, AI for quantum, atomistic, and continuum systems. These areas aim at understanding the physical world from the subatomic (wavefunctions and electron density), atomic (molecules, proteins, materials, and interactions), to macro (fluids, climate, and subsurface) scales and form an important subarea of AI4Science. A unique advantage of focusing on these areas is that they largely share a common set of challenges, thereby allowing a unified and foundational treatment. A key common challenge is how to capture physics first principles, especially symmetries, in natural systems by deep learning methods. We provide an in-depth yet intuitive account of techniques to achieve equivariance to symmetry transformations. We also discuss other common technical challenges, including explainability, out-of-distribution generalization, knowledge transfer with foundation and large language models, and uncertainty quantification. To facilitate learning and education, we provide categorized lists of resources that we found to be useful. We strive to be thorough and unified and hope this initial effort may trigger more community interests and efforts to further advance AI4Science

Generative Prior for Unsupervised Image Restoration

The challenge of restoring real world low-quality images is due to a lack of appropriate training data and difficulty in determining how the image was degraded. Recently, generative models have demonstrated great potential for creating high- quality images by utilizing the rich and diverse information contained within the model’s trained weights and learned latent representations. One popular type of generative model is the generative adversarial network (GAN). Many new methods have been developed to harness the information found in GANs for image manipulation. Our proposed approach is to utilize generative models for both understanding the degradation of an image and restoring it. We propose using a combination of cycle consistency losses and self-attention to enhance face images by first learning the degradation and then using this information to train a style-based neural network. We also aim to use the latent representation to achieve a high level of magnification for face images (x64). By incorporating the weights of a pre-trained StyleGAN into a restoration network with a vision transformer layer, we hope to improve the current state-of-the-art in face image restoration. Finally, we present a projection-based image-denoising algorithm named Noise2Code in the latent space of the VQGAN model with a fixed-point regularization strategy. The fixed-point condition follows the observation that the pre-trained VQGAN affects the clean and noisy images in a drastically different way. Unlike previous projection-based image restoration in the latent space, both the denoising network and VQGAN model parameters are jointly trained, although the latter is not needed during the testing. We report experimental results to demonstrate that the proposed Noise2Code approach is conceptually simple, computationally efficient, and generalizable to real-world degradation scenarios

Sparsity in deep learning: Pruning and growth for efficient inference and training in neural networks

The growing energy and performance costs of deep learning have driven the community to reduce the size of neural networks by selectively pruning components. Similarly to their biological counterparts, sparse networks generalize just as well, sometimes even better than, the original dense networks. Sparsity promises to reduce the memory footprint of regular networks to fit mobile devices, as well as shorten training time for ever growing networks. In this paper, we survey prior work on sparsity in deep learning and provide an extensive tutorial of sparsification for both inference and training. We describe approaches to remove and add elements of neural networks, different training strategies to achieve model sparsity, and mechanisms to exploit sparsity in practice. Our work distills ideas from more than 300 research papers and provides guidance to practitioners who wish to utilize sparsity today, as well as to researchers whose goal is to push the frontier forward. We include the necessary background on mathematical methods in sparsification, describe phenomena such as early structure adaptation, the intricate relations between sparsity and the training process, and show techniques for achieving acceleration on real hardware. We also define a metric of pruned parameter efficiency that could serve as a baseline for comparison of different sparse networks. We close by speculating on how sparsity can improve future workloads and outline major open problems in the field