Joint Spatial-Angular Sparse Coding, Compressed Sensing, and Dictionary Learning for Diffusion MRI

Neuroimaging provides a window into the inner workings of the human brain to diagnose and prevent neurological diseases and understand biological brain function, anatomy, and psychology. Diffusion Magnetic Resonance Imaging (dMRI) is an emerging medical imaging modality used to study the anatomical network of neurons in the brain, which form cohesive bundles, or fiber tracts, that connect various parts of the brain. Since about 73% of the brain is water, measuring the flow, or diffusion of water molecules in the presence of fiber bundles, allows researchers to estimate the orientation of fiber tracts and reconstruct the internal wiring of the brain, in vivo. Diffusion MRI signals can be modeled within two domains: the spatial domain consisting of voxels in a brain volume and the diffusion or angular domain, where fiber orientation is estimated in each voxel. Researchers aim to estimate the probability distribution of fiber orientation in every voxel of a brain volume in order to trace paths of fiber tracts from voxel to voxel over the entire brain. Therefore, the traditional framework for dMRI processing and analysis has been from a voxel-wise vantage point with added spatial regularization considered post-hoc. In contrast, we propose a new joint spatial-angular representation of dMRI data which pairs signals in each voxel with the global spatial environment, jointly. This has the ability to improve many aspects of dMRI processing and analysis and re-envision the core representation of dMRI data from a local perspective to a global one. In this thesis, we propose three main contributions which take advantage of such joint spatial-angular representations to improve major machine learning tasks applied to dMRI: sparse coding, compressed sensing, and dictionary learning. First, we will show that we can achieve sparser representations of dMRI by utilizing a global spatial-angular dictionary instead of a purely voxel-wise angular dictionary. As dMRI data is very large in size, we provide a number of novel extensions to popular spare coding algorithms that perform efficient optimization on a global-scale by exploiting the separability of our dictionaries over the spatial and angular domains. Next, compressed sensing is used to accelerate signal acquisition based on an underlying sparse representation of the data. We will show that our proposed representation has the potential to push the limits of the current state of scanner acceleration within a new compressed sensing model for dMRI. Finally, sparsity can be further increased by learning dictionaries directly from datasets of interest. Prior dictionary learning for dMRI learn angular dictionaries alone. Our third contribution is to learn spatial-angular dictionaries jointly from dMRI data directly to better represent the global structure. Traditionally, the problem of dictionary learning is non-convex with no guarantees of finding a globally optimal solution. We derive the first theoretical results of global optimality for this class of dictionary learning problems. We hope the core foundation of a joint spatial-angular representation will open a new perspective on dMRI with respect to many other processing tasks and analyses. In addition, our contributions are applicable to any general signal types that can benefit from separable dictionaries. We hope the contributions in this thesis may be adopted in the larger signal processing, computer vision, and machine learning communities. dMRI signals can be modeled within two domains: the spatial domain consisting of voxels in a brain volume and the diffusion or angular domain, where fiber orientation is estimated in each voxel. Computationally speaking, researchers aim to estimate the probability distribution of fiber orientation in every voxel of a brain volume in order to trace paths of fiber tracts from voxel to voxel over the entire brain. Therefore, the traditional framework for dMRI processing and analysis is from a voxel-wise, or angular, vantage point with post-hoc consideration of their local spatial neighborhoods. In contrast, we propose a new global spatial-angular representation of dMRI data which pairs signals in each voxel with the global spatial environment, jointly, to improve many aspects of dMRI processing and analysis, including the important need for accelerating the otherwise time-consuming acquisition of advanced dMRI protocols. In this thesis, we propose three main contributions which utilize our joint spatial-angular representation to improve major machine learning tasks applied to dMRI: sparse coding, compressed sensing, and dictionary learning. We will show that sparser codes are possible by utilizing a global dictionary instead of a voxel-wise angular dictionary. This allows for a reduction of the number of measurements needed to reconstruct a dMRI signal to increase acceleration using compressed sensing. Finally, instead of learning angular dictionaries alone, we learn spatial-angular dictionaries jointly from dMRI data directly to better represent the global structure. In addition, this problem is non-convex and so we derive the first theories to guarantee convergence to a global minimum. As dMRI data is very large in size, we provide a number of novel extensions to popular algorithms that perform efficient optimization on a global-scale by exploiting the separability of our global dictionaries over the spatial and angular domains. We hope the core foundation of a joint spatial-angular representation will open a new perspective on dMRI with respect to many other processing tasks and analyses. In addition, our contributions are applicable to any separable dictionary setting which we hope may be adopted in the larger image processing, computer vision, and machine learning communities

Behavior quantification as the missing link between fields: Tools for digital psychiatry and their role in the future of neurobiology

The great behavioral heterogeneity observed between individuals with the same psychiatric disorder and even within one individual over time complicates both clinical practice and biomedical research. However, modern technologies are an exciting opportunity to improve behavioral characterization. Existing psychiatry methods that are qualitative or unscalable, such as patient surveys or clinical interviews, can now be collected at a greater capacity and analyzed to produce new quantitative measures. Furthermore, recent capabilities for continuous collection of passive sensor streams, such as phone GPS or smartwatch accelerometer, open avenues of novel questioning that were previously entirely unrealistic. Their temporally dense nature enables a cohesive study of real-time neural and behavioral signals. To develop comprehensive neurobiological models of psychiatric disease, it will be critical to first develop strong methods for behavioral quantification. There is huge potential in what can theoretically be captured by current technologies, but this in itself presents a large computational challenge -- one that will necessitate new data processing tools, new machine learning techniques, and ultimately a shift in how interdisciplinary work is conducted. In my thesis, I detail research projects that take different perspectives on digital psychiatry, subsequently tying ideas together with a concluding discussion on the future of the field. I also provide software infrastructure where relevant, with extensive documentation. Major contributions include scientific arguments and proof of concept results for daily free-form audio journals as an underappreciated psychiatry research datatype, as well as novel stability theorems and pilot empirical success for a proposed multi-area recurrent neural network architecture.Comment: PhD thesis cop

Reconstruction algorithms for Magnetic Resonance Imaging

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2013.Cataloged from PDF version of thesis.Includes bibliographical references (p. 135-142).This dissertation presents image reconstruction algorithms for Magnetic Resonance Imaging (MRI) that aims to increase the imaging efficiency. Algorithms that reduce imaging time without sacrificing the image quality and mitigate image artifacts are proposed. The goal of increasing the MR efficiency is investigated across multiple imaging techniques: structural imaging with multiple contrasts preparations, Diffusion Spectrum Imaging (DSI), Chemical Shift Imaging (CSI), and Quantitative Susceptibility Mapping (QSM). The main theme connecting the proposed methods is the utilization of prior knowledge on the reconstructed signal. This prior often presents itself in the form of sparsity with respect to either a prespecified or learned signal transformation.by Berkin Bilgic.Ph.D

A Non-Intrusive Multi-Sensor RGB-D System for Preschool Classroom Behavior Analysis

University of Minnesota Ph.D. dissertation. May 2017. Major: Computer Science. Advisor: Nikolaos Papanikolopoulos. 1 computer file (PDF); vii, 121 pages + 2 mp4 video filesMental health disorders are a leading cause of disability in North America and can represent a significant source of financial burden. Early intervention is a key aspect in treating mental disorders as it can dramatically increase the probability of a positive outcome. One key factor to early intervention is the knowledge of risk-markers -- genetic, neural, behavioral and/or social deviations -- that indicate the development of a particular mental disorder. Once these risk-markers are known, it is important to have tools for reliable identification of these risk-markers. For visually observable risk-markers, discovery and screening ideally should occur in a natural environment. However, this often incurs a high cost. Current advances in technology allow for the development of assistive systems that could aid in the detection and screening of visually observable risk-markers in every-day environments, like a preschool classroom. This dissertation covers the development of such a system. The system consists of a series of networked sensors that are able to collect data from a wide baseline. These sensors generate color images and depth maps that can be used to create a 3D point cloud reconstruction of the classroom. The wide baseline nature of the setup helps to minimize the effects of occlusion, since data is captured from multiple distinct perspectives. These point clouds are used to detect occupants in the room and track them throughout their activities. This tracking information is then used to analyze classroom and individual behaviors, enabling the screening for specific risk-markers and also the ability to create a corpus of data that could be used to discover new risk-markers. This system has been installed at the Shirley G. Moore Lab school, a research preschool classroom in the Institute of Child Development at the University of Minnesota. Recordings have been taken and analyzed from actual classes. No instruction or pre-conditioning was given to the instructors or the children in these classes. Portions of this data have also been manually annotated to create groundtruth data that was used to validate the efficacy of the proposed system

Structured representation learning from complex data

This thesis advances several theoretical and practical aspects of the recently introduced restricted Boltzmann machine - a powerful probabilistic and generative framework for modelling data and learning representations. The contributions of this study represent a systematic and common theme in learning structured representations from complex data

Grounding semantic cognition using computational modelling and network analysis

The overarching objective of this thesis is to further the field of grounded semantics using a range of computational and empirical studies. Over the past thirty years, there have been many algorithmic advances in the modelling of semantic cognition. A commonality across these cognitive models is a reliance on hand-engineering “toy-models”. Despite incorporating newer techniques (e.g. Long short-term memory), the model inputs remain unchanged. We argue that the inputs to these traditional semantic models have little resemblance with real human experiences. In this dissertation, we ground our neural network models by training them with real-world visual scenes using naturalistic photographs. Our approach is an alternative to both hand-coded features and embodied raw sensorimotor signals. We conceptually replicate the mutually reinforcing nature of hybrid (feature-based and grounded) representations using silhouettes of concrete concepts as model inputs. We next gradually develop a novel grounded cognitive semantic representation which we call scene2vec, starting with object co-occurrences and then adding emotions and language-based tags. Limitations of our scene-based representation are identified for more abstract concepts (e.g. freedom). We further present a large-scale human semantics study, which reveals small-world semantic network topologies are context-dependent and that scenes are the most dominant cognitive dimension. This finding leads us to conclude that there is no meaning without context. Lastly, scene2vec shows promising human-like context-sensitive stereotypes (e.g. gender role bias), and we explore how such stereotypes are reduced by targeted debiasing. In conclusion, this thesis provides support for a novel computational viewpoint on investigating meaning - scene-based grounded semantics. Future research scaling scene-based semantic models to human-levels through virtual grounding has the potential to unearth new insights into the human mind and concurrently lead to advancements in artificial general intelligence by enabling robots, embodied or otherwise, to acquire and represent meaning directly from the environment

Gaze-Based Human-Robot Interaction by the Brunswick Model

We present a new paradigm for human-robot interaction based on social signal processing, and in particular on the Brunswick model. Originally, the Brunswick model copes with face-to-face dyadic interaction, assuming that the interactants are communicating through a continuous exchange of non verbal social signals, in addition to the spoken messages. Social signals have to be interpreted, thanks to a proper recognition phase that considers visual and audio information. The Brunswick model allows to quantitatively evaluate the quality of the interaction using statistical tools which measure how effective is the recognition phase. In this paper we cast this theory when one of the interactants is a robot; in this case, the recognition phase performed by the robot and the human have to be revised w.r.t. the original model. The model is applied to Berrick, a recent open-source low-cost robotic head platform, where the gazing is the social signal to be considered

A Statistical Approach to the Alignment of fMRI Data

Multi-subject functional Magnetic Resonance Image studies are critical. The anatomical and functional structure varies across subjects, so the image alignment is necessary. We define a probabilistic model to describe functional alignment. Imposing a prior distribution, as the matrix Fisher Von Mises distribution, of the orthogonal transformation parameter, the anatomical information is embedded in the estimation of the parameters, i.e., penalizing the combination of spatially distant voxels. Real applications show an improvement in the classification and interpretability of the results compared to various functional alignment methods