Active MR k-space Sampling with Reinforcement Learning

Deep learning approaches have recently shown great promise in accelerating magnetic resonance image (MRI) acquisition. The majority of existing work have focused on designing better reconstruction models given a pre-determined acquisition trajectory, ignoring the question of trajectory optimization. In this paper, we focus on learning acquisition trajectories given a fixed image reconstruction model. We formulate the problem as a sequential decision process and propose the use of reinforcement learning to solve it. Experiments on a large scale public MRI dataset of knees show that our proposed models significantly outperform the state-of-the-art in active MRI acquisition, over a large range of acceleration factors.Comment: Presented at the 23rd International Conference on Medical Image Computing and Computer Assisted Intervention, MICCAI 202

Optic Nerve Deformation by Eye Movements

Ocular rotation can cause mechanical deformation of the optic nerve head and surrounding tissues. During extreme angles of gaze, the optic nerve can become stretched and impose strain on other ocular tissues. Over a lifetime, the ill effects of repetitive mechanical injury from large adduction can compound, resulting in progressive optic neuropathy in some glaucoma patients.We investigated the etiology of this form of glaucoma through a series of papers focusing on anatomical analysis of the human optic nerve from donated tissue and clinical studies utilizing optical coherence tomography (OCT) and confocal scanning laser ophthalmoscopy (cSLO). The optic nerve is surrounded and protected by a bi-layered dural sheath that bears the bulk of exerted mechanical force. Elastin fibers embedded within the sheath and peripapillary tissues around the nerve head form a three-dimensional meshwork that reinforces the tissue against mechanical strain. While the tissue at the globe optic nerve junction is heavily fortified with organized layers of collagen and elastin fibers, irregularities in the elastin fiber arrangement resulting in large dense elastin deposits were observed to correlate with older age. These elastin deposits could be a pathologic byproduct of optic nerve injury from mechanical strain, or serve as a protective mechanism to further reinforce the ocular tissues.In OCT studies, adduction of angles beyond 26� caused marked deformation of the peripapillary tissues around the optic nerve head, and choroidal volume change. cSLO imaging showed similar deformations of the retina surface during large angle adduction. Ocular tissue of younger subjects appears more compliant, while those of glaucoma patients were stiffer and thus experienced less deformation.We explored possible therapies for optic nerve traction during eye movement. Using collagen crosslinking to fortify ocular tissue, we observed that exposure to riboflavin and UV light can stiffen scleral tissue. In addition, we investigated whether prostaglandin agonists could be used to reduce ocular fat and found that topical administration of these agonists had insignificant effects on the retrobulbar fat

New perspectives and applications for greedy algorithms in machine learning

Approximating probability densities is a core problem in Bayesian statistics, where the inference involves the computation of a posterior distribution. Variational Inference (VI) is a technique to approximate posterior distributions through optimization. It involves specifying a set of tractable densities, out of which the final approximation is to be chosen. While VI is traditionally motivated with the goal of tractability, the focus in this dissertation is to use Bayesian approximation to obtain parsimonious distributions. With this goal in mind, we develop greedy algorithm variants and study their theoretical properties by establishing novel connections of the resulting optimization problems in parsimonious VI with traditional studies in the discrete optimization literature. Specific realizations lead to efficient solutions for many sparse probabilistic models like Sparse regression, Sparse PCA, Sparse Collective Matrix Factorization (CMF) etc. For cases where existing results are insufficient to provide acceptable approximation guarantees, we extend the optimization results for some large scale algorithms to a much larger class of functions.The developed methods are applied to both simulated and real world datasets, including high dimensional functional Magnetic Resonance Imaging (fMRI) datasets, and to the real world tasks of interpreting data exploration and model predictions.Electrical and Computer Engineerin

Adaptive Sensing Techniques for Dynamic Target Tracking and Detection with Applications to Synthetic Aperture Radars.

This thesis studies adaptive allocation of a limited set of sensing or computational resources in order to maximize some criteria, such as detection probability, estimation accuracy, or throughput, with specific application to inference with synthetic aperture radars (SAR). Sparse scenarios are considered where the interesting element is embedded in a much larger signal space. Policies are examined that adaptively distribute the constrained resources by using observed measurements to inform the allocation at subsequent stages. This thesis studies adaptive allocation policies in three main directions. First, a framework for adaptive search for sparse targets is proposed to simultaneously detect and track moving targets. Previous work is extended to include a dynamic target model that incorporates target transitions, birth/death probabilities, and varying target amplitudes. Policies are proposed that are shown empirically to have excellent asymptotic performance in estimation error, detection probability, and robustness to model mismatch. Moreover, policies are provided with low computational complexity as compared to state-of-the-art dynamic programming solutions. Second, adaptive sensor management is studied for stable tracking of targets under different modalities. A sensor scheduling policy is proposed that guarantees that the target spatial uncertainty remains bounded. When stability conditions are met, fundamental performance limits are derived such as the maximum number of targets that can be tracked stably and the maximum spatial uncertainty of those targets. The theory is extended to the case where the system may be engaged in tasks other than tracking, such as wide area search or target classification. Lastly, these developed tools are applied to tracking targets using SAR imagery. A hierarchical Bayesian model is proposed for efficient estimation of the posterior distribution for the target and clutter states given observed SAR imagery. This model provides a unifying framework that models the physical, kinematic, and statistical properties of SAR imagery. It is shown that this method generally outperforms common algorithms for change detection. Moreover, the proposed method has the additional benefits of (a) easily incorporating additional information such as target motion models and/or correlated measurements, (b) having few tuning parameters, and (c) providing a characterization of the uncertainty in the state estimation process.PHDElectrical Engineering-SystemsUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/97931/1/newstage_1.pd

Bayesian M/EEG source localization with possible joint skull conductivity estimation

M/EEG mechanisms allow determining changes in the brain activity, which is useful in diagnosing brain disorders such as epilepsy. They consist of measuring the electric potential at the scalp and the magnetic field around the head. The measurements are related to the underlying brain activity by a linear model that depends on the lead-field matrix. Localizing the sources, or dipoles, of M/EEG measurements consists of inverting this linear model. However, the non-uniqueness of the solution (due to the fundamental law of physics) and the low number of dipoles make the inverse problem ill-posed. Solving such problem requires some sort of regularization to reduce the search space. The literature abounds of methods and techniques to solve this problem, especially with variational approaches. This thesis develops Bayesian methods to solve ill-posed inverse problems, with application to M/EEG. The main idea underlying this work is to constrain sources to be sparse. This hypothesis is valid in many applications such as certain types of epilepsy. We develop different hierarchical models to account for the sparsity of the sources. Theoretically, enforcing sparsity is equivalent to minimizing a cost function penalized by an l0 pseudo norm of the solution. However, since the l0 regularization leads to NP-hard problems, the l1 approximation is usually preferred. Our first contribution consists of combining the two norms in a Bayesian framework, using a Bernoulli-Laplace prior. A Markov chain Monte Carlo (MCMC) algorithm is used to estimate the parameters of the model jointly with the source location and intensity. Comparing the results, in several scenarios, with those obtained with sLoreta and the weighted l1 norm regularization shows interesting performance, at the price of a higher computational complexity. Our Bernoulli-Laplace model solves the source localization problem at one instant of time. However, it is biophysically well-known that the brain activity follows spatiotemporal patterns. Exploiting the temporal dimension is therefore interesting to further constrain the problem. Our second contribution consists of formulating a structured sparsity model to exploit this biophysical phenomenon. Precisely, a multivariate Bernoulli-Laplacian distribution is proposed as an a priori distribution for the dipole locations. A latent variable is introduced to handle the resulting complex posterior and an original Metropolis-Hastings sampling algorithm is developed. The results show that the proposed sampling technique improves significantly the convergence. A comparative analysis of the results is performed between the proposed model, an l21 mixed norm regularization and the Multiple Sparse Priors (MSP) algorithm. Various experiments are conducted with synthetic and real data. Results show that our model has several advantages including a better recovery of the dipole locations. The previous two algorithms consider a fully known leadfield matrix. However, this is seldom the case in practical applications. Instead, this matrix is the result of approximation methods that lead to significant uncertainties. Our third contribution consists of handling the uncertainty of the lead-field matrix. The proposed method consists in expressing this matrix as a function of the skull conductivity using a polynomial matrix interpolation technique. The conductivity is considered as the main source of uncertainty of the lead-field matrix. Our multivariate Bernoulli-Laplacian model is then extended to estimate the skull conductivity jointly with the brain activity. The resulting model is compared to other methods including the techniques of Vallaghé et al and Guttierez et al. Our method provides results of better quality without requiring knowledge of the active dipole positions and is not limited to a single dipole activation

Active Wavelength Selection for Chemical Identification Using Tunable Spectroscopy

Spectrometers are the cornerstone of analytical chemistry. Recent advances in microoptics manufacturing provide lightweight and portable alternatives to traditional spectrometers. In this dissertation, we developed a spectrometer based on Fabry-Perot interferometers (FPIs). A FPI is a tunable (it can only scan one wavelength at a time) optical filter. However, compared to its traditional counterparts such as FTIR (Fourier transform infrared spectroscopy), FPIs provide lower resolution and lower signal-noiseratio (SNR). Wavelength selection can help alleviate these drawbacks. Eliminating uninformative wavelengths not only speeds up the sensing process but also helps improve accuracy by avoiding nonlinearity and noise. Traditional wavelength selection algorithms follow a training-validation process, and thus they are only optimal for the target analyte. However, for chemical identification, the identities are unknown. To address the above issue, this dissertation proposes active sensing algorithms that select wavelengths online while sensing. These algorithms are able to generate analytedependent wavelengths. We envision this algorithm deployed on a portable chemical gas platform that has low-cost sensors and limited computation resources. We develop three algorithms focusing on three different aspects of the chemical identification problems. First, we consider the problem of single chemical identification. We formulate the problem as a typical classification problem where each chemical is considered as a distinct class. We use Bayesian risk as the utility function for wavelength selection, which calculates the misclassification cost between classes (chemicals), and we select the wavelength with the maximum reduction in the risk. We evaluate this approach on both synthesized and experimental data. The results suggest that active sensing outperforms the passive method, especially in a noisy environment. Second, we consider the problem of chemical mixture identification. Since the number of potential chemical mixtures grows exponentially as the number of components increases, it is intractable to formulate all potential mixtures as classes. To circumvent combinatorial explosion, we developed a multi-modal non-negative least squares (MMNNLS) method that searches multiple near-optimal solutions as an approximation of all the solutions. We project the solutions onto spectral space, calculate the variance of the projected spectra at each wavelength, and select the next wavelength using the variance as the guidance. We validate this approach on synthesized and experimental data. The results suggest that active approaches are superior to their passive counterparts especially when the condition number of the mixture grows larger (the analytes consist of more components, or the constituent spectra are very similar to each other). Third, we consider improving the computational speed for chemical mixture identification. MM-NNLS scales poorly as the chemical mixture becomes more complex. Therefore, we develop a wavelength selection method based on Gaussian process regression (GPR). GPR aims to reconstruct the spectrum rather than solving the mixture problem, thus, its computational cost is a function of the number of wavelengths. We evaluate the approach on both synthesized and experimental data. The results again demonstrate more accurate and robust performance in contrast to passive algorithms

Retinotopic connectivity maps of human visual cortex with unconstrained eye movements

Human visual cortex contains topographic visual field maps whose organization can be revealed with retinotopic mapping. Unfortunately, constraints posed by standard mapping hinder its use in patients, atypical subject groups, and individuals at either end of the lifespan. This severely limits the conclusions we can draw about visual processing in such individuals. Here, we present a novel data-driven method to estimate connective fields, resulting in fine-grained maps of the functional connectivity between brain areas. We find that inhibitory connectivity fields accompany, and often surround facilitatory fields. The visual field extent of these inhibitory subfields falls off with cortical magnification. We further show that our method is robust to large eye movements and myopic defocus. Importantly, freed from the controlled stimulus conditions in standard mapping experiments, using entertaining stimuli and unconstrained eye movements our approach can generate retinotopic maps, including the periphery visual field hitherto only possible to map with special stimulus displays. Generally, our results show that the connective field method can gain knowledge about retinotopic architecture of visual cortex in patients and participants where this is at best difficult and confounded, if not impossible, with current methods

Learning to Reduce Annotation Load

Modern machine learning methods and their applications in computer vision are known to crave for large amounts of training data to reach their full potential. Because training data is mostly obtained through humans who manually label samples, it induces a significant cost. Therefore, the problem of reducing the annotation load is of great importance for the success of machine learning methods. We study the problem of reducing the annotation load from two viewpoints, by answering the questions âWhat to annotate?â and âHow to annotate?â. The question âWhat?â addresses the selection of a small portion of the data that would be sufficient to train an accurate model. The question âHow? focuses on minimising the effort of labelling each datapoint. The question âWhat to annotate?â becomes particularly compelling if we can select data to be annotated in an iterative and adaptive way, a setting known as active learning (AL). The key challenge in AL is to identify the datapoints that are the most informative for the model at a given stage. We propose several techniques to address this challenge. Firstly, we consider the problem of segmenting natural images and image volumes. We take advantage of image priors, such as smoothness of objects of interest, and use them in a novel form of geometric uncertainty. Using this, we design an AL technique to efficiently annotate data that is tailored to segmentation applications. Next, we notice that no single manually-designed strategy outperforms others in every application and that often the burden of designing new strategies outweighs the benefits of AL. To overcome this problem we suggest learning an AL strategy from data by formulating the AL problem as a regression task that predicts the reduction in the generalisation error achieved by labelling each datapoint. This enables us to learn AL strategies from simulated data and to transfer them to new datasets. Finally, we turn towards non-myopic data-driven AL strategies. To this end, we formulate the AL problem as a Markov decision process and find the best selection policy using reinforcement learning. We design the decision process such that the policy can be learnt for any ML model and transferred to diverse application domains. Effectively addressing the question âHow to annotate?â is of no less importance as large cost savings can be achieved by labelling each datapoint more efficiently. This can be done with intelligent interfaces that interact with a human annotator. We make two contributions towards answering the question âHow?â. Firstly, we propose an efficient technique to annotate 3D image volumes for image segmentation. Annotating data in 3D is cumbersome and an obvious way to facilitate it is to select a subset of the data lying on a 2D plane. To find the optimal plane (i.e. the one containing the most informative datapoints) we design a branch-and-bound algorithm that quickly eliminates hypotheses about the optimal projection. Secondly, we propose an intelligent data annotation method to train object detectors. Instead of always asking the human annotator to draw bounding boxes in images, we detect automatically in which cases we can rely on the current detector and verify its proposal