Statistical Machine Learning for Breast Cancer Detection with Terahertz Imaging

Breast conserving surgery (BCS) is a common breast cancer treatment option, in which the cancerous tissue is excised while leaving most of the healthy breast tissue intact. The lack of in-situ margin evaluation unfortunately results in a re-excision rate of 20-30% for this type of procedure. This study aims to design statistical and machine learning segmentation algorithms for the detection of breast cancer in BCS by using terahertz (THz) imaging. Given the material characterization properties of the non-ionizing radiation in the THz range, we intend to employ the responses from the THz system to identify healthy and cancerous breast tissue in BCS samples. In particular, this dissertation covers the description of four segmentation algorithms for the detection of breast cancer in THz imaging. We first explore the performance of one-dimensional (1D) Gaussian mixture and t-mixture models with Markov chain Monte Carlo (MCMC). Second, we propose a novel low-dimension ordered orthogonal projection (LOOP) algorithm for the dimension reduction of the THz information through a modified Gram-Schmidt process. Once the key features within the THz waveform have been detected by LOOP, the segmentation algorithm employs a multivariate Gaussian mixture model with MCMC and expectation maximization (EM). Third, we explore the spatial information of each pixel within the THz image through a Markov random field (MRF) approach. Finally, we introduce a supervised multinomial probit regression algorithm with polynomial and kernel data representations. For evaluation purposes, this study makes use of fresh and formalin-fixed paraffin-embedded (FFPE) heterogeneous human and mice tissue models for the quantitative assessment of the segmentation performance in terms of receiver operating characteristics (ROC) curves. Overall, the experimental results demonstrate that the proposed approaches represent a promising technique for tissue segmentation within THz images of freshly excised breast cancer samples

A review of algorithms for medical image segmentation and their applications to the female pelvic cavity

This paper aims to make a review on the current segmentation algorithms used for medical images. Algorithms are classified according to their principal methodologies, namely the ones based on thresholds, the ones based on clustering techniques and the ones based on deformable models. The last type is focused on due to the intensive investigations into the deformable models that have been done in the last few decades. Typical algorithms of each type are discussed and the main ideas, application fields, advantages and disadvantages of each type are summarised. Experiments that apply these algorithms to segment the organs and tissues of the female pelvic cavity are presented to further illustrate their distinct characteristics. In the end, the main guidelines that should be considered for designing the segmentation algorithms of the pelvic cavity are proposed

Machine learning methods for histopathological image analysis

Abundant accumulation of digital histopathological images has led to the increased demand for their analysis, such as computer-aided diagnosis using machine learning techniques. However, digital pathological images and related tasks have some issues to be considered. In this mini-review, we introduce the application of digital pathological image analysis using machine learning algorithms, address some problems specific to such analysis, and propose possible solutions.Comment: 23 pages, 4 figure

Doctor of Philosophy

dissertationScene labeling is the problem of assigning an object label to each pixel of a given image. It is the primary step towards image understanding and unifies object recognition and image segmentation in a single framework. A perfect scene labeling framework detects and densely labels every region and every object that exists in an image. This task is of substantial importance in a wide range of applications in computer vision. Contextual information plays an important role in scene labeling frameworks. A contextual model utilizes the relationships among the objects in a scene to facilitate object detection and image segmentation. Using contextual information in an effective way is one of the main questions that should be answered in any scene labeling framework. In this dissertation, we develop two scene labeling frameworks that rely heavily on contextual information to improve the performance over state-of-the-art methods. The first model, called the multiclass multiscale contextual model (MCMS), uses contextual information from multiple objects and at different scales for learning discriminative models in a supervised setting. The MCMS model incorporates crossobject and interobject information into one probabilistic framework, and thus is able to capture geometrical relationships and dependencies among multiple objects in addition to local information from each single object present in an image. The second model, called the contextual hierarchical model (CHM), learns contextual information in a hierarchy for scene labeling. At each level of the hierarchy, a classifier is trained based on downsampled input images and outputs of previous levels. The CHM then incorporates the resulting multiresolution contextual information into a classifier to segment the input image at original resolution. This training strategy allows for optimization of a joint posterior probability at multiple resolutions through the hierarchy. We demonstrate the performance of CHM on different challenging tasks such as outdoor scene labeling and edge detection in natural images and membrane detection in electron microscopy images. We also introduce two novel classification methods. WNS-AdaBoost speeds up the training of AdaBoost by providing a compact representation of a training set. Disjunctive normal random forest (DNRF) is an ensemble method that is able to learn complex decision boundaries and achieves low generalization error by optimizing a single objective function for each weak classifier in the ensemble. Finally, a segmentation framework is introduced that exploits both shape information and regional statistics to segment irregularly shaped intracellular structures such as mitochondria in electron microscopy images

Learning Discriminative Features and Structured Models for Segmentation in Microscopy and Natural Images

Segmenting images is a significant challenge that has drawn a lot of attention from different fields of artificial intelligence and has many practical applications. One such challenge addressed in this thesis is the segmentation of electron microscope (EM) imaging of neural tissue. EM microscopy is one of the key tools used to analyze neural tissue and understand the brain, but the huge amounts of data it produces make automated analysis necessary. In addition to the challenges specific to EM data, the common problems encountered in image segmentation must also be addressed. These problems include extracting discriminative features from the data and constructing a statistical model using ground-truth data. Although complex models appear to be more attractive because they allow for more expressiveness, they also lead to a higher computational complexity. On the other hand, simple models come with a lower complexity but less faithfully express the real world. Therefore, one of the most challenging tasks in image segmentation is in constructing models that are expressive enough while remaining tractable. In this work, we propose several automated graph partitioning approaches that address these issues. These methods reduce the computational complexity by operating on supervoxels instead of voxels, incorporating features capable of describing the 3D shape of the target objects and using structured models to account for correlation in output variables. One of the non-trivial issues with such models is that their parameters must be carefully chosen for optimal performance. A popular approach to learning model parameters is a maximum-margin approach called Structured SVM (SSVM) that provides optimality guarantees but also suffers from two main drawbacks. First, SSVM-based approaches are usually limited to linear kernels, since more powerful nonlinear kernels cause the learning to become prohibitively expensive. In this thesis, we introduce an approach to “kernelize” the features so that a linear SSVM framework can leverage the power of nonlinear kernels without incurring their high computational cost. Second, the optimality guarentees are violated for complex models with strong inter-relations between the output variables. We propose a new subgradient-based method that is more robust and leads to improved convergence properties and increased reliability. The different approaches presented in this thesis are applicable to both natural and medical images. They are able to segment mitochondria at a performance level close to that of a human annotator, and outperform state-of-the-art segmentation techniques while still benefiting from a low learning time

The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)

In this paper we report the set-up and results of the Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) organized in conjunction with the MICCAI 2012 and 2013 conferences. Twenty state-of-the-art tumor segmentation algorithms were applied to a set of 65 multi-contrast MR scans of low-and high-grade glioma patients-manually annotated by up to four raters-and to 65 comparable scans generated using tumor image simulation software. Quantitative evaluations revealed considerable disagreement between the human raters in segmenting various tumor sub-regions (Dice scores in the range 74%-85%), illustrating the difficulty of this task. We found that different algorithms worked best for different sub-regions (reaching performance comparable to human inter-rater variability), but that no single algorithm ranked in the top for all sub-regions simultaneously. Fusing several good algorithms using a hierarchical majority vote yielded segmentations that consistently ranked above all individual algorithms, indicating remaining opportunities for further methodological improvements. The BRATS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource