Advanced Computational Methods for Oncological Image Analysis

[Cancer is the second most common cause of death worldwide and encompasses highly variable clinical and biological scenarios. Some of the current clinical challenges are (i) early diagnosis of the disease and (ii) precision medicine, which allows for treatments targeted to specific clinical cases. The ultimate goal is to optimize the clinical workflow by combining accurate diagnosis with the most suitable therapies. Toward this, large-scale machine learning research can define associations among clinical, imaging, and multi-omics studies, making it possible to provide reliable diagnostic and prognostic biomarkers for precision oncology. Such reliable computer-assisted methods (i.e., artificial intelligence) together with clinicians’ unique knowledge can be used to properly handle typical issues in evaluation/quantification procedures (i.e., operator dependence and time-consuming tasks). These technical advances can significantly improve result repeatability in disease diagnosis and guide toward appropriate cancer care. Indeed, the need to apply machine learning and computational intelligence techniques has steadily increased to effectively perform image processing operations—such as segmentation, co-registration, classification, and dimensionality reduction—and multi-omics data integration.

IMAGE UNDERSTANDING OF MOLAR PREGNANCY BASED ON ANOMALIES DETECTION

Cancer occurs when normal cells grow and multiply without normal control. As the cells multiply, they form an area of abnormal cells, known as a tumour. Many tumours exhibit abnormal chromosomal segregation at cell division. These anomalies play an important role in detecting molar pregnancy cancer. Molar pregnancy, also known as hydatidiform mole, can be categorised into partial (PHM) and complete (CHM) mole, persistent gestational trophoblastic and choriocarcinoma. Hydatidiform moles are most commonly found in women under the age of 17 or over the age of 35. Hydatidiform moles can be detected by morphological and histopathological examination. Even experienced pathologists cannot easily classify between complete and partial hydatidiform moles. However, the distinction between complete and partial hydatidiform moles is important in order to recommend the appropriate treatment method. Therefore, research into molar pregnancy image analysis and understanding is critical. The hypothesis of this research project is that an anomaly detection approach to analyse molar pregnancy images can improve image analysis and classification of normal PHM and CHM villi. The primary aim of this research project is to develop a novel method, based on anomaly detection, to identify and classify anomalous villi in molar pregnancy stained images. The novel method is developed to simulate expert pathologists’ approach in diagnosis of anomalous villi. The knowledge and heuristics elicited from two expert pathologists are combined with the morphological domain knowledge of molar pregnancy, to develop a heuristic multi-neural network architecture designed to classify the villi into their appropriated anomalous types. This study confirmed that a single feature cannot give enough discriminative power for villi classification. Whereas expert pathologists consider the size and shape before textural features, this thesis demonstrated that the textural feature has a higher discriminative power than size and shape. The first heuristic-based multi-neural network, which was based on 15 elicited features, achieved an improved average accuracy of 81.2%, compared to the traditional multi-layer perceptron (80.5%); however, the recall of CHM villi class was still low (64.3%). Two further textural features, which were elicited and added to the second heuristic-based multi-neural network, have improved the average accuracy from 81.2% to 86.1% and the recall of CHM villi class from 64.3% to 73.5%. The precision of the multi-neural network II has also increased from 82.7% to 89.5% for normal villi class, from 81.3% to 84.7% for PHM villi class and from 80.8% to 86% for CHM villi class. To support pathologists to visualise the results of the segmentation, a software tool, Hydatidiform Mole Analysis Tool (HYMAT), was developed compiling the morphological and pathological data for each villus analysis

A Bottom-Up Review of Image Analysis Methods for Suspicious Region Detection in Mammograms.

Breast cancer is one of the most common death causes amongst women all over the world. Early detection of breast cancer plays a critical role in increasing the survival rate. Various imaging modalities, such as mammography, breast MRI, ultrasound and thermography, are used to detect breast cancer. Though there is a considerable success with mammography in biomedical imaging, detecting suspicious areas remains a challenge because, due to the manual examination and variations in shape, size, other mass morphological features, mammography accuracy changes with the density of the breast. Furthermore, going through the analysis of many mammograms per day can be a tedious task for radiologists and practitioners. One of the main objectives of biomedical imaging is to provide radiologists and practitioners with tools to help them identify all suspicious regions in a given image. Computer-aided mass detection in mammograms can serve as a second opinion tool to help radiologists avoid running into oversight errors. The scientific community has made much progress in this topic, and several approaches have been proposed along the way. Following a bottom-up narrative, this paper surveys different scientific methodologies and techniques to detect suspicious regions in mammograms spanning from methods based on low-level image features to the most recent novelties in AI-based approaches. Both theoretical and practical grounds are provided across the paper sections to highlight the pros and cons of different methodologies. The paper's main scope is to let readers embark on a journey through a fully comprehensive description of techniques, strategies and datasets on the topic

Neuroinformatics in Functional Neuroimaging

This Ph.D. thesis proposes methods for information retrieval in functional neuroimaging through automatic computerized authority identification, and searching and cleaning in a neuroscience database. Authorities are found through cocitation analysis of the citation pattern among scientific articles. Based on data from a single scientific journal it is shown that multivariate analyses are able to determine group structure that is interpretable as particular “known ” subgroups in functional neuroimaging. Methods for text analysis are suggested that use a combination of content and links, in the form of the terms in scientific documents and scientific citations, respectively. These included context sensitive author ranking and automatic labeling of axes and groups in connection with multivariate analyses of link data. Talairach foci from the BrainMap ™ database are modeled with conditional probability density models useful for exploratory functional volumes modeling. A further application is shown with conditional outlier detection where abnormal entries in the BrainMap ™ database are spotted using kernel density modeling and the redundancy between anatomical labels and spatial Talairach coordinates. This represents a combination of simple term and spatial modeling. The specific outliers that were found in the BrainMap ™ database constituted among others: Entry errors, errors in the article and unusual terminology

Computer Vision Algorithms for Mobile Camera Applications

Wearable and mobile sensors have found widespread use in recent years due to their ever-decreasing cost, ease of deployment and use, and ability to provide continuous monitoring as opposed to sensors installed at fixed locations. Since many smart phones are now equipped with a variety of sensors, including accelerometer, gyroscope, magnetometer, microphone and camera, it has become more feasible to develop algorithms for activity monitoring, guidance and navigation of unmanned vehicles, autonomous driving and driver assistance, by using data from one or more of these sensors. In this thesis, we focus on multiple mobile camera applications, and present lightweight algorithms suitable for embedded mobile platforms. The mobile camera scenarios presented in the thesis are: (i) activity detection and step counting from wearable cameras, (ii) door detection for indoor navigation of unmanned vehicles, and (iii) traffic sign detection from vehicle-mounted cameras. First, we present a fall detection and activity classification system developed for embedded smart camera platform CITRIC. In our system, the camera platform is worn by the subject, as opposed to static sensors installed at fixed locations in certain rooms, and, therefore, monitoring is not limited to confined areas, and extends to wherever the subject may travel including indoors and outdoors. Next, we present a real-time smart phone-based fall detection system, wherein we implement camera and accelerometer based fall-detection on Samsung Galaxy S™ 4. We fuse these two sensor modalities to have a more robust fall detection system. Then, we introduce a fall detection algorithm with autonomous thresholding using relative-entropy within the class of Ali-Silvey distance measures. As another wearable camera application, we present a footstep counting algorithm using a smart phone camera. This algorithm provides more accurate step-count compared to using only accelerometer data in smart phones and smart watches at various body locations. As a second mobile camera scenario, we study autonomous indoor navigation of unmanned vehicles. A novel approach is proposed to autonomously detect and verify doorway openings by using the Google Project Tango™ platform. The third mobile camera scenario involves vehicle-mounted cameras. More specifically, we focus on traffic sign detection from lower-resolution and noisy videos captured from vehicle-mounted cameras. We present a new method for accurate traffic sign detection, incorporating Aggregate Channel Features and Chain Code Histograms, with the goal of providing much faster training and testing, and comparable or better performance, with respect to deep neural network approaches, without requiring specialized processors. Proposed computer vision algorithms provide promising results for various useful applications despite the limited energy and processing capabilities of mobile devices

From insights to innovations : data mining, visualization, and user interfaces

This thesis is about data mining (DM) and visualization methods for gaining insight into multidimensional data. Novel, exploratory data analysis tools and adaptive user interfaces are developed by tailoring and combining existing DM and visualization methods in order to advance in different applications. The thesis presents new visual data mining (VDM) methods that are also implemented in software toolboxes and applied to industrial and biomedical signals: First, we propose a method that has been applied to investigating industrial process data. The self-organizing map (SOM) is combined with scatterplots using the traditional color linking or interactive brushing. The original contribution is to apply color linked or brushed scatterplots and the SOM to visually survey local dependencies between a pair of attributes in different parts of the SOM. Clusters can be visualized on a SOM with different colors, and we also present how a color coding can be automatically obtained by using a proximity preserving projection of the SOM model vectors. Second, we present a new method for an (interactive) visualization of cluster structures in a SOM. By using a contraction model, the regular grid of a SOM visualization is smoothly changed toward a presentation that shows better the proximities in the data space. Third, we propose a novel VDM method for investigating the reliability of estimates resulting from a stochastic independent component analysis (ICA) algorithm. The method can be extended also to other problems of similar kind. As a benchmarking task, we rank independent components estimated on a biomedical data set recorded from the brain and gain a reasonable result. We also utilize DM and visualization for mobile-awareness and personalization. We explore how to infer information about the usage context from features that are derived from sensory signals. The signals originate from a mobile phone with on-board sensors for ambient physical conditions. In previous studies, the signals are transformed into descriptive (fuzzy or binary) context features. In this thesis, we present how the features can be transformed into higher-level patterns, contexts, by rather simple statistical methods: we propose and test using minimum-variance cost time series segmentation, ICA, and principal component analysis (PCA) for this purpose. Both time-series segmentation and PCA revealed meaningful contexts from the features in a visual data exploration. We also present a novel type of adaptive soft keyboard where the aim is to obtain an ergonomically better, more comfortable keyboard. The method starts from some conventional keypad layout, but it gradually shifts the keys into new positions according to the user's grasp and typing pattern. Related to the applications, we present two algorithms that can be used in a general context: First, we describe a binary mixing model for independent binary sources. The model resembles the ordinary ICA model, but the summation is replaced by the Boolean operator OR and the multiplication by AND. We propose a new, heuristic method for estimating the binary mixing matrix and analyze its performance experimentally. The method works for signals that are sparse enough. We also discuss differences on the results when using different objective functions in the FastICA estimation algorithm. Second, we propose "global iterative replacement" (GIR), a novel, greedy variant of a merge-split segmentation method. Its performance compares favorably to that of the traditional top-down binary split segmentation algorithm.reviewe

Frugal hypothesis testing and classification

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2010.Cataloged from PDF version of thesis.Includes bibliographical references (p. 157-175).The design and analysis of decision rules using detection theory and statistical learning theory is important because decision making under uncertainty is pervasive. Three perspectives on limiting the complexity of decision rules are considered in this thesis: geometric regularization, dimensionality reduction, and quantization or clustering. Controlling complexity often reduces resource usage in decision making and improves generalization when learning decision rules from noisy samples. A new margin-based classifier with decision boundary surface area regularization and optimization via variational level set methods is developed. This novel classifier is termed the geometric level set (GLS) classifier. A method for joint dimensionality reduction and margin-based classification with optimization on the Stiefel manifold is developed. This dimensionality reduction approach is extended for information fusion in sensor networks. A new distortion is proposed for the quantization or clustering of prior probabilities appearing in the thresholds of likelihood ratio tests. This distortion is given the name mean Bayes risk error (MBRE). The quantization framework is extended to model human decision making and discrimination in segregated populations.by Kush R. Varshney.Ph.D

A precise bare simulation approach to the minimization of some distances. Foundations

In information theory -- as well as in the adjacent fields of statistics, machine learning, artificial intelligence, signal processing and pattern recognition -- many flexibilizations of the omnipresent Kullback-Leibler information distance (relative entropy) and of the closely related Shannon entropy have become frequently used tools. To tackle corresponding constrained minimization (respectively maximization) problems by a newly developed dimension-free bare (pure) simulation method, is the main goal of this paper. Almost no assumptions (like convexity) on the set of constraints are needed, within our discrete setup of arbitrary dimension, and our method is precise (i.e., converges in the limit). As a side effect, we also derive an innovative way of constructing new useful distances/divergences. To illustrate the core of our approach, we present numerous examples. The potential for widespread applicability is indicated, too; in particular, we deliver many recent references for uses of the involved distances/divergences and entropies in various different research fields (which may also serve as an interdisciplinary interface)