Development of Unsupervised Image Segmentation Schemes for Brain MRI using HMRF model

Image segmentation is a classical problem in computer vision and is of paramount importance to medical imaging. Medical image segmentation is an essential step for most subsequent image analysis task. The segmentation of anatomic structure in the brain plays a crucial role in neuro imaging analysis. The study of many brain disorders involves accurate tissue segmentation of brain magnetic resonance (MR) images. Manual segmentation of the brain tissues, namely white matter (WM), gray matter (GM) and cerebrospinal fluid (CSF) in MR images by an human expert is tedious for studies involving larger database. In addition, the lack of clearly defined edges between adjacent tissue classes deteriorates the significance of the analysis of the resulting segmentation. The segmentation is further complicated by the overlap of MR intensities of different tissue classes and by the presence of a spatially and smoothly varying intensity in-homogeneity. The prime objective of this dissertation is to develop strategies and methodologies for an automated brain MR image segmentation scheme

Gaussian Mixture Model based Spatial Information Concept for Image Segmentation

Segmentation of images has found widespread applications in image recognition systems. Over the last two decades, there has been a growing research interest in model-based technique. In this technique, standard Gaussian mixture model (GMM) is a well-known method for image segmentation. The model assumes a common prior distribution, which independently generates the pixel labels. In addition, the spatial relationship between neighboring pixels is not taken into account of the standard GMM. For this reason, its segmentation result is sensitive to noise. To reduce the sensitivity of the segmented result with respect to noise, Markov Random Field (MRF) models provide a powerful way to account for spatial dependencies between image pixels. However, their main drawback is that they are computationally expensive to implement. Based on these considerations, in the first part of this thesis (Chapter 4), we propose an extension of the standard GMM for image segmentation, which utilizes a novel approach to incorporate the spatial relationships between neighboring pixels into the standard GMM. The proposed model is easy to implement and compared with the existing MRF models, requires lesser number of parameters. We also propose a new method to estimate the model parameters in order to minimize the higher bound on the data negative log-likelihood, based on the gradient method. Experimental results obtained on noisy synthetic and real world grayscale images demonstrate the robustness, accuracy and effectiveness of the proposed model in image segmentation. In the final part of this thesis (Chapter 5), another way to incorporate spatial information between the neighboring pixels into the GMM based on MRF is proposed. In comparison to other mixture models that are complex and computationally expensive, the proposed method is robust and fast to implement. In mixture models based on MRF, the M-step of the EM algorithm cannot be directly applied to the prior distribution for maximization of the log-likelihood with respect to the corresponding parameters. Compared with these models, our proposed method directly applies the EM algorithm to optimize the parameters, which makes it much simpler. Finally, our approach is used to segment many images with excellent results

Bayesian Methods and Machine Learning for Processing Text and Image Data

Classification/clustering is an important class of unstructured data processing problems. The classification (supervised, semi-supervised and unsupervised) aims to discover the clusters and group the similar data into categories for information organization and knowledge discovery. My work focuses on using the Bayesian methods and machine learning techniques to classify the free-text and image data, and address how to overcome the limitations of the traditional methods. The Bayesian approach provides a way to allow using more variations(numerical or categorical), and estimate the probabilities instead of explicit rules, which will benefit in the ambiguous cases. The MAP(maximum a posterior) estimation is used to deal with the local maximum problems which the ML(maximum likelihood) method gives inaccurate estimates. The EM(expectation-maximization) algorithm can be applied with MAP estimation for the incomplete/missing data problems. Our proposed framework can be used in both supervised and unsupervised classification. For natural language processing(NLP), we applied the machine learning techniques for sentence/text classification. For 3D CT image segmentation, MAP EM clustering approach is proposed to auto-detect the number of objects in the 3D CT luggage image, and the prior knowledge and constraints in MAP estimation are used to avoid/improve the local maximum problems. The algorithm can automatically determine the number of classes and find the optimal parameters for each class. As a result, it can automatically detect the number of objects and produce better segmentation for each object in the image. For segmented object recognition, we applied machine learning techniques to classify each object into targets or non-targets. We have achieved the good results with 90% PD(probability of detection) and 6% PFA(probability of false alarm). For image restoration, in X-ray imaging, scatter can produce noise, artifacts, and decreased contrast. In practice, hardware such as anti-scatter grid is often used to reduce scatter. However, the remaining scatter can still be significant and additional software-based correction is desirable. Furthermore, good software solutions can potentially reduce the amount of needed anti-scatter hardware, thereby reducing cost. In this work, the scatter correction is formulated as a Bayesian MAP (maximum a posteriori) problem with a non-local prior, which leads to better textural detail preservation in scatter reduction. The efficacy of our algorithm is demonstrated through experimental and simulation results

Machine learning for automatic analysis of affective behaviour

The automated analysis of affect has been gaining rapidly increasing attention by researchers over the past two decades, as it constitutes a fundamental step towards achieving next-generation computing technologies and integrating them into everyday life (e.g. via affect-aware, user-adaptive interfaces, medical imaging, health assessment, ambient intelligence etc.). The work presented in this thesis focuses on several fundamental problems manifesting in the course towards the achievement of reliable, accurate and robust affect sensing systems. In more detail, the motivation behind this work lies in recent developments in the field, namely (i) the creation of large, audiovisual databases for affect analysis in the so-called ''Big-Data`` era, along with (ii) the need to deploy systems under demanding, real-world conditions. These developments led to the requirement for the analysis of emotion expressions continuously in time, instead of merely processing static images, thus unveiling the wide range of temporal dynamics related to human behaviour to researchers. The latter entails another deviation from the traditional line of research in the field: instead of focusing on predicting posed, discrete basic emotions (happiness, surprise etc.), it became necessary to focus on spontaneous, naturalistic expressions captured under settings more proximal to real-world conditions, utilising more expressive emotion descriptions than a set of discrete labels. To this end, the main motivation of this thesis is to deal with challenges arising from the adoption of continuous dimensional emotion descriptions under naturalistic scenarios, considered to capture a much wider spectrum of expressive variability than basic emotions, and most importantly model emotional states which are commonly expressed by humans in their everyday life. In the first part of this thesis, we attempt to demystify the quite unexplored problem of predicting continuous emotional dimensions. This work is amongst the first to explore the problem of predicting emotion dimensions via multi-modal fusion, utilising facial expressions, auditory cues and shoulder gestures. A major contribution of the work presented in this thesis lies in proposing the utilisation of various relationships exhibited by emotion dimensions in order to improve the prediction accuracy of machine learning methods - an idea which has been taken on by other researchers in the field since. In order to experimentally evaluate this, we extend methods such as the Long Short-Term Memory Neural Networks (LSTM), the Relevance Vector Machine (RVM) and Canonical Correlation Analysis (CCA) in order to exploit output relationships in learning. As it is shown, this increases the accuracy of machine learning models applied to this task. The annotation of continuous dimensional emotions is a tedious task, highly prone to the influence of various types of noise. Performed real-time by several annotators (usually experts), the annotation process can be heavily biased by factors such as subjective interpretations of the emotional states observed, the inherent ambiguity of labels related to human behaviour, the varying reaction lags exhibited by each annotator as well as other factors such as input device noise and annotation errors. In effect, the annotations manifest a strong spatio-temporal annotator-specific bias. Failing to properly deal with annotation bias and noise leads to an inaccurate ground truth, and therefore to ill-generalisable machine learning models. This deems the proper fusion of multiple annotations, and the inference of a clean, corrected version of the ``ground truth'' as one of the most significant challenges in the area. A highly important contribution of this thesis lies in the introduction of Dynamic Probabilistic Canonical Correlation Analysis (DPCCA), a method aimed at fusing noisy continuous annotations. By adopting a private-shared space model, we isolate the individual characteristics that are annotator-specific and not shared, while most importantly we model the common, underlying annotation which is shared by annotators (i.e., the derived ground truth). By further learning temporal dynamics and incorporating a time-warping process, we are able to derive a clean version of the ground truth given multiple annotations, eliminating temporal discrepancies and other nuisances. The integration of the temporal alignment process within the proposed private-shared space model deems DPCCA suitable for the problem of temporally aligning human behaviour; that is, given temporally unsynchronised sequences (e.g., videos of two persons smiling), the goal is to generate the temporally synchronised sequences (e.g., the smile apex should co-occur in the videos). Temporal alignment is an important problem for many applications where multiple datasets need to be aligned in time. Furthermore, it is particularly suitable for the analysis of facial expressions, where the activation of facial muscles (Action Units) typically follows a set of predefined temporal phases. A highly challenging scenario is when the observations are perturbed by gross, non-Gaussian noise (e.g., occlusions), as is often the case when analysing data acquired under real-world conditions. To account for non-Gaussian noise, a robust variant of Canonical Correlation Analysis (RCCA) for robust fusion and temporal alignment is proposed. The model captures the shared, low-rank subspace of the observations, isolating the gross noise in a sparse noise term. RCCA is amongst the first robust variants of CCA proposed in literature, and as we show in related experiments outperforms other, state-of-the-art methods for related tasks such as the fusion of multiple modalities under gross noise. Beyond private-shared space models, Component Analysis (CA) is an integral component of most computer vision systems, particularly in terms of reducing the usually high-dimensional input spaces in a meaningful manner pertaining to the task-at-hand (e.g., prediction, clustering). A final, significant contribution of this thesis lies in proposing the first unifying framework for probabilistic component analysis. The proposed framework covers most well-known CA methods, such as Principal Component Analysis (PCA), Linear Discriminant Analysis (LDA), Locality Preserving Projections (LPP) and Slow Feature Analysis (SFA), providing further theoretical insights into the workings of CA. Moreover, the proposed framework is highly flexible, enabling novel CA methods to be generated by simply manipulating the connectivity of latent variables (i.e. the latent neighbourhood). As shown experimentally, methods derived via the proposed framework outperform other equivalents in several problems related to affect sensing and facial expression analysis, while providing advantages such as reduced complexity and explicit variance modelling.Open Acces

Collaborative sparse regression using spatially correlated supports - Application to hyperspectral unmixing

This paper presents a new Bayesian collaborative sparse regression method for linear unmixing of hyperspectral images. Our contribution is twofold; first, we propose a new Bayesian model for structured sparse regression in which the supports of the sparse abundance vectors are a priori spatially correlated across pixels (i.e., materials are spatially organised rather than randomly distributed at a pixel level). This prior information is encoded in the model through a truncated multivariate Ising Markov random field, which also takes into consideration the facts that pixels cannot be empty (i.e, there is at least one material present in each pixel), and that different materials may exhibit different degrees of spatial regularity. Secondly, we propose an advanced Markov chain Monte Carlo algorithm to estimate the posterior probabilities that materials are present or absent in each pixel, and, conditionally to the maximum marginal a posteriori configuration of the support, compute the MMSE estimates of the abundance vectors. A remarkable property of this algorithm is that it self-adjusts the values of the parameters of the Markov random field, thus relieving practitioners from setting regularisation parameters by cross-validation. The performance of the proposed methodology is finally demonstrated through a series of experiments with synthetic and real data and comparisons with other algorithms from the literature

Quantitative evaluation of methods to analyze motion changes in single-particle experiments

The analysis of live-cell single-molecule imaging experiments can reveal valuable information about the heterogeneity of transport processes and interactions between cell components. These characteristics are seen as motion changes in the particle trajectories. Despite the existence of multiple approaches to carry out this type of analysis, no objective assessment of these methods has been performed so far. Here, we have designed a competition to characterize and rank the performance of these methods when analyzing the dynamic behavior of single molecules. To run this competition, we have implemented a software library to simulate realistic data corresponding to widespread diffusion and interaction models, both in the form of trajectories and videos obtained in typical experimental conditions. The competition will constitute the first assessment of these methods, provide insights into the current limits of the field, foster the development of new approaches, and guide researchers to identify optimal tools for analyzing their experiments.Comment: 19 pages, 4 figure, 2 tables. Stage 1 registered report, accepted in principle in Nature Communications (https://springernature.figshare.com/articles/journal_contribution/Quantitative_evaluation_of_methods_to_analyze_motion_changes_in_single-particle_experiments_Registered_Report_Stage_1_Protocol_/24771687