Computer-aided detection and diagnosis of breast cancer in 2D and 3D medical imaging through multifractal analysis

This Thesis describes the research work performed in the scope of a doctoral research program and presents its conclusions and contributions. The research activities were carried on in the industry with Siemens S.A. Healthcare Sector, in integration with a research team. Siemens S.A. Healthcare Sector is one of the world biggest suppliers of products, services and complete solutions in the medical sector. The company offers a wide selection of diagnostic and therapeutic equipment and information systems. Siemens products for medical imaging and in vivo diagnostics include: ultrasound, computer tomography, mammography, digital breast tomosynthesis, magnetic resonance, equipment to angiography and coronary angiography, nuclear imaging, and many others. Siemens has a vast experience in Healthcare and at the beginning of this project it was strategically interested in solutions to improve the detection of Breast Cancer, to increase its competitiveness in the sector. The company owns several patents related with self-similarity analysis, which formed the background of this Thesis. Furthermore, Siemens intended to explore commercially the computer- aided automatic detection and diagnosis eld for portfolio integration. Therefore, with the high knowledge acquired by University of Beira Interior in this area together with this Thesis, will allow Siemens to apply the most recent scienti c progress in the detection of the breast cancer, and it is foreseeable that together we can develop a new technology with high potential. The project resulted in the submission of two invention disclosures for evaluation in Siemens A.G., two articles published in peer-reviewed journals indexed in ISI Science Citation Index, two other articles submitted in peer-reviewed journals, and several international conference papers. This work on computer-aided-diagnosis in breast led to innovative software and novel processes of research and development, for which the project received the Siemens Innovation Award in 2012. It was very rewarding to carry on such technological and innovative project in a socially sensitive area as Breast Cancer.No cancro da mama a deteção precoce e o diagnóstico correto são de extrema importância na prescrição terapêutica e caz e e ciente, que potencie o aumento da taxa de sobrevivência à doença. A teoria multifractal foi inicialmente introduzida no contexto da análise de sinal e a sua utilidade foi demonstrada na descrição de comportamentos siológicos de bio-sinais e até na deteção e predição de patologias. Nesta Tese, três métodos multifractais foram estendidos para imagens bi-dimensionais (2D) e comparados na deteção de microcalci cações em mamogramas. Um destes métodos foi também adaptado para a classi cação de massas da mama, em cortes transversais 2D obtidos por ressonância magnética (RM) de mama, em grupos de massas provavelmente benignas e com suspeição de malignidade. Um novo método de análise multifractal usando a lacunaridade tri-dimensional (3D) foi proposto para classi cação de massas da mama em imagens volumétricas 3D de RM de mama. A análise multifractal revelou diferenças na complexidade subjacente às localizações das microcalci cações em relação aos tecidos normais, permitindo uma boa exatidão da sua deteção em mamogramas. Adicionalmente, foram extraídas por análise multifractal características dos tecidos que permitiram identi car os casos tipicamente recomendados para biópsia em imagens 2D de RM de mama. A análise multifractal 3D foi e caz na classi cação de lesões mamárias benignas e malignas em imagens 3D de RM de mama. Este método foi mais exato para esta classi cação do que o método 2D ou o método padrão de análise de contraste cinético tumoral. Em conclusão, a análise multifractal fornece informação útil para deteção auxiliada por computador em mamogra a e diagnóstico auxiliado por computador em imagens 2D e 3D de RM de mama, tendo o potencial de complementar a interpretação dos radiologistas

Riemannian Flows for Supervised and Unsupervised Geometric Image Labeling

In this thesis we focus on the image labeling problem, which is used as a subroutine in many image processing applications. Our work is based on the assignment flow which was recently introduced as a novel geometric approach to the image labeling problem. This flow evolves over time on the manifold of row-stochastic matrices, whose elements represent label assignments as assignment probabilities. The strict separation of assignment manifold and feature space enables the data to lie in any metric space, while a smoothing operation on the assignment manifold results in an unbiased and spatially regularized labeling. The first part of this work focuses on theoretical statements about the asymptotic behavior of the assignment flow. We show under weak assumptions on the parameters that the assignment flow for data in general position converges towards integral probabilities and thus ensures unique assignment decisions. Furthermore, we investigate the stability of possible limit points depending on the input data and parameters. For stable limits, we derive conditions that allow early evidence of convergence towards these limits and thus provide convergence guarantees. In the second part, we extend the assignment flow approach in order to impose global convex constraints on the labeling results based on linear filter statistics of the assignments. The corresponding filters are learned from examples using an eigendecomposition. The effectiveness of the approach is numerically demonstrated in several academic labeling scenarios. In the last part of this thesis we consider the situation in which no labels are given and therefore these prototypical elements have to be determined from the data as well. To this end we introduce an additional flow on the feature manifold, which is coupled to the assignment flow. The resulting flow adapts the prototypes in time to the assignment probabilities. The simultaneous adaptation and assignment of prototypes not only provides suitable prototypes, but also improves the resulting image segmentation, which is demonstrated by experiments. For this approach it is assumed that the data lie on a Riemannian manifold. We elaborate the approach for a range of manifolds that occur in applications and evaluate the resulting approaches in numerical experiments

Telecommunications Networks

This book guides readers through the basics of rapidly emerging networks to more advanced concepts and future expectations of Telecommunications Networks. It identifies and examines the most pressing research issues in Telecommunications and it contains chapters written by leading researchers, academics and industry professionals. Telecommunications Networks - Current Status and Future Trends covers surveys of recent publications that investigate key areas of interest such as: IMS, eTOM, 3G/4G, optimization problems, modeling, simulation, quality of service, etc. This book, that is suitable for both PhD and master students, is organized into six sections: New Generation Networks, Quality of Services, Sensor Networks, Telecommunications, Traffic Engineering and Routing

Individual-Based Modeling and Nonlinear Analysis for Complex Systems with Application to Theoretical Ecology

One approach to understanding the behaviour of complex systems is individual-based modeling, which provides a bottom-up approach allowing for the consideration of the traits and behaviour of individual organisms. Ecosystem models aim to characterize the major dynamics of ecosystems, in order to synthesize the understanding of such systems and to allow predictions of their behaviour. Moreover, ecosystem simulations have the potential to help scientists address theoretical questions as well as helping with ecological resource management. Because in reality biologists do not have much data regarding variations in ecosystems over long periods of time, using the results of ecological computer simulation for making reasonable predictions can help biologists to better understand the long-term behaviour of ecosystems. Different versions of ecosystem simulations have been developed to investigate several questions in ecology such as how speciation proceeds in the absence of experimenter-defined functions. I have investigated some of these questions relying on complex interactions between the many individuals involved in the system, as well as long-term evolutionary patterns and processes such as speciation and macroevolution. Most scientists now believe that natural phenomena have to be looking as a chaotic system. In the past few years, chaos analysis techniques have gained increasing attention over a variety of applications. I have analyzed results of complex models to see whether chaotic behaviour can emerge, since any attempt to model a realistic system needs to have the capacity to generate patterns as complex as the ones that are observed in real systems. To further understand the complex behaviour of real systems, a new algorithm for long-term prediction of time series behaviour is also proposed based on chaos analysis. We evaluated the performance of our new method with respect to the prediction of the Dow-Jones industrial index time series, epileptic seizure and global temperature anomaly

On incorporating inductive biases into deep neural networks

A machine learning (ML) algorithm can be interpreted as a system that learns to capture patterns in data distributions. Before the modern \emph{deep learning era}, emulating the human brain, the use of structured representations and strong inductive bias have been prevalent in building ML models, partly due to the expensive computational resources and the limited availability of data. On the contrary, armed with increasingly cheaper hardware and abundant data, deep learning has made unprecedented progress during the past decade, showcasing incredible performance on a diverse set of ML tasks. In contrast to \emph{classical ML} models, the latter seeks to minimize structured representations and inductive bias when learning, implicitly favoring the flexibility of learning over manual intervention. Despite the impressive performance, attention is being drawn towards enhancing the (relatively) weaker areas of deep models such as learning with limited resources, robustness, minimal overhead to realize simple relationships, and ability to generalize the learned representations beyond the training conditions, which were (arguably) the forte of classical ML. Consequently, a recent hybrid trend is surfacing that aims to blend structured representations and substantial inductive bias into deep models, with the hope of improving them. Based on the above motivation, this thesis investigates methods to improve the performance of deep models using inductive bias and structured representations across multiple problem domains. To this end, we inject a priori knowledge into deep models in the form of enhanced feature extraction techniques, geometrical priors, engineered features, and optimization constraints. Especially, we show that by leveraging the prior knowledge about the task in hand and the structure of data, the performance of deep learning models can be significantly elevated. We begin by exploring equivariant representation learning. In general, the real-world observations are prone to fundamental transformations (e.g., translation, rotation), and deep models typically demand expensive data-augmentations and a high number of filters to tackle such variance. In comparison, carefully designed equivariant filters possess this ability by nature. Henceforth, we propose a novel \emph{volumetric convolution} operation that can convolve arbitrary functions in the unit-ball ($\mathbb{B}^3$) while preserving rotational equivariance by projecting the input data onto the Zernike basis. We conduct extensive experiments and show that our formulations can be used to construct significantly cheaper ML models. Next, we study generative modeling of 3D objects and propose a principled approach to synthesize 3D point-clouds in the spectral-domain by obtaining a structured representation of 3D points as functions on the unit sphere ($\mathbb{S}^2$). Using the prior knowledge about the spectral moments and the output data manifold, we design an architecture that can maximally utilize the information in the inputs and generate high-resolution point-clouds with minimal computational overhead. Finally, we propose a framework to build normalizing flows (NF) based on increasing triangular maps and Bernstein-type polynomials. Compared to the existing NF approaches, our framework consists of favorable characteristics for fusing inductive bias within the model i.e., theoretical upper bounds for the approximation error, robustness, higher interpretability, suitability for compactly supported densities, and the ability to employ higher degree polynomials without training instability. Most importantly, we present a constructive universality proof, which permits us to analytically derive the optimal model coefficients for known transformations without training

Hidden Markov Models

Hidden Markov Models (HMMs), although known for decades, have made a big career nowadays and are still in state of development. This book presents theoretical issues and a variety of HMMs applications in speech recognition and synthesis, medicine, neurosciences, computational biology, bioinformatics, seismology, environment protection and engineering. I hope that the reader will find this book useful and helpful for their own research

Recent Advances in Indoor Localization Systems and Technologies

Despite the enormous technical progress seen in the past few years, the maturity of indoor localization technologies has not yet reached the level of GNSS solutions. The 23 selected papers in this book present the recent advances and new developments in indoor localization systems and technologies, propose novel or improved methods with increased performance, provide insight into various aspects of quality control, and also introduce some unorthodox positioning methods