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

The Data Big Bang and the Expanding Digital Universe: High-Dimensional, Complex and Massive Data Sets in an Inflationary Epoch

Recent and forthcoming advances in instrumentation, and giant new surveys, are creating astronomical data sets that are not amenable to the methods of analysis familiar to astronomers. Traditional methods are often inadequate not merely because of the size in bytes of the data sets, but also because of the complexity of modern data sets. Mathematical limitations of familiar algorithms and techniques in dealing with such data sets create a critical need for new paradigms for the representation, analysis and scientific visualization (as opposed to illustrative visualization) of heterogeneous, multiresolution data across application domains. Some of the problems presented by the new data sets have been addressed by other disciplines such as applied mathematics, statistics and machine learning and have been utilized by other sciences such as space-based geosciences. Unfortunately, valuable results pertaining to these problems are mostly to be found only in publications outside of astronomy. Here we offer brief overviews of a number of concepts, techniques and developments, some "old" and some new. These are generally unknown to most of the astronomical community, but are vital to the analysis and visualization of complex datasets and images. In order for astronomers to take advantage of the richness and complexity of the new era of data, and to be able to identify, adopt, and apply new solutions, the astronomical community needs a certain degree of awareness and understanding of the new concepts. One of the goals of this paper is to help bridge the gap between applied mathematics, artificial intelligence and computer science on the one side and astronomy on the other.Comment: 24 pages, 8 Figures, 1 Table. Accepted for publication: "Advances in Astronomy, special issue "Robotic Astronomy

Review and classification of variability analysis techniques with clinical applications

Analysis of patterns of variation of time-series, termed variability analysis, represents a rapidly evolving discipline with increasing applications in different fields of science. In medicine and in particular critical care, efforts have focussed on evaluating the clinical utility of variability. However, the growth and complexity of techniques applicable to this field have made interpretation and understanding of variability more challenging. Our objective is to provide an updated review of variability analysis techniques suitable for clinical applications. We review more than 70 variability techniques, providing for each technique a brief description of the underlying theory and assumptions, together with a summary of clinical applications. We propose a revised classification for the domains of variability techniques, which include statistical, geometric, energetic, informational, and invariant. We discuss the process of calculation, often necessitating a mathematical transform of the time-series. Our aims are to summarize a broad literature, promote a shared vocabulary that would improve the exchange of ideas, and the analyses of the results between different studies. We conclude with challenges for the evolving science of variability analysis

An Assessment of Fractal Characterization Methods for 1/f Processes with Application to the Analysis of Stride Interval Time Series

The time evolution and complex interactions of many nonlinear systems, such as in the human body, result in fractal types of parameter outcomes that exhibit self similarity over long time scales by a power law in the frequency spectrum S(f) = 1/f. The scaling exponent can be interpreted as the degree of fractal characteristic and thus as a "biomarker" of relative health and decline. This thesis presents a thorough numerical analysis of fractal characterization techniques with specific consideration given to experimentally measured gait stride interval time series. The ideal fractal signals generated in the numerical analysis are constrained under varying lengths and biases indicative of a range of physiologically conceivable fractal signals. This analysis is to complement previous investigations of fractal characteristics in healthy and pathological gait stride interval time series, with which this study is compared. The comparative numerical analysis and experimental applications provide a thorough basis for determining an appropriate and robust method for measuring and comparing a physiologically meaningful biomarker, the spectral index. In consideration of the constraints in applications, the significant drawbacks of proposed time domain methods are noted, and it is concluded that time-scale domain wavelet methods can provide a reasonably consistent and accurate biomarker technique for these fractal time series

Morphology-based multifractal estimation for texture segmentation

Author name used in this publication: (David) Dagan FengCentre for Multimedia Signal Processing, Department of Electronic and Information Engineering2005-2006 > Academic research: refereed > Publication in refereed journalVersion of RecordPublishe

Uncovering the Correlation between COVID-19 and Neurodegenerative Processes: Toward a New Approach Based on EEG Entropic Analysis

COVID-19 is an ongoing global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. Although it primarily attacks the respiratory tract, inflammation can also affect the central nervous system (CNS), leading to chemo-sensory deficits such as anosmia and serious cognitive problems. Recent studies have shown a connection between COVID-19 and neurodegenerative diseases, particularly Alzheimer’s disease (AD). In fact, AD appears to exhibit neurological mechanisms of protein interactions similar to those that occur during COVID-19. Starting from these considerations, this perspective paper outlines a new approach based on the analysis of the complexity of brain signals to identify and quantify common features between COVID-19 and neurodegenerative disorders. Considering the relation between olfactory deficits, AD, and COVID-19, we present an experimental design involving olfactory tasks using multiscale fuzzy entropy (MFE) for electroencephalographic (EEG) signal analysis. Additionally, we present the open challenges and future perspectives. More specifically, the challenges are related to the lack of clinical standards regarding EEG signal entropy and public data that can be exploited in the experimental phase. Furthermore, the integration of EEG analysis with machine learning still requires further investigatio

New Method for Estimating Fractal Dimension in 3D Space and Its Application to Complex Surfaces

The concept of “surface modeling” generally describes the process of representing a physical or artificial surface by a geometric model, namely a mathematical expression. Among the existing techniques applied for the characterization of a surface, terrain modeling relates to the representation of the natural surface of the Earth. Cartographic terrain or relief models as three-dimensional representations of a part of the Earth's surface convey an immediate and direct impression of a landscape and are much easier to understand than two-dimensional models. This paper addresses a major problem in complex surface modeling and evaluation consisting in the characterization of their topography and comparison among different textures, which can be relevant in different areas of research. A new algorithm is presented that allows calculating the fractal dimension of images of complex surfaces. The method is used to characterize different surfaces and compare their characteristics. The proposed new mathematical method computes the fractal dimension of the 3D space with the average space component of Hurst exponent H, while the estimated fractal dimension is used to evaluate, compare and characterize complex surfaces that are relevant in different areas of research. Various surfaces with both methods were analyzed and the results were compared. The study confirms that with known coordinates of a surface, it is possible to describe its complex structure. The estimated fractal dimension is proved to be an ideal tool for measuring the complexity of the various surfaces considered

New method for estimating fractal dimension in 3d space and its application to complex surfaces

The concept of “surface modeling” generally describes the process of representing a physical or artificial surface by a geometric model, namely a mathematical expression. Among the existing techniques applied for the characterization of a surface, terrain modeling relates to the representation of the natural surface of the Earth. Cartographic terrain or relief models as threedimensional representations of a part of the Earth's surface convey an immediate and direct impression of a landscape and are much easier to understand than two-dimensional models. This paper addresses a major problem in complex surface modeling and evaluation consisting in the characterization of their topography and comparison among different textures, which can be relevant in different areas of research. A new algorithm is presented that allows calculating the fractal dimension of images of complex surfaces. The method is used to characterize different surfaces and compare their characteristics. The proposed new mathematical method computes the fractal dimension of the 3D space with the average space component of Hurst exponent H, while the estimated fractal dimension is used to evaluate, compare and characterize complex surfaces that are relevant in different areas of research. Various surfaces with both methods were analyzed and the results were compared. The study confirms that with known coordinates of a surface, it is possible to describe its complex structure. The estimated fractal dimension is proved to be an ideal tool for measuring the complexity of the various surfaces considered