Radiogenomics Framework for Associating Medical Image Features with Tumour Genetic Characteristics

Significant progress has been made in the understanding of human cancers at the molecular genetics level and it is providing new insights into their underlying pathophysiology. This progress has enabled the subclassification of the disease and the development of targeted therapies that address specific biological pathways. However, obtaining genetic information remains invasive and costly. Medical imaging is a non-invasive technique that captures important visual characteristics (i.e. image features) of abnormalities and plays an important role in routine clinical practice. Advancements in computerised medical image analysis have enabled quantitative approaches to extract image features that can reflect tumour genetic characteristics, leading to the emergence of ‘radiogenomics’. Radiogenomics investigates the relationships between medical imaging features and tumour molecular characteristics, and enables the derivation of imaging surrogates (radiogenomics features) to genetic biomarkers that can provide alternative approaches to non-invasive and accurate cancer diagnosis. This thesis presents a new framework that combines several novel methods for radiogenomics analysis that associates medical image features with tumour genetic characteristics, with the main objectives being: i) a comprehensive characterisation of tumour image features that reflect underlying genetic information; ii) a method that identifies radiogenomics features encoding common pathophysiological information across different diseases, overcoming the dependence on large annotated datasets; and iii) a method that quantifies radiogenomics features from multi-modal imaging data and accounts for unique information encoded in tumour heterogeneity sub-regions. The present radiogenomics methods advance radiogenomics analysis and contribute to improving research in computerised medical image analysis

Reconhecimento de padrões em expressões faciais : algoritmos e aplicações

Orientador: Hélio PedriniTese (doutorado) - Universidade Estadual de Campinas, Instituto de ComputaçãoResumo: O reconhecimento de emoções tem-se tornado um tópico relevante de pesquisa pela comunidade científica, uma vez que desempenha um papel essencial na melhoria contínua dos sistemas de interação humano-computador. Ele pode ser aplicado em diversas áreas, tais como medicina, entretenimento, vigilância, biometria, educação, redes sociais e computação afetiva. Há alguns desafios em aberto relacionados ao desenvolvimento de sistemas emocionais baseados em expressões faciais, como dados que refletem emoções mais espontâneas e cenários reais. Nesta tese de doutorado, apresentamos diferentes metodologias para o desenvolvimento de sistemas de reconhecimento de emoções baseado em expressões faciais, bem como sua aplicabilidade na resolução de outros problemas semelhantes. A primeira metodologia é apresentada para o reconhecimento de emoções em expressões faciais ocluídas baseada no Histograma da Transformada Census (CENTRIST). Expressões faciais ocluídas são reconstruídas usando a Análise Robusta de Componentes Principais (RPCA). A extração de características das expressões faciais é realizada pelo CENTRIST, bem como pelos Padrões Binários Locais (LBP), pela Codificação Local do Gradiente (LGC) e por uma extensão do LGC. O espaço de características gerado é reduzido aplicando-se a Análise de Componentes Principais (PCA) e a Análise Discriminante Linear (LDA). Os algoritmos K-Vizinhos mais Próximos (KNN) e Máquinas de Vetores de Suporte (SVM) são usados para classificação. O método alcançou taxas de acerto competitivas para expressões faciais ocluídas e não ocluídas. A segunda é proposta para o reconhecimento dinâmico de expressões faciais baseado em Ritmos Visuais (VR) e Imagens da História do Movimento (MHI), de modo que uma fusão de ambos descritores codifique informações de aparência, forma e movimento dos vídeos. Para extração das características, o Descritor Local de Weber (WLD), o CENTRIST, o Histograma de Gradientes Orientados (HOG) e a Matriz de Coocorrência em Nível de Cinza (GLCM) são empregados. A abordagem apresenta uma nova proposta para o reconhecimento dinâmico de expressões faciais e uma análise da relevância das partes faciais. A terceira é um método eficaz apresentado para o reconhecimento de emoções audiovisuais com base na fala e nas expressões faciais. A metodologia envolve uma rede neural híbrida para extrair características visuais e de áudio dos vídeos. Para extração de áudio, uma Rede Neural Convolucional (CNN) baseada no log-espectrograma de Mel é usada, enquanto uma CNN construída sobre a Transformada de Census é empregada para a extração das características visuais. Os atributos audiovisuais são reduzidos por PCA e LDA, então classificados por KNN, SVM, Regressão Logística (LR) e Gaussian Naïve Bayes (GNB). A abordagem obteve taxas de reconhecimento competitivas, especialmente em dados espontâneos. A penúltima investiga o problema de detectar a síndrome de Down a partir de fotografias. Um descritor geométrico é proposto para extrair características faciais. Experimentos realizados em uma base de dados pública mostram a eficácia da metodologia desenvolvida. A última metodologia trata do reconhecimento de síndromes genéticas em fotografias. O método visa extrair atributos faciais usando características de uma rede neural profunda e medidas antropométricas. Experimentos são realizados em uma base de dados pública, alcançando taxas de reconhecimento competitivasAbstract: Emotion recognition has become a relevant research topic by the scientific community, since it plays an essential role in the continuous improvement of human-computer interaction systems. It can be applied in various areas, for instance, medicine, entertainment, surveillance, biometrics, education, social networks, and affective computing. There are some open challenges related to the development of emotion systems based on facial expressions, such as data that reflect more spontaneous emotions and real scenarios. In this doctoral dissertation, we propose different methodologies to the development of emotion recognition systems based on facial expressions, as well as their applicability in the development of other similar problems. The first is an emotion recognition methodology for occluded facial expressions based on the Census Transform Histogram (CENTRIST). Occluded facial expressions are reconstructed using an algorithm based on Robust Principal Component Analysis (RPCA). Extraction of facial expression features is then performed by CENTRIST, as well as Local Binary Patterns (LBP), Local Gradient Coding (LGC), and an LGC extension. The generated feature space is reduced by applying Principal Component Analysis (PCA) and Linear Discriminant Analysis (LDA). K-Nearest Neighbor (KNN) and Support Vector Machine (SVM) algorithms are used for classification. This method reached competitive accuracy rates for occluded and non-occluded facial expressions. The second proposes a dynamic facial expression recognition based on Visual Rhythms (VR) and Motion History Images (MHI), such that a fusion of both encodes appearance, shape, and motion information of the video sequences. For feature extraction, Weber Local Descriptor (WLD), CENTRIST, Histogram of Oriented Gradients (HOG), and Gray-Level Co-occurrence Matrix (GLCM) are employed. This approach shows a new direction for performing dynamic facial expression recognition, and an analysis of the relevance of facial parts. The third is an effective method for audio-visual emotion recognition based on speech and facial expressions. The methodology involves a hybrid neural network to extract audio and visual features from videos. For audio extraction, a Convolutional Neural Network (CNN) based on log Mel-spectrogram is used, whereas a CNN built on Census Transform is employed for visual extraction. The audio and visual features are reduced by PCA and LDA, and classified through KNN, SVM, Logistic Regression (LR), and Gaussian Naïve Bayes (GNB). This approach achieves competitive recognition rates, especially in a spontaneous data set. The second last investigates the problem of detecting Down syndrome from photographs. A geometric descriptor is proposed to extract facial features. Experiments performed on a public data set show the effectiveness of the developed methodology. The last methodology is about recognizing genetic disorders in photos. This method focuses on extracting facial features using deep features and anthropometric measurements. Experiments are conducted on a public data set, achieving competitive recognition ratesDoutoradoCiência da ComputaçãoDoutora em Ciência da Computação140532/2019-6CNPQCAPE

Deep Domain Adaptation Learning Framework for Associating Image Features to Tumour Gene Profile

While medical imaging and general pathology are routine in cancer diagnosis, genetic sequencing is not always assessable due to the strong phenotypic and genetic heterogeneity of human cancers. Image-genomics integrates medical imaging and genetics to provide a complementary approach to optimise cancer diagnosis by associating tumour imaging traits with clinical data and has demonstrated its potential in identifying imaging surrogates for tumour biomarkers. However, existing image-genomics research has focused on quantifying tumour visual traits according to human understanding, which may not be optimal across different cancer types. The challenge hence lies in the extraction of optimised imaging representations in an objective data-driven manner. Such an approach requires large volumes of annotated image data that are difficult to acquire. We propose a deep domain adaptation learning framework for associating image features to tumour genetic information, exploiting the ability of domain adaptation technique to learn relevant image features from close knowledge domains. Our proposed framework leverages the current state-of-the-art in image object recognition to provide image features to encode subtle variations of tumour phenotypic characteristics with domain adaptation techniques. The proposed framework was evaluated with current state-of-the-art in: (i) tumour histopathology image classification and; (ii) image-genomics associations. The proposed framework demonstrated improved accuracy of tumour classification, as well as providing additional data-derived representations of tumour phenotypic characteristics that exhibit strong image-genomics association. This thesis advances and indicates the potential of image-genomics research to reveal additional imaging surrogates to genetic biomarkers, which has the potential to facilitate cancer diagnosis

Deep Learning for Brain Age Estimation: A Systematic Review

Over the years, Machine Learning models have been successfully employed on neuroimaging data for accurately predicting brain age. Deviations from the healthy brain aging pattern are associated to the accelerated brain aging and brain abnormalities. Hence, efficient and accurate diagnosis techniques are required for eliciting accurate brain age estimations. Several contributions have been reported in the past for this purpose, resorting to different data-driven modeling methods. Recently, deep neural networks (also referred to as deep learning) have become prevalent in manifold neuroimaging studies, including brain age estimation. In this review, we offer a comprehensive analysis of the literature related to the adoption of deep learning for brain age estimation with neuroimaging data. We detail and analyze different deep learning architectures used for this application, pausing at research works published to date quantitatively exploring their application. We also examine different brain age estimation frameworks, comparatively exposing their advantages and weaknesses. Finally, the review concludes with an outlook towards future directions that should be followed by prospective studies. The ultimate goal of this paper is to establish a common and informed reference for newcomers and experienced researchers willing to approach brain age estimation by using deep learning model