Breast pectoral muscle segmentation in mammograms using a modified holistically-nested edge detection network

This paper presents a method for automatic breast pectoral muscle segmentation in mediolateral oblique mammograms using a Convolutional Neural Network (CNN) inspired by the Holistically-nested Edge Detection (HED) network. Most of the existing methods in the literature are based on hand-crafted models such as straight-line, curve-based techniques or a combination of both. Unfortunately, such models are insufficient when dealing with complex shape variations of the pectoral muscle boundary and when the boundary is unclear due to overlapping breast tissue. To compensate for these issues, we propose a neural network framework that incorporates multi-scale and multi-level learning, capable of learning complex hierarchical features to resolve spatial ambiguity in estimating the pectoral muscle boundary. For this purpose, we modified the HED network architecture to specifically find ‘contour-like’ objects in mammograms. The proposed framework produced a probability map that can be used to estimate the initial pectoral muscle boundary. Subsequently, we process these maps by extracting morphological properties to find the actual pectoral muscle boundary. Finally, we developed two different post-processing steps to find the actual pectoral muscle boundary. Quantitative evaluation results show that the proposed method is comparable with alternative state-of-the-art methods producing on average values of 94.8 ± 8.5% and 97.5 ± 6.3% for the Jaccard and Dice similarity metrics, respectively, across four different databases

Computer aided detection in mammography

Tese de mestrado integrado. Engenharia Electrotécnica e de Computadores. Faculdade de Engenharia. Universidade do Porto. 201

A Decision Support System (DSS) for Breast Cancer Detection Based on Invariant Feature Extraction, Classification, and Retrieval of Masses of Mammographic Images

This paper presents an integrated system for the breast cancer detection from mammograms based on automated mass detection, classification, and retrieval with a goal to support decision-making by retrieving and displaying the relevant past cases as well as predicting the images as benign or malignant. It is hypothesized that the proposed diagnostic aid would refresh the radiologist’s mental memory to guide them to a precise diagnosis with concrete visualizations instead of only suggesting a second diagnosis like many other CAD systems. Towards achieving this goal, a Graph-Based Visual Saliency (GBVS) method is used for automatic mass detection, invariant features are extracted based on using Non-Subsampled Contourlet transform (NSCT) and eigenvalues of the Hessian matrix in a histogram of oriented gradients (HOG), and finally classification and retrieval are performed based on using Support Vector Machines (SVM) and Extreme Learning Machines (ELM), and a linear combination-based similarity fusion approach. The image retrieval and classification performances are evaluated and compared in the benchmark Digital Database for Screening Mammography (DDSM) of 2604 cases by using both the precision-recall and classification accuracies. Experimental results demonstrate the effectiveness of the proposed system and show the viability of a real-time clinical application

Segmentation, Super-resolution and Fusion for Digital Mammogram Classification

Mammography is one of the most common and effective techniques used by radiologists for the early detection of breast cancer. Recently, computer-aided detection/diagnosis (CAD) has become a major research topic in medical imaging and has been widely applied in clinical situations. According to statics, early detection of cancer can reduce the mortality rates by 30% to 70%, therefore detection and diagnosis in the early stage are very important. CAD systems are designed primarily to assist radiologists in detecting and classifying abnormalities in medical scan images, but the main challenges hindering their wider deployment is the difficulty in achieving accuracy rates that help improve radiologists’ performance. The detection and diagnosis of breast cancer face two main issues: the accuracy of the CAD system, and the radiologists’ performance in reading and diagnosing mammograms. This thesis focused on the accuracy of CAD systems. In particular, we investigated two main steps of CAD systems; pre-processing (enhancement and segmentation), feature extraction and classification. Through this investigation, we make five main contributions to the field of automatic mammogram analysis. In automated mammogram analysis, image segmentation techniques are employed in breast boundary or region-of-interest (ROI) extraction. In most Medio-Lateral Oblique (MLO) views of mammograms, the pectoral muscle represents a predominant density region and it is important to detect and segment out this muscle region during pre-processing because it could be bias to the detection of breast cancer. An important reason for the breast border extraction is that it will limit the search-zone for abnormalities in the region of the breast without undue influence from the background of the mammogram. Therefore, we propose a new scheme for breast border extraction, artifact removal and removal of annotations, which are found in the background of mammograms. This was achieved using an local adaptive threshold that creates a binary mask for the images, followed by the use of morphological operations. Furthermore, an adaptive algorithm is proposed to detect and remove the pectoral muscle automatically. Feature extraction is another important step of any image-based pattern classification system. The performance of the corresponding classification depends very much on how well the extracted features represent the object of interest. We investigated a range of different texture feature sets such as Local Binary Pattern Histogram (LBPH), Histogram of Oriented Gradients (HOG) descriptor, and Gray Level Co-occurrence Matrix (GLCM). We propose the use of multi-scale features based on wavelet and local binary patterns for mammogram classification. We extract histograms of LBP codes from the original image as well as the wavelet sub-bands. Extracted features are combined into a single feature set. Experimental results show that our proposed method of combining LBPH features obtained from the original image and with LBPH features obtained from the wavelet domain increase the classification accuracy (sensitivity and specificity) when compared with LBPH extracted from the original image. The feature vector size could be large for some types of feature extraction schemes and they may contain redundant features that could have a negative effect on the performance of classification accuracy. Therefore, feature vector size reduction is needed to achieve higher accuracy as well as efficiency (processing and storage). We reduced the size of the features by applying principle component analysis (PCA) on the feature set and only chose a small number of eigen components to represent the features. Experimental results showed enhancement in the mammogram classification accuracy with a small set of features when compared with using original feature vector. Then we investigated and propose the use of the feature and decision fusion in mammogram classification. In feature-level fusion, two or more extracted feature sets of the same mammogram are concatenated into a single larger fused feature vector to represent the mammogram. Whereas in decision-level fusion, the results of individual classifiers based on distinct features extracted from the same mammogram are combined into a single decision. In this case the final decision is made by majority voting among the results of individual classifiers. Finally, we investigated the use of super resolution as a pre-processing step to enhance the mammograms prior to extracting features. From the preliminary experimental results we conclude that using enhanced mammograms have a positive effect on the performance of the system. Overall, our combination of proposals outperforms several existing schemes published in the literature

Matching of Mammographic Lesions in Different Breast Projections

De todos os cancros, cancro da mama é o que causa mais mortes entre mulheres. Programas de rastreio do cancro da mama podem ajudar a decrescer esta mortalidade, visto que deteção e tratamento do tumor em fases iniciais aumentam a taxa de sobrevivência. Normalmente, um par de radiologistas fazem a interpretação das mamografias, no entanto o processo é longo e cansativo. Isto incentivou o desenvolvimento de sistemas de diagnósitco auxiliado por computador (CADx), para substituir o segundo radiologista, fazendo melhor uso do tempo de especialistas. No entanto, sistemas CADx são associados a taxas elevadas de falsos positivos, dado que a maior parte detes apenas usam uma vista (craniocaudal ou mediolateral oblique) da mamografia. O radiologista, por sua vez, usa ambas as projeções, baseando o seu diagnóstico em diferenças visíveis entre as duas vistas. Quando se consideram as duas projeções da mamografia, a correspondência de lesões é um passo necessário para se fazer o diagnóstico. No entanto, isto é uma tarefa complexa, dado que podem existir vários candidatos a lesão, em cada uma das vistas, para se fazer correspondência. Neste trabalho, um sistema que faz correspondências entre lesões é proposto. Este é composto por três blocos: detetor de candidatos, extração de caraterísticas e correspondência de lesões. O primeiro é uma replicação do trabalho de Ribli et al., e o seu propósito é detetar possíveis candidatos a lesão. O segundo é a extração de vetores de caraterísticas de cada candidato, quer usando a backbone do detetor de candidatos, quer extraindo caraterísticas mais tradicionais, ou usando uma rede neuronal treinada com a triplet loss para distinguir lesões. O terceiro é o cálculo da distância entre os vetores de caraterísticas, usando também heurísticas para restringir possíveis pares de candidatos incorretos, e a ordenação de distâncias para atribuir a correspondência de cada lesão. Este trabalho oferece várias opções de possíveis extractores de caraterísticas e heurísticas a serem incroporados num sistema CADx que seja baseado em detetores de objetos. O facto do modelo treinado com a triplet loss ser competitivo com os restantos modelos, torna o sistema bastante mais viável, sendo que este oferece a possibilidade de a correspondência ser independente da deteção de candidatos. Heurísticas "hard" e "soft" são introduzidas como métodos para limitar correspondências. O sistema é capaz de fazer correspondências de forma satisfatória, dado que a sua exatidão ( 70%85%) é significativamente maior que a probabilidade aleatória (30%40%) dos dados usados. Heurísticas "hard" têm resultados encorajantes na precision@k, dado que estas rejeitam um número significativo de falsos positivos gerados pelo detetor de lesões.Of all cancer diseases, breast cancer is the most lethal among women. It has been shown that breast cancer screening programs can decrease mortality, since early detection increases the chances of survival. Usually, a pair of radiologists interpret the screening mammograms, however the process is long and exhausting. This has encouraged the development of computer aided diagnosis (CADx) systems to replace the second radiologist, making a better use of human-experts' time. But CADx systems are associated with high false positive rates, since most of them only use one view (craniocaudal or mediolateral oblique) of the screening mammogram. Radiologist, on the other hand, use both views; frequently reasoning about the diagnosis by noticeable differences between the two views. When considering both projections of a mammogram, lesion matching is a necessary step to perform diagnosis. However this is a complex task, since there might be various lesion candidates on both projections to match. In this work, a matching system is proposed. The system is a cascade of three blocks: candidates detector, feature extraction and lesion matching. The first is a replication of Ribli et al.'s Faster R-CNN and its purpose is to find possible lesion candidates. The second is the feature vector extraction of each candidate, either by using the candidates detector's backbone, handcrafted features or a siamese network model trained for distinguish lesions. The third is the calculus of the distance between feature vector, also using some heuristics to restrain possible non-lesion pairs, and the ranking of the distances to match the lesions. This work provides several options of possible feature extractors and heuristics to be incorporated into a CADx system based on object detectors. The fact that the triplet loss trained models obtained competitive results with the other features extractors is valuable, since it offers some independence between the detection and matching tasks. "Hard" heuristics and "soft" heurisitcs are introduced as methods to restrain matching. The system is able to detect matches satisfactorily, since its accuracy (70%85%) is significantly higher than chance level (30%40%). "Hard" heuristics proposals achieved encouraging results on precision@k, due to its match and candidates exclusion methods, which rejects a significant number of false positives generated by the object detector

Healthcare data heterogeneity and its contribution to machine learning performance

Tesis por compendio[EN] The data quality assessment has many dimensions, from those so obvious as the data completeness and consistency to other less evident such as the correctness or the ability to represent the target population. In general, it is possible to classify them as those produced by an external effect, and those that are inherent in the data itself. This work will be focused on those inherent to data, such as the temporal and the multisource variability applied to healthcare data repositories. Every process is usually improved over time, and that has a direct impact on the data distribution. Similarly, how a process is executed in different sources may vary due to many factors, such as the diverse interpretation of standard protocols by human beings or different previous experiences of experts. Artificial Intelligence has become one of the most widely extended technological paradigms in almost all the scientific and industrial fields. Advances not only in models but also in hardware have led to their use in almost all areas of science. Although the solved problems using this technology often have the drawback of not being interpretable, or at least not as much as other classical mathematical or statistical techniques. This motivated the emergence of the "explainable artificial intelligence" concept, that study methods to quantify and visualize the training process of models based on machine learning. On the other hand, real systems may often be represented by large networks (graphs), and one of the most relevant features in such networks is the community or clustering structure. Since sociology, biology, or clinical situations could usually be modeled using graphs, community detection algorithms are becoming more and more extended in a biomedical field. In the present doctoral thesis, contributions have been made in the three above mentioned areas. On the one hand, temporal and multisource variability assessment methods based on information geometry were used to detect variability in data distribution that may hinder data reuse and, hence, the conclusions which can be extracted from them. This methodology's usability was proved by a temporal variability analysis to detect data anomalies in the electronic health records of a hospital over 7 years. Besides, it showed that this methodology could have a positive impact if it applied previously to any study. To this end, firstly, we extracted the variables that highest influenced the intensity of headache in migraine patients using machine learning techniques. One of the principal characteristics of machine learning algorithms is its capability of fitting the training set. In those datasets with a small number of observations, the model can be biased by the training sample. The observed variability, after the application of the mentioned methodology and considering as sources the registries of migraine patients with different headache intensity, served as evidence for the truthfulness of the extracted features. Secondly, such an approach was applied to measure the variability among the gray-level histograms of digital mammographies. We demonstrated that the acquisition device produced the observed variability, and after defining an image preprocessing step, the performance of a deep learning model, which modeled a marker of breast cancer risk estimation, increased. Given a dataset containing the answers to a survey formed by psychometric scales, or in other words, questionnaires to measure psychologic factors, such as depression, cope, etcetera, two deep learning architectures that used the data structure were defined. Firstly, we designed a deep learning architecture using the conceptual structure of such psychometric scales. This architecture was trained to model the happiness degree of the participants, improved the performance compared to classical statistical approaches. A second architecture, automatically designed using community detection in graphs, was not only a contribution[ES] El análisis de la calidad de los datos abarca muchas dimensiones, desde aquellas tan obvias como la completitud y la coherencia, hasta otras menos evidentes como la correctitud o la capacidad de representar a la población objetivo. En general, es posible clasificar estas dimensiones como las producidas por un efecto externo y las que son inherentes a los propios datos. Este trabajo se centrará en la evaluación de aquellas inherentes a los datos en repositorios de datos sanitarios, como son la variabilidad temporal y multi-fuente. Los procesos suelen evolucionar con el tiempo, y esto tiene un impacto directo en la distribución de los datos. Análogamente, la subjetividad humana puede influir en la forma en la que un mismo proceso, se ejecuta en diferentes fuentes de datos, influyendo en su cuantificación o recogida. La inteligencia artificial se ha convertido en uno de los paradigmas tecnológicos más extendidos en casi todos los campos científicos e industriales. Los avances, no sólo en los modelos sino también en el hardware, han llevado a su uso en casi todas las áreas de la ciencia. Es cierto que, los problemas resueltos mediante esta tecnología, suelen tener el inconveniente de no ser interpretables, o al menos, no tanto como otras técnicas de matemáticas o de estadística clásica. Esta falta de interpretabilidad, motivó la aparición del concepto de "inteligencia artificial explicable", que estudia métodos para cuantificar y visualizar el proceso de entrenamiento de modelos basados en aprendizaje automático. Por otra parte, los sistemas reales pueden representarse a menudo mediante grandes redes (grafos), y una de las características más relevantes de esas redes, es la estructura de comunidades. Dado que la sociología, la biología o las situaciones clínicas, usualmente pueden modelarse mediante grafos, los algoritmos de detección de comunidades se están extendiendo cada vez más en el ámbito biomédico. En la presente tesis doctoral, se han hecho contribuciones en los tres campos anteriormente mencionados. Por una parte, se han utilizado métodos de evaluación de variabilidad temporal y multi-fuente, basados en geometría de la información, para detectar la variabilidad en la distribución de los datos que pueda dificultar la reutilización de los mismos y, por tanto, las conclusiones que se puedan extraer. Esta metodología demostró ser útil tras ser aplicada a los registros electrónicos sanitarios de un hospital a lo largo de 7 años, donde se detectaron varias anomalías. Además, se demostró el impacto positivo que este análisis podría añadir a cualquier estudio. Para ello, en primer lugar, se utilizaron técnicas de aprendizaje automático para extraer las características más relevantes, a la hora de clasificar la intensidad del dolor de cabeza en pacientes con migraña. Una de las propiedades de los algoritmos de aprendizaje automático es su capacidad de adaptación a los datos de entrenamiento, en bases de datos en los que el número de observaciones es pequeño, el estimador puede estar sesgado por la muestra de entrenamiento. La variabilidad observada, tras la utilización de la metodología y considerando como fuentes, los registros de los pacientes con diferente intensidad del dolor, sirvió como evidencia de la veracidad de las características extraídas. En segundo lugar, se aplicó para medir la variabilidad entre los histogramas de los niveles de gris de mamografías digitales. Se demostró que esta variabilidad estaba producida por el dispositivo de adquisición, y tras la definición de un preproceso de imagen, se mejoró el rendimiento de un modelo de aprendizaje profundo, capaz de estimar un marcador de imagen del riesgo de desarrollar cáncer de mama. Dada una base de datos que recogía las respuestas de una encuesta formada por escalas psicométricas, o lo que es lo mismo cuestionarios que sirven para medir un factor psicológico, tales como depresión, resiliencia, etc., se definieron nuevas arquitecturas de aprendizaje profundo utilizando la estructura de los datos. En primer lugar, se dise˜no una arquitectura, utilizando la estructura conceptual de las citadas escalas psicom´etricas. Dicha arquitectura, que trataba de modelar el grado de felicidad de los participantes, tras ser entrenada, mejor o la precisión en comparación con otros modelos basados en estadística clásica. Una segunda aproximación, en la que la arquitectura se diseño de manera automática empleando detección de comunidades en grafos, no solo fue una contribución de por sí por la automatización del proceso, sino que, además, obtuvo resultados comparables a su predecesora.[CA] L'anàlisi de la qualitat de les dades comprén moltes dimensions, des d'aquelles tan òbvies com la completesa i la coherència, fins a altres menys evidents com la correctitud o la capacitat de representar a la població objectiu. En general, és possible classificar estes dimensions com les produïdes per un efecte extern i les que són inherents a les pròpies dades. Este treball se centrarà en l'avaluació d'aquelles inherents a les dades en reposadors de dades sanitaris, com són la variabilitat temporal i multi-font. Els processos solen evolucionar amb el temps i açò té un impacte directe en la distribució de les dades. Anàlogament, la subjectivitat humana pot influir en la forma en què un mateix procés, s'executa en diferents fonts de dades, influint en la seua quantificació o arreplega. La intel·ligència artificial s'ha convertit en un dels paradigmes tecnològics més estesos en quasi tots els camps científics i industrials. Els avanços, no sols en els models sinó també en el maquinari, han portat al seu ús en quasi totes les àrees de la ciència. És cert que els problemes resolts per mitjà d'esta tecnologia, solen tindre l'inconvenient de no ser interpretables, o almenys, no tant com altres tècniques de matemàtiques o d'estadística clàssica. Esta falta d'interpretabilitat, va motivar l'aparició del concepte de "inteligencia artificial explicable", que estudia mètodes per a quantificar i visualitzar el procés d'entrenament de models basats en aprenentatge automàtic. D'altra banda, els sistemes reals poden representar-se sovint per mitjà de grans xarxes (grafs) i una de les característiques més rellevants d'eixes xarxes, és l'estructura de comunitats. Atés que la sociologia, la biologia o les situacions clíniques, poden modelar-se usualment per mitjà de grafs, els algoritmes de detecció de comunitats s'estan estenent cada vegada més en l'àmbit biomèdic. En la present tesi doctoral, s'han fet contribucions en els tres camps anteriorment mencionats. D'una banda, s'han utilitzat mètodes d'avaluació de variabilitat temporal i multi-font, basats en geometria de la informació, per a detectar la variabilitat en la distribució de les dades que puga dificultar la reutilització dels mateixos i, per tant, les conclusions que es puguen extraure. Esta metodologia va demostrar ser útil després de ser aplicada als registres electrònics sanitaris d'un hospital al llarg de 7 anys, on es van detectar diverses anomalies. A més, es va demostrar l'impacte positiu que esta anàlisi podria afegir a qualsevol estudi. Per a això, en primer lloc, es van utilitzar tècniques d'aprenentatge automàtic per a extraure les característiques més rellevants, a l'hora de classificar la intensitat del mal de cap en pacients amb migranya. Una de les propietats dels algoritmes d'aprenentatge automàtic és la seua capacitat d'adaptació a les dades d'entrenament, en bases de dades en què el nombre d'observacions és xicotet, l'estimador pot estar esbiaixat per la mostra d'entrenament. La variabilitat observada després de la utilització de la metodologia, i considerant com a fonts els registres dels pacients amb diferent intensitat del dolor, va servir com a evidència de la veracitat de les característiques extretes. En segon lloc, es va aplicar per a mesurar la variabilitat entre els histogrames dels nivells de gris de mamografies digitals. Es va demostrar que esta variabilitat estava produïda pel dispositiu d'adquisició i després de la definició d'un preprocés d'imatge, es va millorar el rendiment d'un model d'aprenentatge profund, capaç d'estimar un marcador d'imatge del risc de desenrotllar càncer de mama. Donada una base de dades que arreplegava les respostes d'una enquesta formada per escales psicomètriques, o el que és el mateix qüestionaris que servixen per a mesurar un factor psicològic, com ara depressió, resiliència, etc., es van definir noves arquitectures d'aprenentatge profund utilitzant l’estructura de les dades. En primer lloc, es disseny`a una arquitectura, utilitzant l’estructura conceptual de les esmentades escales psicom`etriques. La dita arquitectura, que tractava de modelar el grau de felicitat dels participants, despr´es de ser entrenada, va millorar la precisió en comparació amb altres models basats en estad´ıstica cl`assica. Una segona aproximació, en la que l’arquitectura es va dissenyar de manera autoàtica emprant detecció de comunitats en grafs, no sols va ser una contribució de per si per l’automatització del procés, sinó que, a més, va obtindre resultats comparables a la seua predecessora.También me gustaría mencionar al Instituto Tecnológico de la Informáica, en especial al grupo de investigación Percepción, Reconocimiento, Aprendizaje e Inteligencia Artificial, no solo por darme la oportunidad de seguir creciendo en el mundo de la ciencia, sino también, por apoyarme en la consecución de mis objetivos personalesPérez Benito, FJ. (2020). Healthcare data heterogeneity and its contribution to machine learning performance [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/154414TESISCompendi