Multimodal representation learning with neural networks

Abstract: Representation learning methods have received a lot of attention by researchers and practitioners because of their successful application to complex problems in areas such as computer vision, speech recognition and text processing [1]. Many of these promising results are due to the development of methods to automatically learn the representation of complex objects directly from large amounts of sample data [2]. These efforts have concentrated on data involving one type of information (images, text, speech, etc.), despite data being naturally multimodal. Multimodality refers to the fact that the same real-world concept can be described by different views or data types. Addressing multimodal automatic analysis faces three main challenges: feature learning and extraction, modeling of relationships between data modalities and scalability to large multimodal collections [3, 4]. This research considers the problem of leveraging multiple sources of information or data modalities in neural networks. It defines a novel model called gated multimodal unit (GMU), designed as an internal unit in a neural network architecture whose purpose is to find an intermediate representation based on a combination of data from different modalities. The GMU learns to decide how modalities influence the activation of the unit using multiplicative gates. The GMU can be used as a building block for different kinds of neural networks and can be seen as a form of intermediate fusion. The model was evaluated on four supervised learning tasks in conjunction with fully-connected and convolutional neural networks. We compare the GMU with other early and late fusion methods, outperforming classification scores in the evaluated datasets. Strategies to understand how the model gives importance to each input were also explored. By measuring correlation between gate activations and predictions, we were able to associate modalities with classes. It was found that some classes were more correlated with some particular modality. Interesting findings in genre prediction show, for instance, that the model associates the visual information with animation movies while textual information is more associated with drama or romance movies. During the development of this project, three new benchmark datasets were built and publicly released. The BCDR-F03 dataset which contains 736 mammography images and serves as benchmark for mass lesion classification. The MM-IMDb dataset containing around 27000 movie plots, poster along with 50 metadata annotations and that motivates new research in multimodal analysis. And the Goodreads dataset, a collection of 1000 books that encourages the research on success prediction based on the book content. This research also facilitates reproducibility of the present work by releasing source code implementation of the proposed methods.Doctorad

Representation learning for histopathology image analysis

Abstract. Nowadays, automatic methods for image representation and analysis have been successfully applied in several medical imaging problems leading to the emergence of novel research areas like digital pathology and bioimage informatics. The main challenge of these methods is to deal with the high visual variability of biological structures present in the images, which increases the semantic gap between their visual appearance and their high level meaning. Particularly, the visual variability in histopathology images is also related to the noise added by acquisition stages such as magnification, sectioning and staining, among others. Many efforts have focused on the careful selection of the image representations to capture such variability. This approach requires expert knowledge as well as hand-engineered design to build good feature detectors that represent the relevant visual information. Current approaches in classical computer vision tasks have replaced such design by the inclusion of the image representation as a new learning stage called representation learning. This paradigm has outperformed the state-of-the-art results in many pattern recognition tasks like speech recognition, object detection, and image scene classification. The aim of this research was to explore and define a learning-based histopathology image representation strategy with interpretative capabilities. The main contribution was a novel approach to learn the image representation for cancer detection. The proposed approach learns the representation directly from a Basal-cell carcinoma image collection in an unsupervised way and was extended to extract more complex features from low-level representations. Additionally, this research proposed the digital staining module, a complementary interpretability stage to support diagnosis through a visual identification of discriminant and semantic features. Experimental results showed a performance of 92% in F-Score, improving the state-of-the-art representation by 7%. This research concluded that representation learning improves the feature detectors generalization as well as the performance for the basal cell carcinoma detection task. As additional contributions, a bag of features image representation was extended and evaluated for Alzheimer detection, obtaining 95% in terms of equal error classification rate. Also, a novel perspective to learn morphometric measures in cervical cells based on bag of features was presented and evaluated obtaining promising results to predict nuclei and cytoplasm areas.Los métodos automáticos para la representación y análisis de imágenes se han aplicado con éxito en varios problemas de imagen médica que conducen a la aparición de nuevas áreas de investigación como la patología digital. El principal desafío de estos métodos es hacer frente a la alta variabilidad visual de las estructuras biológicas presentes en las imágenes, lo que aumenta el vacío semántico entre su apariencia visual y su significado de alto nivel. Particularmente, la variabilidad visual en imágenes de histopatología también está relacionada con el ruido añadido por etapas de adquisición tales como magnificación, corte y tinción entre otros. Muchos esfuerzos se han centrado en la selección de la representacion de las imágenes para capturar dicha variabilidad. Este enfoque requiere el conocimiento de expertos y el diseño de ingeniería para construir buenos detectores de características que representen la información visual relevante. Los enfoques actuales en tareas de visión por computador han reemplazado ese diseño por la inclusión de la representación en la etapa de aprendizaje. Este paradigma ha superado los resultados del estado del arte en muchas de las tareas de reconocimiento de patrones tales como el reconocimiento de voz, la detección de objetos y la clasificación de imágenes. El objetivo de esta investigación es explorar y definir una estrategia basada en el aprendizaje de la representación para imágenes histopatológicas con capacidades interpretativas. La contribución principal de este trabajo es un enfoque novedoso para aprender la representación de la imagen para la detección de cáncer. El enfoque propuesto aprende la representación directamente de una colección de imágenes de carcinoma basocelular en forma no supervisada que permite extraer características más complejas a partir de las representaciones de bajo nivel. También se propone el módulo de tinción digital, una nueva etapa de interpretabilidad para apoyar el diagnóstico a través de una identificación visual de las funciones discriminantes y semánticas. Los resultados experimentales mostraron un rendimiento del 92% en términos de F-Score, mejorando la representación del estado del arte en un 7%. Esta investigación concluye que el aprendizaje de la representación mejora la generalización de los detectores de características así como el desempeño en la detección de carcinoma basocelular. Como contribuciones adicionales, una representación de bolsa de caracteristicas (BdC) fue ampliado y evaluado para la detección de la enfermedad de Alzheimer, obteniendo un 95% en términos de EER. Además, una nueva perspectiva para aprender medidas morfométricas en las células del cuello uterino basado en BdC fue presentada y evaluada obteniendo resultados prometedores para predecir las areás del nucleo y el citoplasma.Maestrí