Deep convolutional neural networks for segmenting 3D in vivo multiphoton images of vasculature in Alzheimer disease mouse models

The health and function of tissue rely on its vasculature network to provide reliable blood perfusion. Volumetric imaging approaches, such as multiphoton microscopy, are able to generate detailed 3D images of blood vessels that could contribute to our understanding of the role of vascular structure in normal physiology and in disease mechanisms. The segmentation of vessels, a core image analysis problem, is a bottleneck that has prevented the systematic comparison of 3D vascular architecture across experimental populations. We explored the use of convolutional neural networks to segment 3D vessels within volumetric in vivo images acquired by multiphoton microscopy. We evaluated different network architectures and machine learning techniques in the context of this segmentation problem. We show that our optimized convolutional neural network architecture, which we call DeepVess, yielded a segmentation accuracy that was better than both the current state-of-the-art and a trained human annotator, while also being orders of magnitude faster. To explore the effects of aging and Alzheimer's disease on capillaries, we applied DeepVess to 3D images of cortical blood vessels in young and old mouse models of Alzheimer's disease and wild type littermates. We found little difference in the distribution of capillary diameter or tortuosity between these groups, but did note a decrease in the number of longer capillary segments ($>75\mu m$) in aged animals as compared to young, in both wild type and Alzheimer's disease mouse models.Comment: 34 pages, 9 figure

Optimization of neural networks for deep learning and applications to CT image segmentation

[eng] During the last few years, AI development in deep learning has been going so fast that even important researchers, politicians, and entrepreneurs are signing petitions to try to slow it down. The newest methods for natural language processing and image generation are achieving results so unbelievable that people are seriously starting to think they can be dangerous for society. In reality, they are not dangerous (at the moment) even if we have to admit we reached a point where we have no more control over the flux of data inside the deep networks. It is impossible to open a modern deep neural network and interpret how it processes the information and, in many cases, explain how or why it gives back that particular result. One of the goals of this doctoral work has been to study the behavior of weights in convolutional neural networks and in transformers. We hereby present a work that demonstrates how to invert 3x3 convolutions after training a neural network able to learn how to classify images, with the future aim of having precisely invertible convolutional neural networks. We demonstrate that a simple network can learn to classify images on an open-source dataset without loss in accuracy, with respect to a non-invertible one. All that with the ability to reconstruct the original image without detectable error (on 8-bit images) in up to 20 convolutions stacked in a row. We present a thorough comparison between our method and the standard. We tested the performances of the five most used transformers for image classification on an open- source dataset. Studying the embedded matrices, we have been able to provide two criteria that can help transformers learn with a training time reduction of up to 30% and with no impact on classification accuracy. The evolution of deep learning techniques is also touching the field of digital health. With tens of thousands of new start-ups and more than 1B $ of investments only in the last year, this field is growing rapidly and promising to revolutionize healthcare. In this thesis, we present several neural networks for the segmentation of lungs, lung nodules, and areas affected by pneumonia induced by COVID-19, in chest CT scans. The architecturesm we used are all residual convolutional neural networks inspired by UNet and Inception. We customized them with novel loss functions and layers studied to achieve high performances on these particular applications. The errors on the surface of nodule segmentation masks are not over 1mm in more than 99% of the cases. Our algorithm for COVID-19 lesion detection has a specificity of 100% and overall accuracy of 97.1%. In general, it surpasses the state-of-the-art in all the considered statistics, using UNet as a benchmark. Combining these with other algorithms able to detect and predict lung cancer, the whole work was presented in a European innovation program and judged of high interest by worldwide experts. With this work, we set the basis for the future development of better AI tools in healthcare and scientific investigation into the fundamentals of deep learning.[spa] Durante los últimos años, el desarrollo de la IA en el aprendizaje profundo ha ido tan rápido que Incluso importantes investigadores, políticos y empresarios están firmando peticiones para intentar para ralentizarlo. Los métodos más nuevos para el procesamiento y la generación de imágenes y lenguaje natural, están logrando resultados tan increíbles que la gente está empezando a preocuparse seriamente. Pienso que pueden ser peligrosos para la sociedad. En realidad, no son peligrosos (al menos de momento) incluso si tenemos que admitir que llegamos a un punto en el que ya no tenemos control sobre el flujo de datos dentro de las redes profundas. Es imposible abrir una moderna red neuronal profunda e interpretar cómo procesa la información y, en muchos casos, explique cómo o por qué devuelve ese resultado en particular, uno de los objetivos de este doctorado. El trabajo ha consistido en estudiar el comportamiento de los pesos en redes neuronales convolucionales y en transformadores. Por la presente presentamos un trabajo que demuestra cómo invertir 3x3 convoluciones después de entrenar una red neuronal capaz de aprender a clasificar imágenes, con el objetivo futuro de tener redes neuronales convolucionales precisamente invertibles. Nosotros queremos demostrar que una red simple puede aprender a clasificar imágenes en un código abierto conjunto de datos sin pérdida de precisión, con respecto a uno no invertible. Todo eso con la capacidad de reconstruir la imagen original sin errores detectables (en imágenes de 8 bits) en hasta 20 convoluciones apiladas en fila. Presentamos una exhaustiva comparación entre nuestro método y el estándar. Probamos las prestaciones de los cinco transformadores más utilizados para la clasificación de imágenes en abierto. conjunto de datos de origen. Al estudiar las matrices incrustadas, hemos sido capaz de proporcionar dos criterios que pueden ayudar a los transformadores a aprender con un tiempo de capacitación reducción de hasta el 30% y sin impacto en la precisión de la clasificación. La evolución de las técnicas de aprendizaje profundo también está afectando al campo de la salud digital. Con decenas de miles de nuevas empresas y más de mil millones de dólares en inversiones sólo en el año pasado, este campo está creciendo rápidamente y promete revolucionar la atención médica. En esta tesis, presentamos varias redes neuronales para la segmentación de pulmones, nódulos pulmonares, y zonas afectadas por neumonía inducida por COVID-19, en tomografías computarizadas de tórax. La arquitectura que utilizamos son todas redes neuronales convolucionales residuales inspiradas en UNet. Las personalizamos con nuevas funciones y capas de pérdida, estudiado para lograr altos rendimientos en estas aplicaciones particulares. Los errores en la superficie de las máscaras de segmentación de los nódulos no supera 1 mm en más del 99% de los casos. Nuestro algoritmo para la detección de lesiones de COVID-19 tiene una especificidad del 100% y en general precisión del 97,1%. En general supera el estado del arte en todos los aspectos considerados, estadísticas, utilizando UNet como punto de referencia. Combinando estos con otros algoritmos capaces de detectar y predecir el cáncer de pulmón, todo el trabajo se presentó en una innovación europea programa y considerado de gran interés por expertos de todo el mundo. Con este trabajo, sentamos las bases para el futuro desarrollo de mejores herramientas de IA en Investigación sanitaria y científica sobre los fundamentos del aprendizaje profundo

Image Denoising: Invertible and General Denoising Frameworks

The widespread use of digital cameras has resulted in a massive number of images being taken every day. However, due to the limitations of sensors and environments such as light conditions, the images are usually contaminated by noise. Obtaining visually clean images are essential for the accuracy of downstream high-level vision tasks. Thus, denoising is a crucial preprocessing step. A fundamental challenge in image denoising is to restore recognizable frequencies in edge and fine-scaled texture regions. Traditional methods usually employ hand-crafted priors to enhance the restoration of these high frequency regions, which seem to be omitted in current deep learning models. We explored whether the clean gradients can be utilized in deep networks as a prior as well as how to incorporate this prior in the networks to boost recovery of missing or obscured picture elements. We present results showing that fusing the pre-denoised images' gradient in the shallow layer contributes to recovering better edges and textures. We also propose a regularization loss term to ensure that the reconstructed images' gradients are close to the clean gradients. Both techniques are indispensable for enhancing the restored image frequencies. We also studied how to make the network preserve input information for better restoration of the high-frequency details. According to the definition of mutual information, we presented that invertibility is indispensable for information losslessness. Then, we proposed the Invertible Restoring Autoencoder (IRAE) network, a multiscale invertible encoder-decoder network. The superiority of this network was verified on three different low-level tasks, image denoising, JPEG image decompression and image inpainting. IRAE showed a good direction to explore more invertible architectures for image restoration. We attempted to further reduce the model size of invertible restoration networks. Our intuition was to use the same learned parameters to encode the noisy images in the forward pass and reconstruct the clean images in the backward pass. However, existing invertible networks use the same distribution for both the input and output obtained in the reversed pass. For our noise removal purpose, the input is noisy, but the reversed output is clean, following two different distributions. It was challenging to design lightweight invertible architectures for denoising. We presented InvDN, converting the noisy input to a clean low-resolution image and a noisy latent representation. To address the challenge mentioned above, we replaced the noisy representation with a clean one random sampled from Gaussian during the reverse pass. InvDN achieved state-of-the-art on real image denoising with much fewer parameters and less run time than existing state-of-the-art models. In addition, InvDN could also generate new noisy images for data augmentation. We also rethought image denoising from a novel aspect and introduced a more general denoising framework. Our framework utilized invertible networks to learn a noisy image distribution, which could be considered as the joint distribution of clean content and noise. The noisy input was mapped to representations in the latent space. A novel disentanglement strategy was applied to the latent representations to obtain the representations for the clean content, which were passed to the reversed network to get the clean image. Since this concept was a novel attempt, we also explored different data augmentation and training strategies for this framework. The proposed FDN was trained and tested from simple to complex tasks on distribution-clear class-specific synthetic noisy datasets, more general remote sensing datasets, and real noisy datasets and achieved competitive results with fewer parameters and faster speed. This work contributed a novel perspective and potential direction to design low-level task models in the future

Seamless Multimodal Biometrics for Continuous Personalised Wellbeing Monitoring

Artificially intelligent perception is increasingly present in the lives of every one of us. Vehicles are no exception, (...) In the near future, pattern recognition will have an even stronger role in vehicles, as self-driving cars will require automated ways to understand what is happening around (and within) them and act accordingly. (...) This doctoral work focused on advancing in-vehicle sensing through the research of novel computer vision and pattern recognition methodologies for both biometrics and wellbeing monitoring. The main focus has been on electrocardiogram (ECG) biometrics, a trait well-known for its potential for seamless driver monitoring. Major efforts were devoted to achieving improved performance in identification and identity verification in off-the-person scenarios, well-known for increased noise and variability. Here, end-to-end deep learning ECG biometric solutions were proposed and important topics were addressed such as cross-database and long-term performance, waveform relevance through explainability, and interlead conversion. Face biometrics, a natural complement to the ECG in seamless unconstrained scenarios, was also studied in this work. The open challenges of masked face recognition and interpretability in biometrics were tackled in an effort to evolve towards algorithms that are more transparent, trustworthy, and robust to significant occlusions. Within the topic of wellbeing monitoring, improved solutions to multimodal emotion recognition in groups of people and activity/violence recognition in in-vehicle scenarios were proposed. At last, we also proposed a novel way to learn template security within end-to-end models, dismissing additional separate encryption processes, and a self-supervised learning approach tailored to sequential data, in order to ensure data security and optimal performance. (...)Comment: Doctoral thesis presented and approved on the 21st of December 2022 to the University of Port