Anatomical Priors in Convolutional Networks for Unsupervised Biomedical Segmentation

We consider the problem of segmenting a biomedical image into anatomical regions of interest. We specifically address the frequent scenario where we have no paired training data that contains images and their manual segmentations. Instead, we employ unpaired segmentation images to build an anatomical prior. Critically these segmentations can be derived from imaging data from a different dataset and imaging modality than the current task. We introduce a generative probabilistic model that employs the learned prior through a convolutional neural network to compute segmentations in an unsupervised setting. We conducted an empirical analysis of the proposed approach in the context of structural brain MRI segmentation, using a multi-study dataset of more than 14,000 scans. Our results show that an anatomical prior can enable fast unsupervised segmentation which is typically not possible using standard convolutional networks. The integration of anatomical priors can facilitate CNN-based anatomical segmentation in a range of novel clinical problems, where few or no annotations are available and thus standard networks are not trainable. The code is freely available at http://github.com/adalca/neuron.Comment: Presented at CVPR 2018. IEEE CVPR proceedings pp. 9290-929

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Deep Learning Approaches for Data Augmentation in Medical Imaging: A Review

Deep learning has become a popular tool for medical image analysis, but the limited availability of training data remains a major challenge, particularly in the medical field where data acquisition can be costly and subject to privacy regulations. Data augmentation techniques offer a solution by artificially increasing the number of training samples, but these techniques often produce limited and unconvincing results. To address this issue, a growing number of studies have proposed the use of deep generative models to generate more realistic and diverse data that conform to the true distribution of the data. In this review, we focus on three types of deep generative models for medical image augmentation: variational autoencoders, generative adversarial networks, and diffusion models. We provide an overview of the current state of the art in each of these models and discuss their potential for use in different downstream tasks in medical imaging, including classification, segmentation, and cross-modal translation. We also evaluate the strengths and limitations of each model and suggest directions for future research in this field. Our goal is to provide a comprehensive review about the use of deep generative models for medical image augmentation and to highlight the potential of these models for improving the performance of deep learning algorithms in medical image analysis

Advancing Land Cover Mapping in Remote Sensing with Deep Learning

Automatic mapping of land cover in remote sensing data plays an increasingly significant role in several earth observation (EO) applications, such as sustainable development, autonomous agriculture, and urban planning. Due to the complexity of the real ground surface and environment, accurate classification of land cover types is facing many challenges. This thesis provides novel deep learning-based solutions to land cover mapping challenges such as how to deal with intricate objects and imbalanced classes in multi-spectral and high-spatial resolution remote sensing data. The first work presents a novel model to learn richer multi-scale and global contextual representations in very high-resolution remote sensing images, namely the dense dilated convolutions' merging (DDCM) network. The proposed method is light-weighted, flexible and extendable, so that it can be used as a simple yet effective encoder and decoder module to address different classification and semantic mapping challenges. Intensive experiments on different benchmark remote sensing datasets demonstrate that the proposed method can achieve better performance but consume much fewer computation resources compared with other published methods. Next, a novel graph model is developed for capturing long-range pixel dependencies in remote sensing images to improve land cover mapping. One key component in the method is the self-constructing graph (SCG) module that can effectively construct global context relations (latent graph structure) without requiring prior knowledge graphs. The proposed SCG-based models achieved competitive performance on different representative remote sensing datasets with faster training and lower computational cost compared to strong baseline models. The third work introduces a new framework, namely the multi-view self-constructing graph (MSCG) network, to extend the vanilla SCG model to be able to capture multi-view context representations with rotation invariance to achieve improved segmentation performance. Meanwhile, a novel adaptive class weighting loss function is developed to alleviate the issue of class imbalance commonly found in EO datasets for semantic segmentation. Experiments on benchmark data demonstrate the proposed framework is computationally efficient and robust to produce improved segmentation results for imbalanced classes. To address the key challenges in multi-modal land cover mapping of remote sensing data, namely, 'what', 'how' and 'where' to effectively fuse multi-source features and to efficiently learn optimal joint representations of different modalities, the last work presents a compact and scalable multi-modal deep learning framework (MultiModNet) based on two novel modules: the pyramid attention fusion module and the gated fusion unit. The proposed MultiModNet outperforms the strong baselines on two representative remote sensing datasets with fewer parameters and at a lower computational cost. Extensive ablation studies also validate the effectiveness and flexibility of the framework

Methods for generating and evaluating synthetic longitudinal patient data: a systematic review

The proliferation of data in recent years has led to the advancement and utilization of various statistical and deep learning techniques, thus expediting research and development activities. However, not all industries have benefited equally from the surge in data availability, partly due to legal restrictions on data usage and privacy regulations, such as in medicine. To address this issue, various statistical disclosure and privacy-preserving methods have been proposed, including the use of synthetic data generation. Synthetic data are generated based on some existing data, with the aim of replicating them as closely as possible and acting as a proxy for real sensitive data. This paper presents a systematic review of methods for generating and evaluating synthetic longitudinal patient data, a prevalent data type in medicine. The review adheres to the PRISMA guidelines and covers literature from five databases until the end of 2022. The paper describes 17 methods, ranging from traditional simulation techniques to modern deep learning methods. The collected information includes, but is not limited to, method type, source code availability, and approaches used to assess resemblance, utility, and privacy. Furthermore, the paper discusses practical guidelines and key considerations for developing synthetic longitudinal data generation methods

Locality and compositionality in representation learning for complex visual tasks

L'utilisation d'architectures neuronales profondes associée à des innovations spécifiques telles que les méthodes adversarielles, l’entraînement préalable sur de grands ensembles de données et l'estimation de l'information mutuelle a permis, ces dernières années, de progresser rapidement dans de nombreuses tâches de vision par ordinateur complexes telles que la classification d'images de catégories préalablement inconnues (apprentissage zéro-coups), la génération de scènes ou la classification multimodale. Malgré ces progrès, il n’est pas certain que les méthodes actuelles d’apprentissage de représentations suffiront à atteindre une performance équivalente au niveau humain sur des tâches visuelles arbitraires et, de fait, cela pose des questions quant à la direction de la recherche future. Dans cette thèse, nous nous concentrerons sur deux aspects des représentations qui semblent nécessaires pour atteindre de bonnes performances en aval pour l'apprentissage des représentations : la localité et la compositionalité. La localité peut être comprise comme la capacité d'une représentation à retenir des informations locales. Ceci sera pertinent dans de nombreux cas, et bénéficiera particulièrement à la vision informatique, domaine dans lequel les images naturelles comportent intrinsèquement des informations locales, par exemple des parties pertinentes d’une image, des objets multiples présents dans une scène... D'autre part, une représentation compositionnelle peut être comprise comme une représentation qui résulte d'une combinaison de parties plus simples. Les réseaux neuronaux convolutionnels sont intrinsèquement compositionnels, et de nombreuses images complexes peuvent être considérées comme la composition de sous-composantes pertinentes : les objets et attributs individuels dans une scène, les attributs sémantiques dans l'apprentissage zéro-coups en sont deux exemples. Nous pensons que ces deux propriétés détiennent la clé pour concevoir de meilleures méthodes d'apprentissage de représentations. Dans cette thèse, nous présentons trois articles traitant de la localité et/ou de la compositionnalité, et de leur application à l'apprentissage de représentations pour des tâches visuelles complexes. Dans le premier article, nous introduisons des méthodes de mesure de la localité et de la compositionnalité pour les représentations d'images, et nous démontrons que les représentations locales et compositionnelles sont plus performantes dans l'apprentissage zéro-coups. Nous utilisons également ces deux notions comme base pour concevoir un nouvel algorithme d'apprentissage des représentations qui atteint des performances de pointe dans notre cadre expérimental, une variante de l'apprentissage "zéro-coups" plus difficile où les informations externes, par exemple un pré-entraînement sur d'autres ensembles de données d'images, ne sont pas autorisées. Dans le deuxième article, nous montrons qu'en encourageant un générateur à conserver des informations locales au niveau de l'objet, à l'aide d'un module dit de similarité de graphes de scène, nous pouvons améliorer les performances de génération de scènes. Ce modèle met également en évidence l'importance de la composition, car de nombreux composants fonctionnent individuellement sur chaque objet présent. Pour démontrer pleinement la portée de notre approche, nous effectuons une analyse détaillée et proposons un nouveau cadre pour évaluer les modèles de génération de scènes. Enfin, dans le troisième article, nous montrons qu'en encourageant une forte information mutuelle entre les représentations multimodales locales et globales des images médicales en 2D et 3D, nous pouvons améliorer la classification et la segmentation des images. Ce cadre général peut être appliqué à une grande variété de contextes et démontre les avantages non seulement de la localité, mais aussi de la compositionnalité, car les représentations multimodales sont combinées pour obtenir une représentation plus générale.The use of deep neural architectures coupled with specific innovations such as adversarial methods, pre-training on large datasets and mutual information estimation has in recent years allowed rapid progress in many complex vision tasks such as zero-shot learning, scene generation, or multi-modal classification. Despite such progress, it is still not clear if current representation learning methods will be enough to attain human-level performance on arbitrary visual tasks, and if not, what direction should future research take. In this thesis, we will focus on two aspects of representations that seem necessary to achieve good downstream performance for representation learning: locality and compositionality. Locality can be understood as a representation's ability to retain local information. This will be relevant in many cases, and will specifically benefit computer vision where natural images inherently feature local information, i.e. relevant patches of an image, multiple objects present in a scene... On the other hand, a compositional representation can be understood as one that arises from a combination of simpler parts. Convolutional neural networks are inherently compositional, and many complex images can be seen as composition of relevant sub-components: individual objects and attributes in a scene, semantic attributes in zero-shot learning are two examples. We believe both properties hold the key to designing better representation learning methods. In this thesis, we present 3 articles dealing with locality and/or compositionality, and their application to representation learning for complex visual tasks. In the first article, we introduce ways of measuring locality and compositionality for image representations, and demonstrate that local and compositional representations perform better at zero-shot learning. We also use these two notions as the basis for designing class-matching deep info-max, a novel representation learning algorithm that achieves state-of-the-art performance on our proposed "Zero-shot from scratch" setting, a harder zero-shot setting where external information, e.g. pre-training on other image datasets is not allowed. In the second article, we show that by encouraging a generator to retain local object-level information, using a scene-graph similarity module, we can improve scene generation performance. This model also showcases the importance of compositionality as many components operate individually on each object present. To fully demonstrate the reach of our approach, we perform detailed analysis, and propose a new framework to evaluate scene generation models. Finally, in the third article, we show that encouraging high mutual information between local and global multi-modal representations of 2D and 3D medical images can lead to improvements in image classification and segmentation. This general framework can be applied to a wide variety of settings, and demonstrates the benefits of not only locality, but also of compositionality as multi-modal representations are combined to obtain a more general one