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Deep learning methods are increasingly becoming instrumental as modeling tools in computational neuroscience, employing optimality principles to build bridges between neural responses and perception or behavior. Developing models that adequately represent uncertainty is however challenging for deep learning methods, which often suffer from calibration problems. This constitutes a difficulty in particular when modeling cortical circuits in terms of Bayesian inference, beyond single point estimates such as the posterior mean or the maximum a posteriori. In this work we systematically studied uncertainty representations in latent representations of variational auto-encoders (VAEs), both in a perceptual task from natural images and in two other canonical tasks of computer vision, finding a poor alignment between uncertainty and informativeness or ambiguities in the images. We next showed how a novel approach which we call explaining-away variational auto-encoders (EA-VAEs), fixes these issues, producing meaningful reports of uncertainty in a variety of scenarios, including interpolation, image corruption, and even out-of-distribution detection. We show EA-VAEs may prove useful both as models of perception in computational neuroscience and as inference tools in computer vision.

Cardiovascular magnetic resonance imaging is emerging as a crucial tool to examine cardiac morphology and function. Essential to this endeavour are anatomical 3D surface and volumetric meshes derived from CMR images, which facilitate computational anatomy studies, biomarker discovery, and in-silico simulations. However, conventional surface mesh generation methods, such as active shape models and multi-atlas segmentation, are highly time-consuming and require complex processing pipelines to generate simulation-ready 3D meshes. In response, we introduce HybridVNet, a novel architecture for direct image-to-mesh extraction seamlessly integrating standard convolutional neural networks with graph convolutions, which we prove can efficiently handle surface and volumetric meshes by encoding them as graph structures. To further enhance accuracy, we propose a multiview HybridVNet architecture which processes both long axis and short axis CMR, showing that it can increase the performance of cardiac MR mesh generation. Our model combines traditional convolutional networks with variational graph generative models, deep supervision and mesh-specific regularisation. Experiments on a comprehensive dataset from the UK Biobank confirm the potential of HybridVNet to significantly advance cardiac imaging and computational cardiology by efficiently generating high-fidelity and simulation ready meshes from CMR images.

It has recently been shown that deep learning models for anatomical segmentation in medical images can exhibit biases against certain sub-populations defined in terms of protected attributes like sex or ethnicity. In this context, auditing fairness of deep segmentation models becomes crucial. However, such audit process generally requires access to ground-truth segmentation masks for the target population, which may not always be available, especially when going from development to deployment. Here we propose a new method to anticipate model biases in biomedical image segmentation in the absence of ground-truth annotations. Our unsupervised bias discovery method leverages the reverse classification accuracy framework to estimate segmentation quality. Through numerical experiments in synthetic and realistic scenarios we show how our method is able to successfully anticipate fairness issues in the absence of ground-truth labels, constituting a novel and valuable tool in this field., Comment: Accepted for publication at FAIMI 2023 (Fairness of AI in Medical Imaging) at MICCAI

The development of successful artificial intelligence models for chest X-ray analysis relies on large, diverse datasets with high-quality annotations. While several databases of chest X-ray images have been released, most include disease diagnosis labels but lack detailed pixel-level anatomical segmentation labels. To address this gap, we introduce an extensive chest X-ray multi-center segmentation dataset with uniform and fine-grain anatomical annotations for images coming from five well-known publicly available databases: ChestX-ray8, Chexpert, MIMIC-CXR-JPG, Padchest, and VinDr-CXR, resulting in 657,566 segmentation masks. Our methodology utilizes the HybridGNet model to ensure consistent and high-quality segmentations across all datasets. Rigorous validation, including expert physician evaluation and automatic quality control, was conducted to validate the resulting masks. Additionally, we provide individualized quality indices per mask and an overall quality estimation per dataset. This dataset serves as a valuable resource for the broader scientific community, streamlining the development and assessment of innovative methodologies in chest X-ray analysis. The CheXmask dataset is publicly available at: https://physionet.org/content/chexmask-cxr-segmentation-data/, Comment: The CheXmask dataset is publicly available at https://physionet.org/content/chexmask-cxr-segmentation-data/

Learning anatomical segmentation from heterogeneous labels in multi-center datasets is a common situation encountered in clinical scenarios, where certain anatomical structures are only annotated in images coming from particular medical centers, but not in the full database. Here we first show how state-of-the-art pixel-level segmentation models fail in naively learning this task due to domain memorization issues and conflicting labels. We then propose to adopt HybridGNet, a landmark-based segmentation model which learns the available anatomical structures using graph-based representations. By analyzing the latent space learned by both models, we show that HybridGNet naturally learns more domain-invariant feature representations, and provide empirical evidence in the context of chest X-ray multiclass segmentation. We hope these insights will shed light on the training of deep learning models with heterogeneous labels from public and multi-center datasets.

Precision livestock farming optimizes livestock production through the use of sensor information and communication technologies to support decision making, proactively and near real-time. Among available technologies to monitor foraging behavior, the acoustic method has been highly reliable and repeatable, but can be subject to further computational improvements to increase precision and specificity of recognition of foraging activities. In this study, an algorithm called Jaw Movement segment-based Foraging Activity Recognizer (JMFAR) is proposed. The method is based on the computation and analysis of temporal, statistical and spectral features of jaw movement sounds for detection of rumination and grazing bouts. They are called JM-segment features because they are extracted from a sound segment and expect to capture JM information of the whole segment rather than individual JMs. Two variants of the method are proposed and tested: (i) the temporal and statistical features only JMFAR-ns; and (ii) a feature selection process (JMFAR-sel). The JMFAR was tested on signals registered in a free grazing environment, achieving an average weighted F1-score of 93%. Then, it was compared with a state-of-the-art algorithm, showing improved performance for estimation of grazing bouts (+19%). The JMFAR-ns variant reduced the computational cost by 25.4%, but achieved a slightly lower performance than the JMFAR. The good performance and low computational cost of JMFAR-ns supports the feasibility of using this algorithm variant for real-time implementation in low-cost embedded systems. The method presented within this publication is protected by a pending patent application: AR P20220100910., Comment: Preprint submitted to journal

Anatomical segmentation is a fundamental task in medical image computing, generally tackled with fully convolutional neural networks which produce dense segmentation masks. These models are often trained with loss functions such as cross-entropy or Dice, which assume pixels to be independent of each other, thus ignoring topological errors and anatomical inconsistencies. We address this limitation by moving from pixel-level to graph representations, which allow to naturally incorporate anatomical constraints by construction. To this end, we introduce HybridGNet, an encoder-decoder neural architecture that leverages standard convolutions for image feature encoding and graph convolutional neural networks (GCNNs) to decode plausible representations of anatomical structures. We also propose a novel image-to-graph skip connection layer which allows localized features to flow from standard convolutional blocks to GCNN blocks, and show that it improves segmentation accuracy. The proposed architecture is extensively evaluated in a variety of domain shift and image occlusion scenarios, and audited considering different types of demographic domain shift. Our comprehensive experimental setup compares HybridGNet with other landmark and pixel-based models for anatomical segmentation in chest x-ray images, and shows that it produces anatomically plausible results in challenging scenarios where other models tend to fail., Comment: Source code at https://github.com/ngaggion/HybridGNet Accepted for publication at IEEE TMI

In real-life applications, machine learning models often face scenarios where there is a change in data distribution between training and test domains. When the aim is to make predictions on distributions different from those seen at training, we incur in a domain generalization problem. Methods to address this issue learn a model using data from multiple source domains, and then apply this model to the unseen target domain. Our hypothesis is that when training with multiple domains, conflicting gradients within each mini-batch contain information specific to the individual domains which is irrelevant to the others, including the test domain. If left untouched, such disagreement may degrade generalization performance. In this work, we characterize the conflicting gradients emerging in domain shift scenarios and devise novel gradient agreement strategies based on gradient surgery to alleviate their effect. We validate our approach in image classification tasks with three multi-domain datasets, showing the value of the proposed agreement strategy in enhancing the generalization capability of deep learning models in domain shift scenarios., Comment: Accepted for publication at ICCV 2021

Theories for autism spectrum disorder (ASD) have been formulated at different levels: ranging from physiological observations to perceptual and behavioral descriptions. Understanding the physiological underpinnings of perceptual traits in ASD remains a significant challenge in the field. Here we show how a recurrent neural circuit model which was optimized to perform sampling-based inference and displays characteristic features of cortical dynamics can help bridge this gap. The model was able to establish a mechanistic link between two descriptive levels for ASD: a physiological level, in terms of inhibitory dysfunction, neural variability and oscillations, and a perceptual level, in terms of hypopriors in Bayesian computations. We took two parallel paths: inducing hypopriors in the probabilistic model, and an inhibitory dysfunction in the network model, which lead to consistent results in terms of the represented posteriors, providing support for the view that both descriptions might constitute two sides of the same coin., Comment: Accepted for publication in Network Neuroscience

Deformable image registration is a fundamental problem in the field of medical image analysis. During the last years, we have witnessed the advent of deep learning-based image registration methods which achieve state-of-the-art performance, and drastically reduce the required computational time. However, little work has been done regarding how can we encourage our models to produce not only accurate, but also anatomically plausible results, which is still an open question in the field. In this work, we argue that incorporating anatomical priors in the form of global constraints into the learning process of these models, will further improve their performance and boost the realism of the warped images after registration. We learn global non-linear representations of image anatomy using segmentation masks, and employ them to constraint the registration process. The proposed AC-RegNet architecture is evaluated in the context of chest X-ray image registration using three different datasets, where the high anatomical variability makes the task extremely challenging. Our experiments show that the proposed anatomically constrained registration model produces more realistic and accurate results than state-of-the-art methods, demonstrating the potential of this approach., Comment: Accepted for publication in Neural Networks (Elsevier). Source code and resulting segmentation masks for the NIH Chest-XRay14 dataset with estimated quality index available at https://github.com/lucasmansilla/ACRN_Chest_X-ray_IA

Markov networks are extensively used to model complex sequential, spatial, and relational interactions in a wide range of fields. By learning the structure of independences of a domain, more accurate joint probability distributions can be obtained for inference tasks or, more directly, for interpreting the most significant relations among the variables. Recently, several researchers have investigated techniques for automatically learning the structure from data by obtaining the probabilistic maximum-a-posteriori structure given the available data. However, all the approximations proposed decompose the posterior of the whole structure into local sub-problems, by assuming that the posteriors of the Markov blankets of all the variables are mutually independent. In this work, we propose a scoring function for relaxing such assumption. The Blankets Joint Posterior score computes the joint posterior of structures as a joint distribution of the collection of its Markov blankets. Essentially, the whole posterior is obtained by computing the posterior of the blanket of each variable as a conditional distribution that takes into account information from other blankets in the network. We show in our experimental results that the proposed approximation can improve the sample complexity of state-of-the-art scores when learning complex networks, where the independence assumption between blanket variables is clearly incorrect., Comment: 33 pages, 5 figures

Detection of desaturations on the pulse oximetry signal is of great importance for the diagnosis of sleep apneas. Using the counting of desaturations, an index can be built to help in the diagnosis of severe cases of obstructive sleep apnea-hypopnea syndrome. It is important to have automatic detection methods that allows the screening for this syndrome, reducing the need of the expensive polysomnography based studies. In this paper a novel recognition method based on the empirical mode decomposition of the pulse oximetry signal is proposed. The desaturations produce a very specific wave pattern that is extracted in the modes of the decomposition. Using this information, a detector based on properly selected thresholds and a set of simple rules is built. The oxygen desaturation index constructed from these detections produces a detector for obstructive sleep apnea-hypopnea syndrome with high sensitivity ($0.838$) and specificity ($0.855$) and yields better results than standard desaturation detection approaches., Comment: Accepted in Medical Engineering and Physics