Variational autoencoders (VAE) encode data into lower-dimensional latent vectors before decoding those vectors back to data. Once trained, decoding a random latent vector from the prior usually does not produce meaningful data, at least when the latent space has more than a dozen dimensions. In this paper, we investigate this issue by drawing insight from high dimensional statistics: in these regimes, the latent vectors of a standard VAE are by construction distributed uniformly on a hypersphere. We propose to formulate the latent variables of a VAE using hyperspherical coordinates, which allows compressing the latent vectors towards an island on the hypersphere, thereby reducing the latent sparsity and we show that this improves the generation ability of the VAE. We propose a new parameterization of the latent space with limited computational overhead.

Managing chronic wounds is a global challenge that can be alleviated by the adoption of automatic systems for clinical wound assessment from consumer-grade videos. While 2D image analysis approaches are insufficient for handling the 3D features of wounds, existing approaches utilizing 3D reconstruction methods have not been thor-oughly evaluated. To address this gap, this paper presents a comprehensive study on 3D wound reconstruction from consumer-grade videos. Specifically, we introduce the SALVE dataset, comprising video recordings of realistic wound phantoms captured with different cameras. Using this dataset, we assess the accuracy and precision of state-of-the-art methods for 3D reconstruction, ranging from traditional photogrammetry pipelines to advanced neural rendering approaches. In our experiments, we observe that photogrammetry approaches do not provide smooth surfaces suitable for precise clinical measurements of wounds. Neural rendering approaches show promise in addressing this issue, advancing the use of this technology in wound care practices. We encourage the readers to visit the project page: https://rcmichierchia.github.io/SALVE/.

Neural Rendering representations have significantly contributed to the field of 3D computer vision. Given their potential, considerable efforts have been invested to improve their performance. Nonetheless, the essential question of selecting training views is yet to be thoroughly investigated. This key aspect plays a vital role in achieving high-quality results and aligns with the well-known tenet of deep learning: “garbage in, garbage out”. In this paper, we first illustrate the importance of view selection by demonstrating how a simple rotation of the test views within the most pervasive NeRF dataset can lead to consequential shifts in the performance rankings of state-of-the-art techniques. To address this challenge, we introduce a unified framework for view selection methods and devise a thorough benchmark to assess its impact. Significant improvements can be achieved without leveraging error or uncertainty estimation but focusing on uniform view coverage of the reconstructed object, resulting in a training-free approach. Using this technique, we show that high-quality renderings can be achieved faster by using fewer views. We conduct extensive experiments on both synthetic datasets and realistic data to demonstrate the effectiveness of our proposed method compared with random, conventional error-based, and uncertainty-guided view selection.

Saliency methods are critical tools that allow the estimation of the most important features of an input image that contribute to the network’s prediction. These tools are pivotal in high-stakes applications such as medical diagnosis or autonomous driving. Additionally, these tools can help identify models’ biasedness, such as a strong prior on object placement, easily distinguishable background features, or frequent object co-occurrence. We introduce RankPix, a novel saliency method for visual bias identification in image classification tasks. RankPix is a derivative-free approach that allows the identification of a minimum subset of pixels/features at a given network layer that changes the output of a classifier. Surprisingly, this approaches provides equivalent performance to gradient-based approaches on the standard pointing game benchmark. More interestingly, RankPix outperforms traditional approaches for systematic bias identification.

Deep learning models are powerful tools for addressing challenging medical imaging problems. However, for an ever-growing range of applications, interpreting a model’s prediction remains non-trivial. Understanding decisions made by black-box algorithms is critical, and assessing their fairness and susceptibility to bias is a key step towards healthcare deployment. In this paper, we propose DBCE (Deformation Based Counterfactual Explainability). We optimise a diffeomorphic transformation that deforms a given input image to change the prediction of the model. This provides anatomically meaningful saliency maps indicating tissue atrophy and expansion, which can be easily interpreted by clinicians. In our test case, DBCE replicates the transition of a patient from healthy control (HC) to Alzheimer’s disease (AD). We benchmark DBCE against three commonly used saliency methods. We show that it provides more meaningful saliency maps when applied to one subject and disease-consistent atrophy patterns when used over a larger cohort. In addition, our method fulfils a recent sanity check and is repeatable for different model initialisations in contrast to classical sensitivity-based methods.

Cortical thickness (CTh) is routinely used to quantify grey matter atrophy as it is a significant biomarker in studying neurodegenerative and neurological conditions. Clinical studies commonly employ one of several available CTh estimation software tools to estimate CTh from brain MRI scans. In recent years, machine learning-based methods emerged as a faster alternative to the main-stream CTh estimation methods (e.g. FreeSurfer). Evaluation and comparison of CTh estimation methods often include various metrics and downstream tasks, but none fully covers the sensitivity to sub-voxel atrophy characteristic of neurodegeneration. In addition, current evaluation methods do not provide a framework for the intra-method region-wise evaluation of CTh estimation methods. Therefore, we propose a method for brain MRI synthesis capable of generating a range of sub-voxel atrophy levels (global and local) with quantifiable changes from the baseline scan. We further create a synthetic test set and evaluate four different CTh estimation methods: FreeSurfer (cross-sectional), FreeSurfer (longitudinal), DL+DiReCT and HerstonNet. DL+DiReCT showed superior sensitivity to sub-voxel atrophy over other methods in our testing framework. The obtained results indicate that our synthetic test set is suitable for benchmarking CTh estimation methods on both global and local scales as well as regional inter-and intra-method performance comparison.

Recent advances in geometric deep-learning introduce complex computational challenges for evaluating the distance between meshes. From a mesh model, point clouds are necessary along with a robust distance metric to assess surface quality or as part of the loss function for training models. Current methods often rely on a uniform random mesh discretization, which yields irregular sampling and noisy distance estimation. In this paper we introduce MongeNet, a fast and optimal transport based sampler that allows for an accurate discretization of a mesh with better approximation properties. We compare our method to the ubiquitous random uniform sampling and show that the approximation error is almost half with a very small computational overhead.

In this paper, we introduce CorticalFlow, a new geometric deep-learning model that, given a 3-dimensional image, learns to deform a reference template towards a targeted object. To conserve the template mesh’s topological properties, we train our model over a set of diffeomorphic transformations. This new implementation of a flow Ordinary Differential Equation (ODE) framework benefits from a small GPU memory footprint, allowing the generation of surfaces with several hundred thousand vertices. To reduce topological errors introduced by its discrete resolution, we derive numeric conditions which improve the manifoldness of the predicted triangle mesh. To exhibit the utility of CorticalFlow, we demonstrate its performance for the challenging task of brain cortical surface reconstruction. In contrast to the current state-of-the-art, CorticalFlow produces superior surfaces while reducing the computation time from nine and a half minutes to one second. More significantly, CorticalFlow enforces the generation of anatomically plausible surfaces; the absence of which has been a major impediment restricting the clinical relevance of such surface reconstruction methods.

The study of neurodegenerative diseases relies on the reconstruction and analysis of the brain cortex from magnetic resonance imaging (MRI). Traditional frameworks for this task like FreeSurfer demand lengthy runtimes, while its accelerated variant FastSurfer still relies on a voxel-wise segmentation which is limited by its resolution to capture narrow continuous objects as cortical surfaces. Having these limitations in mind, we propose DeepCSR, a 3D deep learning framework for cortical surface reconstruction from MRI. Towards this end, we train a neural network model with hypercolumn features to predict implicit surface representations for points in a brain template space. After training, the cortical surface at a desired level of detail is obtained by evaluating surface representations at specific coordinates, and subsequently applying a topology correction algorithm and an isosurface extraction method. Thanks to the continuous nature of this approach and the efficacy of its hypercolumn features scheme, DeepCSR efficiently reconstructs cortical surfaces at high resolution capturing fine details in the cortical folding. Moreover, DeepCSR is as accurate, more precise, and faster than the widely used FreeSurfer toolbox and its deep learning powered variant FastSurfer on reconstructing cortical surfaces from MRI which should facilitate large-scale medical studies and new healthcare applications.

We propose a fast and scalable algorithm to project a given density on a set of structured measures defined over a compact 2D domain. The measures can be discrete or supported on curves, for instance. The proposed principle and algorithm are a natural generalization of previous results revolving around the generation of blue-noise point distributions, such as Lloyd's algorithm or more advanced techniques based on power diagrams. We analyze the convergence properties and propose new approaches to accelerate the generation of point distributions. We also design new algorithms to project curves onto spaces of curves with bounded length and curvature or speed and acceleration. We illustrate the algorithm's interest through applications in advanced sampling theory, nonphotorealistic rendering, and path planning.