Michaël Clément

Huy-Dung Nguyen, Michaël Clément, Vincent Planche et al.

Alzheimer's disease and Frontotemporal dementia are common forms of neurodegenerative dementia. Behavioral alterations and cognitive impairments are found in the clinical courses of both diseases and their differential diagnosis is sometimes difficult for physicians. Therefore, an accurate tool dedicated to this diagnostic challenge can be valuable in clinical practice. However, current structural imaging methods mainly focus on the detection of each disease but rarely on their differential diagnosis. In this paper, we propose a deep learning based approach for both problems of disease detection and differential diagnosis. We suggest utilizing two types of biomarkers for this application: structure grading and structure atrophy. First, we propose to train a large ensemble of 3D U-Nets to locally determine the anatomical patterns of healthy people, patients with Alzheimer's disease and patients with Frontotemporal dementia using structural MRI as input. The output of the ensemble is a 2-channel disease's coordinate map able to be transformed into a 3D grading map which is easy to interpret for clinicians. This 2-channel map is coupled with a multi-layer perceptron classifier for different classification tasks. Second, we propose to combine our deep learning framework with a traditional machine learning strategy based on volume to improve the model discriminative capacity and robustness. After both cross-validation and external validation, our experiments based on 3319 MRI demonstrated competitive results of our method compared to the state-of-the-art methods for both disease detection and differential diagnosis.

Huy-Dung Nguyen, Michaël Clément, Boris Mansencal et al.

Age is an important variable to describe the expected brain's anatomy status across the normal aging trajectory. The deviation from that normative aging trajectory may provide some insights into neurological diseases. In neuroimaging, predicted brain age is widely used to analyze different diseases. However, using only the brain age gap information (\ie the difference between the chronological age and the estimated age) can be not enough informative for disease classification problems. In this paper, we propose to extend the notion of global brain age by estimating brain structure ages using structural magnetic resonance imaging. To this end, an ensemble of deep learning models is first used to estimate a 3D aging map (\ie voxel-wise age estimation). Then, a 3D segmentation mask is used to obtain the final brain structure ages. This biomarker can be used in several situations. First, it enables to accurately estimate the brain age for the purpose of anomaly detection at the population level. In this situation, our approach outperforms several state-of-the-art methods. Second, brain structure ages can be used to compute the deviation from the normal aging process of each brain structure. This feature can be used in a multi-disease classification task for an accurate differential diagnosis at the subject level. Finally, the brain structure age deviations of individuals can be visualized, providing some insights about brain abnormality and helping clinicians in real medical contexts.

Coloma Ballester, Aurélie Bugeau, Hernan Carrillo et al.

Colorization is a process that converts a grayscale image into a color one that looks as natural as possible. Over the years this task has received a lot of attention. Existing colorization methods rely on different color spaces: RGB, YUV, Lab, etc. In this chapter, we aim to study their influence on the results obtained by training a deep neural network, to answer the question: "Is it crucial to correctly choose the right color space in deep-learning based colorization?". First, we briefly summarize the literature and, in particular, deep learning-based methods. We then compare the results obtained with the same deep neural network architecture with RGB, YUV and Lab color spaces. Qualitative and quantitative analysis do not conclude similarly on which color space is better. We then show the importance of carefully designing the architecture and evaluation protocols depending on the types of images that are being processed and their specificities: strong/small contours, few/many objects, recent/archive images.

Huy-Dung Nguyen, Michaël Clément, Boris Mansencal et al.

Alzheimer's Disease is the most common cause of dementia. Accurate diagnosis and prognosis of this disease are essential to design an appropriate treatment plan, increasing the life expectancy of the patient. Intense research has been conducted on the use of machine learning to identify Alzheimer's Disease from neuroimaging data, such as structural magnetic resonance imaging. In recent years, advances of deep learning in computer vision suggest a new research direction for this problem. Current deep learning-based approaches in this field, however, have a number of drawbacks, including the interpretability of model decisions, a lack of generalizability information and a lower performance compared to traditional machine learning techniques. In this paper, we design a two-stage framework to overcome these limitations. In the first stage, an ensemble of 125 U-Nets is used to grade the input image, producing a 3D map that reflects the disease severity at voxel-level. This map can help to localize abnormal brain areas caused by the disease. In the second stage, we model a graph per individual using the generated grading map and other information about the subject. We propose to use a graph convolutional neural network classifier for the final classification. As a result, our framework demonstrates comparative performance to the state-of-the-art methods in different datasets for both diagnosis and prognosis. We also demonstrate that the use of a large ensemble of U-Nets offers a better generalization capacity for our framework.

Huy-Dung Nguyen, Michaël Clément, Boris Mansencal et al.

Alzheimer's disease and Frontotemporal dementia are two major types of dementia. Their accurate diagnosis and differentiation is crucial for determining specific intervention and treatment. However, differential diagnosis of these two types of dementia remains difficult at the early stage of disease due to similar patterns of clinical symptoms. Therefore, the automatic classification of multiple types of dementia has an important clinical value. So far, this challenge has not been actively explored. Recent development of deep learning in the field of medical image has demonstrated high performance for various classification tasks. In this paper, we propose to take advantage of two types of biomarkers: structure grading and structure atrophy. To this end, we propose first to train a large ensemble of 3D U-Nets to locally discriminate healthy versus dementia anatomical patterns. The result of these models is an interpretable 3D grading map capable of indicating abnormal brain regions. This map can also be exploited in various classification tasks using graph convolutional neural network. Finally, we propose to combine deep grading and atrophy-based classifications to improve dementia type discrimination. The proposed framework showed competitive performance compared to state-of-the-art methods for different tasks of disease detection and differential diagnosis.

Coloma Ballester, Aurélie Bugeau, Hernan Carrillo et al.

Image colorization aims to add color information to a grayscale image in a realistic way. Recent methods mostly rely on deep learning strategies. While learning to automatically colorize an image, one can define well-suited objective functions related to the desired color output. Some of them are based on a specific type of error between the predicted image and ground truth one, while other losses rely on the comparison of perceptual properties. But, is the choice of the objective function that crucial, i.e., does it play an important role in the results? In this chapter, we aim to answer this question by analyzing the impact of the loss function on the estimated colorization results. To that goal, we review the different losses and evaluation metrics that are used in the literature. We then train a baseline network with several of the reviewed objective functions: classic L1 and L2 losses, as well as more complex combinations such as Wasserstein GAN and VGG-based LPIPS loss. Quantitative results show that the models trained with VGG-based LPIPS provide overall slightly better results for most evaluation metrics. Qualitative results exhibit more vivid colors when with Wasserstein GAN plus the L2 loss or again with the VGG-based LPIPS. Finally, the convenience of quantitative user studies is also discussed to overcome the difficulty of properly assessing on colorized images, notably for the case of old archive photographs where no ground truth is available.

Huy-Dung Nguyen, Michaël Clément, Boris Mansencal et al.

Alzheimer's disease and Frontotemporal dementia are common types of neurodegenerative disorders that present overlapping clinical symptoms, making their differential diagnosis very challenging. Numerous efforts have been done for the diagnosis of each disease but the problem of multi-class differential diagnosis has not been actively explored. In recent years, transformer-based models have demonstrated remarkable success in various computer vision tasks. However, their use in disease diagnostic is uncommon due to the limited amount of 3D medical data given the large size of such models. In this paper, we present a novel 3D transformer-based architecture using a deformable patch location module to improve the differential diagnosis of Alzheimer's disease and Frontotemporal dementia. Moreover, to overcome the problem of data scarcity, we propose an efficient combination of various data augmentation techniques, adapted for training transformer-based models on 3D structural magnetic resonance imaging data. Finally, we propose to combine our transformer-based model with a traditional machine learning model using brain structure volumes to better exploit the available data. Our experiments demonstrate the effectiveness of the proposed approach, showing competitive results compared to state-of-the-art methods. Moreover, the deformable patch locations can be visualized, revealing the most relevant brain regions used to establish the diagnosis of each disease.

Julien Walther, Rémi Giraud, Michaël Clément

Superpixels are widely used in computer vision to simplify image representation and reduce computational complexity. While traditional methods rely on low-level features, deep learning-based approaches leverage high-level features but also tend to sacrifice regularity of superpixels to capture complex objects, leading to accurate but less interpretable segmentations. In this work, we introduce SPAM (SuperPixel Anything Model), a versatile framework for segmenting images into accurate yet regular superpixels. We train a model to extract image features for superpixel generation, and at inference, we leverage a large-scale pretrained model for semantic-agnostic segmentation to ensure that superpixels align with object masks. SPAM can handle any prior high-level segmentation, resolving uncertainty regions, and is able to interactively focus on specific objects. Comprehensive experiments demonstrate that SPAM qualitatively and quantitatively outperforms state-of-the-art methods on segmentation tasks, making it a valuable and robust tool for various applications. Code and pre-trained models are available here: https://github.com/waldo-j/spam.

Rémi Giraud, Michaël Clément

For many years, image over-segmentation into superpixels has been essential to computer vision pipelines, by creating homogeneous and identifiable regions of similar sizes. Such constrained segmentation problem would require a clear definition and specific evaluation criteria. However, the validation framework for superpixel methods, typically viewed as standard object segmentation, has rarely been thoroughly studied. In this work, we first take a step back to show that superpixel segmentation is fundamentally an ill-posed problem, due to the implicit regularity constraint on the shape and size of superpixels. We also demonstrate through a novel comprehensive study that the literature suffers from only evaluating certain aspects, sometimes incorrectly and with inappropriate metrics. Concurrently, recent deep learning-based superpixel methods mainly focus on the object segmentation task at the expense of regularity. In this ill-posed context, we show that we can achieve competitive results using a recent architecture like the Segment Anything Model (SAM), without dedicated training for the superpixel segmentation task. This leads to rethinking superpixel segmentation and the necessary properties depending on the targeted downstream task.

Manuel Ricardo Guevara Garban, Yves Chemisky, Étienne Prulière et al.

We propose a physics-informed machine learning framework called P-DivGNN to reconstruct local stress fields at the micro-scale, in the context of multi-scale simulation given a periodic micro-structure mesh and mean, macro-scale, stress values. This method is based in representing a periodic micro-structure as a graph, combined with a message passing graph neural network. We are able to retrieve local stress field distributions, providing average stress values produced by a mean field reduced order model (ROM) or Finite Element (FE) simulation at the macro-scale. The prediction of local stress fields are of utmost importance considering fracture analysis or the definition of local fatigue criteria. Our model incorporates physical constraints during training to constraint local stress field equilibrium state and employs a periodic graph representation to enforce periodic boundary conditions. The benefits of the proposed physics-informed GNN are evaluated considering linear and non linear hyperelastic responses applied to varying geometries. In the non-linear hyperelastic case, the proposed method achieves significant computational speed-ups compared to FE simulation, making it particularly attractive for large-scale applications.

Pierrick Coupé, Boris Mansencal, Michaël Clément et al.

Whole brain segmentation using deep learning (DL) is a very challenging task since the number of anatomical labels is very high compared to the number of available training images. To address this problem, previous DL methods proposed to use a single convolution neural network (CNN) or few independent CNNs. In this paper, we present a novel ensemble method based on a large number of CNNs processing different overlapping brain areas. Inspired by parliamentary decision-making systems, we propose a framework called AssemblyNet, made of two "assemblies" of U-Nets. Such a parliamentary system is capable of dealing with complex decisions, unseen problem and reaching a consensus quickly. AssemblyNet introduces sharing of knowledge among neighboring U-Nets, an "amendment" procedure made by the second assembly at higher-resolution to refine the decision taken by the first one, and a final decision obtained by majority voting. During our validation, AssemblyNet showed competitive performance compared to state-of-the-art methods such as U-Net, Joint label fusion and SLANT. Moreover, we investigated the scan-rescan consistency and the robustness to disease effects of our method. These experiences demonstrated the reliability of AssemblyNet. Finally, we showed the interest of using semi-supervised learning to improve the performance of our method.

Pierrick Coupé, Boris Mansencal, Michaël Clément et al.

Whole brain segmentation using deep learning (DL) is a very challenging task since the number of anatomical labels is very high compared to the number of available training images. To address this problem, previous DL methods proposed to use a global convolution neural network (CNN) or few independent CNNs. In this paper, we present a novel ensemble method based on a large number of CNNs processing different overlapping brain areas. Inspired by parliamentary decision-making systems, we propose a framework called AssemblyNet, made of two "assemblies" of U-Nets. Such a parliamentary system is capable of dealing with complex decisions and reaching a consensus quickly. AssemblyNet introduces sharing of knowledge among neighboring U-Nets, an "amendment" procedure made by the second assembly at higher-resolution to refine the decision taken by the first one, and a final decision obtained by majority voting. When using the same 45 training images, AssemblyNet outperforms global U-Net by 28% in terms of the Dice metric, patch-based joint label fusion by 15% and SLANT-27 by 10%. Finally, AssemblyNet demonstrates high capacity to deal with limited training data to achieve whole brain segmentation in practical training and testing times.