3D Transformer based on deformable patch location for differential diagnosis between Alzheimer's disease and Frontotemporal dementia

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.

Brain Structure Ages -- A new biomarker for multi-disease classification

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.

Sport Task: Fine Grained Action Detection and Classification of Table Tennis Strokes from Videos for MediaEval 2022

Sports video analysis is a widespread research topic. Its applications are very diverse, like events detection during a match, video summary, or fine-grained movement analysis of athletes. As part of the MediaEval 2022 benchmarking initiative, this task aims at detecting and classifying subtle movements from sport videos. We focus on recordings of table tennis matches. Conducted since 2019, this task provides a classification challenge from untrimmed videos recorded under natural conditions with known temporal boundaries for each stroke. Since 2021, the task also provides a stroke detection challenge from unannotated, untrimmed videos. This year, the training, validation, and test sets are enhanced to ensure that all strokes are represented in each dataset. The dataset is now similar to the one used in [1, 2]. This research is intended to build tools for coaches and athletes who want to further evaluate their sport performances.

Deep Grading based on Collective Artificial Intelligence for AD Diagnosis and Prognosis

Accurate diagnosis and prognosis of Alzheimer's disease are crucial to develop new therapies and reduce the associated costs. Recently, with the advances of convolutional neural networks, methods have been proposed to automate these two tasks using structural MRI. However, these methods often suffer from lack of interpretability, generalization, and can be limited in terms of performance. In this paper, we propose a novel deep framework designed to overcome these limitations. Our framework consists of two stages. In the first stage, we propose a deep grading model to extract meaningful features. To enhance the robustness of these features against domain shift, we introduce an innovative collective artificial intelligence strategy for training and evaluating steps. In the second stage, we use a graph convolutional neural network to better capture AD signatures. Our experiments based on 2074 subjects show the competitive performance of our deep framework compared to state-of-the-art methods on different datasets for both AD diagnosis and prognosis.

Deep grading for MRI-based differential diagnosis of Alzheimer's disease and Frontotemporal dementia

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.

Longitudinal detection of new MS lesions using Deep Learning

The detection of new multiple sclerosis (MS) lesions is an important marker of the evolution of the disease. The applicability of learning-based methods could automate this task efficiently. However, the lack of annotated longitudinal data with new-appearing lesions is a limiting factor for the training of robust and generalizing models. In this work, we describe a deep-learning-based pipeline addressing the challenging task of detecting and segmenting new MS lesions. First, we propose to use transfer-learning from a model trained on a segmentation task using single time-points. Therefore, we exploit knowledge from an easier task and for which more annotated datasets are available. Second, we propose a data synthesis strategy to generate realistic longitudinal time-points with new lesions using single time-point scans. In this way, we pretrain our detection model on large synthetic annotated datasets. Finally, we use a data-augmentation technique designed to simulate data diversity in MRI. By doing that, we increase the size of the available small annotated longitudinal datasets. Our ablation study showed that each contribution lead to an enhancement of the segmentation accuracy. Using the proposed pipeline, we obtained the best score for the segmentation and the detection of new MS lesions in the MSSEG2 MICCAI challenge.

Interpretable differential diagnosis for Alzheimer's disease and Frontotemporal dementia

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.

Towards better Interpretable and Generalizable AD detection using Collective Artificial Intelligence

Accurate diagnosis and prognosis of Alzheimer's disease are crucial for developing new therapies and reducing the associated costs. Recently, with the advances of convolutional neural networks, deep learning methods have been proposed to automate these two tasks using structural MRI. However, these methods often suffer from a lack of interpretability and generalization and have limited prognosis performance. In this paper, we propose a novel deep framework designed to overcome these limitations. Our pipeline consists of two stages. In the first stage, 125 3D U-Nets are used to estimate voxelwise grade scores over the whole brain. The resulting 3D maps are then fused to construct an interpretable 3D grading map indicating the disease severity at the structure level. As a consequence, clinicians can use this map to detect the brain structures affected by the disease. In the second stage, the grading map and subject's age are used to perform classification with a graph convolutional neural network. Experimental results based on 2106 subjects demonstrated competitive performance of our deep framework compared to state-of-the-art methods on different datasets for both AD diagnosis and prognosis. Moreover, we found that using a large number of U-Nets processing different overlapping brain areas improved the generalization capacity of the proposed methods.

Sports Video: Fine-Grained Action Detection and Classification of Table Tennis Strokes from Videos for MediaEval 2021

Sports video analysis is a prevalent research topic due to the variety of application areas, ranging from multimedia intelligent devices with user-tailored digests up to analysis of athletes' performance. The Sports Video task is part of the MediaEval 2021 benchmark. This task tackles fine-grained action detection and classification from videos. The focus is on recordings of table tennis games. Running since 2019, the task has offered a classification challenge from untrimmed video recorded in natural conditions with known temporal boundaries for each stroke. This year, the dataset is extended and offers, in addition, a detection challenge from untrimmed videos without annotations. This work aims at creating tools for sports coaches and players in order to analyze sports performance. Movement analysis and player profiling may be built upon such technology to enrich the training experience of athletes and improve their performance.

Towards broader generalization of deep learning methods for multiple sclerosis lesion segmentation

Recently, segmentation methods based on Convolutional Neural Networks (CNNs) showed promising performance in automatic Multiple Sclerosis (MS) lesions segmentation. These techniques have even outperformed human experts in controlled evaluation condition. However state-of-the-art approaches trained to perform well on highly-controlled datasets fail to generalize on clinical data from unseen datasets. Instead of proposing another improvement of the segmentation accuracy, we propose a novel method robust to domain shift and performing well on unseen datasets, called DeepLesionBrain (DLB). This generalization property results from three main contributions. First, DLB is based on a large ensemble of compact 3D CNNs. This ensemble strategy ensures a robust prediction despite the risk of generalization failure of some individual networks. Second, DLB includes a new image quality data augmentation to reduce dependency to training data specificity (e.g., acquisition protocol). Finally, to learn a more generalizable representation of MS lesions, we propose a hierarchical specialization learning (HSL). HSL is performed by pre-training a generic network over the whole brain, before using its weights as initialization to locally specialized networks. By this end, DLB learns both generic features extracted at global image level and specific features extracted at local image level. At the time of publishing this paper, DLB is among the Top 3 performing published methods on ISBI Challenge while using only half of the available modalities. DLB generalization has also been compared to other state-of-the-art approaches, during cross-dataset experiments on MSSEG'16, ISBI challenge, and in-house datasets. DLB improves the segmentation performance and generalization over classical techniques, and thus proposes a robust approach better suited for clinical practice.