Weakly supervised deep learning model with size constraint for prostate cancer detection in multiparametric MRI and generalization to unseen domains

Fully supervised deep models have shown promising performance for many medical segmentation tasks. Still, the deployment of these tools in clinics is limited by the very timeconsuming collection of manually expert-annotated data. Moreover, most of the state-ofthe-art models have been trained and validated on moderately homogeneous datasets. It is known that deep learning methods are often greatly degraded by domain or label shifts and are yet to be built in such a way as to be robust to unseen data or label distributions. In the clinical setting, this problematic is particularly relevant as the deployment institutions may have different scanners or acquisition protocols than those from which the data has been collected to train the model. In this work, we propose to address these two challenges on the detection of clinically significant prostate cancer (csPCa) from bi-parametric MRI. We evaluate the method proposed by (Kervadec et al., 2018), which introduces a size constaint loss to produce fine semantic cancer lesions segmentations from weak circle scribbles annotations. Performance of the model is based on two public (PI-CAI and Prostate158) and one private databases. First, we show that the model achieves on-par performance with strong fully supervised baseline models, both on in-distribution validation data and unseen test images. Second, we observe a performance decrease for both fully supervised and weakly supervised models when tested on unseen data domains. This confirms the crucial need for efficient domain adaptation methods if deep learning models are aimed to be deployed in a clinical environment. Finally, we show that ensemble predictions from multiple trainings increase generalization performance.

Whole-brain radiomics for clustered federated personalization in brain tumor segmentation

Federated learning and its application to medical image segmentation have recently become a popular research topic. This training paradigm suffers from statistical heterogeneity between participating institutions' local datasets, incurring convergence slowdown as well as potential accuracy loss compared to classical training. To mitigate this effect, federated personalization emerged as the federated optimization of one model per institution. We propose a novel personalization algorithm tailored to the feature shift induced by the usage of different scanners and acquisition parameters by different institutions. This method is the first to account for both inter and intra-institution feature shift (multiple scanners used in a single institution). It is based on the computation, within each centre, of a series of radiomic features capturing the global texture of each 3D image volume, followed by a clustering analysis pooling all feature vectors transferred from the local institutions to the central server. Each computed clustered decentralized dataset (potentially including data from different institutions) then serves to finetune a global model obtained through classical federated learning. We validate our approach on the Federated Brain Tumor Segmentation 2022 Challenge dataset (FeTS2022). Our code is available at (https://github.com/MatthisManthe/radiomics_CFFL).

Time CNN and Graph Convolution Network for Epileptic Spike Detection in MEG Data

Magnetoencephalography (MEG) recordings of patients with epilepsy exhibit spikes, a typical biomarker of the pathology. Detecting those spikes allows accurate localization of brain regions triggering seizures. Spike detection is often performed manually. However, it is a burdensome and error prone task due to the complexity of MEG data. To address this problem, we propose a 1D temporal convolutional neural network (Time CNN) coupled with a graph convolutional network (GCN) to classify short time frames of MEG recording as containing a spike or not. Compared to other recent approaches, our models have fewer parameters to train and we propose to use a GCN to account for MEG sensors spatial relationships. Our models produce clinically relevant results and outperform deep learning-based state-of-the-art methods reaching a classification f1-score of 76.7% on a balanced dataset and of 25.5% on a realistic, highly imbalanced dataset, for the spike class.

Towards frugal unsupervised detection of subtle abnormalities in medical imaging

Anomaly detection in medical imaging is a challenging task in contexts where abnormalities are not annotated. This problem can be addressed through unsupervised anomaly detection (UAD) methods, which identify features that do not match with a reference model of normal profiles. Artificial neural networks have been extensively used for UAD but they do not generally achieve an optimal trade-o$\hookleftarrow$ between accuracy and computational demand. As an alternative, we investigate mixtures of probability distributions whose versatility has been widely recognized for a variety of data and tasks, while not requiring excessive design e$\hookleftarrow$ort or tuning. Their expressivity makes them good candidates to account for complex multivariate reference models. Their much smaller number of parameters makes them more amenable to interpretation and e cient learning. However, standard estimation procedures, such as the Expectation-Maximization algorithm, do not scale well to large data volumes as they require high memory usage. To address this issue, we propose to incrementally compute inferential quantities. This online approach is illustrated on the challenging detection of subtle abnormalities in MR brain scans for the follow-up of newly diagnosed Parkinsonian patients. The identified structural abnormalities are consistent with the disease progression, as accounted by the Hoehn and Yahr scale.

Anomaly detection in image or latent space of patch-based auto-encoders for industrial image analysis

We study several methods for detecting anomalies in color images, constructed on patch-based auto-encoders. Wecompare the performance of three types of methods based, first, on the error between the original image and its reconstruction,second, on the support estimation of the normal image distribution in the latent space, and third, on the error between the originalimage and a restored version of the reconstructed image. These methods are evaluated on the industrial image database MVTecADand compared to two competitive state-of-the-art methods.

One-Class SVM on siamese neural network latent space for Unsupervised Anomaly Detection on brain MRI White Matter Hyperintensities

Anomaly detection remains a challenging task in neuroimaging when little to no supervision is available and when lesions can be very small or with subtle contrast. Patch-based representation learning has shown powerful representation capacities when applied to industrial or medical imaging and outlier detection methods have been applied successfully to these images. In this work, we propose an unsupervised anomaly detection (UAD) method based on a latent space constructed by a siamese patch-based auto-encoder and perform the outlier detection with a One-Class SVM training paradigm tailored to the lesion detection task in multi-modality neuroimaging. We evaluate performances of this model on a public database, the White Matter Hyperintensities (WMH) challenge and show in par performance with the two best performing state-of-the-art methods reported so far.

Brain subtle anomaly detection based on auto-encoders latent space analysis : application to de novo parkinson patients

Neural network-based anomaly detection remains challenging in clinical applications with little or no supervised information and subtle anomalies such as hardly visible brain lesions. Among unsupervised methods, patch-based auto-encoders with their efficient representation power provided by their latent space, have shown good results for visible lesion detection. However, the commonly used reconstruction error criterion may limit their performance when facing less obvious lesions. In this work, we design two alternative detection criteria. They are derived from multivariate analysis and can more directly capture information from latent space representations. Their performance compares favorably with two additional supervised learning methods, on a difficult de novo Parkinson Disease (PD) classification task.

ProstAttention-Net: A deep attention model for prostate cancer segmentation by aggressiveness in MRI scans

Multiparametric magnetic resonance imaging (mp-MRI) has shown excellent results in the detection of prostate cancer (PCa). However, characterizing prostate lesions aggressiveness in mp-MRI sequences is impossible in clinical practice, and biopsy remains the reference to determine the Gleason score (GS). In this work, we propose a novel end-to-end multi-class network that jointly segments the prostate gland and cancer lesions with GS group grading. After encoding the information on a latent space, the network is separated in two branches: 1) the first branch performs prostate segmentation 2) the second branch uses this zonal prior as an attention gate for the detection and grading of prostate lesions. The model was trained and validated with a 5-fold cross-validation on an heterogeneous series of 219 MRI exams acquired on three different scanners prior prostatectomy. In the free-response receiver operating characteristics (FROC) analysis for clinically significant lesions (defined as GS > 6) detection, our model achieves 69.0% $\pm$14.5% sensitivity at 2.9 false positive per patient on the whole prostate and 70.8% $\pm$14.4% sensitivity at 1.5 false positive when considering the peripheral zone (PZ) only. Regarding the automatic GS group

Perfusion imaging in deep prostate cancer detection from mp-MRI: can we take advantage of it?

To our knowledge, all deep computer-aided detection and diagnosis (CAD) systems for prostate cancer (PCa) detection consider bi-parametric magnetic resonance imaging (bp-MRI) only, including T2w and ADC sequences while excluding the 4D perfusion sequence,which is however part of standard clinical protocols for this diagnostic task. In this paper, we question strategies to integrate information from perfusion imaging in deep neural architectures. To do so, we evaluate several ways to encode the perfusion information in a U-Net like architecture, also considering early versus mid fusion strategies. We compare performance of multiparametric MRI (mp-MRI) models with the baseline bp-MRI model based on a private dataset of 219 mp-MRI exams. Perfusion maps derived from dynamic contrast enhanced MR exams are shown to positively impact segmentation and grading performance of PCa lesions, especially the 3D MR volume corresponding to the maximum slope of the wash-in curve as well as Tmax perfusion maps. The latter mp-MRI models indeed outperform the bp-MRI one whatever the fusion strategy, with Cohen's kappa score of 0.318$\pm$0.019 for the bp-MRI model and 0.378 $\pm$ 0.033 for the model including the maximum slope with a mid fusion strategy, also achieving competitive Cohen's kappa score compared to state of the art.

Learning to segment prostate cancer by aggressiveness from scribbles in bi-parametric MRI

In this work, we propose a deep U-Net based model to tackle the challenging task of prostate cancer segmentation by aggressiveness in MRI based on weak scribble annotations. This model extends the size constraint loss proposed by Kervadec et al. 1 in the context of multiclass detection and segmentation task. This model is of high clinical interest as it allows training on prostate biopsy samples and avoids time-consuming full annotation process. Performance is assessed on a private dataset (219 patients) where the full ground truth is available as well as on the ProstateX-2 challenge database, where only biopsy results at different localisations serve as reference. We show that we can approach the fully-supervised baseline in grading the lesions by using only 6.35% of voxels for training. We report a lesion-wise Cohen's kappa score of 0.29 $\pm$ 0.07 for the weak model versus 0.32 $\pm$ 0.05 for the baseline. We also report a kappa score (0.276 $\pm$ 0.037) on the ProstateX-2 challenge dataset with our weak U-Net trained on a combination of ProstateX-2 and our dataset, which is the highest reported value on this challenge dataset for a segmentation task to our knowledge.