Machine learning in clinical neuroimaging : 7th international workshop, MLCN 2024, held in conjunction with MICCAI 2024, Marrakesh, Morocco, October 10, 2024, proceedings. MLCN (Workshop) (7th : 2024 : Marrakesh, Morocco)最新文献

Deep learning can help uncover patterns in resting-state functional Magnetic Resonance Imaging (rs-fMRI) associated with psychiatric disorders and personal traits. Yet the problem of interpreting deep learning findings is rarely more evident than in fMRI analyses, as the data is sensitive to scanning effects and inherently difficult to visualize. We propose a simple approach to mitigate these challenges grounded on sparsification and self-supervision. Instead of extracting post-hoc feature attributions to uncover functional connections that are important to the target task, we identify a small subset of highly informative connections during training and occlude the rest. To this end, we jointly train a (1) sparse input mask, (2) variational autoencoder (VAE), and (3) downstream classifier in an end-to-end fashion. While we need a portion of labeled samples to train the classifier, we optimize the sparse mask and VAE with unlabeled data from additional acquisition sites, retaining only the input features that generalize well. We evaluate our method - Sparsely Reconstructed Graphs (SpaRG) - on the public ABIDE dataset for the task of sex classification, training with labeled cases from 18 sites and adapting the model to two additional out-of-distribution sites with a portion of unlabeled samples. For a relatively coarse parcellation (64 regions), SpaRG utilizes only 1% of the original connections while improving the classification accuracy across domains. Our code can be found at www.github.com/yanismiraoui/SpaRG.

Many longitudinal neuroimaging studies aim to improve the understanding of brain aging and diseases by studying the dynamic interactions between brain function and cognition. Doing so requires accurate encoding of their multidimensional relationship while accounting for individual variability over time. For this purpose, we propose an unsupervised learning model (called Contrastive Learning-based Graph Generalized Canonical Correlation Analysis (CoGraCa)) that encodes their relationship via Graph Attention Networks and generalized Canonical Correlational Analysis. To create brain-cognition fingerprints reflecting unique neural and cognitive phenotype of each person, the model also relies on individualized and multimodal contrastive learning. We apply CoGraCa to longitudinal dataset of healthy individuals consisting of resting-state functional MRI and cognitive measures acquired at multiple visits for each participant. The generated fingerprints effectively capture significant individual differences and outperform current single-modal and CCA-based multimodal models in identifying sex and age. More importantly, our encoding provides interpretable interactions between those two modalities.

Autism Spectrum Disorder (ASD) is a neurodevelopmental condition that encompasses a wide variety of symptoms and degrees of impairment, which makes the diagnosis and treatment challenging. Functional magnetic resonance imaging (fMRI) has been extensively used to study brain activity in ASD, and machine learning methods have been applied to analyze resting state fMRI (rs-fMRI) data. However, fewer studies have explored the recent transformer-based models on rs-fMRI data. Given the superiority of transformer models in capturing long-range dependencies in sequence data, we have developed a transformer-based self-supervised framework that directly analyzes time-series fMRI data without computing functional connectivity. To address over-fitting in small datasets and enhance the model performance, we propose self-supervised pre-training tasks to reconstruct the randomly masked fMRI time-series data, investigating the effects of various masking strategies. We then fine-tune the model for the ASD classification task and evaluate it using two public datasets and five-fold cross-validation with different amounts of training data. The experiments show that randomly masking entire ROIs gives better model performance than randomly masking time points in the pre-training step, resulting in an average improvement of 10.8% for AUC and 9.3% for subject accuracy compared with the transformer model trained from scratch across different levels of training data availability. Our code is available on GitHub .

Deep neural networks have demonstrated exceptional efficacy in stroke lesion segmentation. However, the delineation of small lesions, critical for stroke diagnosis, remains a challenge. In this study, we propose two straightforward yet powerful approaches that can be seamlessly integrated into a variety of networks: Multi-Size Labeling (MSL) and Distance-Based Labeling (DBL), with the aim of enhancing the segmentation accuracy of small lesions. MSL divides lesion masks into various categories based on lesion volume while DBL emphasizes the lesion boundaries. Experimental evaluations on the Anatomical Tracings of Lesions After Stroke (ATLAS) v2.0 dataset showcase that an ensemble of MSL and DBL achieves consistently better or equal performance on recall (3.6% and 3.7%), F1 (2.4% and 1.5%), and Dice scores (1.3% and 0.0%) compared to the top-1 winner of the 2022 MICCAI ATLAS Challenge on both the subset only containing small lesions and the entire dataset, respectively. Notably, on the mini-lesion subset, a single MSL model surpasses the previous best ensemble strategy, with enhancements of 1.0% and 0.3% on F1 and Dice scores, respectively. Our code is available at: https://github.com/nadluru/StrokeLesSeg.

Quantitative Susceptibility Mapping (QSM) is a technique that derives tissue magnetic susceptibility distributions from phase measurements obtained through Magnetic Resonance (MR) imaging. This involves solving an ill-posed dipole inversion problem, however, and thus time-consuming and cumbersome data acquisition from several distinct head orientations becomes necessary to obtain an accurate solution. Most recent (supervised) deep learning methods for single-phase QSM require training data obtained via multiple orientations. In this work, we present an alternative unsupervised learning approach that can efficiently train on single-orientation measurement data alone, named ProxiMO (Proximal Multi-Operator), combining Learned Proximal Convolutional Neural Networks (LP-CNN) with multi-operator imaging (MOI). This integration enables LP-CNN training for QSM on single-phase data without ground truth reconstructions. We further introduce a semi-supervised variant, which further boosts the reconstruction performance, compared to the traditional supervised fashions. Extensive experiments on multicenter datasets illustrate the advantage of unsupervised training and the superiority of the proposed approach for QSM reconstruction. Code is available at https://github.com/shmuelor/ProxiMO.