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Multi-modality magnetic resonance imaging (MRI) can provide complementary information for computer-aided diagnosis. Traditional deep learning algorithms are suitable for identifying specific anatomical structures segmenting lesions and classifying diseases with magnetic resonance images. However, manual labels are limited due to high expense, which hinders further improvement of model accuracy. Self-supervised learning (SSL) can effectively learn feature representations from unlabeled data by pre-training and is demonstrated to be effective in natural image analysis. Most SSL methods ignore the similarity of multi-modality MRI, leading to model collapse. This limits the efficiency of pre-training, causing low accuracy in downstream segmentation and classification tasks. To solve this challenge, we establish and validate a multi-modality MRI masked autoencoder consisting of hybrid mask pattern (HMP) and pyramid barlow twin (PBT) module for SSL on multi-modality MRI analysis. The HMP concatenates three masking steps forcing the SSL to learn the semantic connections of multi-modality images by reconstructing the masking patches. We have proved that the proposed HMP can avoid model collapse. The PBT module exploits the pyramidal hierarchy of the network to construct barlow twin loss between masked and original views, aligning the semantic representations of image patches at different vision scales in latent space. Experiments on BraTS2023, PI-CAI, and lung gas MRI datasets further demonstrate the superiority of our framework over the state-of-the-art. The performance of the segmentation and classification is substantially enhanced, supporting the accurate detection of small lesion areas. The code is available at https://github.com/LinxuanHan/M2-MAE.

Significance testing aims to determine whether a proposition about the population distribution is the truth or not given observations. However, traditional significance testing often needs to derive the distribution of the testing statistic, failing to deal with complex nonlinear relationships. In this paper, we propose to conduct Full Bayesian Significance Testing for neural networks, called \textit{n}FBST, to overcome the limitation in relationship characterization of traditional approaches. A Bayesian neural network is utilized to fit the nonlinear and multi-dimensional relationships with small errors and avoid hard theoretical derivation by computing the evidence value. Besides, \textit{n}FBST can test not only global significance but also local and instance-wise significance, which previous testing methods don't focus on. Moreover, \textit{n}FBST is a general framework that can be extended based on the measures selected, such as Grad-\textit{n}FBST, LRP-\textit{n}FBST, DeepLIFT-\textit{n}FBST, LIME-\textit{n}FBST. A range of experiments on both simulated and real data are conducted to show the advantages of our method., Comment: Published as a conference paper at AAAI 2024

Magnetic resonance imaging (MRI) using hyperpolarized noble gases provides a way to visualize the structure and function of human lung, but the long imaging time limits its broad research and clinical applications. Deep learning has demonstrated great potential for accelerating MRI by reconstructing images from undersampled data. However, most existing deep conventional neural networks (CNN) directly apply square convolution to k-space data without considering the inherent properties of k-space sampling, limiting k-space learning efficiency and image reconstruction quality. In this work, we propose an encoding enhanced (EN2) complex CNN for highly undersampled pulmonary MRI reconstruction. EN2 employs convolution along either the frequency or phase-encoding direction, resembling the mechanisms of k-space sampling, to maximize the utilization of the encoding correlation and integrity within a row or column of k-space. We also employ complex convolution to learn rich representations from the complex k-space data. In addition, we develop a feature-strengthened modularized unit to further boost the reconstruction performance. Experiments demonstrate that our approach can accurately reconstruct hyperpolarized 129Xe and 1H lung MRI from 6-fold undersampled k-space data and provide lung function measurements with minimal biases compared with fully-sampled image. These results demonstrate the effectiveness of the proposed algorithmic components and indicate that the proposed approach could be used for accelerated pulmonary MRI in research and clinical lung disease patient care.

Drug-drug interaction (DDI) prediction provides a drug combination strategy for systemically effective treatment. Previous studies usually model drug information constrained on a single view such as the drug itself, leading to incomplete and noisy information, which limits the accuracy of DDI prediction. In this work, we propose a novel multi- view drug substructure network for DDI prediction (MSN-DDI), which learns chemical substructures from both the representations of the single drug (intra-view) and the drug pair (inter-view) simultaneously and utilizes the substructures to update the drug representation iteratively. Comprehensive evaluations demonstrate that MSN-DDI has almost solved DDI prediction for existing drugs by achieving a relatively improved accuracy of 19.32% and an over 99% accuracy under the transductive setting. More importantly, MSN-DDI exhibits better generalization ability to unseen drugs with a relatively improved accuracy of 7.07% under more challenging inductive scenarios. Finally, MSN-DDI improves prediction performance for real-world DDI applications to new drugs.