Xi Chen

Yiran Wei, Xi Chen, Lei Zhu et al.

The isocitrate dehydrogenase (IDH) gene mutation is an essential biomarker for the diagnosis and prognosis of glioma. It is promising to better predict glioma genotype by integrating focal tumor image and geometric features with brain network features derived from MRI. Convolutions neural networks show reasonable performance in predicting IDH mutation, which, however, cannot learn from non-Euclidean data, e.g., geometric and network data. In this study, we propose a multi-modal learning framework using three separate encoders to extract features of focal tumor image, tumor geometrics and global brain networks. To mitigate the limited availability of diffusion MRI, we develop a self-supervised approach to generate brain networks from anatomical multi-sequence MRI. Moreover, to extract tumor-related features from the brain network, we design a hierarchical attention module for the brain network encoder. Further, we design a bi-level multi-modal contrastive loss to align the multi-modal features and tackle the domain gap at the focal tumor and global brain. Finally, we propose a weighted population graph to integrate the multi-modal features for genotype prediction. Experimental results on the testing set show that the proposed model outperforms the baseline deep learning models. The ablation experiments validate the performance of different components of the framework. The visualized interpretation corresponds to clinical knowledge with further validation. In conclusion, the proposed learning framework provides a novel approach for predicting the genotype of glioma.

Lan Jiang, Ye Mao, Xi Chen et al.

MRI synthesis promises to mitigate the challenge of missing MRI modality in clinical practice. Diffusion model has emerged as an effective technique for image synthesis by modelling complex and variable data distributions. However, most diffusion-based MRI synthesis models are using a single modality. As they operate in the original image domain, they are memory-intensive and less feasible for multi-modal synthesis. Moreover, they often fail to preserve the anatomical structure in MRI. Further, balancing the multiple conditions from multi-modal MRI inputs is crucial for multi-modal synthesis. Here, we propose the first diffusion-based multi-modality MRI synthesis model, namely Conditioned Latent Diffusion Model (CoLa-Diff). To reduce memory consumption, we design CoLa-Diff to operate in the latent space. We propose a novel network architecture, e.g., similar cooperative filtering, to solve the possible compression and noise in latent space. To better maintain the anatomical structure, brain region masks are introduced as the priors of density distributions to guide diffusion process. We further present auto-weight adaptation to employ multi-modal information effectively. Our experiments demonstrate that CoLa-Diff outperforms other state-of-the-art MRI synthesis methods, promising to serve as an effective tool for multi-modal MRI synthesis.

Chaoyang Zhang, Shaojie Chang, Ti Bai et al.

Photon counting spectral CT (PCCT) can produce reconstructed attenuation maps in different energy channels, reflecting energy properties of the scanned object. Due to the limited photon numbers and the non-ideal detector response of each energy channel, the reconstructed images usually contain much noise. With the development of Deep Learning (DL) technique, different kinds of DL-based models have been proposed for noise reduction. However, most of the models require clean data set as the training labels, which are not always available in medical imaging field. Inspiring by the similarities of each channel's reconstructed image, we proposed a self-supervised learning based PCCT image enhancement framework via multi-spectral channels (S2MS). In S2MS framework, both the input and output labels are noisy images. Specifically, one single channel image was used as output while images of other single channels and channel-sum image were used as input to train the network, which can fully use the spectral data information without extra cost. The simulation results based on the AAPM Low-dose CT Challenge database showed that the proposed S2MS model can suppress the noise and preserve details more effectively in comparison with the traditional DL models, which has potential to improve the image quality of PCCT in clinical applications.

Yiran Wei, Chao Li, Xi Chen et al.

The isocitrate dehydrogenase (IDH) gene mutation status is an important biomarker for glioma patients. The gold standard of IDH mutation detection requires tumour tissue obtained via invasive approaches and is usually expensive. Recent advancement in radiogenomics provides a non-invasive approach for predicting IDH mutation based on MRI. Meanwhile, tumor geometrics encompass crucial information for tumour phenotyping. Here we propose a collaborative learning framework that learns both tumor images and tumor geometrics using convolutional neural networks (CNN) and graph neural networks (GNN), respectively. Our results show that the proposed model outperforms the baseline model of 3D-DenseNet121. Further, the collaborative learning model achieves better performance than either the CNN or the GNN alone. The model interpretation shows that the CNN and GNN could identify common and unique regions of interest for IDH mutation prediction. In conclusion, collaborating image and geometric learners provides a novel approach for predicting genotype and characterising glioma.

Yifan Li, Chao Li, Yiran Wei et al.

Glioblastoma is profoundly heterogeneous in regional microstructure and vasculature. Characterizing the spatial heterogeneity of glioblastoma could lead to more precise treatment. With unsupervised learning techniques, glioblastoma MRI-derived radiomic features have been widely utilized for tumor sub-region segmentation and survival prediction. However, the reliability of algorithm outcomes is often challenged by both ambiguous intermediate process and instability introduced by the randomness of clustering algorithms, especially for data from heterogeneous patients. In this paper, we propose an adaptive unsupervised learning approach for efficient MRI intra-tumor partitioning and glioblastoma survival prediction. A novel and problem-specific Feature-enhanced Auto-Encoder (FAE) is developed to enhance the representation of pairwise clinical modalities and therefore improve clustering stability of unsupervised learning algorithms such as K-means. Moreover, the entire process is modelled by the Bayesian optimization (BO) technique with a custom loss function that the hyper-parameters can be adaptively optimized in a reasonably few steps. The results demonstrate that the proposed approach can produce robust and clinically relevant MRI sub-regions and statistically significant survival predictions.

Chao Li, Yiran Wei, Xi Chen et al.

Alzheimer's disease (AD) is the most common age-related dementia. It remains a challenge to identify the individuals at risk of dementia for precise management. Brain MRI offers a noninvasive biomarker to detect brain aging. Previous evidence shows that the brain structural change detected by diffusion MRI is associated with dementia. Mounting studies has conceptualised the brain as a complex network, which has shown the utility of this approach in characterising various neurological and psychiatric disorders. Therefore, the structural connectivity shows promise in dementia classification. The proposed BrainNetGAN is a generative adversarial network variant to augment the brain structural connectivity matrices for binary dementia classification tasks. Structural connectivity matrices between separated brain regions are constructed using tractography on diffusion MRI data. The BrainNetGAN model is trained to generate fake brain connectivity matrices, which are expected to reflect latent distribution of the real brain network data. Finally, a convolutional neural network classifier is proposed for binary dementia classification. Numerical results show that the binary classification performance in the testing set was improved using the BrainNetGAN augmented dataset. The proposed methodology allows quick synthesis of an arbitrary number of augmented connectivity matrices and can be easily transferred to similar classification tasks.

Yifan Li, Chao Li, Stephen Price et al.

Glioblastoma is profoundly heterogeneous in microstructure and vasculature, which may lead to tumor regional diversity and distinct treatment response. Although successful in tumor sub-region segmentation and survival prediction, radiomics based on machine learning algorithms, is challenged by its robustness, due to the vague intermediate process and track changes. Also, the weak interpretability of the model poses challenges to clinical application. Here we proposed a machine learning framework to semi-automatically fine-tune the clustering algorithms and quantitatively identify stable sub-regions for reliable clinical survival prediction. Hyper-parameters are automatically determined by the global minimum of the trained Gaussian Process (GP) surrogate model through Bayesian optimization(BO) to alleviate the difficulty of tuning parameters for clinical researchers. To enhance the interpretability of the survival prediction model, we incorporated the prior knowledge of intra-tumoral heterogeneity, by segmenting tumor sub-regions and extracting sub-regional features. The results demonstrated that the global minimum of the trained GP surrogate can be used as sub-optimal hyper-parameter solutions for efficient. The sub-regions segmented based on physiological MRI can be applied to predict patient survival, which could enhance the clinical interpretability for the machine learning model.

Zhiguo Zhou, Zhi-Jie Zhou, Hongxia Hao et al.

Radiomics aims to extract and analyze large numbers of quantitative features from medical images and is highly promising in staging, diagnosing, and predicting outcomes of cancer treatments. Nevertheless, several challenges need to be addressed to construct an optimal radiomics predictive model. First, the predictive performance of the model may be reduced when features extracted from an individual imaging modality are blindly combined into a single predictive model. Second, because many different types of classifiers are available to construct a predictive model, selecting an optimal classifier for a particular application is still challenging. In this work, we developed multi-modality and multi-classifier radiomics predictive models that address the aforementioned issues in currently available models. Specifically, a new reliable classifier fusion strategy was proposed to optimally combine output from different modalities and classifiers. In this strategy, modality-specific classifiers were first trained, and an analytic evidential reasoning (ER) rule was developed to fuse the output score from each modality to construct an optimal predictive model. One public data set and two clinical case studies were performed to validate model performance. The experimental results indicated that the proposed ER rule based radiomics models outperformed the traditional models that rely on a single classifier or simply use combined features from different modalities.