Jinxi Xiang

Inverse problems are essential to imaging applications. In this paper, we propose a model-based deep learning network, named FISTA-Net, by combining the merits of interpretability and generality of the model-based Fast Iterative Shrinkage/Thresholding Algorithm (FISTA) and strong regularization and tuning-free advantages of the data-driven neural network. By unfolding the FISTA into a deep network, the architecture of FISTA-Net consists of multiple gradient descent, proximal mapping, and momentum modules in cascade. Different from FISTA, the gradient matrix in FISTA-Net can be updated during iteration and a proximal operator network is developed for nonlinear thresholding which can be learned through end-to-end training. Key parameters of FISTA-Net including the gradient step size, thresholding value and momentum scalar are tuning-free and learned from training data rather than hand-crafted. We further impose positive and monotonous constraints on these parameters to ensure they converge properly. The experimental results, evaluated both visually and quantitatively, show that the FISTA-Net can optimize parameters for different imaging tasks, i.e. Electromagnetic Tomography (EMT) and X-ray Computational Tomography (X-ray CT). It outperforms the state-of-the-art model-based and deep learning methods and exhibits good generalization ability over other competitive learning-based approaches under different noise levels.

The large-scale whole-slide images (WSIs) facilitate the learning-based computational pathology methods. However, the gigapixel size of WSIs makes it hard to train a conventional model directly. Current approaches typically adopt multiple-instance learning (MIL) to tackle this problem. Among them, MIL combined with graph convolutional network (GCN) is a significant branch, where the sampled patches are regarded as the graph nodes to further discover their correlations. However, it is difficult to build correspondence across patches from different WSIs. Therefore, most methods have to perform non-ordered node pooling to generate the bag-level representation. Direct non-ordered pooling will lose much structural and contextual information, such as patch distribution and heterogeneous patterns, which is critical for WSI representation. In this paper, we propose a hierarchical global-to-local clustering strategy to build a Node-Aligned GCN (NAGCN) to represent WSI with rich local structural information as well as global distribution. We first deploy a global clustering operation based on the instance features in the dataset to build the correspondence across different WSIs. Then, we perform a local clustering-based sampling strategy to select typical instances belonging to each cluster within the WSI. Finally, we employ the graph convolution to obtain the representation. Since our graph construction strategy ensures the alignment among different WSIs, WSI-level representation can be easily generated and used for the subsequent classification. The experiment results on two cancer subtype classification datasets demonstrate our method achieves better performance compared with the state-of-the-art methods.

Nuclear detection, segmentation and morphometric profiling are essential in helping us further understand the relationship between histology and patient outcome. To drive innovation in this area, we setup a community-wide challenge using the largest available dataset of its kind to assess nuclear segmentation and cellular composition. Our challenge, named CoNIC, stimulated the development of reproducible algorithms for cellular recognition with real-time result inspection on public leaderboards. We conducted an extensive post-challenge analysis based on the top-performing models using 1,658 whole-slide images of colon tissue. With around 700 million detected nuclei per model, associated features were used for dysplasia grading and survival analysis, where we demonstrated that the challenge's improvement over the previous state-of-the-art led to significant boosts in downstream performance. Our findings also suggest that eosinophils and neutrophils play an important role in the tumour microevironment. We release challenge models and WSI-level results to foster the development of further methods for biomarker discovery.