Genomics-guided Representation Learning for Pathologic Pan-cancer Tumor Microenvironment Subtype Prediction

The characterization of Tumor MicroEnvironment (TME) is challenging due to its complexity and heterogeneity. Relatively consistent TME characteristics embedded within highly specific tissue features, render them difficult to predict. The capability to accurately classify TME subtypes is of critical significance for clinical tumor diagnosis and precision medicine. Based on the observation that tumors with different origins share similar microenvironment patterns, we propose PathoTME, a genomics-guided Siamese representation learning framework employing Whole Slide Image (WSI) for pan-cancer TME subtypes prediction. Specifically, we utilize Siamese network to leverage genomic information as a regularization factor to assist WSI embeddings learning during the training phase. Additionally, we employ Domain Adversarial Neural Network (DANN) to mitigate the impact of tissue type variations. To eliminate domain bias, a dynamic WSI prompt is designed to further unleash the model's capabilities. Our model achieves better performance than other state-of-the-art methods across 23 cancer types on TCGA dataset. Our code is available at https://github.com/Mengflz/PathoTME.

Domain Game: Disentangle Anatomical Feature for Single Domain Generalized Segmentation

Single domain generalization aims to address the challenge of out-of-distribution generalization problem with only one source domain available. Feature distanglement is a classic solution to this purpose, where the extracted task-related feature is presumed to be resilient to domain shift. However, the absence of references from other domains in a single-domain scenario poses significant uncertainty in feature disentanglement (ill-posedness). In this paper, we propose a new framework, named \textit{Domain Game}, to perform better feature distangling for medical image segmentation, based on the observation that diagnostic relevant features are more sensitive to geometric transformations, whilist domain-specific features probably will remain invariant to such operations. In domain game, a set of randomly transformed images derived from a singular source image is strategically encoded into two separate feature sets to represent diagnostic features and domain-specific features, respectively, and we apply forces to pull or repel them in the feature space, accordingly. Results from cross-site test domain evaluation showcase approximately an ~11.8% performance boost in prostate segmentation and around ~10.5% in brain tumor segmentation compared to the second-best method.

D-CoRP: Differentiable Connectivity Refinement for Functional Brain Networks

Brain network is an important tool for understanding the brain, offering insights for scientific research and clinical diagnosis. Existing models for brain networks typically primarily focus on brain regions or overlook the complexity of brain connectivities. MRI-derived brain network data is commonly susceptible to connectivity noise, underscoring the necessity of incorporating connectivities into the modeling of brain networks. To address this gap, we introduce a differentiable module for refining brain connectivity. We develop the multivariate optimization based on information bottleneck theory to address the complexity of the brain network and filter noisy or redundant connections. Also, our method functions as a flexible plugin that is adaptable to most graph neural networks. Our extensive experimental results show that the proposed method can significantly improve the performance of various baseline models and outperform other state-of-the-art methods, indicating the effectiveness and generalizability of the proposed method in refining brain network connectivity. The code will be released for public availability.

Weakly supervised segmentation with point annotations for histopathology images via contrast-based variational model

Image segmentation is a fundamental task in the field of imaging and vision. Supervised deep learning for segmentation has achieved unparalleled success when sufficient training data with annotated labels are available. However, annotation is known to be expensive to obtain, especially for histopathology images where the target regions are usually with high morphology variations and irregular shapes. Thus, weakly supervised learning with sparse annotations of points is promising to reduce the annotation workload. In this work, we propose a contrast-based variational model to generate segmentation results, which serve as reliable complementary supervision to train a deep segmentation model for histopathology images. The proposed method considers the common characteristics of target regions in histopathology images and can be trained in an end-to-end manner. It can generate more regionally consistent and smoother boundary segmentation, and is more robust to unlabeled `novel' regions. Experiments on two different histology datasets demonstrate its effectiveness and efficiency in comparison to previous models.

DTFD-MIL: Double-Tier Feature Distillation Multiple Instance Learning for Histopathology Whole Slide Image Classification

Multiple instance learning (MIL) has been increasingly used in the classification of histopathology whole slide images (WSIs). However, MIL approaches for this specific classification problem still face unique challenges, particularly those related to small sample cohorts. In these, there are limited number of WSI slides (bags), while the resolution of a single WSI is huge, which leads to a large number of patches (instances) cropped from this slide. To address this issue, we propose to virtually enlarge the number of bags by introducing the concept of pseudo-bags, on which a double-tier MIL framework is built to effectively use the intrinsic features. Besides, we also contribute to deriving the instance probability under the framework of attention-based MIL, and utilize the derivation to help construct and analyze the proposed framework. The proposed method outperforms other latest methods on the CAMELYON-16 by substantially large margins, and is also better in performance on the TCGA lung cancer dataset. The proposed framework is ready to be extended for wider MIL applications. The code is available at: https://github.com/hrzhang1123/DTFD-MIL

BI-GCN: Boundary-Aware Input-Dependent Graph Convolution Network for Biomedical Image Segmentation

Segmentation is an essential operation of image processing. The convolution operation suffers from a limited receptive field, while global modelling is fundamental to segmentation tasks. In this paper, we apply graph convolution into the segmentation task and propose an improved \textit{Laplacian}. Different from existing methods, our \textit{Laplacian} is data-dependent, and we introduce two attention diagonal matrices to learn a better vertex relationship. In addition, it takes advantage of both region and boundary information when performing graph-based information propagation. Specifically, we model and reason about the boundary-aware region-wise correlations of different classes through learning graph representations, which is capable of manipulating long range semantic reasoning across various regions with the spatial enhancement along the object's boundary. Our model is well-suited to obtain global semantic region information while also accommodates local spatial boundary characteristics simultaneously. Experiments on two types of challenging datasets demonstrate that our method outperforms the state-of-the-art approaches on the segmentation of polyps in colonoscopy images and of the optic disc and optic cup in colour fundus images.

Spatial Uncertainty-Aware Semi-Supervised Crowd Counting

Semi-supervised approaches for crowd counting attract attention, as the fully supervised paradigm is expensive and laborious due to its request for a large number of images of dense crowd scenarios and their annotations. This paper proposes a spatial uncertainty-aware semi-supervised approach via regularized surrogate task (binary segmentation) for crowd counting problems. Different from existing semi-supervised learning-based crowd counting methods, to exploit the unlabeled data, our proposed spatial uncertainty-aware teacher-student framework focuses on high confident regions' information while addressing the noisy supervision from the unlabeled data in an end-to-end manner. Specifically, we estimate the spatial uncertainty maps from the teacher model's surrogate task to guide the feature learning of the main task (density regression) and the surrogate task of the student model at the same time. Besides, we introduce a simple yet effective differential transformation layer to enforce the inherent spatial consistency regularization between the main task and the surrogate task in the student model, which helps the surrogate task to yield more reliable predictions and generates high-quality uncertainty maps. Thus, our model can also address the task-level perturbation problems that occur spatial inconsistency between the primary and surrogate tasks in the student model. Experimental results on four challenging crowd counting datasets demonstrate that our method achieves superior performance to the state-of-the-art semi-supervised methods.