Hao Du

Hao Du, Qihua Dong, Yan Xu et al.

Medical image segmentation is almost the most important pre-processing procedure in computer-aided diagnosis but is also a very challenging task due to the complex shapes of segments and various artifacts caused by medical imaging, (i.e., low-contrast tissues, and non-homogenous textures). In this paper, we propose a simple yet effective segmentation framework that incorporates the geometric prior and contrastive similarity into the weakly-supervised segmentation framework in a loss-based fashion. The proposed geometric prior built on point cloud provides meticulous geometry to the weakly-supervised segmentation proposal, which serves as better supervision than the inherent property of the bounding-box annotation (i.e., height and width). Furthermore, we propose contrastive similarity to encourage organ pixels to gather around in the contrastive embedding space, which helps better distinguish low-contrast tissues. The proposed contrastive embedding space can make up for the poor representation of the conventionally-used gray space. Extensive experiments are conducted to verify the effectiveness and the robustness of the proposed weakly-supervised segmentation framework. The proposed framework is superior to state-of-the-art weakly-supervised methods on the following publicly accessible datasets: LiTS 2017 Challenge, KiTS 2021 Challenge, and LPBA40. We also dissect our method and evaluate the performance of each component.

Xinzhe Zheng, Hao Du, Fanding Xu et al.

Deep learning-based computational methods have achieved promising results in predicting protein-protein interactions (PPIs). However, existing benchmarks predominantly focus on isolated pairwise evaluations, overlooking a model's capability to reconstruct biologically meaningful PPI networks, which is crucial for biology research. To address this gap, we introduce PRING, the first comprehensive benchmark that evaluates protein-protein interaction prediction from a graph-level perspective. PRING curates a high-quality, multi-species PPI network dataset comprising 21,484 proteins and 186,818 interactions, with well-designed strategies to address both data redundancy and leakage. Building on this golden-standard dataset, we establish two complementary evaluation paradigms: (1) topology-oriented tasks, which assess intra and cross-species PPI network construction, and (2) function-oriented tasks, including protein complex pathway prediction, GO module analysis, and essential protein justification. These evaluations not only reflect the model's capability to understand the network topology but also facilitate protein function annotation, biological module detection, and even disease mechanism analysis. Extensive experiments on four representative model categories, consisting of sequence similarity-based, naive sequence-based, protein language model-based, and structure-based approaches, demonstrate that current PPI models have potential limitations in recovering both structural and functional properties of PPI networks, highlighting the gap in supporting real-world biological applications. We believe PRING provides a reliable platform to guide the development of more effective PPI prediction models for the community. The dataset and source code of PRING are available at https://github.com/SophieSarceau/PRING.

Fangzhou Han, Can Wang, Hao Du et al.

Despite recent breakthroughs in deep learning methods for image lighting enhancement, they are inferior when applied to portraits because 3D facial information is ignored in their models. To address this, we present a novel deep learning framework for portrait lighting enhancement based on 3D facial guidance. Our framework consists of two stages. In the first stage, corrected lighting parameters are predicted by a network from the input bad lighting image, with the assistance of a 3D morphable model and a differentiable renderer. Given the predicted lighting parameter, the differentiable renderer renders a face image with corrected shading and texture, which serves as the 3D guidance for learning image lighting enhancement in the second stage. To better exploit the long-range correlations between the input and the guidance, in the second stage, we design an image-to-image translation network with a novel transformer architecture, which automatically produces a lighting-enhanced result. Experimental results on the FFHQ dataset and in-the-wild images show that the proposed method outperforms state-of-the-art methods in terms of both quantitative metrics and visual quality. We will publish our dataset along with more results on https://cassiepython.github.io/egsr/index.html.

Hao Du, Melissa Min-Szu Yao, Liangyu Chen et al.

The morphology and distribution of microcalcifications in a cluster are the most important characteristics for radiologists to diagnose breast cancer. However, it is time-consuming and difficult for radiologists to identify these characteristics, and there also lacks of effective solutions for automatic characterization. In this study, we proposed a multi-task deep graph convolutional network (GCN) method for the automatic characterization of morphology and distribution of microcalcifications in mammograms. Our proposed method transforms morphology and distribution characterization into node and graph classification problem and learns the representations concurrently. Through extensive experiments, we demonstrate significant improvements with the proposed multi-task GCN comparing to the baselines. Moreover, the achieved improvements can be related to and enhance clinical understandings. We explore, for the first time, the application of GCNs in microcalcification characterization that suggests the potential of graph learning for more robust understanding of medical images.