Peng Wan

Junjie Zhou, Yingli Zuo, Shichang Feng et al.

With the development of generative artificial intelligence and instruction tuning techniques, multimodal large language models (MLLMs) have made impressive progress on general reasoning tasks. Benefiting from the chain-of-thought (CoT) methodology, MLLMs can solve the visual reasoning problem step-by-step. However, existing MLLMs still face significant challenges when applied to pathology visual reasoning tasks: (1) LLMs often underperforms because they lack domain-specific information, which can lead to model hallucinations. (2) The additional reasoning steps in CoT may introduce errors, leading to the divergence of answers. To address these limitations, we propose PathCoT, a novel zero-shot CoT prompting method which integrates the pathology expert-knowledge into the reasoning process of MLLMs and incorporates self-evaluation to mitigate divergence of answers. Specifically, PathCoT guides the MLLM with prior knowledge to perform as pathology experts, and provides comprehensive analysis of the image with their domain-specific knowledge. By incorporating the experts' knowledge, PathCoT can obtain the answers with CoT reasoning. Furthermore, PathCoT incorporates a self-evaluation step that assesses both the results generated directly by MLLMs and those derived through CoT, finally determining the reliable answer. The experimental results on the PathMMU dataset demonstrate the effectiveness of our method on pathology visual understanding and reasoning.

Junjie Zhou, Jiao Tang, Yingli Zuo et al.

The integrative analysis of histopathological images and genomic data has received increasing attention for survival prediction of human cancers. However, the existing studies always hold the assumption that full modalities are available. As a matter of fact, the cost for collecting genomic data is high, which sometimes makes genomic data unavailable in testing samples. A common way of tackling such incompleteness is to generate the genomic representations from the pathology images. Nevertheless, such strategy still faces the following two challenges: (1) The gigapixel whole slide images (WSIs) are huge and thus hard for representation. (2) It is difficult to generate the genomic embeddings with diverse function categories in a unified generative framework. To address the above challenges, we propose a Conditional Latent Differentiation Variational AutoEncoder (LD-CVAE) for robust multimodal survival prediction, even with missing genomic data. Specifically, a Variational Information Bottleneck Transformer (VIB-Trans) module is proposed to learn compressed pathological representations from the gigapixel WSIs. To generate different functional genomic features, we develop a novel Latent Differentiation Variational AutoEncoder (LD-VAE) to learn the common and specific posteriors for the genomic embeddings with diverse functions. Finally, we use the product-of-experts technique to integrate the genomic common posterior and image posterior for the joint latent distribution estimation in LD-CVAE. We test the effectiveness of our method on five different cancer datasets, and the experimental results demonstrate its superiority in both complete and missing modality scenarios.

Junjie Zhou, Wei Shao, Yagao Yue et al.

Prompt learning has emerged as a promising paradigm for adapting pre-trained vision-language models (VLMs) to few-shot whole slide image (WSI) classification by aligning visual features with textual representations, thereby reducing annotation cost and enhancing model generalization. Nevertheless, existing methods typically rely on slide-level prompts and fail to capture the subtype-specific phenotypic variations of histological entities (\emph{e.g.,} nuclei, glands) that are critical for cancer diagnosis. To address this gap, we propose Multi-scale Attribute-enhanced Prompt Learning (\textbf{MAPLE}), a hierarchical framework for few-shot WSI classification that jointly integrates multi-scale visual semantics and performs prediction at both the entity and slide levels. Specifically, we first leverage large language models (LLMs) to generate entity-level prompts that can help identify multi-scale histological entities and their phenotypic attributes, as well as slide-level prompts to capture global visual descriptions. Then, an entity-guided cross-attention module is proposed to generate entity-level features, followed by aligning with their corresponding subtype-specific attributes for fine-grained entity-level prediction. To enrich entity representations, we further develop a cross-scale entity graph learning module that can update these representations by capturing their semantic correlations within and across scales. The refined representations are then aggregated into a slide-level representation and aligned with the corresponding prompts for slide-level prediction. Finally, we combine both entity-level and slide-level outputs to produce the final prediction results. Results on three cancer cohorts confirm the effectiveness of our approach in addressing few-shot pathology diagnosis tasks.

Lingyu Chen, Yawen Zeng, Yue Wang et al.

Conventional single-dataset training often fails with new data distributions, especially in ultrasound (US) image analysis due to limited data, acoustic shadows, and speckle noise. Therefore, constructing a universal framework for multi-heterogeneous US datasets is imperative. However, a key challenge arises: how to effectively mitigate inter-dataset interference while preserving dataset-specific discriminative features for robust downstream task? Previous approaches utilize either a single source-specific decoder or a domain adaptation strategy, but these methods experienced a decline in performance when applied to other domains. Considering this, we propose a Universal Collaborative Mixture of Heterogeneous Source-Specific Experts (COME). Specifically, COME establishes dual structure-semantic shared experts that create a universal representation space and then collaborate with source-specific experts to extract discriminative features through providing complementary features. This design enables robust generalization by leveraging cross-datasets experience distributions and providing universal US priors for small-batch or unseen data scenarios. Extensive experiments under three evaluation modes (single-dataset, intra-organ, and inter-organ integration datasets) demonstrate COME's superiority, achieving significant mean AP improvements over state-of-the-art methods. Our project is available at: https://universalcome.github.io/UniversalCOME/.

Jie Shao, Wei Yao, Peng Wan et al.

Registration of unmanned aerial vehicle laser scanning (ULS) and ground light detection and ranging (LiDAR) point clouds in forests is critical to create a detailed representation of a forest structure and an accurate inversion of forest parameters. However, forest occlusion poses challenges for marker-based registration methods, and some marker-free automated registration methods have low efficiency due to the process of object (e.g., tree, crown) segmentation. Therefore, we use a divide-and-conquer strategy and propose an automated and efficient method to register ULS and ground LiDAR point clouds in forests. Registration involves coarse alignment and fine registration, where the coarse alignment of point clouds is divided into vertical and horizontal alignment. The vertical alignment is achieved by ground alignment, which is achieved by the transformation relationship between normal vectors of the ground point cloud and the horizontal plane, and the horizontal alignment is achieved by canopy projection image matching. During image matching, vegetation points are first distinguished by the ground filtering algorithm, and then, vegetation points are projected onto the horizontal plane to obtain two binary images. To match the two images, a matching strategy is used based on canopy shape context features, which are described by a two-point congruent set and canopy overlap. Finally, we implement coarse alignment of ULS and ground LiDAR datasets by combining the results of ground alignment and image matching and finish fine registration. Also, the effectiveness, accuracy, and efficiency of the proposed method are demonstrated by field measurements of forest plots. Experimental results show that the ULS and ground LiDAR data in different plots are registered, of which the horizontal alignment errors are less than 0.02 m, and the average runtime of the proposed method is less than 1 second.

Peng Wan, Zhenbo Song, Jianfeng Lu

In this paper, we present a novel end-to-end deep neural network model for autonomous driving that takes monocular image sequence as input, and directly generates the steering control angle. Firstly, we model the end-to-end driving problem as a local path planning process. Inspired by the environmental representation in the classical planning algorithms(i.e. the beam curvature method), pixel-wise orientations are fed into the network to learn direction-aware features. Next, to handle the imbalanced distribution of steering values in training datasets, we propose an improvement on a cost-sensitive loss function named SteeringLoss2. Besides, we also present a new end-to-end driving dataset, which provides corresponding LiDAR and image sequences, as well as standard driving behaviors. Our dataset includes multiple driving scenarios, such as urban, country, and off-road. Numerous experiments are conducted on both public available LiVi-Set and our own dataset, and the results show that the model using our proposed methods can predict steering angle accurately.

Kai Ma, Peng Wan, Daoqiang Zhang

Graph kernel is a powerful tool measuring the similarity between graphs. Most of the existing graph kernels focused on node labels or attributes and ignored graph hierarchical structure information. In order to effectively utilize graph hierarchical structure information, we propose pyramid graph kernel based on optimal transport (OT). Each graph is embedded into hierarchical structures of the pyramid. Then, the OT distance is utilized to measure the similarity between graphs in hierarchical structures. We also utilize the OT distance to measure the similarity between subgraphs and propose subgraph kernel based on OT. The positive semidefinite (p.s.d) of graph kernels based on optimal transport distance is not necessarily possible. We further propose regularized graph kernel based on OT where we add the kernel regularization to the original optimal transport distance to obtain p.s.d kernel matrix. We evaluate the proposed graph kernels on several benchmark classification tasks and compare their performance with the existing state-of-the-art graph kernels. In most cases, our proposed graph kernel algorithms outperform the competing methods.

Zhongnian Li, Tao Zhang, Peng Wan et al.

Generative Adversarial Networks (GANs) are powerful tools for reconstructing Compressed Sensing Magnetic Resonance Imaging (CS-MRI). However most recent works lack exploration of structure information of MRI images that is crucial for clinical diagnosis. To tackle this problem, we propose the Structure-Enhanced GAN (SEGAN) that aims at restoring structure information at both local and global scale. SEGAN defines a new structure regularization called Patch Correlation Regularization (PCR) which allows for efficient extraction of structure information. In addition, to further enhance the ability to uncover structure information, we propose a novel generator SU-Net by incorporating multiple-scale convolution filters into each layer. Besides, we theoretically analyze the convergence of stochastic factors contained in training process. Experimental results show that SEGAN is able to learn target structure information and achieves state-of-the-art performance for CS-MRI reconstruction.