Chaoyi Li

Meng Li, Chaoyi Li, Can Peng et al.

Deep learning techniques have become widely utilized in histopathology image classification due to their superior performance. However, this success heavily relies on the availability of substantial labeled data, which necessitates extensive and costly manual annotation by domain experts. To address this challenge, researchers have recently employed generative models to synthesize data for augmentation, thereby enhancing classification model performance. Traditionally, this involves generating synthetic data first and then training the classification model with both synthetic and real data, which creates a two-stage, time-consuming workflow. To overcome this limitation, we propose an innovative unified framework that integrates the data generation and model training stages into a unified process. Our approach utilizes a pure Vision Transformer (ViT)-based conditional Generative Adversarial Network (cGAN) model to simultaneously handle both image synthesis and classification. An additional classification head is incorporated into the cGAN model to enable simultaneous classification of histopathology images. To improve training stability and enhance the quality of generated data, we introduce a conditional class projection technique that helps maintain class separation during the generation process. We also employ a dynamic multi-loss weighting mechanism to effectively balance the losses of the classification tasks. Furthermore, our selective augmentation mechanism actively selects the most suitable generated images for data augmentation to further improve performance. Extensive experiments on histopathology datasets show that our unified synthetic augmentation framework consistently enhances the performance of histopathology image classification models.

Peng Zhou, Lai Hou Tim, Zhixiang Cheng et al.

Predicting molecular properties is a critical component of drug discovery. Recent advances in deep learning, particularly Graph Neural Networks (GNNs), have enabled end-to-end learning from molecular structures, reducing reliance on manual feature engineering. However, while GNNs and self-supervised learning approaches have advanced molecular property prediction (MPP), the integration of human prior knowledge remains indispensable, as evidenced by recent methods that leverage large language models (LLMs) for knowledge extraction. Despite their strengths, LLMs are constrained by knowledge gaps and hallucinations, particularly for less-studied molecular properties. In this work, we propose a novel framework that, for the first time, integrates knowledge extracted from LLMs with structural features derived from pre-trained molecular models to enhance MPP. Our approach prompts LLMs to generate both domain-relevant knowledge and executable code for molecular vectorization, producing knowledge-based features that are subsequently fused with structural representations. We employ three state-of-the-art LLMs, GPT-4o, GPT-4.1, and DeepSeek-R1, for knowledge extraction. Extensive experiments demonstrate that our integrated method outperforms existing approaches, confirming that the combination of LLM-derived knowledge and structural information provides a robust and effective solution for MPP.

Teng Qiu, Kaifu Yang, Chaoyi Li et al.

In this paper, we propose a physically inspired graph-theoretical clustering method, which first makes the data points organized into an attractive graph, called In-Tree, via a physically inspired rule, called Nearest Descent (ND). In particular, the rule of ND works to select the nearest node in the descending direction of potential as the parent node of each node, which is in essence different from the classical Gradient Descent or Steepest Descent. The constructed In-Tree proves a very good candidate for clustering due to its particular features and properties. In the In-Tree, the original clustering problem is reduced to a problem of removing a very few of undesired edges from this graph. Pleasingly, the undesired edges in In-Tree are so distinguishable that they can be easily determined in either automatic or interactive way, which is in stark contrast to the cases in the widely used Minimal Spanning Tree and k-nearest-neighbor graph. The cluster number in the proposed method can be easily determined based on some intermediate plots, and the cluster assignment for each node is easily made by quickly searching its root node in each sub-graph (also an In-Tree). The proposed method is extensively evaluated on both synthetic and real-world datasets. Overall, the proposed clustering method is a density-based one, but shows significant differences and advantages in comparison to the traditional ones. The proposed method is simple yet efficient and reliable, and is applicable to various datasets with diverse shapes, attributes and any high dimensionality