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.

Tengfei Ma, Xuan Lin, Tianle Li et al.

Large Language Models (LLMs) have recently demonstrated remarkable performance in general tasks across various fields. However, their effectiveness within specific domains such as drug development remains challenges. To solve these challenges, we introduce \textbf{Y-Mol}, forming a well-established LLM paradigm for the flow of drug development. Y-Mol is a multiscale biomedical knowledge-guided LLM designed to accomplish tasks across lead compound discovery, pre-clinic, and clinic prediction. By integrating millions of multiscale biomedical knowledge and using LLaMA2 as the base LLM, Y-Mol augments the reasoning capability in the biomedical domain by learning from a corpus of publications, knowledge graphs, and expert-designed synthetic data. The capability is further enriched with three types of drug-oriented instructions: description-based prompts from processed publications, semantic-based prompts for extracting associations from knowledge graphs, and template-based prompts for understanding expert knowledge from biomedical tools. Besides, Y-Mol offers a set of LLM paradigms that can autonomously execute the downstream tasks across the entire process of drug development, including virtual screening, drug design, pharmacological properties prediction, and drug-related interaction prediction. Our extensive evaluations of various biomedical sources demonstrate that Y-Mol significantly outperforms general-purpose LLMs in discovering lead compounds, predicting molecular properties, and identifying drug interaction events.

Yuqin He, Tengfei Ma, Chaoyi Li et al.

To mitigate the potential adverse health effects of simultaneous multi-drug use, including unexpected side effects and interactions, accurately identifying and predicting drug-drug interactions (DDIs) is considered a crucial task in the field of deep learning. Although existing methods have demonstrated promising performance, they suffer from the bottleneck of limited functional motif-based representation learning, as DDIs are fundamentally caused by motif interactions rather than the overall drug structures. In this paper, we propose an Image-enhanced molecular motif sequence representation framework for \textbf{DDI} prediction, called ImageDDI, which represents a pair of drugs from both global and local structures. Specifically, ImageDDI tokenizes molecules into functional motifs. To effectively represent a drug pair, their motifs are combined into a single sequence and embedded using a transformer-based encoder, starting from the local structure representation. By leveraging the associations between drug pairs, ImageDDI further enhances the spatial representation of molecules using global molecular image information (e.g. texture, shadow, color, and planar spatial relationships). To integrate molecular visual information into functional motif sequence, ImageDDI employs Adaptive Feature Fusion, enhancing the generalization of ImageDDI by dynamically adapting the fusion process of feature representations. Experimental results on widely used datasets demonstrate that ImageDDI outperforms state-of-the-art methods. Moreover, extensive experiments show that ImageDDI achieved competitive performance in both 2D and 3D image-enhanced scenarios compared to other 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