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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., Comment: 12 pages, Under Review

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.

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, Comment: 28 pages: text part(1-14), supplementary material(15-28)