Huanhuan Dai

Xiangyu Meng, Xue Li, Qing Yang et al.

Benefiting from the advancements in deep learning, various genomic analytical techniques, such as survival analysis, classification of tumors and their subtypes, and exploration of specific pathways, have significantly enhanced our understanding of the biological mechanisms driving cancer. However, the overfitting issue, arising from the limited number of patient samples, poses a challenge in improving the accuracy of genome analysis by deepening the neural network. Furthermore, it remains uncertain whether novel approaches such as the sparsely gated mixture of expert (MOE) and self-attention mechanisms can improve the accuracy of genomic analysis. In this paper, we introduce a novel sparsely gated RNA-seq analysis framework called Gene-MOE. This framework exploits the potential of the MOE layers and the proposed mixture of attention expert (MOAE) layers to enhance the analysis accuracy. Additionally, it addresses overfitting challenges by integrating pan-cancer information from 33 distinct cancer types through pre-training.We pre-trained Gene-MOE on TCGA pan-cancer RNA-seq dataset with 33 cancer types. Subsequently, we conducted experiments involving cancer classification and survival analysis based on the pre-trained Gene-MOE. According to the survival analysis results on 14 cancer types, Gene-MOE outperformed state-of-the-art models on 12 cancer types. Through detailed feature analysis, we found that the Gene-MOE model could learn rich feature representations of high-dimensional genes. According to the classification results, the total accuracy of the classification model for 33 cancer classifications reached 95.8%, representing the best performance compared to state-of-the-art models. These results indicate that Gene-MOE holds strong potential for use in cancer classification and survival analysis.

Xiangyu Meng, Xudong Zhang, Gan Wang et al.

Liver cancer is one of the most common malignant diseases in the world. Segmentation and labeling of liver tumors and blood vessels in CT images can provide convenience for doctors in liver tumor diagnosis and surgical intervention. In the past decades, many state-of-the-art medical image segmentation algorithms appeared during this period. With the development of embedded devices, embedded deployment for medical segmentation and automatic reconstruction brings prospects for future automated surgical tasks. Yet, most of the existing segmentation methods mostly care about the spatial feature context and have a perception defect in the semantic relevance of medical images, which significantly affects the segmentation accuracy of liver tumors and blood vessels. Deploying large and complex models into embedded devices requires a reasonable trade-off between model accuracy, reasoning speed and model capacity. Given these problems, we introduce a multi-scale feature fusion network called TransFusionNet based on Transformer. This network achieved very competitive performance for liver vessel and liver tumor segmentation tasks, meanwhile it can improve the recognition of morphologic margins of liver tumors by exploiting the global information of CT images. Experiments show that in vessel segmentation task TransFusionNet achieved mean Dice coefficients of 0.899 and in liver tumor segmentation task TransFusionNet achieved mean Dice coefficients of 0.961. Compared with the state-of-the-art framework, our model achieves the best segmentation result. In addition, we deployed the model into an embedded micro-structure and constructed an integrated model for liver tumor vascular segmentation and reconstruction. This proprietary structure will be the exclusive component of the future medical field.