A Multimodal Graph Neural Network Framework for Cancer Molecular Subtype Classification

The recent development of high-throughput sequencing creates a large collection of multi-omics data, which enables researchers to better investigate cancer molecular profiles and cancer taxonomy based on molecular subtypes. Integrating multi-omics data has been proven to be effective for building more precise classification models. Current multi-omics integrative models mainly use early fusion by concatenation or late fusion based on deep neural networks. Due to the nature of biological systems, graphs are a better representation of bio-medical data. Although few graph neural network (GNN) based multi-omics integrative methods have been proposed, they suffer from three common disadvantages. One is most of them use only one type of connection, either inter-omics or intra-omic connection; second, they only consider one kind of GNN layer, either graph convolution network (GCN) or graph attention network (GAT); and third, most of these methods lack testing on a more complex cancer classification task. We propose a novel end-to-end multi-omics GNN framework for accurate and robust cancer subtype classification. The proposed model utilizes multi-omics data in the form of heterogeneous multi-layer graphs that combines both inter-omics and intra-omic connections from established biological knowledge. The proposed model incorporates learned graph features and global genome features for accurate classification. We test the proposed model on TCGA Pan-cancer dataset and TCGA breast cancer dataset for molecular subtype and cancer subtype classification, respectively. The proposed model outperforms four current state-of-the-art baseline models in multiple evaluation metrics. The comparative analysis of GAT-based models and GCN-based models reveals that GAT-based models are preferred for smaller graphs with less information and GCN-based models are preferred for larger graphs with extra information.

Color Recognition for Rubik's Cube Robot

In this paper, we proposed three methods to solve color recognition of Rubik's cube, which includes one offline method and two online methods. Scatter balance \& extreme learning machine (SB-ELM), a offline method, is proposed to illustrate the efficiency of training based method. We also point out the conception of color drifting which indicates offline methods are always ineffectiveness and can not work well in continuous change circumstance. By contrast, dynamic weight label propagation is proposed for labeling blocks color by known center blocks color of Rubik's cube. Furthermore, weak label hierarchic propagation, another online method, is also proposed for unknown all color information but only utilizes weak label of center block in color recognition. We finally design a Rubik's cube robot and construct a dataset to illustrate the efficiency and effectiveness of our online methods and to indicate the ineffectiveness of offline method by color drifting in our dataset.