Related papers: Hierarchical Pooling and Explainability in Graph N…

Graph neural networks (GNN) extends deep learning to graph-structure dataset. Similar to Convolutional Neural Networks (CNN) using on image prediction, convolutional and pooling layers are the foundation to success for GNN on graph…

Graph Neural Networks (GNNs), which generalize deep neural networks to graph-structured data, have drawn considerable attention and achieved state-of-the-art performance in numerous graph related tasks. However, existing GNN models mainly…

Graph neural networks (GNN) has been demonstrated to be effective in classifying graph structures. To further improve the graph representation learning ability, hierarchical GNN has been explored. It leverages the differentiable pooling to…

Cancer is responsible for millions of deaths worldwide every year. Although significant progress hasbeen achieved in cancer medicine, many issues remain to be addressed for improving cancer therapy.Appropriate cancer patient stratification…

Graph convolutional networks (GCNs) have been successfully applied in node classification tasks of network mining. However, most of these models based on neighborhood aggregation are usually shallow and lack the "graph pooling" mechanism,…

The spatial convolution layer which is widely used in the Graph Neural Networks (GNNs) aggregates the feature vector of each node with the feature vectors of its neighboring nodes. The GNN is not aware of the locations of the nodes in the…

Graph Neural Networks (GNNs) are attracting growing attention due to their effectiveness and flexibility in modeling a variety of graph-structured data. Exiting GNN architectures usually adopt simple pooling operations (eg. sum, average,…

Deep Graph Neural Networks (GNNs) are useful models for graph classification and graph-based regression tasks. In these tasks, graph pooling is a critical ingredient by which GNNs adapt to input graphs of varying size and structure. We…

Graph neural networks (GNNs) extends the functionality of traditional neural networks to graph-structured data. Similar to CNNs, an optimized design of graph convolution and pooling is key to success. Borrowing ideas from physics, we…

Spatial arrangement of cells of various types, such as tumor infiltrating lymphocytes and the advancing edge of a tumor, are important features for detecting and characterizing cancers. However, convolutional neural networks (CNNs) do not…

Graph neural networks, which generalize deep neural network models to graph structured data, have attracted increasing attention in recent years. They usually learn node representations by transforming, propagating and aggregating node…

The identification of cancer genes is a critical yet challenging problem in cancer genomics research. Existing computational methods, including deep graph neural networks, fail to exploit the multilayered gene-gene interactions or provide…

Graph neural networks (GNNs) are increasingly used to model biological systems, yet the reliability of post-hoc explanation methods for recovering meaningful molecular mechanisms remains unclear. Here, we systematically evaluate four widely…

The exploration of cellular heterogeneity within the tumor microenvironment (TME) via single-cell RNA sequencing (scRNA-seq) is essential for understanding cancer progression and response to therapy. Current scRNA-seq approaches, however,…

Graph neural networks (GNNs) have revolutionized the field of machine learning on non-Euclidean data such as graphs and networks. GNNs effectively implement node representation learning through neighborhood aggregation and achieve…

We present a novel and hierarchical approach for supervised classification of signals spanning over a fixed graph, reflecting shared properties of the dataset. To this end, we introduce a Convolutional Cluster Pooling layer exploiting a…

Graph neural networks (GNNs) have shown promise in integrating protein-protein interaction (PPI) networks for identifying cancer genes in recent studies. However, due to the insufficient modeling of the biological information in PPI…

Graph convolutional neural networks (GCNNs) are a powerful extension of deep learning techniques to graph-structured data problems. We empirically evaluate several pooling methods for GCNNs, and combinations of those graph pooling methods…

Gigapixel medical images provide massive data, both morphological textures and spatial information, to be mined. Due to the large data scale in histology, deep learning methods play an increasingly significant role as feature extractors.…

Early detection of cancer plays a key role in improving survival rates, but identifying reliable biomarkers from RNA-seq data is still a major challenge. The data are high-dimensional, and conventional statistical methods often fail to…