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Understanding protein structure-function relationships is a key challenge in computational biology, with applications across the biotechnology and pharmaceutical industries. While it is known that protein structure directly impacts protein…

Graph Convolutional Networks (GCNs) achieve an impressive performance due to the remarkable representation ability in learning the graph information. However, GCNs, when implemented on a deep network, require expensive computation power,…

Graph Neural Networks (GNNs) have recently gained widespread attention as a successful tool for analyzing graph-structured data. However, imperfect graph structure with noisy links lacks enough robustness and may damage graph…

As proteins with similar structures often have similar functions, analysis of protein structures can help predict protein functions and is thus important. We consider the problem of protein structure classification, which computationally…

Graph Convolution Networks (GCNs) are becoming more and more popular for learning node representations on graphs. Though there exist various developments on sampling and aggregation to accelerate the training process and improve the…

Predicting interactions between biomolecules, such as protein-protein complexes, remains a challenging problem. Despite the many advancements done so far, the performances of docking protocols are deeply dependent on their capability of…

Modern recommender systems (RS) work by processing a number of signals that can be inferred from large sets of user-item interaction data. The main signal to analyze stems from the raw matrix that represents interactions. However, we can…

Identifying influential nodes in complex networks is of great importance, and has many applications in practice. For example, finding influential nodes in e-commerce network can provide merchants with customers with strong purchase intent;…

Important advances have been made using convolutional neural network (CNN) approaches to solve complicated problems in areas that rely on grid structured data such as image processing and object classification. Recently, research on graph…

Skeleton-based action recognition has attracted considerable attention in computer vision since skeleton data is more robust to the dynamic circumstance and complicated background than other modalities. Recently, many researchers have used…

Graph Convolutional Networks (GCNs) are extensively utilized for deep learning on graphs. The large data sizes of graphs and their vertex features make scalable training algorithms and distributed memory systems necessary. Since the…

Learning on 3D structures of large biomolecules is emerging as a distinct area in machine learning, but there has yet to emerge a unifying network architecture that simultaneously leverages the graph-structured and geometric aspects of the…

In representation learning on the graph-structured data, under heterophily (or low homophily), many popular GNNs may fail to capture long-range dependencies, which leads to their performance degradation. To solve the above-mentioned issue,…

Graph Convolutional Networks (GCNs) have proven to be highly effective for skeleton-based action recognition, primarily due to their ability to leverage graph topology for feature aggregation, a key factor in extracting meaningful…

Geometric deep learning provides a principled and versatile manner for the integration of imaging and non-imaging modalities in the medical domain. Graph Convolutional Networks (GCNs) in particular have been explored on a wide variety of…

Multi-modal neuroimaging technology has greatlly facilitated the efficiency and diagnosis accuracy, which provides complementary information in discovering objective disease biomarkers. Conventional deep learning methods, e.g. convolutional…

Graph convolutional networks (GCNs), which can model the human body skeletons as spatial and temporal graphs, have shown remarkable potential in skeleton-based action recognition. However, in the existing GCN-based methods, graph-structured…

Graph Convolutional Networks (GCNs) have emerged as a promising approach to machine learning on Electronic Health Records (EHRs). By constructing a graph representation of patient data and performing convolutions on neighborhoods of nodes,…

Graph embedding, aiming to learn low-dimensional representations (aka. embeddings) of nodes, has received significant attention recently. Recent years have witnessed a surge of efforts made on static graphs, among which Graph Convolutional…

Pre-trained models have been successful in many protein engineering tasks. Most notably, sequence-based models have achieved state-of-the-art performance on protein fitness prediction while structure-based models have been used…