Related papers: Tri-graph Information Propagation for Polypharmacy…

Accurately predicting the binding affinity between drugs and proteins is an essential step for computational drug discovery. Since graph neural networks (GNNs) have demonstrated remarkable success in various graph-related tasks, GNNs have…

Graph convolutional neural networks have recently shown great potential for the task of zero-shot learning. These models are highly sample efficient as related concepts in the graph structure share statistical strength allowing…

Protein function prediction may be framed as predicting subgraphs (with certain closure properties) of a directed acyclic graph describing the hierarchy of protein functions. Graph neural networks (GNNs), with their built-in inductive bias…

Motivation: Identifying drug-target interactions (DTIs) is a key step in drug repositioning. In recent years, the accumulation of a large number of genomics and pharmacology data has formed mass drug and target related heterogeneous…

Mixed Integer Programming (MIP) is one of the most widely used modeling techniques for combinatorial optimization problems. In many applications, a similar MIP model is solved on a regular basis, maintaining remarkable similarities in model…

Learning invariant graph representations for out-of-distribution (OOD) generalization remains challenging because the learned representations often retain spurious components. To address this challenge, this work introduces a new tool from…

Hypergraphs model higher-order relations that drive real-world decisions, from drug prescriptions to recommendations. A central structural signal in such data, beyond what pairwise relations can express, is interaction compositionality:…

The computational drug repositioning aims to discover new uses for marketed drugs, which can accelerate the drug development process and play an important role in the existing drug discovery system. However, the number of validated…

Drug recommendation (DR) systems aim to support healthcare professionals in selecting appropriate medications based on patients' medical conditions. State-of-the-art approaches utilize deep learning techniques for improving DR, but fall…

The emergence of Graph Convolutional Network (GCN) has greatly boosted the progress of graph learning. However, two disturbing factors, noise and redundancy in graph data, and lack of interpretation for prediction results, impede further…

Graph neural networks (GNNs) have been popularly used in analyzing graph-structured data, showing promising results in various applications such as node classification, link prediction and network recommendation. In this paper, we present a…

Adverse Drug Reaction (ADR) is a significant public health concern world-wide. Numerous graph-based methods have been applied to biomedical graphs for predicting ADRs in pre-marketing phases. ADR detection in post-market surveillance is no…

Adverse Drug Reactions (ADRs) are a leading cause of morbidity and mortality. Existing prediction methods rely mainly on chemical similarity, machine learning on structured databases, or isolated target profiles, but often fail to integrate…

We propose Embedding Propagation (EP), an unsupervised learning framework for graph-structured data. EP learns vector representations of graphs by passing two types of messages between neighboring nodes. Forward messages consist of label…

Do higher-order network structures aid graph semi-supervised learning? Given a graph and a few labeled vertices, labeling the remaining vertices is a high-impact problem with applications in several tasks, such as recommender systems, fraud…

In this study, we intend to solve a mutual information problem in interacting molecules of any type, such as proteins, nucleic acids, and small molecules. Using machine learning techniques, we accurately predict pairwise interactions, which…

Scalable graph neural networks (GNNs) have emerged as a promising technique, which exhibits superior predictive performance and high running efficiency across numerous large-scale graph-based web applications. However, (i) Most scalable…

Estimating a 3D human pose has proven to be a challenging task, primarily because of the complexity of the human body joints, occlusions, and variability in lighting conditions. In this paper, we introduce a higher-order graph convolutional…

Temporal graphs exhibit dynamic interactions between nodes over continuous time, whose topologies evolve with time elapsing. The whole temporal neighborhood of nodes reveals the varying preferences of nodes. However, previous works usually…

Subgraph-based methods have proven to be effective and interpretable in predicting drug-drug interactions (DDIs), which are essential for medical practice and drug development. Subgraph selection and encoding are critical stages in these…