Related papers: Hierarchical Protein Function Prediction with Tail…

Many machine learning techniques have been proposed in the last few years to process data represented in graph-structured form. Graphs can be used to model several scenarios, from molecules and materials to RNA secondary structures. Several…

The message-passing mechanism underlying Graph Neural Networks (GNNs) is not naturally suited for heterophilic datasets, where adjacent nodes often have different labels. Most solutions to this problem remain confined to the task of node…

Protein function prediction is a crucial task in bioinformatics, with significant implications for understanding biological processes and disease mechanisms. While the relationship between sequence and function has been extensively…

Graph neural networks (GNNs) have emerged as powerful tools for learning protein structures by capturing spatial relationships at the residue level. However, existing GNN-based methods often face challenges in learning multiscale…

Protein-protein interactions (PPIs) play key roles in a broad range of biological processes. Numerous strategies have been proposed for predicting PPIs, and among them, graph-based methods have demonstrated promising outcomes owing to the…

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 neural networks (GNNs) are shown to be successful in modeling applications with graph structures. However, training an accurate GNN model requires a large collection of labeled data and expressive features, which might be inaccessible…

The task of inferring the missing links in a graph based on its current structure is referred to as link prediction. Link prediction methods that are based on pairwise node similarity are well-established approaches in the literature. They…

Studying the function of proteins is important for understanding the molecular mechanisms of life. The number of publicly available protein structures has increasingly become extremely large. Still, the determination of the function of a…

Link prediction is a fundamental task in graph learning, inherently shaped by the topology of the graph. While traditional heuristics are grounded in graph topology, they encounter challenges in generalizing across diverse graphs. Recent…

Graph Neural Networks (GNNs) extend basic Neural Networks (NNs) by additionally making use of graph structure based on the relational inductive bias (edge bias), rather than treating the nodes as collections of independent and identically…

Graph Neural Networks (GNNs) extend the success of neural networks to graph-structured data by accounting for their intrinsic geometry. While extensive research has been done on developing GNN models with superior performance according to a…

Machine learning (ML) is revolutionizing protein structural analysis, including an important subproblem of predicting protein residue contact maps, i.e., which amino-acid residues are in close spatial proximity given the amino-acid sequence…

In this survey, we dive into Tabular Data Learning (TDL) using Graph Neural Networks (GNNs), a domain where deep learning-based approaches have increasingly shown superior performance in both classification and regression tasks compared to…

Graph Neural Networks (GNNs) have been widely applied to various fields for learning over graph-structured data. They have shown significant improvements over traditional heuristic methods in various tasks such as node classification and…

Graph neural networks (GNNs) have been demonstrated to be powerful in modeling graph-structured data. However, training GNNs usually requires abundant task-specific labeled data, which is often arduously expensive to obtain. One effective…

Graph Neural Networks (GNNs) are characterized by their capacity of processing graph-structured data. However, due to the sparsity of labels under semi-supervised learning, they have been found to exhibit biased performance on specific…

Graphs are essential for modeling complex relationships and capturing structured interactions in data. Graph Neural Networks (GNNs) are particularly effective when such relational structure is explicitly available, but many real-world…

Link prediction, which consists of predicting edges based on graph features, is a fundamental task in many graph applications. As for several related problems, Graph Neural Networks (GNNs), which are based on an attribute-centric…

Many applications of machine learning require a model to make accurate pre-dictions on test examples that are distributionally different from training ones, while task-specific labels are scarce during training. An effective approach to…