Related papers: Enhancing the functional content of protein intera…

Graph Neural Networks (GNNs) achieve state-of-the-art performance on graph-structured data across numerous domains. Their underlying ability to represent nodes as summaries of their vicinities has proven effective for homophilous graphs in…

Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…

Many real-world networks such as the gene networks, protein-protein interaction networks and metabolic networks exhibit community structures, meaning the existence of groups of densely connected vertices in the networks. Many local…

We propose a biologically motivated quantity, twinness, to evaluate local similarity between nodes in a network. The twinness of a pair of nodes is the number of connected, labeled subgraphs of size n in which the two nodes possess…

Networks describe a variety of interacting complex systems in social science, biology and information technology. Usually the nodes of real networks are identified not only by their connections but also by some other characteristics.…

The prediction of protein interactions (CPIs) is crucial for the in-silico screening step in drug discovery. Recently, many end-to-end representation learning methods using deep neural networks have achieved significantly better performance…

Background:Typically, proteins perform key biological functions by interacting with each other. As a consequence, predicting which protein pairs interact is a fundamental problem. Experimental methods are slow, expensive, and may be error…

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…

Motivation: Machine learning based prediction of compound-protein interactions (CPIs) is important for drug design, screening and repurposing studies and can improve the efficiency and cost-effectiveness of wet lab assays. Despite the…

We introduce a new centrality measure that characterizes the participation of each node in all subgraphs in a network. Smaller subgraphs are given more weight than larger ones, which makes this measure appropriate for characterizing network…

High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions…

We present a method that compares the protein interaction networks of two species to detect functionally similar (conserved) protein modules between them. The method is based on an algorithm we developed to identify matching subgraphs…

Initial protein structural comparisons were sequence-based. Since amino acids that are distant in the sequence can be close in the 3-dimensional (3D) structure, 3D contact approaches can complement sequence approaches. Traditional 3D…

Graph Neural Networks (GNNs) have emerged as a powerful technique for learning on relational data. Owing to the relatively limited number of message passing steps they perform -- and hence a smaller receptive field -- there has been…

Heterogeneous information network (HIN) has been widely used to characterize entities of various types and their complex relations. Recent attempts either rely on explicit path reachability to leverage path-based semantic relatedness or…

Measures of complex network analysis, such as vertex centrality, have the potential to unveil existing network patterns and behaviors. They contribute to the understanding of networks and their components by analyzing their structural…

Heterogeneous molecular entities and their interactions, commonly depicted as a network, are crucial for advancing our systems-level understanding of biology. With recent advancements in high-throughput data generation and a significant…

Protein interaction networks (PINs) are often used to "learn" new biological function from their topology. Since current PINs are noisy, their computational de-noising via link prediction (LP) could improve the learning accuracy. LP uses…

In this work, we propose a novel centrality metric, referred to as star centrality, which incorporates information from the closed neighborhood of a node, rather than solely from the node itself, when calculating its topological importance.…

The structure of a social network contains information useful for predicting its evolution. Nodes that are "close" in some sense are more likely to become linked in the future than more distant nodes. We show that structural information can…