相关论文: Parallel Protein Community Detection in Large-scal…

This study introduces a framework that integrates nonlinear feature extraction, classification, and efficient optimization. First, kernel principal component analysis with a radial basis function kernel reduces dimensionality while…

Many systems can be described using graphs, or networks. Detecting communities in these networks can provide information about the underlying structure and functioning of the original systems. Yet this detection is a complex task and a…

Molecular interactions have widely been modelled as networks. The local wiring patterns around molecules in molecular networks are linked with their biological functions. However, networks model only pairwise interactions between molecules…

Motivation: Protein-protein interactions (PPIs) are usually modelled as networks. These networks have extensively been studied using graphlets, small induced subgraphs capturing the local wiring patterns around nodes in networks. They…

Over the last few years, several computational techniques have been devised to recover protein complexes from the protein interaction (PPI) networks of organisms. These techniques model "dense" subnetworks within PPI networks as complexes.…

Protein-ligand interactions (PLIs) are fundamental to biochemical research and their identification is crucial for estimating biophysical and biochemical properties for rational therapeutic design. Currently, experimental characterization…

Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. However, with the fast-paced growth of biomedical literature, there is a growing need for automated and…

Computationally predicting protein-protein interactions (PPIs) is challenging due to the lack of integrated, multimodal protein representations. DPEB is a curated collection of 22,043 human proteins that integrates four embedding types:…

Functional protein-protein interactions are crucial in most cellular processes. They enable multi-protein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between…

Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…

Community detection is a task of fundamental importance in social network analysis that can be used in a variety of knowledge-based domains. While there exist many works on community detection based on connectivity structures, they suffer…

While there has been a plethora of approaches for detecting disjoint communities from real-world complex networks, some methods for detecting overlapping community structures have also been recently proposed. In this work, we argue that,…

Recent advances in AI for science have highlighted the power of contrastive learning in bridging heterogeneous biological data modalities. Building on this paradigm, we propose HIPPO (HIerarchical Protein-Protein interaction prediction…

Understanding how molecular alterations propagate across biological systems to drive disease remains a central challenge. Although high-throughput profiling enables comprehensive characterization of tumor states, most models neglect…

The protein-protein interaction (PPI) network is crucial for cellular information processing and decision-making. With suitable inputs, PPI networks drive the cells to diverse functional outcomes such as cell proliferation or cell death.…

Community detection plays a crucial role in understanding the structural organization of complex networks. Previous methods, particularly those from statistical physics, primarily focus on the analysis of mesoscopic network structures and…

Membership diversity is a characteristic aspect of social networks in which a person may belong to more than one social group. For this reason, discovering overlapping structures is necessary for realistic social analysis. In this paper, we…

Protein-protein interactions are of great importance in biochemical processes. Accurate prediction of protein-protein interaction sites (PPIs) is crucial for our understanding of biological mechanism. Although numerous approaches have been…

Protein-protein interactions (PPIs) are fundamental for deciphering cellular functions,disease pathways,and drug discovery.Although existing neural networks and machine learning methods have achieved high accuracy in PPI prediction,their…

Community detection in online social networks has been a hot research topic in recent years. Meanwhile, to enjoy more social network services, users nowadays are usually involved in multiple online social networks simultaneously, some of…