Interaction Network Ontology
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Related Articles from SNS
ECHO-PPI: Trustworthy AI for Evidence-Bundled Detection of Overlapping Protein Modules in Protein-Protein Interaction Networks
arXiv:2605.21216v2 Announce Type: replace Abstract: Protein-protein interaction networks provide a graph-level view of cellular organization, yet their functional modules are overlapping, noisy, and difficult to interpret from cluster assignments alone. Existing community-detection methods can recover candidate protein complexes, but they rarely explain why an individual protein is assigned to a specific module or whether that assignment should be treated as core, peripheral, or uncertain....
Ignet 2.0 and Vignet: An Ontology-Driven Web Platform for Biomedical Gene Interaction Discovery and Visualization
Background: The expansion of biomedical literature demands systematic ontology-guided discovery of gene interactions, vaccine mechanisms, drug associations, and adverse events. Existing platforms such as STRING, DisGeNET, and PubTator fall short of providing a unified, freely accessible system that integrates ontology-based semantic interaction classification, vaccine-focused heterogeneous network construction, and Artificial Intelligence-assisted evidence retrieval. Ignet 2.0 and Vignet are...
Defining and classifying models of groups: The social ontology of higher-order networks
arXiv:2507.02758v2 Announce Type: replace Abstract: In complex systems research, the study of higher-order interactions has exploded in recent years. Researchers have formalized various types of group interactions, such as public goods games, biological contagion, and information broadcasting, showing how higher-order networks can capture group effects more directly than pairwise models. However, equating hyperedges-edges involving more than two agents-with groups can be misleading, as it...
Interpretable Graph Kolmogorov-Arnold Networks for Multi-Cancer Classification and Biomarker Identification using Multi-Omics Data
arXiv:2503.22939v4 Announce Type: replace Abstract: The integration of heterogeneous multi-omics datasets at a systems level remains a central challenge for developing analytical and computational models in precision cancer diagnostics. This paper introduces Multi-Omics Graph Kolmogorov-Arnold Network (MOGKAN), a deep learning framework that utilizes messenger-RNA, micro-RNA sequences, and DNA methylation samples together with Protein-Protein Interaction (PPI) networks for cancer...
Evidence-Aware Protein Complex Detection: Methods, Benchmarks, and Reproducibility Challenges
arXiv:2606.03178v1 Announce Type: new Abstract: Protein complexes are central units of cellular organization, yet their identification from protein-protein interaction (PPI) networks remains difficult because interactome maps are noisy, incomplete, context dependent, and unevenly annotated. This focused methodological review examines evidence-aware approaches that combine PPI topology with Gene Ontology (GO) annotations, expression profiles, subcellular localization, sequence or domain...
Whole-genome duplication shaped cell-type evolution in the vertebrate brain
Abstract The complex brains of vertebrates have more cell types than those of their closest relatives. Whole-genome duplications (WGDs) occurred during early vertebrate evolution1, but it is unclear whether the duplicated genes (ohnologues) facilitated cell-type evolution. Here using brain single-cell transcriptomes from five chordates—human2, mouse3, lizard4, lamprey5 and amphioxus—we report that many cell-type families with conserved core transcription factors in vertebrates do not show...