{"paper":{"title":"Graph neural network explanations reveal a topological signature of disease-associated hubs in biological networks","license":"http://creativecommons.org/licenses/by/4.0/","headline":"","cross_cats":["cs.AI","cs.LG"],"primary_cat":"q-bio.MN","authors_text":"Dennis Veselkov, Ivan Laponogov, Kirill Veselkov, Kyle Higgins","submitted_at":"2026-05-08T15:29:36Z","abstract_excerpt":"Graph neural networks (GNNs) are increasingly used to model biological systems, yet the reliability of post-hoc explanation methods for recovering meaningful molecular mechanisms remains unclear. Here, we systematically evaluate four widely used approaches: Saliency Attribution (SA), Integrated Gradients (IG), GNNExplainer, and Layer-wise Relevance Propagation (LRP) for identifying disease-relevant structure in breast cancer RNA-seq data projected onto a protein-protein interaction network. Using synthetic benchmarks with known ground-truth motifs, we show that explanation methods recover dist"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2605.21502","kind":"arxiv","version":1},"verdict":{"id":null,"model_set":{},"created_at":null,"strongest_claim":"","one_line_summary":"","pipeline_version":null,"weakest_assumption":"","pith_extraction_headline":""},"integrity":{"clean":true,"summary":{"advisory":0,"critical":0,"by_detector":{},"informational":0},"endpoint":"/pith/2605.21502/integrity.json","findings":[],"available":true,"detectors_run":[],"snapshot_sha256":"c28c3603d3b5d939e8dc4c7e95fa8dfce3d595e45f758748cecf8e644a296938"},"references":{"count":0,"sample":[],"resolved_work":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57","internal_anchors":0},"formal_canon":{"evidence_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"author_claims":{"count":0,"strong_count":0,"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"builder_version":"pith-number-builder-2026-05-17-v1"}