{"paper":{"title":"Interpretable Neural ODEs for Gene Regulatory Network Discovery under Perturbations","license":"http://arxiv.org/licenses/nonexclusive-distrib/1.0/","headline":"","cross_cats":["cs.AI","cs.CE","q-bio.MN","stat.ME"],"primary_cat":"cs.LG","authors_text":"Aaron Zweig, David A. Knowles, Elham Azizi, Fabian J. Theis, Minseo Kang, Sei Chang, Zaikang Lin","submitted_at":"2025-01-05T01:04:23Z","abstract_excerpt":"Modern high-throughput biological datasets containing thousands of perturbations enable large-scale discovery of causal graphs that represent regulatory interactions between genes. Differentiable causal graphical models and regression-based methods have been developed to infer gene regulatory networks (GRNs) from interventional datasets. However, existing approaches fail to capture the non-linear dynamics of biological processes such as cellular differentiation. To address this limitation, we propose PerturbODE, a novel framework that employs interpretable neural ordinary differential equation"},"claims":{"count":0,"items":[],"snapshot_sha256":"258153158e38e3291e3d48162225fcdb2d5a3ed65a07baac614ab91432fd4f57"},"source":{"id":"2501.02409","kind":"arxiv","version":6},"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/2501.02409/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"}