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[CS.AI] CASCADE: An Agentic Regulatory Network Framework for Downstream Perturbation Prediction

Published at: 2026-08-07 22:00 Last updated: 2026-08-08 01:08
#Machine Learning #Neural #Artificial Intelligence

CASCADE is an agentic framework that predicts downstream transcriptional effects of gene perturbation from precomputed ARACNe regulatory networks, exposed via MCP. Prior work validates such tools by checking whether predicted genes are known cancer genes (membership); we instead test whether the predicted direction of change matches reality, using focal-gene copy-number amplification as a dosage-based proxy for the inverse of knockdown against real TCGA patient tumor data. For MYC, CASCADE's predicted knockdown targets show strong concordance with real amplified-vs-non-amplified tumor expression across three cancer types (BRCA: 90.0%, COAD: 72.0%, STAD: 85.7%; all p-values are significant). Blogger's Review: CASCADE framework provides an intelligent solution for predicting downstream transcriptional effects in gene regulatory networks, with accuracy and robustness validated by real data, which has important implications for cancer research and personalized treatment.

Original Source: https://arxiv.org/abs/2608.05359

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