# CN-SBM: Categorical Block Modelling For Primary and Residual Copy Number Variation

arXiv: https://arxiv.org/abs/2506.22963 · HTML: https://mlsanity.com/paper/2506.22963/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 2 of its 31 references that are in the map.
- First posted on arXiv 28 Jun 2025.

## Builds on (most cited first, 2 of 2)

- [Convex optimization](https://mlsanity.com/paper/2106.01946/) (2021)
- [Variational Inference: A Review for Statisticians](https://mlsanity.com/paper/1601.00670/) (2016)

## Abstract (arXiv)

Cancer is a genetic disorder whose clonal evolution can be monitored by tracking noisy genome-wide copy number variants. We introduce the Copy Number Stochastic Block Model (CN-SBM), a probabilistic framework that jointly clusters samples and genomic regions based on discrete copy number states using a bipartite categorical block model. Unlike models relying on Gaussian or Poisson assumptions, CN-SBM respects the discrete nature of CNV calls and captures subpopulation-specific patterns through block-wise structure. Using a two-stage approach, CN-SBM decomposes CNV data into primary and residual components, enabling detection of both large-scale chromosomal alterations and finer aberrations. We derive a scalable variational inference algorithm for application to large cohorts and high-resolution data. Benchmarks on simulated and real datasets show improved model fit over existing methods. Applied to TCGA low-grade glioma data, CN-SBM reveals clinically relevant subtypes and structured residual variation, aiding patient stratification in survival analysis. These results establish CN-SBM as an interpretable, scalable framework for CNV analysis with direct relevance for tumor heterogeneity and prognosis.