# Amortized Bayesian Causal Discovery of Extended Factor Graphs

arXiv: https://arxiv.org/abs/2607.22934 · HTML: https://mlsanity.com/paper/2607.22934/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 20 of its 33 references that are in the map.
- First posted on arXiv 24 Jul 2026.

## Builds on (most cited first, 20 of 20)

- [Categorical Reparameterization with Gumbel-Softmax](https://mlsanity.com/paper/1611.01144/) (2016)
- [DAGs with NO TEARS: Continuous Optimization for Structure Learning](https://mlsanity.com/paper/1803.01422/) (2018)
- [Differentiable Causal Discovery from Interventional Data](https://mlsanity.com/paper/2007.01754/) (2020)
- [DAGMA: Learning DAGs via M-matrices and a Log-Determinant Acyclicity Characterization](https://mlsanity.com/paper/2209.08037/) (2022)
- [Deep End-to-end Causal Inference](https://mlsanity.com/paper/2202.02195/) (2022)
- [Efficient Neural Causal Discovery without Acyclicity Constraints](https://mlsanity.com/paper/2107.10483/) (2021)
- [Characterizing and Learning Equivalence Classes of Causal DAGs under Interventions](https://mlsanity.com/paper/1802.06310/) (2018)
- [BCD Nets: Scalable Variational Approaches for Bayesian Causal Discovery](https://mlsanity.com/paper/2112.02761/) (2021)
- [SoftSort: A Continuous Relaxation for the argsort Operator](https://mlsanity.com/paper/2006.16038/) (2020)
- [DAGs with No Curl: An Efficient DAG Structure Learning Approach](https://mlsanity.com/paper/2106.07197/) (2021)
- [Differentiable DAG Sampling](https://mlsanity.com/paper/2203.08509/) (2022)
- [Large-Scale Differentiable Causal Discovery of Factor Graphs](https://mlsanity.com/paper/2206.07824/) (2022)
- [Scaling structural learning with NO-BEARS to infer causal transcriptome networks](https://mlsanity.com/paper/1911.00081/) (2019)
- [Advances in Black-Box VI: Normalizing Flows, Importance Weighting, and Optimization](https://mlsanity.com/paper/2006.10343/) (2020)
- [BayesDAG: Gradient-Based Posterior Inference for Causal Discovery](https://mlsanity.com/paper/2307.13917/) (2023)
- [Stable Differentiable Causal Discovery](https://mlsanity.com/paper/2311.10263/) (2023)
- [BaCaDI: Bayesian Causal Discovery with Unknown Interventions](https://mlsanity.com/paper/2206.01665/) (2022)
- [Probabilistic Circuits for Variational Inference in Discrete Graphical Models](https://mlsanity.com/paper/2010.11446/) (2020)
- [Learning Unknown Intervention Targets in Structural Causal Models from Heterogeneous Data](https://mlsanity.com/paper/2312.06091/) (2023)
- [iSCAN: Identifying Causal Mechanism Shifts among Nonlinear Additive Noise Models](https://mlsanity.com/paper/2306.17361/) (2023)

## Abstract (arXiv)

Learning causal graphs from interventional data is a challenging problem with broad applications. In molecular biology, for example, a central goal is to uncover gene regulatory networks from large-scale perturbation data. An ideal algorithm for this task should scale to thousands of nodes, incorporate interventions even when their targets are unknown, quantify uncertainty, and provide identifiability guarantees. However, existing approaches---e.g. approaches using score-based optimization or approximate Bayesian inference---often fail to meet all of these criteria. To address these limitations, we develop Amortized Bayesian Causal Discovery of Extended Factor Graphs (ABCDEFG). Our method guarantees exact acyclicity, scales to graphs with thousands of nodes, and naturally handles interventions even when their targets are unknown. Additionally, ABCDEFG estimates a posterior distribution whose maximum a posteriori estimate provably identifies the true causal graph up to an equivalence class. On simulated datasets, ABCDEFG achieves state-of-the-art accuracy, producing a well-calibrated posterior distribution while outperforming previous score-based and approximate Bayesian methods. Applied to large-scale single-cell perturbation data, ABCDEFG identifies both established and novel gene targets of growth factors.