# CausalDisenSeg: A Causality-Guided Disentanglement Framework with Counterfactual Reasoning for Robust Brain Tumor Segmentation Under Missing Modalities

arXiv: https://arxiv.org/abs/2604.13409 · HTML: https://mlsanity.com/paper/2604.13409/

## Key facts

- No citing papers in the map yet (data through 14 Oct 2026).
- Builds on 12 of its 31 references that are in the map.
- First posted on arXiv 15 Apr 2026.

## Builds on (most cited first, 12 of 12)

- [Dropout as a Bayesian Approximation: Representing Model Uncertainty in Deep Learning](https://mlsanity.com/paper/1506.02142/) (2015)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Multi-modal Learning with Missing Modality via Shared-Specific Feature Modelling](https://mlsanity.com/paper/2307.14126/) (2023)
- [Brain Tumor Segmentation with Deep Neural Networks](https://mlsanity.com/paper/1505.03540/) (2015)
- [Domain Adaptation by Using Causal Inference to Predict Invariant Conditional Distributions](https://mlsanity.com/paper/1707.06422/) (2017)
- [Deep Multimodal Fusion by Channel Exchanging](https://mlsanity.com/paper/2011.05005/) (2020)
- [HeMIS: Hetero-Modal Image Segmentation](https://mlsanity.com/paper/1607.05194/) (2016)
- [mmFormer: Multimodal Medical Transformer for Incomplete Multimodal Learning of Brain Tumor Segmentation](https://mlsanity.com/paper/2206.02425/) (2022)
- [The HSIC Bottleneck: Deep Learning without Back-Propagation](https://mlsanity.com/paper/1908.01580/) (2019)
- [Robust Multimodal Brain Tumor Segmentation via Feature Disentanglement and Gated Fusion](https://mlsanity.com/paper/2002.09708/) (2020)
- [ACN: Adversarial Co-training Network for Brain Tumor Segmentation with Missing Modalities](https://mlsanity.com/paper/2106.14591/) (2021)
- [SMU-Net: Style matching U-Net for brain tumor segmentation with missing modalities](https://mlsanity.com/paper/2204.02961/) (2022)

## Abstract (arXiv)

In clinical practice, the robustness of deep learning models for multimodal brain tumor segmentation is severely compromised by incomplete MRI data. This vulnerability stems primarily from modality bias, where models exploit spurious correlations as shortcuts rather than learning true anatomical structures. Existing feature fusion methods fail to fundamentally eliminate this dependency. To address this, we propose CausalDisenSeg, a novel Structural Causal Model (SCM)-grounded framework that achieves robust segmentation via causality-guided disentanglement and counterfactual reasoning. We reframe the problem as isolating the anatomical Causal Factor from the stylistic Bias Factor. Our framework implements a three-stage causal intervention: (1) Explicit Causal Disentanglement: A Conditional Variational Autoencoder (CVAE) coupled with an HSIC constraint mathematically enforces statistical orthogonality between anatomical and style features. (2) Causal Representation Reinforcement: A Region Causality Module (RCM) explicitly grounds causal features in physical tumor regions. (3) Counterfactual Reasoning: A dual-adversarial strategy actively suppresses the residual Natural Direct Effect (NDE) of the bias, forcing its spatial attention to be mutually exclusive from the causal path. Extensive experiments on the BraTS 2020 dataset demonstrate that CausalDisenSeg significantly outperforms state-of-the-art methods in accuracy and consistency across severe missing-modality scenarios. Furthermore, cross-dataset evaluation on BraTS 2023 under the same protocol yields a state-of-the-art macro-average DSC of 84.49.