Learning to Trim: End-to-End Causal Graph Pruning with Dynamic Anatomical Feature Banks for Medical VQA

Medical Visual Question Answering (MedVQA) aims to generate clinically reliable answers conditioned on complex medical images and questions. However, existing methods often overfit to superficial cross-modal correlations, neglecting the intrinsic biases embedded in multimodal medical data. Consequently, models become vulnerable to cross-modal confounding effects, severely hindering their ability to provide trustworthy diagnostic reasoning. To address this limitation, we propose a novel Dual Causal Inference (DCI) framework for MedVQA. To the best of our knowledge, DCI is the first unified architecture that integrates Backdoor Adjustment (BDA) and Instrumental Variable (IV) learning to jointly tackle both observable and unobserved confounders. Specifically, we formulate a Structural Causal Model (SCM) where observable cross-modal biases (e.g., frequent visual and textual co-occurrences) are mitigated via BDA, while unobserved confounders are compensated using an IV learned from a shared latent space. To guarantee the validity of the IV, we design mutual information constraints that maximize its dependence on the fused multimodal representations while minimizing its associations with the unobserved confounders and target answers. Through this dual mechanism, DCI extracts deconfounded representations that capture genuine causal relationships. Extensive experiments on four benchmark datasets, SLAKE, SLAKE-CP, VQA-RAD, and PathVQA, demonstrate that our method consistently outperforms existing approaches, particularly in out-of-distribution (OOD) generalization. Furthermore, qualitative analyses confirm that DCI significantly enhances the interpretability and robustness of cross-modal reasoning by explicitly disentangling true causal effects from spurious cross-modal shortcuts.

Medical vision-language models (VLMs) for visual question answering (VQA) often pass long visual-token sequences to the language model, making visual-token pruning attractive but risky for medical images, where answers may depend on localized boundary and texture evidence. We study training free pre-decoding pruning and treat pruning as a subspace stable evidence preservation problem. The retained tokens should remain close to the dominant visual evidence subspace induced by the full token set. To this end, we propose Subspace-Transition Token Pruning (\method{}), which estimates each token's spectral support from principal component space and constructs a compact representation subspace. To better reflect medical image structure, \method{} further uses a bounded token-grid transition prior to promote boundary and texture sensitive tokens. We evaluate \method{} on the closed-ended SLAKE and OmniMedVQA benchmarks and on RadImageNet-VQA, which provides both closed-ended and open-ended evaluations, using Lingshu-7B and Qwen3-VL-8B backbones. \method{} delivers consistently strong performance on both the closed-ended and open-ended RadImageNet-VQA evaluations. These results show that \method{} is an effective training free pruning framework for medical domain VQA.

Vision-Language Models (VLMs) have enabled interpretable medical diagnosis by integrating visual perception with linguistic reasoning. Yet, existing medical chain-of-thought (CoT) models lack explicit mechanisms to represent and enforce causal reasoning, leaving them vulnerable to spurious correlations and limiting their clinical reliability. We pinpoint three core challenges in medical CoT reasoning: how to adaptively trigger causal correction, construct high-quality causal-spurious contrastive samples, and maintain causal consistency across reasoning trajectories. To address these challenges, we propose MedCausalX, an end-to-end framework explicitly models causal reasoning chains in medical VLMs. We first introduce the CRMed dataset providing fine-grained anatomical annotations, structured causal reasoning chains, and counterfactual variants that guide the learning of causal relationships beyond superficial correlations. Building upon CRMed, MedCausalX employs a two-stage adaptive reflection architecture equipped with $\langle$causal$\rangle$ and $\langle$verify$\rangle$ tokens, enabling the model to autonomously determine when and how to perform causal analysis and verification. Finally, a trajectory-level causal correction objective optimized through error-attributed reinforcement learning refines the reasoning chain, allowing the model to distinguish genuine causal dependencies from shortcut associations. Extensive experiments on multiple benchmarks show that MedCausalX consistently outperforms state-of-the-art methods, improving diagnostic consistency by +5.4 points, reducing hallucination by over 10 points, and attaining top spatial grounding IoU, thereby setting a new standard for causally grounded medical reasoning. The code and dataset are available at https://github.com/zhcz328/MedCausalX.