Counterfactual Image Generation

Visual counterfactual explanations (VCEs) should alter a classifier's prediction while remaining realistic and preserving decision-irrelevant content. Image-space methods provide high-quality counterfactuals but are computationally costly, whereas latent-space methods are more efficient but often less faithful. We identify two sources responsible for this gap. First, latent generation recovers a natural sample from a perturbed representation, whereas classifier guidance pushes it toward a target class, so their update directions may oppose. Second, VAE reconstruction can alter regions that should remain unchanged. We introduce CLEAR, a latent Flow Matching framework for VCEs. CLEAR uses Flow Matching's explicit instantaneous velocity as a reference for the generative direction to decompose classifier guidance into cooperative and conflicting components. It preserves the cooperative component and adaptively attenuates only the conflicting one according to conflict strength. We further analyze conflict frequency and strength throughout generation to reveal how classifier guidance interacts with the generative process. CLEAR also dynamically identifies editable regions, constrains latent modifications, and directly preserves factual content outside them to reduce VAE-induced changes. Across five bidirectional tasks on two datasets, CLEAR retains latent-space efficiency while achieving counterfactual quality comparable to or better than strong image-space baselines, with a 2.5x speedup over the strongest baseline. Project page: https://yan-zen9.github.io/CLEAR/

Counterfactual cardiac anatomy can support risk modelling and intervention planning, by predicting how a patient's heart would change under altered clinical conditions. However, current shape generative models are conditional on clinical variables and disregard causal links between these variables. Thus, they cannot answer counterfactual questions about how a given subject's anatomy would change under a different clinical profile. Modelling the heart's continuous movement over the cardiac cycle requires a representation that is itself continuous in space and time. Spatio-temporal neural distance fields provide this while separating clinical conditioning from subject-specific shape. We place a structural causal model (SCM) over the set of clinical variables (age, sex, smoking, BMI, heart rate, systolic blood pressure), before the condition encoding of the spatio-temporal neural distance field which represents the left atrial complex over a cardiac cycle by signed distance fields. An intervention of the clinical variables, propagated through a SCM before the 4D counterfactual, is constructed from the neural distance field. The generated counterfactuals follow dose-response under age interventions and transforms the male distribution to closely match the female distribution under the intervention $\mathrm{do(\mathrm{female}{=}1)}$. By doing inverse interventions the model also approximates the original anatomy with sub millimeter precision. To our knowledge, this is the first counterfactual generation of 4D cardiac anatomy and the first integration of an SCM with an implicit neural representation as its imaging mechanism.

Current explanation methods for contrastive vision-language models such as CLIP mainly identify important regions without showing how to change the input in order to get a target prediction. We introduce Mask-guided Adaptive Counterfactual Explanations (MACE), a targeted visual counterfactual method designed specifically for CLIP zero-shot classification. MACE constructs an editable region from either source attribution or source-target attribution differences and expands the mask only when needed to reach a specified target class. A latent diffusion inpainting model then modifies the selected region, while a frozen CLIP model provides modification guidance and anchors the remaining image content to the original input. We evaluate MACE on ImageNet, Food-101, Oxford Pets, and CUB-200. The source-mask variant achieves the highest target top-1 success rate across all four datasets, while the difference-mask variant produces the smallest pixel level and perceptual changes and the best realism scores. Both variants improve proximity and realism over a Stable Diffusion-only baseline using the same generative backbone. These results show that adaptive mask-guided editing produces effective CLIP counterfactuals. They further reveal a tradeoff between counterfactual validity and source-image preservation.

Counterfactual image generation answers questions about how a subject would have looked under retrospective, hypothetical scenarios. Recent methods have improved perceptual quality, identity preservation and faithfulness to an underlying causal model, but their adoption in healthcare is limited by scarce annotated data, distribution shift between datasets, and mismatches between pretrained generative models and those required for counterfactual inference. We propose specialisation, a data and parameter-efficient framework for adapting pretrained, non-causal generative models into causal mechanisms under distribution shift. Based on this framework, we train a radiology counterfactual image generation model, called RadCF, using latent flow matching. We validate our approach on three chest X-ray datasets spanning different dataset shifts, data volumes, and counterfactual questions, associated with challenging, highly-localised interventions. Our results show that RadCF and specialisation improve counterfactual soundness over existing methods while being data and parameter efficient, and that the resulting counterfactuals can detect and mitigate shortcut learning in a downstream medical classifier. Code is available at https://github.com/GSK-AI/RadCF/.

Medical counterfactual generation modifies images to change model predictions for interpretability. However, existing diffusion-based approaches are often prohibitively slow and memory-intensive, making them difficult to apply in high-resolution settings. Moreover, existing masking strategies are tightly coupled with pixel-space representations, making them incompatible with latent-space diffusion editing. To address these challenges, we propose MedDiME, a latent-space classifier-guided diffusion framework that reduces computational and memory overhead while introducing a latent-compatible, gradient-driven adaptive masking mechanism for spatially precise medical counterfactual generation. Extensive experiments demonstrate that MedDiME achieves high-quality counterfactual generation with significant efficiency gains compared to prior classifier-guided diffusion baselines, achieving up to 40 times faster inference and 13 times lower peak GPU memory usage.

Medical image analysis is often hindered by biased datasets, which can lead to biased models and limited clinical applicability. A promising strategy for mitigating such biases is to augment training data with synthetic images. Counterfactual (CF) generation is one such strategy, though the term is used in two different senses: in some works, CFs are produced through causality-based interventions derived from structural causal models, whereas in others, they are produced by non-causal image edits or conventional conditional generative models, such as altering anatomy or adding pathologies. In this work, we study this distinction and evaluate its practical consequences for medical image augmentation. We compare three conditioning strategies: $\textit{Deterministic}$, which changes selected variables while holding the remaining variables fixed; $\textit{Undirected}$, which updates variables according to learned statistical associations without assigning causal directions; and $\textit{Causal}$, which propagates interventions along a directed causal graph. We analyse how these choices affect the resulting images, and explore when causally grounded methods improve dataset augmentation or bring limited benefit. In particular, we assess downstream performance and fairness, where fairness refers to reduced sensitivity to dataset biases across sensitive subgroups. Our experiments demonstrate that using a causal approach to synthetic training data generation can lead to tangible benefits, with these insights offering valuable guidance to machine learning practitioners for the effective design of data generation protocols.

Deep learning models have achieved impressive performance in medical image diagnosis, yet their deployment in clinical settings remains constrained by limited explainability. Counterfactual images provide one means of auditing model behavior by showing how an image would need to change for a classifier to produce a different prediction. Existing approaches typically generate such explanations using auxiliary models, including generative adversarial networks and diffusion models. While often capable of producing visually realistic images, these methods explain one black-box model using another, making it difficult to separate the classifier's decision-making process from the inductive biases of the generator. We propose a novel counterfactual-generation framework that requires no generative model. Instead, counterfactuals are constructed directly from causal evidence extracted from the classifier. The resulting approach is deterministic, requires no additional model training, and enables controllable edits within user-specified regions of interest. Experiments on real-world medical imaging datasets demonstrate that the proposed method successfully changes classifier predictions while remaining closer to the original image than generative baselines, providing a more direct and transparent view of the classifier's decision boundary.

Counterfactual medical image generation aims to modify an existing image to reflect a hypothetical scenario in which certain characteristics of the imaged subject are altered, while keeping their identity fixed. Most existing works repurpose established image editing methods, which do not directly supervise identity preservation. Instead, they assume that identity is implicitly preserved by anchoring generation to the source image. This assumption is rarely tested and may fail in domains where biometric cues are subtle, such as retinal optical coherence tomography (OCT). In this work, we explicitly measure identity preservation for three groups of text-conditioned editing methods - source-anchored, structured-prompt, and paired-training - using referee classifiers, embedding alignment scores, and a blind reader study. We find that all methods produce high-quality OCT images with comparable editing success, yet their identity preservation differs markedly. Source-anchored editing frequently alters the depicted subject, while paired-training preserves it best. We argue that future work on medical counterfactual generation must explicitly measure and report identity preservation alongside image realism and editing success.

Reinforcement learning (RL) enables direct preference optimization for image editing through editing-specific rewards, which remain less developed due to costly triplet supervision and complex task-dependent calibration. In contrast, text-to-image (T2I) generation benefits from a mature and diverse reward ecosystem spanning semantic alignment, aesthetics, realism, glyph shape, and other visual preferences. Extending this ecosystem to image editing would substantially broaden the range of visual preferences accessible to RL-based optimization, prompting the central question: Can We Perform Image Editing RL without Editing Rewards? In this paper, we argue that the standard image editing dimensions have potential to be mapped to the T2I reward space: image quality can transfer directly, prompt following can be aligned through a description of the desired visual state, and reference consistency admits a coarse semantic conversion by encoding the source content to preserve. However, editing instructions specify relative changes, whereas T2I rewards require self-contained target descriptions; moreover, semantically valid captions from generic vision-language models may be incompatible with the frozen reward. Hence, we further introduce Lever-Edit, a two-stage framework that learns a reward-aligned captioner for counterfactual target descriptions, freezes it, and optimizes the editing policy solely with the transferred T2I reward. Experiments show competitive editing alignment and source preservation against editing-reward-based fine-tuning, while outperforming intuitive transfer baselines.

Visual Counterfactual Explanations (VCEs) aim to explain image classifiers by generating minimally edited and realistic versions of an input image that change the classifier's prediction. Existing VCE methods are inherently classifier-dependent and therefore susceptible to classifier biases and failure modes, such as sensitivity to shortcut features and calibration errors. In this paper, we propose a classifier-free approach for visual counterfactual generation based on Contrastive Analysis (CA). Given two datasets corresponding to different classes (e.g., healthy and patients), we disentangle the generative factors that are common across the two datasets from those that are salient to each dataset, and generate counterfactual images by swapping only the salient factors. By operating directly on data distributions rather than decision boundaries, our method provides model-agnostic VCEs that are less sensitive to classifier biases. Our approach leverages the high-quality synthesis and well-structured latent space of StyleGAN2. We use the feature space F, instead than the usual W-space, to improve detail preservation. Unlike conventional CA approaches, which typically assume salient factors in only one dataset, we introduce an adapted framework and loss functions for VCE that allow multiple salient factors in each dataset. We evaluate our method on three medical imaging datasets and demonstrate superior counterfactual generation quality compared to existing approaches.

Visual counterfactual explanations aim to change classifier decisions through realistic and localized edits while preserving decision-irrelevant content. Existing DDPM-based methods typically perform classifier-guided editing along a long reverse denoising trajectory. The changing noise levels make semantic editability and spatial control difficult to balance, and the editable state is noisy, whereas the target classifier is trained on clean images. As a result, these methods require either costly recursive denoising or low-quality one-step estimates to obtain classifier-facing clean images. We propose FiRe, a Fixed-noise Refinement framework for visual counterfactual explanations. Rather than following a reverse denoising trajectory, FiRe maps the input to a fixed noise level and iteratively refines the noisy state at that level. To provide clean images for classifier guidance, FiRe first adapts Pixel Mean Flow to visual counterfactual explanation, enabling direct clean-image prediction from noisy states. To make fixed-noise refinement produce minimal and localized counterfactual edits, FiRe introduces three FiRe-specific controls: a dynamic dual-mask strategy, adaptive guidance, and early stopping, which determine where edits accumulate, which changes become visible, and when refinement stops. Experiments on five tasks across three datasets show that, compared with the strongest recent baseline, FiRe achieves about 3$\times$ faster online inference and 8$\times$ fewer FLOPs while obtaining comparable or state-of-the-art counterfactual quality.

Text-to-image (T2I) generation models have achieved remarkable progress in producing visually realistic images from natural language prompts. Yet it remains unclear whether their success reflects genuine causal understanding or sophisticated pattern matching over visual-textual correlations. Inspired by Russell's inductivist turkey, we introduce Counterfactual-World (CF-World), a counterfactual benchmark designed to investigate whether text-to-image models can generate images under rules that systematically contradict real-world priors. CF-World organizes each scenario into three progressive levels: factual generation under ordinary world knowledge, explicit counterfactual generation with direct visual instructions, and implicit counterfactual generation requiring causal deduction from altered rules. We evaluate both open-source and closed-source T2I models using a Vision Language Model (VLM)-based evaluator (CF-Eval). Furthermore, we introduce two metrics: Prior Resistance Rate (PRR), which measures a models' ability to overcome entrenched real-world priors, and Reasoning Retention Rate (RRR), which assesses whether models can maintain reasoning-dependent counterfactual generation without explicit visual cues. Experiments show that all models exhibit sharp degradation from factual to counterfactual settings. Further analyses suggest that these failures arise because current T2I models encode world knowledge and visual appearances as tightly coupled patterns. Consequently, their heavy reliance on frequent visual co-occurrences within the training data forces them to default to familiar commonsense priors when tasked with rendering counterfactual worlds.

Causal generative modeling is essential for developing reliable and transparent AI systems capable of counterfactual reasoning. While existing approaches focus on integrating causal constraints during the training of generative models, they often lack a unified framework to leverage the zero-shot reasoning capabilities of pretrained foundation models. We introduce FM-CGM, a modular framework for end-to-end visual causal reasoning using pretrained foundation models. FM-CGM formalizes the causal pipeline through three core components: a concept extractor, a concept manipulator, and a counterfactual generator. By leveraging a large reasoning model for causal inference and a text-to-image diffusion model for generation, our approach enables zero-shot causal discovery, intervention, and counterfactual generation. We then develop Causal Semantic Guidance (CSG), a cross-attention-based mechanism that ensures semantic interventions propagate to descendant concepts while preserving invariant regions. We empirically show that our approach can identify plausible causal structures and is suitable for faithful counterfactual image generation.

Dual-energy X-ray absorptiometry (DXA) is widely used for large-scale skeletal assessment, yet learning controllable and interpretable factor-specific anatomical variation remains challenging. We propose a metadata-conditioned causal hierarchical variational autoencoder (CHVAE) for causally consistent generation of anteroposterior (AP) spine DXA images from the UK Biobank (UKB). The model is trained on 3,743 raw AP spine scans from the first imaging visit and conditioned on basic participant attributes and lumbar morphometry. Causal consistency is evaluated in a baseline-to-follow-up setting using abduction--action--prediction (AAP): latent variables are abducted from baseline images, age is intervened to the repeat-imaging value, and the resulting counterfactual follow-up morphometry is compared with observed repeat-imaging measurements. Results show strong absolute-level agreement for key vertebral morphometry variables under age intervention, supporting intervention-aligned synthesis of anatomically plausible DXA images.

Ascription of an image gives insights into the objects that influence the classification of the whole image or its pixels towards a specific category. These insights help radiologists to visualize deformities in medical imaging. Most of the existing visualization techniques are based on discriminative models and highlight regions of the input image participating in the decision-making of a classifier. However, these approaches do not take all noticeable objects into account as their objective is to classify the input by using a minimal set of discriminative features. To overcome the issue, a counterfactual explanation (CX) based class-oriented feature attribution method is proposed. A counterfactual explanation (CX) explicates a causal reasoning process of the form: "if X had not happened, then Y would not have happened". The method is built on generative adversarial networks (GANs) with a cyclical-consistent loss function. We evaluate our method on three datasets: synthetic, tuberculosis and BraTS. All experiments confirm the efficacy of the proposed method. This study also highlighted the limitations of existing counterfactual explanation techniques in producing plausible counterfactual instances (CIs). Accompanying CXs with believable CIs thus provides self-explanatory analogy-based explanations. To this end, a CI generation method is proposed. Also, a novel technique is used to evaluate the quality of CI. The baseline results are produced on the BraTS dataset.

Counterfactual image generation enables controlled data augmentation, bias mitigation, and disease modeling. However, existing methods guided by external classifiers or regressors are limited to subject-level factors (e.g., age) and fail to produce localized structural changes, often resulting in global artifacts. Pixel-level guidance using segmentation masks has been explored, but requires user-defined counterfactual masks, which are tedious and impractical. Segmentor-guided Counterfactual Fine-Tuning (Seg-CFT) addressed this by using segmentation-derived measurements to supervise structure-specific variables, yet it remains restricted to global interventions. We propose Positional Seg-CFT, which subdivides each structure into regional segments and derives independent measurements per region, enabling spatially localized and anatomically coherent counterfactuals. Experiments on coronary CT angiography show that Pos-Seg-CFT generates realistic, region-specific modifications, providing finer spatial control for modeling disease progression.

Generative diffusion models are increasingly used for medical imaging data augmentation, but text prompting cannot produce causal training data. Re-prompting rerolls the entire generation trajectory, altering anatomy, texture, and background. Inversion-based editing methods introduce reconstruction error that causes structural drift. We propose PolypSteer, a training-free activation-steering framework for endoscopic synthesis. PolypSteer identifies a pathology vector for each contrastive prompt pair in the cross-attention layers of a diffusion transformer. At inference time, it steers image activations along this vector, generating counterfactual pairs from scratch where the only difference is the steered concept. All other structure is preserved by construction. We evaluate PolypSteer across three experiments on Kvasir v3 and HyperKvasir. On counterfactual generation across three clinical concept pairs, PolypSteer achieves flip rates of 0.800, 0.925, and 0.950, outperforming the best inversion-based baseline in both concept flip rate and structural preservation. On dye disentanglement, PolypSteer achieves 75% dye removal against 20% (PnP) and 10% (h-Edit). On downstream polyp detection, augmenting with PolypSteer counterfactual pairs achieves ViT AUC of 0.9755 versus 0.9083 for quantity-matched re-prompting, confirming that counterfactual structure drives the gain. Code is at link https://github.com/UARK-AICV/PolypSteer

Visual counterfactual explanations aim to reveal the minimal semantic modifications that can alter a model's prediction, providing causal and interpretable insights into deep neural networks. However, existing diffusion-based counterfactual generation methods are often computationally expensive, slow to sample, and imprecise in localizing the modified regions. To address these limitations, we propose MaskDiME, a simple, fast, yet effective diffusion framework that unifies semantic consistency and spatial precision through localized sampling. Our approach adaptively focuses on decision-relevant regions to achieve localized and semantically consistent counterfactual generation while preserving high image fidelity. Our training-free framework, MaskDiME, performs inference over 30x faster than the baseline and achieves comparable or state-of-the-art performance across five benchmark datasets spanning diverse visual domains, establishing a practical and generalizable solution for efficient counterfactual explanation.