COGENT: Counterfactual Gaussian Explanations for Volumetric Medical Images
Authors: Dorian Rząsa, Bartosz Zabdyr, Krzysztof Piekarz, Jakub Grzywaczewski, Bartlomiej Sobieski, Przemyslaw Biecek, Żaneta Świderska-Chadaj, Olga Śliwicka, +2 more
Explainability is essential for deploying deep learning models in high-stakes medical applications. Existing explainability methods for volumetric imaging predominantly operate in voxel space, overlooking the structured representations introduced by recent advances in 3D scene modeling. We present COGENT (Counterfactual Gaussian Explanations), a framework that generates counterfactual explanations directly in the parameter space of Gaussian-based volumetric representations. Built upon MedGS and the Sybil lung cancer risk prediction model, COGENT optimizes selected Gaussian primitives through a differentiable rendering pipeline, enabling gradients from the downstream predictor to identify representation components that most influence model decisions. Unlike conventional pixel- or voxel-level attribution methods, our approach formulates explainability as a counterfactual optimization problem over an explicit 3D scene representation, producing sparse and spatially localized explanations while preserving anatomical consistency. We evaluate COGENT on lung CT scans using quantitative comparisons with existing explainability methods together with qualitative analysis by medical experts. The results demonstrate that representation-space counterfactual optimization provides clinically meaningful explanations while offering a new perspective on interpreting volumetric deep learning models.
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.
Attention and saliency heatmaps are widely used to explain medical Vision-Language Model (VLM) outputs on chest X-rays, yet whether they truly highlight the image evidence driving predictions has not been causally tested. We audit faithfulness via overlap with radiologist bounding boxes on PadChest (n=637), attribution mass within radiologist masks on CheXlocalize (n=643), and 16x16 patch-occlusion maps that record which regions, when hidden, change the answer. We study three MedGemma-4B variants, cross-family probes on LLaVA-RAD and Qwen3-VL-8B-Instruct, and the specialist CheXagent-2-3b, with two CXR-trained classifiers (DenseNet121, ResNet50) as positive controls. A heatmap is faithful only if the model uses the image and attention concentrates on regions whose occlusion alters the prediction. No evaluated VLM meets both criteria. MedGemma and Qwen3-VL use the image, but attention anti-correlates with patch-occlusion importance (rho < 0 with 95% bootstrap CIs below zero). LLaVA-RAD's attention correlates positively, but the model is almost text-only (99.1% text-only agreement, near-zero causal mass), so correlation ties two near-zero signals. Attention also misses annotated anatomy: overlap with true regions never beats shifted or random controls, and no method places more than 22% of its mass inside radiologist masks. The two CXR classifiers pass all metrics, indicating the failure is specific to VLM heatmaps, not the evaluation. These heatmaps are visually reassuring but not faithful; clinical explanations require controlled localization metrics and causal perturbation, not visual inspection alone.
Deep neural networks for medical image diagnosis often achieve high predictive accuracy while relying on spurious or clinically irrelevant visual cues, limiting their trustworthiness in practice. Post-hoc explanation methods are widely used to visualize model decisions in the form of saliency maps; however, these explanations do not influence how models learn during training, allowing non-causal or confounding features to persist. This motivates the incorporation of explanation supervision directly into the training objective to guide model attention toward clinically meaningful regions and promote clinically grounded decision-making. This paper presents a systematic approach to integrate explanation loss into model training and analyzes how different explanation loss designs and supervision strengths influence both predictive performance and spatial faithfulness of explanations. To quantitatively assess interpretability, two complementary explanation performance metrics-annotation coverage and saliency precision-are introduced, enabling rigorous evaluation beyond qualitative visualization. Our experimental results reveal a clear trade-off between explanation quality and explanation loss coefficients. Furthermore, quantitative statistical analysis yields consistently improved explanation alignment while maintaining comparable accuracy. Experiments were conducted on annotated chest X-ray datasets; however, the proposed framework is applicable to a broad range of annotated biomedical imaging modalities. Overall, these findings demonstrate that explanation supervision is not a monolithic design choice and provide practical guidance for incorporating explanation loss into training objectives under noisy clinical annotations.