Counterfactual explainability seeks to uncover model decisions by identifying minimal changes to the input that alter the predicted outcome. This task becomes particularly challenging for graph data due to preserving structural integrity and semantic meaning. Unlike prior approaches that rely on forward perturbation mechanisms, we introduce Graph Inverse Style Transfer (GIST), the first framework to re-imagine graph counterfactual generation as a backtracking process, leveraging spectral style transfer. By aligning the global structure with the original input spectrum and preserving local content faithfulness, GIST produces valid counterfactuals as interpolations between the input style and counterfactual content. Tested on 8 binary and multi-class graph classification benchmarks, GIST achieves a remarkable +7.6% improvement in the validity of produced counterfactuals and significant gains (+45.5%) in faithfully explaining the true class distribution. Additionally, GIST's backtracking mechanism effectively mitigates overshooting the underlying predictor's decision boundary, minimizing the spectral differences between the input and the counterfactuals. These results challenge traditional forward perturbation methods, offering a novel perspective that advances graph explainability.
Graph neural networks (GNNs) have been widely used in various domains such as social networks, molecular biology, or recommendation systems. Concurrently, different explanations methods of GNNs have arisen to complement its black-box nature. Explanations of the GNNs' predictions can be categorized into two types--factual and counterfactual. Given a GNN trained on binary classification into ''accept'' and ''reject'' classes, a global counterfactual explanation consists in generating a small set of ''accept'' graphs relevant to all of the input ''reject'' graphs. The transformation of a ''reject'' graph into an ''accept'' graph is called a recourse. A common recourse explanation is a small set of recourse, from which every ''reject'' graph can be turned into an ''accept'' graph. Although local counterfactual explanations have been studied extensively, the problem of finding common recourse for global counterfactual explanation remains unexplored, particularly for GNNs. In this paper, we formalize the common recourse explanation problem, and design an effective algorithm, COMRECGC, to solve it. We benchmark our algorithm against strong baselines on four different real-world graphs datasets and demonstrate the superior performance of COMRECGC against the competitors. We also compare the common recourse explanations to the graph counterfactual explanation, showing that common recourse explanations are either comparable or superior, making them worth considering for applications such as drug discovery or computational biology.
This study presents Latent Diffusion Autoencoder (LDAE), a novel encoder-decoder diffusion-based framework for efficient and meaningful unsupervised learning in medical imaging, focusing on Alzheimer disease (AD) using brain MR from the ADNI database as a case study. Unlike conventional diffusion autoencoders operating in image space, LDAE applies the diffusion process in a compressed latent representation, improving computational efficiency and making 3D medical imaging representation learning tractable. To validate the proposed approach, we explore two key hypotheses: (i) LDAE effectively captures meaningful semantic representations on 3D brain MR associated with AD and ageing, and (ii) LDAE achieves high-quality image generation and reconstruction while being computationally efficient. Experimental results support both hypotheses: (i) linear-probe evaluations demonstrate promising diagnostic performance for AD (ROC-AUC: 90%, ACC: 84%) and age prediction (MAE: 4.1 years, RMSE: 5.2 years); (ii) the learned semantic representations enable attribute manipulation, yielding anatomically plausible modifications; (iii) semantic interpolation experiments show strong reconstruction of missing scans, with SSIM of 0.969 (MSE: 0.0019) for a 6-month gap. Even for longer gaps (24 months), the model maintains robust performance (SSIM > 0.93, MSE < 0.004), indicating an ability to capture temporal progression trends; (iv) compared to conventional diffusion autoencoders, LDAE significantly increases inference throughput (20x faster) while also enhancing reconstruction quality. These findings position LDAE as a promising framework for scalable medical imaging applications, with the potential to serve as a foundation model for medical image analysis. Code available at https://github.com/GabrieleLozupone/LDAE
The objective of few-shot object detection (FSOD) is to detect novel objects with few training samples. The core challenge of this task is how to construct a generalized feature space for novel categories with limited data on the basis of the base category space, which could adapt the learned detection model to unknown scenarios. However, limited by insufficient samples for novel categories, two issues still exist: (1) the features of the novel category are easily implicitly represented by the features of the base category, leading to inseparable classifier boundaries, (2) novel categories with fewer data are not enough to fully represent the distribution, where the model fine-tuning is prone to overfitting. To address these issues, we introduce the side information to alleviate the negative influences derived from the feature space and sample viewpoints and formulate a novel generalized feature representation learning method for FSOD. Specifically, we first utilize embedding side information to construct a knowledge matrix to quantify the semantic relationship between the base and novel categories. Then, to strengthen the discrimination between semantically similar categories, we further develop contextual semantic supervised contrastive learning which embeds side information. Furthermore, to prevent overfitting problems caused by sparse samples, a side-information guided region-aware masked module is introduced to augment the diversity of samples, which finds and abandons biased information that discriminates between similar categories via counterfactual explanation, and refines the discriminative representation space further. Extensive experiments using ResNet and ViT backbones on PASCAL VOC, MS COCO, LVIS V1, FSOD-1K, and FSVOD-500 benchmarks demonstrate that our model outperforms the previous state-of-the-art methods, significantly improving the ability of FSOD in most shots/splits.
Deep Learning systems excel in complex tasks but often lack transparency, limiting their use in critical applications. Counterfactual explanations, a core tool within eXplainable Artificial Intelligence (XAI), offer insights into model decisions by identifying minimal changes to an input to alter its predicted outcome. However, existing methods for time series data are limited by univariate assumptions, rigid constraints on modifications, or lack of validity guarantees. This paper introduces Multi-SpaCE, a multi-objective counterfactual explanation method for multivariate time series. Using non-dominated ranking genetic algorithm II (NSGA-II), Multi-SpaCE balances proximity, sparsity, plausibility, and contiguity. Unlike most methods, it ensures perfect validity, supports multivariate data and provides a Pareto front of solutions, enabling flexibility to different end-user needs. Comprehensive experiments in diverse datasets demonstrate the ability of Multi-SpaCE to consistently achieve perfect validity and deliver superior performance compared to existing methods.
Over the past decade, multivariate time series classification has received great attention. Machine learning (ML) models for multivariate time series classification have made significant strides and achieved impressive success in a wide range of applications and tasks. The challenge of many state-of-the-art ML models is a lack of transparency and interpretability. In this work, we introduce M-CELS, a counterfactual explanation model designed to enhance interpretability in multidimensional time series classification tasks. Our experimental validation involves comparing M-CELS with leading state-of-the-art baselines, utilizing seven real-world time-series datasets from the UEA repository. The results demonstrate the superior performance of M-CELS in terms of validity, proximity, and sparsity, reinforcing its effectiveness in providing transparent insights into the decisions of machine learning models applied to multivariate time series data.
As machine learning models evolve, maintaining transparency demands more human-centric explainable AI techniques. Counterfactual explanations, with roots in human reasoning, identify the minimal input changes needed to obtain a given output and, hence, are crucial for supporting decision-making. Despite their importance, the evaluation of these explanations often lacks grounding in user studies and remains fragmented, with existing metrics not fully capturing human perspectives. To address this challenge, we developed a diverse set of 30 counterfactual scenarios and collected ratings across 8 evaluation metrics from 206 respondents. Subsequently, we fine-tuned different Large Language Models (LLMs) to predict average or individual human judgment across these metrics. Our methodology allowed LLMs to achieve an accuracy of up to 63% in zero-shot evaluations and 85% (over a 3-classes prediction) with fine-tuning across all metrics. The fine-tuned models predicting human ratings offer better comparability and scalability in evaluating different counterfactual explanation frameworks.
In recent years, Graph Neural Networks (GNNs) have become successful in molecular property prediction tasks such as toxicity analysis. However, due to the black-box nature of GNNs, their outputs can be concerning in high-stakes decision-making scenarios, e.g., drug discovery. Facing such an issue, Graph Counterfactual Explanation (GCE) has emerged as a promising approach to improve GNN transparency. However, current GCE methods usually fail to take domain-specific knowledge into consideration, which can result in outputs that are not easily comprehensible by humans. To address this challenge, we propose a novel GCE method, LLM-GCE, to unleash the power of large language models (LLMs) in explaining GNNs for molecular property prediction. Specifically, we utilize an autoencoder to generate the counterfactual graph topology from a set of counterfactual text pairs (CTPs) based on an input graph. Meanwhile, we also incorporate a CTP dynamic feedback module to mitigate LLM hallucination, which provides intermediate feedback derived from the generated counterfactuals as an attempt to give more faithful guidance. Extensive experiments demonstrate the superior performance of LLM-GCE. Our code is released on https://github.com/YinhanHe123/new\_LLM4GNNExplanation.
Visual counterfactual explanation (CF) methods modify image concepts, e.g, shape, to change a prediction to a predefined outcome while closely resembling the original query image. Unlike self-explainable models (SEMs) and heatmap techniques, they grant users the ability to examine hypothetical "what-if" scenarios. Previous CF methods either entail post-hoc training, limiting the balance between transparency and CF quality, or demand optimization during inference. To bridge the gap between transparent SEMs and CF methods, we introduce the GdVAE, a self-explainable model based on a conditional variational autoencoder (CVAE), featuring a Gaussian discriminant analysis (GDA) classifier and integrated CF explanations. Full transparency is achieved through a generative classifier that leverages class-specific prototypes for the downstream task and a closed-form solution for CFs in the latent space. The consistency of CFs is improved by regularizing the latent space with the explainer function. Extensive comparisons with existing approaches affirm the effectiveness of our method in producing high-quality CF explanations while preserving transparency. Code and models are public.
Counterfactual explanations of Graph Neural Networks (GNNs) offer a powerful way to understand data that can naturally be represented by a graph structure. Furthermore, in many domains, it is highly desirable to derive data-driven global explanations or rules that can better explain the high-level properties of the models and data in question. However, evaluating global counterfactual explanations is hard in real-world datasets due to a lack of human-annotated ground truth, which limits their use in areas like molecular sciences. Additionally, the increasing scale of these datasets provides a challenge for random search-based methods. In this paper, we develop a novel global explanation model RLHEX for molecular property prediction. It aligns the counterfactual explanations with human-defined principles, making the explanations more interpretable and easy for experts to evaluate. RLHEX includes a VAE-based graph generator to generate global explanations and an adapter to adjust the latent representation space to human-defined principles. Optimized by Proximal Policy Optimization (PPO), the global explanations produced by RLHEX cover 4.12% more input graphs and reduce the distance between the counterfactual explanation set and the input set by 0.47% on average across three molecular datasets. RLHEX provides a flexible framework to incorporate different human-designed principles into the counterfactual explanation generation process, aligning these explanations with domain expertise. The code and data are released at https://github.com/dqwang122/RLHEX.
Vulnerability detection is crucial for ensuring the security and reliability of software systems. Recently, Graph Neural Networks (GNNs) have emerged as a prominent code embedding approach for vulnerability detection, owing to their ability to capture the underlying semantic structure of source code. However, GNNs face significant challenges in explainability due to their inherently black-box nature. To this end, several factual reasoning-based explainers have been proposed. These explainers provide explanations for the predictions made by GNNs by analyzing the key features that contribute to the outcomes. We argue that these factual reasoning-based explanations cannot answer critical what-if questions: What would happen to the GNN's decision if we were to alter the code graph into alternative structures? Inspired by advancements of counterfactual reasoning in artificial intelligence, we propose CFExplainer, a novel counterfactual explainer for GNN-based vulnerability detection. Unlike factual reasoning-based explainers, CFExplainer seeks the minimal perturbation to the input code graph that leads to a change in the prediction, thereby addressing the what-if questions for vulnerability detection. We term this perturbation a counterfactual explanation, which can pinpoint the root causes of the detected vulnerability and furnish valuable insights for developers to undertake appropriate actions for fixing the vulnerability. Extensive experiments on four GNN-based vulnerability detection models demonstrate the effectiveness of CFExplainer over existing state-of-the-art factual reasoning-based explainers.
Although counterfactual explanations are a popular approach to explain ML black-box classifiers, they are less widespread in NLP. Most methods find those explanations by iteratively perturbing the target document until it is classified differently by the black box. We identify two main families of counterfactual explanation methods in the literature, namely, (a) \emph{transparent} methods that perturb the target by adding, removing, or replacing words, and (b) \emph{opaque} approaches that project the target document into a latent, non-interpretable space where the perturbation is carried out subsequently. This article offers a comparative study of the performance of these two families of methods on three classical NLP tasks. Our empirical evidence shows that opaque approaches can be an overkill for downstream applications such as fake news detection or sentiment analysis since they add an additional level of complexity with no significant performance gain. These observations motivate our discussion, which raises the question of whether it makes sense to explain a black box using another black box.
Machine-learning models, which are known to accurately predict patterns from large datasets, are crucial in decision making. Consequently, counterfactual explanations-methods explaining predictions by introducing input perturbations-have become prominent. These perturbations often suggest ways to alter the predictions, leading to actionable recommendations. However, the current techniques require resolving the optimization problems for each input change, rendering them computationally expensive. In addition, traditional encoding methods inadequately address the perturbations of categorical variables in tabular data. Thus, this study propose FastDCFlow, an efficient counterfactual explanation method using normalizing flows. The proposed method captures complex data distributions, learns meaningful latent spaces that retain proximity, and improves predictions. For categorical variables, we employed TargetEncoding, which respects ordinal relationships and includes perturbation costs. The proposed method outperformed existing methods in multiple metrics, striking a balance between trade offs for counterfactual explanations. The source code is available in the following repository: https://github.com/sumugit/FastDCFlow.
Deep learning is dramatically transforming the field of medical imaging and radiology, enabling the identification of pathologies in medical images, including computed tomography (CT) and X-ray scans. However, the performance of deep learning models, particularly in segmentation tasks, is often limited by the need for extensive annotated datasets. To address this challenge, the capabilities of weakly supervised semantic segmentation are explored through the lens of Explainable AI and the generation of counterfactual explanations. The scope of this research is development of a novel counterfactual inpainting approach (COIN) that flips the predicted classification label from abnormal to normal by using a generative model. For instance, if the classifier deems an input medical image X as abnormal, indicating the presence of a pathology, the generative model aims to inpaint the abnormal region, thus reversing the classifier's original prediction label. The approach enables us to produce precise segmentations for pathologies without depending on pre-existing segmentation masks. Crucially, image-level labels are utilized, which are substantially easier to acquire than creating detailed segmentation masks. The effectiveness of the method is demonstrated by segmenting synthetic targets and actual kidney tumors from CT images acquired from Tartu University Hospital in Estonia. The findings indicate that COIN greatly surpasses established attribution methods, such as RISE, ScoreCAM, and LayerCAM, as well as an alternative counterfactual explanation method introduced by Singla et al. This evidence suggests that COIN is a promising approach for semantic segmentation of tumors in CT images, and presents a step forward in making deep learning applications more accessible and effective in healthcare, where annotated data is scarce.
In Precision Agriculture, the utilization of management zones (MZs) that take into account within-field variability facilitates effective fertilizer management. This approach enables the optimization of nitrogen (N) rates to maximize crop yield production and enhance agronomic use efficiency. However, existing works often neglect the consideration of responsivity to fertilizer as a factor influencing MZ determination. In response to this gap, we present a MZ clustering method based on fertilizer responsivity. We build upon the statement that the responsivity of a given site to the fertilizer rate is described by the shape of its corresponding N fertilizer-yield response (N-response) curve. Thus, we generate N-response curves for all sites within the field using a convolutional neural network (CNN). The shape of the approximated N-response curves is then characterized using functional principal component analysis. Subsequently, a counterfactual explanation (CFE) method is applied to discern the impact of various variables on MZ membership. The genetic algorithm-based CFE solves a multi-objective optimization problem and aims to identify the minimum combination of features needed to alter a site's cluster assignment. Results from two yield prediction datasets indicate that the features with the greatest influence on MZ membership are associated with terrain characteristics that either facilitate or impede fertilizer runoff, such as terrain slope or topographic aspect.
Graph neural networks (GNNs) are widely utilized to capture the information spreading patterns in graphs. While remarkable performance has been achieved, there is a new trending topic of evaluating node influence. We propose a new method of evaluating node influence, which measures the prediction change of a trained GNN model caused by removing a node. A real-world application is, "In the task of predicting Twitter accounts' polarity, had a particular account been removed, how would others' polarity change?". We use the GNN as a surrogate model whose prediction could simulate the change of nodes or edges caused by node removal. Our target is to obtain the influence score for every node, and a straightforward way is to alternately remove every node and apply the trained GNN on the modified graph to generate new predictions. It is reliable but time-consuming, so we need an efficient method. The related lines of work, such as graph adversarial attack and counterfactual explanation, cannot directly satisfy our needs, since their problem settings are different. We propose an efficient, intuitive, and effective method, NOde-Removal-based fAst GNN inference (NORA), which uses the gradient information to approximate the node-removal influence. It only costs one forward propagation and one backpropagation to approximate the influence score for all nodes. Extensive experiments on six datasets and six GNN models verify the effectiveness of NORA. Our code is available at https://github.com/weikai-li/NORA.git.
Machine learning models are widely used in real-world applications. However, their complexity makes it often challenging to interpret the rationale behind their decisions. Counterfactual explanations (CEs) have emerged as a viable solution for generating comprehensible explanations in eXplainable Artificial Intelligence (XAI). CE provides actionable information to users on how to achieve the desired outcome with minimal modifications to the input. However, current CE algorithms usually operate within the entire feature space when optimizing changes to turn over an undesired outcome, overlooking the identification of key contributors to the outcome and disregarding the practicality of the suggested changes. In this study, we introduce a novel methodology, that is named as user feedback-based counterfactual explanation (UFCE), which addresses these limitations and aims to bolster confidence in the provided explanations. UFCE allows for the inclusion of user constraints to determine the smallest modifications in the subset of actionable features while considering feature dependence, and evaluates the practicality of suggested changes using benchmark evaluation metrics. We conducted three experiments with five datasets, demonstrating that UFCE outperforms two well-known CE methods in terms of \textit{proximity}, \textit{sparsity}, and \textit{feasibility}. Reported results indicate that user constraints influence the generation of feasible CEs.
A new model for generating survival trajectories and data based on applying an autoencoder of a specific structure is proposed. It solves three tasks. First, it provides predictions in the form of the expected event time and the survival function for a new generated feature vector on the basis of the Beran estimator. Second, the model generates additional data based on a given training set that would supplement the original dataset. Third, the most important, it generates a prototype time-dependent trajectory for an object, which characterizes how features of the object could be changed to achieve a different time to an event. The trajectory can be viewed as a type of the counterfactual explanation. The proposed model is robust during training and inference due to a specific weighting scheme incorporating into the variational autoencoder. The model also determines the censored indicators of new generated data by solving a classification task. The paper demonstrates the efficiency and properties of the proposed model using numerical experiments on synthetic and real datasets. The code of the algorithm implementing the proposed model is publicly available.
The need to explain decisions made by AI systems is driven by both recent regulation and user demand. The decisions are often explainable only post hoc. In counterfactual explanations, one may ask what constitutes the best counterfactual explanation. Clearly, multiple criteria must be taken into account, although "distance from the sample" is a key criterion. Recent methods that consider the plausibility of a counterfactual seem to sacrifice this original objective. Here, we present a system that provides high-likelihood explanations that are, at the same time, close and sparse. We show that the search for the most likely explanations satisfying many common desiderata for counterfactual explanations can be modeled using Mixed-Integer Optimization (MIO). We use a Sum-Product Network (SPN) to estimate the likelihood of a counterfactual. To achieve that, we propose an MIO formulation of an SPN, which can be of independent interest. The source code with examples is available at https://github.com/Epanemu/LiCE.
Social media platforms are being increasingly used by malicious actors to share unsafe content, such as images depicting sexual activity, cyberbullying, and self-harm. Consequently, major platforms use artificial intelligence (AI) and human moderation to obfuscate such images to make them safer. Two critical needs for obfuscating unsafe images is that an accurate rationale for obfuscating image regions must be provided, and the sensitive regions should be obfuscated (\textit{e.g.} blurring) for users' safety. This process involves addressing two key problems: (1) the reason for obfuscating unsafe images demands the platform to provide an accurate rationale that must be grounded in unsafe image-specific attributes, and (2) the unsafe regions in the image must be minimally obfuscated while still depicting the safe regions. In this work, we address these key issues by first performing visual reasoning by designing a visual reasoning model (VLM) conditioned on pre-trained unsafe image classifiers to provide an accurate rationale grounded in unsafe image attributes, and then proposing a counterfactual explanation algorithm that minimally identifies and obfuscates unsafe regions for safe viewing, by first utilizing an unsafe image classifier attribution matrix to guide segmentation for a more optimal subregion segmentation followed by an informed greedy search to determine the minimum number of subregions required to modify the classifier's output based on attribution score. Extensive experiments on uncurated data from social networks emphasize the efficacy of our proposed method. We make our code available at: https://github.com/SecureAIAutonomyLab/ConditionalVLM