The development of biologically interpretable and explainable models remains a key challenge in computational pathology, particularly for multistain immunohistochemistry (IHC) analysis. We present BioX-CPath, an explainable graph neural network architecture for whole slide image (WSI) classification that leverages both spatial and semantic features across multiple stains. At its core, BioX-CPath introduces a novel Stain-Aware Attention Pooling (SAAP) module that generates biologically meaningful, stain-aware patient embeddings. Our approach achieves state-of-the-art performance on both Rheumatoid Arthritis and Sjogren's Disease multistain datasets. Beyond performance metrics, BioX-CPath provides interpretable insights through stain attention scores, entropy measures, and stain interaction scores, that permit measuring model alignment with known pathological mechanisms. This biological grounding, combined with strong classification performance, makes BioX-CPath particularly suitable for clinical applications where interpretability is key. Source code and documentation can be found at: https://github.com/AmayaGS/BioX-CPath.
The ever growing realism and quality of generated videos makes it increasingly harder for humans to spot deepfake content, who need to rely more and more on automatic deepfake detectors. However, deepfake detectors are also prone to errors, and their decisions are not explainable, leaving humans vulnerable to deepfake-based fraud and misinformation. To this end, we introduce ExDDV, the first dataset and benchmark for Explainable Deepfake Detection in Video. ExDDV comprises around 5.4K real and deepfake videos that are manually annotated with text descriptions (to explain the artifacts) and clicks (to point out the artifacts). We evaluate a number of vision-language models on ExDDV, performing experiments with various fine-tuning and in-context learning strategies. Our results show that text and click supervision are both required to develop robust explainable models for deepfake videos, which are able to localize and describe the observed artifacts. Our novel dataset and code to reproduce the results are available at https://github.com/vladhondru25/ExDDV.
The integration of machine learning (ML) into chemistry offers transformative potential in the design of molecules with targeted properties. However, the focus has often been on creating highly efficient predictive models, sometimes at the expense of interpretability. In this study, we leverage explainable AI techniques to explore the rational design of boron-based Lewis acids, which play a pivotal role in organic reactions due to their electron-ccepting properties. Using Fluoride Ion Affinity as a proxy for Lewis acidity, we developed interpretable ML models based on chemically meaningful descriptors, including ab initio computed features and substituent-based parameters derived from the Hammett linear free-energy relationship. By constraining the chemical space to well-defined molecular scaffolds, we achieved highly accurate predictions (mean absolute error < 6 kJ/mol), surpassing conventional black-box deep learning models in low-data regimes. Interpretability analyses of the models shed light on the origin of Lewis acidity in these compounds and identified actionable levers to modulate it through the nature and positioning of substituents on the molecular scaffold. This work bridges ML and chemist's way of thinking, demonstrating how explainable models can inspire molecular design and enhance scientific understanding of chemical reactivity.
Rolling element bearings are critical components of rotating machinery, with their performance directly influencing the efficiency and reliability of industrial systems. At the same time, bearing faults are a leading cause of machinery failures, often resulting in costly downtime, reduced productivity, and, in extreme cases, catastrophic damage. This study presents a methodology that utilizes Kolmogorov-Arnold Networks to address these challenges through automatic feature selection, hyperparameter tuning and interpretable fault analysis within a unified framework. By training shallow network architectures and minimizing the number of selected features, the framework produces lightweight models that deliver explainable results through feature attribution and symbolic representations of their activation functions. Validated on two widely recognized datasets for bearing fault diagnosis, the framework achieved perfect F1-Scores for fault detection and high performance in fault and severity classification tasks, including 100% F1-Scores in most cases. Notably, it demonstrated adaptability by handling diverse fault types, such as imbalance and misalignment, within the same dataset. The symbolic representations enhanced model interpretability, while feature attribution offered insights into the optimal feature types or signals for each studied task. These results highlight the framework's potential for practical applications, such as real-time machinery monitoring, and for scientific research requiring efficient and explainable models.
MRI and CT are essential clinical cross-sectional imaging techniques for diagnosing complex conditions. However, large 3D datasets with annotations for deep learning are scarce. While methods like DINOv2 are encouraging for 2D image analysis, these methods have not been applied to 3D medical images. Furthermore, deep learning models often lack explainability due to their "black-box" nature. This study aims to extend 2D self-supervised models, specifically DINOv2, to 3D medical imaging while evaluating their potential for explainable outcomes. We introduce the Medical Slice Transformer (MST) framework to adapt 2D self-supervised models for 3D medical image analysis. MST combines a Transformer architecture with a 2D feature extractor, i.e., DINOv2. We evaluate its diagnostic performance against a 3D convolutional neural network (3D ResNet) across three clinical datasets: breast MRI (651 patients), chest CT (722 patients), and knee MRI (1199 patients). Both methods were tested for diagnosing breast cancer, predicting lung nodule dignity, and detecting meniscus tears. Diagnostic performance was assessed by calculating the Area Under the Receiver Operating Characteristic Curve (AUC). Explainability was evaluated through a radiologist's qualitative comparison of saliency maps based on slice and lesion correctness. P-values were calculated using Delong's test. MST achieved higher AUC values compared to ResNet across all three datasets: breast (0.94$\pm$0.01 vs. 0.91$\pm$0.02, P=0.02), chest (0.95$\pm$0.01 vs. 0.92$\pm$0.02, P=0.13), and knee (0.85$\pm$0.04 vs. 0.69$\pm$0.05, P=0.001). Saliency maps were consistently more precise and anatomically correct for MST than for ResNet. Self-supervised 2D models like DINOv2 can be effectively adapted for 3D medical imaging using MST, offering enhanced diagnostic accuracy and explainability compared to convolutional neural networks.
The growing reproducibility crisis in machine learning has brought forward a need for careful examination of research findings. This paper investigates the claims made by Lei et al. (2023) regarding their proposed method, LICO, for enhancing post-hoc interpretability techniques and improving image classification performance. LICO leverages natural language supervision from a vision-language model to enrich feature representations and guide the learning process. We conduct a comprehensive reproducibility study, employing (Wide) ResNets and established interpretability methods like Grad-CAM and RISE. We were mostly unable to reproduce the authors' results. In particular, we did not find that LICO consistently led to improved classification performance or improvements in quantitative and qualitative measures of interpretability. Thus, our findings highlight the importance of rigorous evaluation and transparent reporting in interpretability research.
In the field of explainable AI, a vibrant effort is dedicated to the design of self-explainable models, as a more principled alternative to post-hoc methods that attempt to explain the decisions after a model opaquely makes them. However, this productive line of research suffers from common downsides: lack of reproducibility, unfeasible comparison, diverging standards. In this paper, we propose CaBRNet, an open-source, modular, backward-compatible framework for Case-Based Reasoning Networks: https://github.com/aiser-team/cabrnet.
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.
Stereotypes are generalised assumptions about societal groups, and even state-of-the-art LLMs using in-context learning struggle to identify them accurately. Due to the subjective nature of stereotypes, where what constitutes a stereotype can vary widely depending on cultural, social, and individual perspectives, robust explainability is crucial. Explainable models ensure that these nuanced judgments can be understood and validated by human users, promoting trust and accountability. We address these challenges by introducing HEARTS (Holistic Framework for Explainable, Sustainable, and Robust Text Stereotype Detection), a framework that enhances model performance, minimises carbon footprint, and provides transparent, interpretable explanations. We establish the Expanded Multi-Grain Stereotype Dataset (EMGSD), comprising 57,201 labelled texts across six groups, including under-represented demographics like LGBTQ+ and regional stereotypes. Ablation studies confirm that BERT models fine-tuned on EMGSD outperform those trained on individual components. We then analyse a fine-tuned, carbon-efficient ALBERT-V2 model using SHAP to generate token-level importance values, ensuring alignment with human understanding, and calculate explainability confidence scores by comparing SHAP and LIME outputs...
Attribution maps are one of the most established tools to explain the functioning of computer vision models. They assign importance scores to input features, indicating how relevant each feature is for the prediction of a deep neural network. While much research has gone into proposing new attribution methods, their proper evaluation remains a difficult challenge. In this work, we propose a novel evaluation protocol that overcomes two fundamental limitations of the widely used incremental-deletion protocol, i.e., the out-of-domain issue and lacking inter-model comparisons. This allows us to evaluate 23 attribution methods and how different design choices of popular vision backbones affect their attribution quality. We find that intrinsically explainable models outperform standard models and that raw attribution values exhibit a higher attribution quality than what is known from previous work. Further, we show consistent changes in the attribution quality when varying the network design, indicating that some standard design choices promote attribution quality.
Time-series data are fundamentally important for many critical domains such as healthcare, finance, and climate, where explainable models are necessary for safe automated decision making. To develop explainable artificial intelligence in these domains therefore implies explaining salient information in the time series. Current methods for obtaining saliency maps assume localized information in the raw input space. In this paper, we argue that the salient information of a number of time series is more likely to be localized in the frequency domain. We propose FreqRISE, which uses masking-based methods to produce explanations in the frequency and time-frequency domain, and outperforms strong baselines across a number of tasks. The source code is available here: \url{https://github.com/theabrusch/FreqRISE}.
Prototypical networks aim to build intrinsically explainable models based on the linear summation of concepts. Concepts are coherent entities that we, as humans, can recognize and associate with a certain object or entity. However, important challenges remain in the fair evaluation of explanation quality provided by these models. This work first proposes an extensive set of quantitative and qualitative metrics which allow to identify drawbacks in current prototypical networks. It then introduces a novel architecture which provides compact explanations, outperforming current prototypical models in terms of explanation quality. Overall, the proposed architecture demonstrates how frozen pre-trained ViT backbones can be effectively turned into prototypical models for both general and domain-specific tasks, in our case biomedical image classifiers. Code is available at \url{https://github.com/hturbe/protosvit}.
Image classification is a primary task in data analysis where explainable models are crucially demanded in various applications. Although amounts of methods have been proposed to obtain explainable knowledge from the black-box classifiers, these approaches lack the efficiency of extracting global knowledge regarding the classification task, thus is vulnerable to local traps and often leads to poor accuracy. In this study, we propose a generative explanation model that combines the advantages of global and local knowledge for explaining image classifiers. We develop a representation learning method called class association embedding (CAE), which encodes each sample into a pair of separated class-associated and individual codes. Recombining the individual code of a given sample with altered class-associated code leads to a synthetic real-looking sample with preserved individual characters but modified class-associated features and possibly flipped class assignments. A building-block coherency feature extraction algorithm is proposed that efficiently separates class-associated features from individual ones. The extracted feature space forms a low-dimensional manifold that visualizes the classification decision patterns. Explanation on each individual sample can be then achieved in a counter-factual generation manner which continuously modifies the sample in one direction, by shifting its class-associated code along a guided path, until its classification outcome is changed. We compare our method with state-of-the-art ones on explaining image classification tasks in the form of saliency maps, demonstrating that our method achieves higher accuracies. The code is available at https://github.com/xrt11/XAI-CODE.
Society's capacity for algorithmic problem-solving has never been greater. Artificial Intelligence is now applied across more domains than ever, a consequence of powerful abstractions, abundant data, and accessible software. As capabilities have expanded, so have risks, with models often deployed without fully understanding their potential impacts. Interpretable and interactive machine learning aims to make complex models more transparent and controllable, enhancing user agency. This review synthesizes key principles from the growing literature in this field. We first introduce precise vocabulary for discussing interpretability, like the distinction between glass box and explainable models. We then explore connections to classical statistical and design principles, like parsimony and the gulfs of interaction. Basic explainability techniques -- including learned embeddings, integrated gradients, and concept bottlenecks -- are illustrated with a simple case study. We also review criteria for objectively evaluating interpretability approaches. Throughout, we underscore the importance of considering audience goals when designing interactive data-driven systems. Finally, we outline open challenges and discuss the potential role of data science in addressing them. Code to reproduce all examples can be found at https://go.wisc.edu/3k1ewe.
The rapid advancement of Large Language Models (LLMs) has opened up new opportunities for leveraging artificial intelligence in various domains, including cybersecurity. As the volume and sophistication of cyber threats continue to grow, there is an increasing need for intelligent systems that can automatically detect vulnerabilities, analyze malware, and respond to attacks. In this survey, we conduct a comprehensive review of the literature on the application of LLMs in cybersecurity (LLM4Security). By comprehensively collecting over 30K relevant papers and systematically analyzing 127 papers from top security and software engineering venues, we aim to provide a holistic view of how LLMs are being used to solve diverse problems across the cybersecurity domain. Through our analysis, we identify several key findings. First, we observe that LLMs are being applied to a wide range of cybersecurity tasks, including vulnerability detection, malware analysis, network intrusion detection, and phishing detection. Second, we find that the datasets used for training and evaluating LLMs in these tasks are often limited in size and diversity, highlighting the need for more comprehensive and representative datasets. Third, we identify several promising techniques for adapting LLMs to specific cybersecurity domains, such as fine-tuning, transfer learning, and domain-specific pre-training. Finally, we discuss the main challenges and opportunities for future research in LLM4Security, including the need for more interpretable and explainable models, the importance of addressing data privacy and security concerns, and the potential for leveraging LLMs for proactive defense and threat hunting. Overall, our survey provides a comprehensive overview of the current state-of-the-art in LLM4Security and identifies several promising directions for future research.
Deep learning models have achieved high performance in medical applications, however, their adoption in clinical practice is hindered due to their black-box nature. Self-explainable models, like prototype-based models, can be especially beneficial as they are interpretable by design. However, if the learnt prototypes are of low quality then the prototype-based models are as good as black-box. Having high quality prototypes is a pre-requisite for a truly interpretable model. In this work, we propose a prototype evaluation framework for coherence (PEF-C) for quantitatively evaluating the quality of the prototypes based on domain knowledge. We show the use of PEF-C in the context of breast cancer prediction using mammography. Existing works on prototype-based models on breast cancer prediction using mammography have focused on improving the classification performance of prototype-based models compared to black-box models and have evaluated prototype quality through anecdotal evidence. We are the first to go beyond anecdotal evidence and evaluate the quality of the mammography prototypes systematically using our PEF-C. Specifically, we apply three state-of-the-art prototype-based models, ProtoPNet, BRAIxProtoPNet++ and PIP-Net on mammography images for breast cancer prediction and evaluate these models w.r.t. i) classification performance, and ii) quality of the prototypes, on three public datasets. Our results show that prototype-based models are competitive with black-box models in terms of classification performance, and achieve a higher score in detecting ROIs. However, the quality of the prototypes are not yet sufficient and can be improved in aspects of relevance, purity and learning a variety of prototypes. We call the XAI community to systematically evaluate the quality of the prototypes to check their true usability in high stake decisions and improve such models further.
Prototypical self-explainable classifiers have emerged to meet the growing demand for interpretable AI systems. These classifiers are designed to incorporate high transparency in their decisions by basing inference on similarity with learned prototypical objects. While these models are designed with diversity in mind, the learned prototypes often do not sufficiently represent all aspects of the input distribution, particularly those in low density regions. Such lack of sufficient data representation, known as representation bias, has been associated with various detrimental properties related to machine learning diversity and fairness. In light of this, we introduce pantypes, a new family of prototypical objects designed to capture the full diversity of the input distribution through a sparse set of objects. We show that pantypes can empower prototypical self-explainable models by occupying divergent regions of the latent space and thus fostering high diversity, interpretability and fairness.
Deep neural networks have revolutionized many fields, but their black-box nature also occasionally prevents their wider adoption in fields such as healthcare and finance, where interpretable and explainable models are required. The recent development of Neural Additive Models (NAMs) is a significant step in the direction of interpretable deep learning for tabular datasets. In this paper, we propose a new subclass of NAMs that use a single-layer neural network construction of the Gaussian process via random Fourier features, which we call Gaussian Process Neural Additive Models (GP-NAM). GP-NAMs have the advantage of a convex objective function and number of trainable parameters that grows linearly with feature dimensionality. It suffers no loss in performance compared to deeper NAM approaches because GPs are well-suited for learning complex non-parametric univariate functions. We demonstrate the performance of GP-NAM on several tabular datasets, showing that it achieves comparable or better performance in both classification and regression tasks with a large reduction in the number of parameters.
In Federated Learning, clients train models on local data and send updates to a central server, which aggregates them into a global model using a fusion algorithm. This collaborative yet privacy-preserving training comes at a cost. FL developers face significant challenges in attributing global model predictions to specific clients. Localizing responsible clients is a crucial step towards (a) excluding clients primarily responsible for incorrect predictions and (b) encouraging clients who contributed high-quality models to continue participating in the future. Existing ML debugging approaches are inherently inapplicable as they are designed for single-model, centralized training. We introduce TraceFL, a fine-grained neuron provenance capturing mechanism that identifies clients responsible for a global model's prediction by tracking the flow of information from individual clients to the global model. Since inference on different inputs activates a different set of neurons of the global model, TraceFL dynamically quantifies the significance of the global model's neurons in a given prediction, identifying the most crucial neurons in the global model. It then maps them to the corresponding neurons in every participating client to determine each client's contribution, ultimately localizing the responsible client. We evaluate TraceFL on six datasets, including two real-world medical imaging datasets and four neural networks, including advanced models such as GPT. TraceFL achieves 99% accuracy in localizing the responsible client in FL tasks spanning both image and text classification tasks. At a time when state-of-the-artML debugging approaches are mostly domain-specific (e.g., image classification only), TraceFL is the first technique to enable highly accurate automated reasoning across a wide range of FL applications.
Explainable AI (XAI) has unfolded in two distinct research directions with, on the one hand, post-hoc methods that explain the predictions of a pre-trained black-box model and, on the other hand, self-explainable models (SEMs) which are trained directly to provide explanations alongside their predictions. While the latter is preferred in safety-critical scenarios, post-hoc approaches have received the majority of attention until now, owing to their simplicity and ability to explain base models without retraining. Current SEMs, instead, require complex architectures and heavily regularized loss functions, thus necessitating specific and costly training. To address this shortcoming and facilitate wider use of SEMs, we propose a simple yet efficient universal method called KMEx (K-Means Explainer), which can convert any existing pre-trained model into a prototypical SEM. The motivation behind KMEx is to enhance transparency in deep learning-based decision-making via class-prototype-based explanations that are diverse and trustworthy without retraining the base model. We compare models obtained from KMEx to state-of-the-art SEMs using an extensive qualitative evaluation to highlight the strengths and weaknesses of each model, further paving the way toward a more reliable and objective evaluation of SEMs (The code is available at https://github.com/SrishtiGautam/KMEx).