1. arXiv

   Interpretable machine learning for survival analysis

   S. H. Langbein, M. Krzyzinski, M. Spytek, H. Baniecki, P. Biecek, M. N. Wright

   arXiv:2403.10250v1

   Abstract arXiv Code

   With the spread and rapid advancement of black box machine learning models, the field of interpretable machine learning (IML) or explainable artificial intelligence (XAI) has become increasingly important over the last decade. This is particularly relevant for survival analysis, where the adoption of IML techniques promotes transparency, accountability and fairness in sensitive areas, such as clinical decision making processes, the development of targeted therapies, interventions or in other medical or healthcare related contexts. More specifically, explainability can uncover a survival model's potential biases and limitations and provide more mathematically sound ways to understand how and which features are influential for prediction or constitute risk factors. However, the lack of readily available IML methods may have deterred medical practitioners and policy makers in public health from leveraging the full potential of machine learning for predicting time-to-event data. We present a comprehensive review of the limited existing amount of work on IML methods for survival analysis within the context of the general IML taxonomy. In addition, we formally detail how commonly used IML methods, such as such as individual conditional expectation (ICE), partial dependence plots (PDP), accumulated local effects (ALE), different feature importance measures or Friedman's H-interaction statistics can be adapted to survival outcomes. An application of several IML methods to real data on data on under-5 year mortality of Ghanaian children from the Demographic and Health Surveys (DHS) Program serves as a tutorial or guide for researchers, on how to utilize the techniques in practice to facilitate understanding of model decisions or predictions.

2. ICLR

   Red teaming models for hyperspectral image analysis using explainable AI

   V. Zaigrajew, H. Baniecki, L. Tulczyjew, A. M. Wijata, J. Nalepa, N. Longepe, P. Biecek

   ICLR 2024 Workshops

   Abstract arXiv

   Remote sensing (RS) applications in the space domain demand machine learning (ML) models that are reliable, robust, and quality-assured, making red teaming a vital approach for identifying and exposing potential flaws and biases. Since both fields advance independently, there is a notable gap in integrating red teaming strategies into RS. This paper introduces a methodology for examining ML models operating on hyperspectral images within the HYPERVIEW challenge, focusing on soil parameters' estimation. We use post-hoc explanation methods from the Explainable AI (XAI) domain to critically assess the best performing model that won the HYPERVIEW challenge and served as an inspiration for the model deployed on board the INTUITION-1 hyperspectral mission. Our approach effectively red teams the model by pinpointing and validating key shortcomings, constructing a model that achieves comparable performance using just 1% of the input features and a mere up to 5% performance loss. Additionally, we propose a novel way of visualizing explanations that integrate domain-specific information about hyperspectral bands (wavelengths) and data transformations to better suit interpreting models for hyperspectral image analysis.

3. arXiv

   Be careful when evaluating explanations regarding ground truth

   H. Baniecki*, M. Chrabaszcz*, A. Holzinger, B. Pfeifer, A. Saranti, P. Biecek

   arXiv:2311.04813v1

   Abstract arXiv Code

   Evaluating explanations of image classifiers regarding ground truth, e.g. segmentation masks defined by human perception, primarily evaluates the quality of the models under consideration rather than the explanation methods themselves. Driven by this observation, we propose a framework for jointly evaluating the robustness of safety-critical systems that combine a deep neural network with an explanation method. These are increasingly used in real-world applications like medical image analysis or robotics. We introduce a fine-tuning procedure to (mis)align model–explanation pipelines with ground truth and use it to quantify the potential discrepancy between worst and best-case scenarios of human alignment. Experiments across various model architectures and post-hoc local interpretation methods provide insights into the robustness of vision transformers and the overall vulnerability of such AI systems to potential adversarial attacks.

4. arXiv

   Explaining and visualizing black-box models through counterfactual paths

   B. Pfeifer, M. Krzyzinski, H. Baniecki, A. Saranti, A. Holzinger, P. Biecek

   arXiv:2307.07764v3

   Abstract arXiv Code

   Explainable AI (XAI) is an increasingly important area of machine learning research, which aims to make black-box models transparent and interpretable. In this paper, we propose a novel approach to XAI that uses the so-called counterfactual paths generated by conditional permutations of features. The algorithm measures feature importance by identifying sequential permutations of features that most influence changes in model predictions. It is particularly suitable for generating explanations based on counterfactual paths in knowledge graphs incorporating domain knowledge. Counterfactual paths introduce an additional graph dimension to current XAI methods in both explaining and visualizing black-box models. Experiments with synthetic and medical data demonstrate the practical applicability of our approach.

preprints / in review / non-archival

accepted / in press / published

1. JCGS

   Performance is not enough: The story told by a Rashomon quartet

   P. Biecek, H. Baniecki, M. Krzyzinski, D. Cook

   Journal of Computational and Graphical Statistics, 2024

   Abstract arXiv Code

   The usual goal of supervised learning is to find the best model, the one that optimizes a particular performance measure. However, what if the explanation provided by this model is completely different from another model and different again from another model despite all having similarly good fit statistics? Is it possible that the equally effective models put the spotlight on different relationships in the data? Inspired by Anscombe's quartet, this paper introduces a Rashomon Quartet, i.e. a set of four models built on a synthetic dataset which have practically identical predictive performance. However, the visual exploration reveals distinct explanations of the relations in the data. This illustrative example aims to encourage the use of methods for model visualization to compare predictive models beyond their performance.

2. CVPR

   Red-teaming segment anything model

   K. Jankowski*, B. Sobieski*, M. Kwiatkowski, J. Szulc, M. Janik, H. Baniecki, P. Biecek

   CVPR 2024 Workshops

   Abstract arXiv Code

   Foundation models have emerged as pivotal tools, tackling many complex tasks through pre-training on vast datasets and subsequent fine-tuning for specific applications. The Segment Anything Model is one of the first and most well-known foundation models for computer vision segmentation tasks. This work presents a multi-faceted red-teaming analysis that tests the Segment Anything Model against challenging tasks: (1) We analyze the impact of style transfer on segmentation masks, demonstrating that applying adverse weather conditions and raindrops to dashboard images of city roads significantly distorts generated masks. (2) We focus on assessing whether the model can be used for attacks on privacy, such as recognizing celebrities' faces, and show that the model possesses some undesired knowledge in this task. (3) Finally, we check how robust the model is to adversarial attacks on segmentation masks under text prompts. We not only show the effectiveness of popular white-box attacks and resistance to black-box attacks but also introduce a novel approach – Focused Iterative Gradient Attack (FIGA) that combines white-box approaches to construct an efficient attack resulting in a smaller number of modified pixels. All of our testing methods and analyses indicate a need for enhanced safety measures in foundation models for image segmentation.

3. Inf. Fus.

   Adversarial attacks and defenses in explainable artificial intelligence: A survey

   H. Baniecki, P. Biecek

   Information Fusion, 2024
   Review of adversarial attacks on explanations and how to defend them.

   Abstract Paper arXiv Website

   Explainable artificial intelligence (XAI) methods are portrayed as a remedy for debugging and trusting statistical and deep learning models, as well as interpreting their predictions. However, recent advances in adversarial machine learning (AdvML) highlight the limitations and vulnerabilities of state-of-the-art explanation methods, putting their security and trustworthiness into question. The possibility of manipulating, fooling or fairwashing evidence of the model's reasoning has detrimental consequences when applied in high-stakes decision-making and knowledge discovery. This survey provides a comprehensive overview of research concerning adversarial attacks on explanations of machine learning models, as well as fairness metrics. We introduce a unified notation and taxonomy of methods facilitating a common ground for researchers and practitioners from the intersecting research fields of AdvML and XAI. We discuss how to defend against attacks and design robust interpretation methods. We contribute a list of existing insecurities in XAI and outline the emerging research directions in adversarial XAI (AdvXAI). Future work should address improving explanation methods and evaluation protocols to take into account the reported safety issues.

4. Bioinf.

   survex: an R package for explaining machine learning survival models

   M. Spytek, M. Krzyzinski, S. H. Langbein, H. Baniecki, M. N. Wright, P. Biecek

   Bioinformatics, 2023

   Abstract Paper arXiv Code

   Due to their flexibility and superior performance, machine learning models frequently complement and outperform traditional statistical survival models. However, their widespread adoption is hindered by a lack of user-friendly tools to explain their internal operations and prediction rationales. To tackle this issue, we introduce the survex R package, which provides a cohesive framework for explaining any survival model by applying explainable artificial intelligence techniques. The capabilities of the proposed software encompass understanding and diagnosing survival models, which can lead to their improvement. By revealing insights into the decision-making process, such as variable effects and importances, survex enables the assessment of model reliability and the detection of biases. Thus, transparency and responsibility may be promoted in sensitive areas, such as biomedical research and healthcare applications.

5. CVPR

   Towards evaluating explanations of vision transformers for medical imaging

   P. Komorowski, H. Baniecki, P. Biecek

   CVPR 2023 Workshops

   Abstract Paper arXiv Code

   As deep learning models increasingly find applications in critical domains such as medical imaging, the need for transparent and trustworthy decision-making becomes paramount. Many explainability methods provide insights into how these models make predictions by attributing importance to input features. As Vision Transformer (ViT) becomes a promising alternative to convolutional neural networks for image classification, its interpretability remains an open research question. This paper investigates the performance of various interpretation methods on a ViT applied to classify chest X-ray images. We introduce the notion of evaluating faithfulness, sensitivity, and complexity of ViT explanations. The obtained results indicate that Layerwise relevance propagation for transformers outperforms Local interpretable model-agnostic explanations and Attention visualization, providing a more accurate and reliable representation of what a ViT has actually learned. Our findings provide insights into the applicability of ViT explanations in medical imaging and highlight the importance of using appropriate evaluation criteria for comparing them.

6. AIME

   Hospital length of stay prediction based on multi-modal data towards trustworthy human-AI collaboration in radiomics

   H. Baniecki, B. Sobieski, P. Bombinski, P. Szatkowski, P. Biecek

   AIME 2023

   Abstract Paper arXiv Code

   To what extent can the patient's length of stay in a hospital be predicted using only an X-ray image? We answer this question by comparing the performance of machine learning survival models on a novel multi-modal dataset created from 1235 images with textual radiology reports annotated by humans. Although black-box models predict better on average than interpretable ones, like Cox proportional hazards, they are not inherently understandable. To overcome this trust issue, we introduce time-dependent model explanations into the human-AI decision making process. Explaining models built on both: human-annotated and algorithm-extracted radiomics features provides valuable insights for physicians working in a hospital. We believe the presented approach to be general and widely applicable to other time-to-event medical use cases. For reproducibility, we open-source code and the TLOS dataset at https://github.com/mi2datalab/xlungs-trustworthy-los-prediction.

7. Kno. Sys.

   SurvSHAP(t): Time-dependent explanations of machine learning survival models

   M. Krzyzinski, M. Spytek, H. Baniecki, P. Biecek

   Knowledge-Based Systems, 2023

   Abstract Paper arXiv Code

   Machine and deep learning survival models demonstrate similar or even improved time-to-event prediction capabilities compared to classical statistical learning methods yet are too complex to be interpreted by humans. Several model-agnostic explanations are available to overcome this issue; however, none directly explain the survival function prediction. In this paper, we introduce SurvSHAP(t), the first time-dependent explanation that allows for interpreting survival black-box models. It is based on SHapley Additive exPlanations with solid theoretical foundations and a broad adoption among machine learning practitioners. The proposed methods aim to enhance precision diagnostics and support domain experts in making decisions. Experiments on synthetic and medical data confirm that SurvSHAP(t) can detect variables with a time-dependent effect, and its aggregation is a better determinant of the importance of variables for a prediction than SurvLIME. SurvSHAP(t) is model-agnostic and can be applied to all models with functional output. We provide an accessible implementation of time-dependent explanations in Python at https://github.com/MI2DataLab/survshap.

8. DAMI

   The grammar of interactive explanatory model analysis

   H. Baniecki, D. Parzych, P. Biecek

   Data Mining and Knowledge Discovery, 2023
   Interactive explanation of a model improves the performance of human decision making.

   Abstract Paper arXiv Code Website

   The growing need for in-depth analysis of predictive models leads to a series of new methods for explaining their local and global properties. Which of these methods is the best? It turns out that this is an ill-posed question. One cannot sufficiently explain a black-box machine learning model using a single method that gives only one perspective. Isolated explanations are prone to misunderstanding, leading to wrong or simplistic reasoning. This problem is known as the Rashomon effect and refers to diverse, even contradictory, interpretations of the same phenomenon. Surprisingly, most methods developed for explainable and responsible machine learning focus on a single-aspect of the model behavior. In contrast, we showcase the problem of explainability as an interactive and sequential analysis of a model. This paper proposes how different Explanatory Model Analysis (EMA) methods complement each other and discusses why it is essential to juxtapose them. The introduced process of Interactive EMA (IEMA) derives from the algorithmic side of explainable machine learning and aims to embrace ideas developed in cognitive sciences. We formalize the grammar of IEMA to describe human-model interaction. It is implemented in a widely used human-centered open-source software framework that adopts interactivity, customizability and automation as its main traits. We conduct a user study to evaluate the usefulness of IEMA, which indicates that an interactive sequential analysis of a model may increase the accuracy and confidence of human decision making.

9. Sci. Rep.

   Multi-omics disease module detection with an explainable greedy decision forest

   B. Pfeifer, H. Baniecki, A. Saranti, P. Biecek, A. Holzinger

   Scientific Reports, 2022

   Abstract Paper arXiv Code

   Machine learning methods can detect complex relationships between variables, but usually do not exploit domain knowledge. This is a limitation because in many scientific disciplines, such as systems biology, domain knowledge is available in the form of graphs or networks, and its use can improve model performance. We need network-based algorithms that are versatile and applicable in many research areas. In this work, we demonstrate subnetwork detection based on multi-modal node features using a novel Greedy Decision Forest (GDF) with inherent interpretability. The latter will be a crucial factor to retain experts and gain their trust in such algorithms. To demonstrate a concrete application example, we focus on bioinformatics, systems biology and particularly biomedicine, but the presented methodology is applicable in many other domains as well. Systems biology is a good example of a field in which statistical data-driven machine learning enables the analysis of large amounts of multi-modal biomedical data. This is important to reach the future goal of precision medicine, where the complexity of patients is modeled on a system level to best tailor medical decisions, health practices and therapies to the individual patient. Our proposed explainable approach can help to uncover disease-causing network modules from multi-omics data to better understand complex diseases such as cancer.

10. ECML PKDD

    Fooling partial dependence via data poisoning

    H. Baniecki, W. Kretowicz, P. Biecek

    ECML PKDD 2022
    Feature effect explanations can be manipulated in an adversarial manner.

    Abstract Paper arXiv Code Slides

    Many methods have been developed to understand complex predictive models and high expectations are placed on post-hoc model explainability. It turns out that such explanations are not robust nor trustworthy, and they can be fooled. This paper presents techniques for attacking Partial Dependence (plots, profiles, PDP), which are among the most popular methods of explaining any predictive model trained on tabular data. We showcase that PD can be manipulated in an adversarial manner, which is alarming, especially in financial or medical applications where auditability became a must-have trait supporting black-box models. The fooling is performed via poisoning the data to bend and shift explanations in the desired direction using genetic and gradient algorithms. To the best of our knowledge, this is the first work using a genetic algorithm for attacking explanations, which is highly transferable as it generalizes both ways: in a model-agnostic and an explanation-agnostic manner.

11. AAAI

    Manipulating SHAP via adversarial data perturbations (student abstract)

    H. Baniecki, P. Biecek

    AAAI 2022

    Abstract Paper Code Poster

    We introduce a model-agnostic algorithm for manipulating SHapley Additive exPlanations (SHAP) with perturbation of tabular data. It is evaluated on predictive tasks from healthcare and financial domains to illustrate how crucial is the context of data distribution in interpreting machine learning models. Our method supports checking the stability of the explanations used by various stakeholders apparent in the domain of responsible AI; moreover, the result highlights the explanations' vulnerability that can be exploited by an adversary.

12. JMLR

    dalex: Responsible machine learning with interactive explainability and fairness in Python

    H. Baniecki, W. Kretowicz, P. Piatyszek, J. Wisniewski, P. Biecek

    Journal of Machine Learning Research, 2021
    2022 John M. Chambers Statistical Software Award

    Abstract Paper arXiv Code Website

    In modern machine learning, we observe the phenomenon of opaqueness debt, which manifests itself by an increased risk of discrimination, lack of reproducibility, and deflated performance due to data drift. An increasing amount of available data and computing power results in the growing complexity of black-box predictive models. To manage these issues, good MLOps practice asks for better validation of model performance and fairness, higher explainability, and continuous monitoring. The necessity for deeper model transparency comes from both scientific and social domains and is also caused by emerging laws and regulations on artificial intelligence. To facilitate the responsible development of machine learning models, we introduce dalex, a Python package which implements a model-agnostic interface for interactive explainability and fairness. It adopts the design crafted through the development of various tools for explainable machine learning; thus, it aims at the unification of existing solutions. This library's source code and documentation are available under open license at https://python.drwhy.ai.

13. AAAI

    Responsible prediction making of COVID-19 mortality (student abstract)

    H. Baniecki, P. Biecek

    AAAI 2021

    Abstract Paper Poster Website

    For high-stakes prediction making, the Responsible Artificial Intelligence (RAI) is more important than ever. It builds upon Explainable Artificial Intelligence (XAI) to advance the efforts in providing fairness, model explainability, and accountability to the AI systems. During the literature review of COVID-19 related prognosis and diagnosis, we found out that most of the predictive models are not faithful to the RAI principles, which can lead to biassed results and wrong reasoning. To solve this problem, we show how novel XAI techniques boost transparency, reproducibility and quality of models.

14. JOSS

    modelStudio: Interactive studio with explanations for ML predictive models

    H. Baniecki, P. Biecek

    Journal of Open Source Software, 2019

    Paper Code