Bartlomiej Sobieski

Hubert Baniecki, Bartlomiej Sobieski, Patryk Szatkowski et al.

Time-to-event prediction, e.g. cancer survival analysis or hospital length of stay, is a highly prominent machine learning task in medical and healthcare applications. However, only a few interpretable machine learning methods comply with its challenges. To facilitate a comprehensive explanatory analysis of survival models, we formally introduce time-dependent feature effects and global feature importance explanations. We show how post-hoc interpretation methods allow for finding biases in AI systems predicting length of stay using a novel multi-modal dataset created from 1235 X-ray images with textual radiology reports annotated by human experts. Moreover, we evaluate cancer survival models beyond predictive performance to include the importance of multi-omics feature groups based on a large-scale benchmark comprising 11 datasets from The Cancer Genome Atlas (TCGA). Model developers can use the proposed methods to debug and improve machine learning algorithms, while physicians can discover disease biomarkers and assess their significance. We hope the contributed open data and code resources facilitate future work in the emerging research direction of explainable survival analysis.

Bartlomiej Sobieski, Jakub Grzywaczewski, Karol Dobiczek et al.

Lung cancer remains the leading cause of cancer mortality, driving the development of automated screening tools to alleviate radiologist workload. Standing at the frontier of this effort is Sybil, a deep learning model capable of predicting future risk solely from computed tomography (CT) with high precision. However, despite extensive clinical validation, current assessments rely purely on observational metrics. This correlation-based approach overlooks the model's actual reasoning mechanism, necessitating a shift to causal verification to ensure robust decision-making before clinical deployment. We propose S(H)NAP, a model-agnostic auditing framework that constructs generative interventional attributions validated by expert radiologists. By leveraging realistic 3D diffusion bridge modeling to systematically modify anatomical features, our approach isolates object-specific causal contributions to the risk score. Providing the first interventional audit of Sybil, we demonstrate that while the model often exhibits behavior akin to an expert radiologist, differentiating malignant pulmonary nodules from benign ones, it suffers from critical failure modes, including dangerous sensitivity to clinically unjustified artifacts and a distinct radial bias.

Bartlomiej Sobieski, Matthew Tivnan, Dawid Płudowski et al.

Diffusion models are prone to generating structural hallucinations - samples that match the statistical properties of the training data yet defy underlying structural rules, resulting in anomalies like hands with more than five fingers. Recent research studied this failure mode from several viewpoints, offering partial explanations to their occurrence, such as mode interpolation. In this work, we propose a complementary perspective that treats hallucinations as instabilities on the model-induced manifold. We begin by showing that a hallucination filter based on such instabilities matches or exceeds the performance of the recently proposed temporal one. By tracing the source of these instabilities, we identify local intrinsic dimension (LID) as their primary driver and propose Intrinsic Quenching (IQ), a direct corrective mechanism that deflates it to alleviate hallucinations. IQ consistently outperforms standard hallucination reduction baselines across a wide array of benchmarks and offers a highly promising solution for enforcing anatomical consistency in downstream medical imaging tasks.

Bartlomiej Sobieski, Przemysław Biecek

Despite increasing progress in development of methods for generating visual counterfactual explanations, especially with the recent rise of Denoising Diffusion Probabilistic Models, previous works consider them as an entirely local technique. In this work, we take the first step at globalizing them. Specifically, we discover that the latent space of Diffusion Autoencoders encodes the inference process of a given classifier in the form of global directions. We propose a novel proxy-based approach that discovers two types of these directions with the use of only single image in an entirely black-box manner. Precisely, g-directions allow for flipping the decision of a given classifier on an entire dataset of images, while h-directions further increase the diversity of explanations. We refer to them in general as Global Counterfactual Directions (GCDs). Moreover, we show that GCDs can be naturally combined with Latent Integrated Gradients resulting in a new black-box attribution method, while simultaneously enhancing the understanding of counterfactual explanations. We validate our approach on existing benchmarks and show that it generalizes to real-world use-cases.

Bartlomiej Sobieski, Jakub Grzywaczewski, Bartlomiej Sadlej et al.

Visual counterfactual explanations (VCEs) have recently gained immense popularity as a tool for clarifying the decision-making process of image classifiers. This trend is largely motivated by what these explanations promise to deliver -- indicate semantically meaningful factors that change the classifier's decision. However, we argue that current state-of-the-art approaches lack a crucial component -- the region constraint -- whose absence prevents from drawing explicit conclusions, and may even lead to faulty reasoning due to phenomenons like confirmation bias. To address the issue of previous methods, which modify images in a very entangled and widely dispersed manner, we propose region-constrained VCEs (RVCEs), which assume that only a predefined image region can be modified to influence the model's prediction. To effectively sample from this subclass of VCEs, we propose Region-Constrained Counterfactual Schrödinger Bridges (RCSB), an adaptation of a tractable subclass of Schrödinger Bridges to the problem of conditional inpainting, where the conditioning signal originates from the classifier of interest. In addition to setting a new state-of-the-art by a large margin, we extend RCSB to allow for exact counterfactual reasoning, where the predefined region contains only the factor of interest, and incorporating the user to actively interact with the RVCE by predefining the regions manually.

Krzysztof Jankowski, Bartlomiej Sobieski, Mateusz Kwiatkowski et al.

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.

Bartlomiej Sobieski, Matthew Tivnan, Yuang Wang et al.

Solving inverse problems -- recovering signals from incomplete or noisy measurements -- is fundamental in science and engineering. Score-based generative models (SGMs) have recently emerged as a powerful framework for this task. Two main paradigms have formed: unsupervised approaches that adapt pretrained generative models to inverse problems, and supervised bridge methods that train stochastic processes conditioned on paired clean and corrupted data. While the former typically assume knowledge of the measurement model, the latter have largely overlooked this structural information. We introduce System embedded Diffusion Bridge Models (SDBs), a new class of supervised bridge methods that explicitly embed the known linear measurement system into the coefficients of a matrix-valued SDE. This principled integration yields consistent improvements across diverse linear inverse problems and demonstrates robust generalization under system misspecification between training and deployment, offering a promising solution to real-world applications.