Duway Nicolas Lesmes-Leon, Shumpei Takezaki, Fabian Schmeisser, Ryoma Bise, Gillian Lovell, Bianca Migliori, Andreas Dengel, Sheraz Ahmed
Generative models increasingly produce realistic microscopy images, yet conventional evaluation primarily characterizes visual fidelity and distributional coverage rather than the biological information represented by synthetic data. We introduce biological congruence as an evaluation principle describing whether biologically relevant information forms a coherent description across representations and remains consistent with its empirical biological context. To study this principle, we develop a text-conditioned diffusion framework that jointly generates microscopy images and instance masks, exposing the same generated biological state through conditioning, visual appearance, and instance structure. Across prompt--mask, prompt--image, image--mask, and population-level analyses, we find strongly feature-dependent behavior: density and confluency are consistently preserved, morphology exhibits recurrent disagreement, while nearest-neighbor distance reveals that strong image--mask agreement can coexist with weaker conditioning and population fidelity. Stress testing increasingly unsupported phenotype combinations further shows that target controllability can increase while untargeted phenotypes reorganize and the complete generated state moves toward configurations better supported by real data. These findings demonstrate that generative quality, controllability, cross-representation agreement, and population fidelity capture complementary properties, motivating biological congruence as a relational perspective for evaluating scientific generative models.
Saifullah Saifullah, David Dembinsky, Stefan Agne, Andreas Dengel, Sheraz Ahmed
Multimodal transformer models have driven unprecedented performance breakthroughs in modern document understanding. However, the inherent black-box nature of these models remains a major obstacle to their safe deployment in high-stakes sectors. Despite significant progress in explainability for vision and language tasks, explainable AI (XAI) research tailored to multimodal document understanding has received little attention. To address this gap, we present \ourframework{}, the first comprehensive explainability framework that adapts existing XAI methods and evaluation metrics to the multimodal (text, layout, and image) document understanding context, while introducing efficient multi-target adaptations of both methods and metrics for domain-specific tasks such as semantic entity recognition. Using \ourframework{}, we systematically evaluate 13 XAI methods across 3 document understanding tasks, 8 datasets, 4 models, and 17 evaluation metrics, and find that only a few methods perform consistently across all evaluation criteria, with Occlusion emerging as the most faithful and interpretable method overall. Through a dedicated meta-evaluation, we observe moderate to strong agreement among several faithfulness and complexity metrics while identifying certain ones that produce unreliable results. Finally, through multiple dataset-wide diagnostic analyses, we uncover key insights into model behavior, including the contribution of individual modalities across tasks and labels, spatial attribution patterns around target entities, and potential dataset biases. Overall, this work serves as both a benchmark and a practical guide for future XAI research in multimodal document understanding. To support reproducibility, we publicly release our code at https://github.com/saifullah3396/docxeval/.