Sander P. J. Moonemans

Sander Moonemans, Sebastiaan Ram, Frédérique Meeuwsen et al.

Vision-language models (VLMs) have the potential to become co-pilots for pathologists. However, most VLMs either focus on small regions of interest within whole-slide images, provide only static slide-level outputs, or rely on data that is not publicly available, limiting reproducibility. Furthermore, training data containing WSIs paired with detailed clinical reports is scarce, restricting progress toward transparent and generalisable VLMs. We address these limitations with three main contributions. First, we introduce Polysome, a standardised tool for synthetic instruction generation. Second, we apply Polysome to the public HISTAI dataset, generating HISTAI-Instruct, a large whole-slide instruction tuning dataset spanning 24,259 slides and over 1.1 million instruction-response pairs. Finally, we use HISTAI-Instruct to train ANTONI-α, a VLM capable of visual-question answering (VQA). We show that ANTONI-α outperforms MedGemma on WSI-level VQA tasks of tissue identification, neoplasm detection, and differential diagnosis. We also compare the performance of multiple incarnations of ANTONI-α trained with different amounts of data. All methods, data, and code are publicly available.

Ruben T. Lucassen, Sander P. J. Moonemans, Tijn van de Luijtgaarden et al.

Millions of melanocytic skin lesions are examined by pathologists each year, the majority of which concern common nevi (i.e., ordinary moles). While most of these lesions can be diagnosed in seconds, writing the corresponding pathology report is much more time-consuming. Automating part of the report writing could, therefore, alleviate the increasing workload of pathologists. In this work, we develop a vision-language model specifically for the pathology domain of cutaneous melanocytic lesions. The model follows the Contrastive Captioner framework and was trained and evaluated using a melanocytic lesion dataset of 42,512 H&E-stained whole slide images and 19,645 corresponding pathology reports. Our results show that the quality scores of model-generated reports were on par with pathologist-written reports for common nevi, assessed by an expert pathologist in a reader study. While report generation revealed to be more difficult for rare melanocytic lesion subtypes, the cross-modal retrieval performance for these cases was considerably better.

Ruben T. Lucassen, Tijn van de Luijtgaarden, Sander P. J. Moonemans et al.

Vision-language models in pathology enable multimodal case retrieval and automated report generation. Many of the models developed so far, however, have been trained on pathology reports that include information which cannot be inferred from paired whole slide images (e.g., patient history), potentially leading to hallucinated sentences in generated reports. To this end, we investigate how the selection of information from pathology reports for vision-language modeling affects the quality of the multimodal representations and generated reports. More concretely, we compare a model trained on full reports against a model trained on preprocessed reports that only include sentences describing the cell and tissue appearances based on the H&E-stained slides. For the experiments, we built upon the BLIP-2 framework and used a cutaneous melanocytic lesion dataset of 42,433 H&E-stained whole slide images and 19,636 corresponding pathology reports. Model performance was assessed using image-to-text and text-to-image retrieval, as well as qualitative evaluation of the generated reports by an expert pathologist. Our results demonstrate that text preprocessing prevents hallucination in report generation. Despite the improvement in the quality of the generated reports, training the vision-language model on full reports showed better cross-modal retrieval performance.