Performance Evaluation of Open-Source Large Language Models for Assisting Pathology Report Writing in Japanese

The performance of large language models (LLMs) for supporting pathology report writing in Japanese remains unexplored. We evaluated seven open-source LLMs from three perspectives: (A) generation and information extraction of pathology diagnosis text following predefined formats, (B) correction of typographical errors in Japanese pathology reports, and (C) subjective evaluation of model-generated explanatory text by pathologists and clinicians. Thinking models and medical-specialized models showed advantages in structured reporting tasks that required reasoning and in typo correction. In contrast, preferences for explanatory outputs varied substantially across raters. Although the utility of LLMs differed by task, our findings suggest that open-source LLMs can be useful for assisting Japanese pathology report writing in limited but clinically relevant scenarios.

Large-scale pretraining on pathological images for fine-tuning of small pathological benchmarks

Pretraining a deep learning model on large image datasets is a standard step before fine-tuning the model on small targeted datasets. The large dataset is usually general images (e.g. imagenet2012) while the small dataset can be specialized datasets that have different distributions from the large dataset. However, this 'large-to-small' strategy is not well-validated when the large dataset is specialized and has a similar distribution to small datasets. We newly compiled three hematoxylin and eosin-stained image datasets, one large (PTCGA200) and two magnification-adjusted small datasets (PCam200 and segPANDA200). Major deep learning models were trained with supervised and self-supervised learning methods and fine-tuned on the small datasets for tumor classification and tissue segmentation benchmarks. ResNet50 pretrained with MoCov2, SimCLR, and BYOL on PTCGA200 was better than imagenet2012 pretraining when fine-tuned on PTCGA200 (accuracy of 83.94%, 86.41%, 84.91%, and 82.72%, respectively). ResNet50 pre-trained on PTCGA200 with MoCov2 exceeded the COCOtrain2017-pretrained baseline and was the best in ResNet50 for the tissue segmentation benchmark (mIoU of 63.53% and 63.22%). We found re-training imagenet-pretrained models (ResNet50, BiT-M-R50x1, and ViT-S/16) on PTCGA200 improved downstream benchmarks.