A New Era in Computational Pathology: A Survey on Foundation and Vision-Language Models

Recent advances in deep learning have completely transformed the domain of computational pathology (CPath), which in turn altered the diagnostic workflow of pathologists by integrating foundation models (FMs) and vision-language models (VLMs) in their assessment and decision-making process. FMs overcome the limitations of existing deep learning approaches in CPath by learning a representation space that can be adapted to a wide variety of downstream tasks without explicit supervision. VLMs allow pathology reports written in natural language to be used as a rich semantic information source to improve existing models as well as generate predictions in natural language form. In this survey, a holistic and systematic overview of recent innovations in FMs and VLMs in CPath is presented. Furthermore, the tools, datasets and training schemes for these models are summarized in addition to categorizing them into distinct groups. This extensive survey highlights the current trends in CPath and the way it is going to be transformed through FMs and VLMs in the future.

Adversary-Robust Graph-Based Learning of WSIs

Enhancing the robustness of deep learning models against adversarial attacks is crucial, especially in critical domains like healthcare where significant financial interests heighten the risk of such attacks. Whole slide images (WSIs) are high-resolution, digitized versions of tissue samples mounted on glass slides, scanned using sophisticated imaging equipment. The digital analysis of WSIs presents unique challenges due to their gigapixel size and multi-resolution storage format. In this work, we aim at improving the robustness of cancer Gleason grading classification systems against adversarial attacks, addressing challenges at both the image and graph levels. As regards the proposed algorithm, we develop a novel and innovative graph-based model which utilizes GNN to extract features from the graph representation of WSIs. A denoising module, along with a pooling layer is incorporated to manage the impact of adversarial attacks on the WSIs. The process concludes with a transformer module that classifies various grades of prostate cancer based on the processed data. To assess the effectiveness of the proposed method, we conducted a comparative analysis using two scenarios. Initially, we trained and tested the model without the denoiser using WSIs that had not been exposed to any attack. We then introduced a range of attacks at either the image or graph level and processed them through the proposed network. The performance of the model was evaluated in terms of accuracy and kappa scores. The results from this comparison showed a significant improvement in cancer diagnosis accuracy, highlighting the robustness and efficiency of the proposed method in handling adversarial challenges in the context of medical imaging.

Artifact-Robust Graph-Based Learning in Digital Pathology

Whole slide images~(WSIs) are digitized images of tissues placed in glass slides using advanced scanners. The digital processing of WSIs is challenging as they are gigapixel images and stored in multi-resolution format. A common challenge with WSIs is that perturbations/artifacts are inevitable during storing the glass slides and digitizing them. These perturbations include motion, which often arises from slide movement during placement, and changes in hue and brightness due to variations in staining chemicals and the quality of digitizing scanners. In this work, a novel robust learning approach to account for these artifacts is presented. Due to the size and resolution of WSIs and to account for neighborhood information, graph-based methods are called for. We use graph convolutional network~(GCN) to extract features from the graph representing WSI. Through a denoiser {and pooling layer}, the effects of perturbations in WSIs are controlled and the output is followed by a transformer for the classification of different grades of prostate cancer. To compare the efficacy of the proposed approach, the model without denoiser is trained and tested with WSIs without any perturbation and then different perturbations are introduced in WSIs and passed through the network with the denoiser. The accuracy and kappa scores of the proposed model with prostate cancer dataset compared with non-robust algorithms show significant improvement in cancer diagnosis.