Joseph DiPalma

Joseph DiPalma, Lorenzo Torresani, Saeed Hassanpour

Deep learning has been effective for histology image analysis in digital pathology. However, many current deep learning approaches require large, strongly- or weakly-labeled images and regions of interest, which can be time-consuming and resource-intensive to obtain. To address this challenge, we present HistoPerm, a view generation method for representation learning using joint embedding architectures that enhances representation learning for histology images. HistoPerm permutes augmented views of patches extracted from whole-slide histology images to improve classification performance. We evaluated the effectiveness of HistoPerm on two histology image datasets for Celiac disease and Renal Cell Carcinoma, using three widely used joint embedding architecture-based representation learning methods: BYOL, SimCLR, and VICReg. Our results show that HistoPerm consistently improves patch- and slide-level classification performance in terms of accuracy, F1-score, and AUC. Specifically, for patch-level classification accuracy on the Celiac disease dataset, HistoPerm boosts BYOL and VICReg by 8% and SimCLR by 3%. On the Renal Cell Carcinoma dataset, patch-level classification accuracy is increased by 2% for BYOL and VICReg, and by 1% for SimCLR. In addition, on the Celiac disease dataset, models with HistoPerm outperform the fully-supervised baseline model by 6%, 5%, and 2% for BYOL, SimCLR, and VICReg, respectively. For the Renal Cell Carcinoma dataset, HistoPerm lowers the classification accuracy gap for the models up to 10% relative to the fully-supervised baseline. These findings suggest that HistoPerm can be a valuable tool for improving representation learning of histopathology features when access to labeled data is limited and can lead to whole-slide classification results that are comparable to or superior to fully-supervised methods.

Weiyi Wu, Chongyang Gao, Joseph DiPalma et al.

Recent advances in whole-slide image (WSI) scanners and computational capabilities have significantly propelled the application of artificial intelligence in histopathology slide analysis. While these strides are promising, current supervised learning approaches for WSI analysis come with the challenge of exhaustively labeling high-resolution slides - a process that is both labor-intensive and time-consuming. In contrast, self-supervised learning (SSL) pretraining strategies are emerging as a viable alternative, given that they don't rely on explicit data annotations. These SSL strategies are quickly bridging the performance disparity with their supervised counterparts. In this context, we introduce an SSL framework. This framework aims for transferable representation learning and semantically meaningful clustering by synergizing invariance loss and clustering loss in WSI analysis. Notably, our approach outperforms common SSL methods in downstream classification and clustering tasks, as evidenced by tests on the Camelyon16 and a pancreatic cancer dataset.

Joseph DiPalma, Arief A. Suriawinata, Laura J. Tafe et al.

Developing deep learning models to analyze histology images has been computationally challenging, as the massive size of the images causes excessive strain on all parts of the computing pipeline. This paper proposes a novel deep learning-based methodology for improving the computational efficiency of histology image classification. The proposed approach is robust when used with images that have reduced input resolution and can be trained effectively with limited labeled data. Pre-trained on the original high-resolution (HR) images, our method uses knowledge distillation (KD) to transfer learned knowledge from a teacher model to a student model trained on the same images at a much lower resolution. To address the lack of large-scale labeled histology image datasets, we perform KD in a self-supervised manner. We evaluate our approach on two histology image datasets associated with celiac disease (CD) and lung adenocarcinoma (LUAD). Our results show that a combination of KD and self-supervision allows the student model to approach, and in some cases, surpass the classification accuracy of the teacher, while being much more efficient. Additionally, we observe an increase in student classification performance as the size of the unlabeled dataset increases, indicating that there is potential to scale further. For the CD data, our model outperforms the HR teacher model, while needing 4 times fewer computations. For the LUAD data, our student model results at 1.25x magnification are within 3% of the teacher model at 10x magnification, with a 64 times computational cost reduction. Moreover, our CD outcomes benefit from performance scaling with the use of more unlabeled data. For 0.625x magnification, using unlabeled data improves accuracy by 4% over the baseline. Thus, our method can improve the feasibility of deep learning solutions for digital pathology with standard computational hardware.