Dennis H. Murphree

Saghir Alfasly, Peyman Nejat, Sobhan Hemati et al.

Recently, several studies have reported on the fine-tuning of foundation models for image-text modeling in the field of medicine, utilizing images from online data sources such as Twitter and PubMed. Foundation models are large, deep artificial neural networks capable of learning the context of a specific domain through training on exceptionally extensive datasets. Through validation, we have observed that the representations generated by such models exhibit inferior performance in retrieval tasks within digital pathology when compared to those generated by significantly smaller, conventional deep networks.

Peyman Nejat, Areej Alsaafin, Ghazal Alabtah et al.

Patching gigapixel whole slide images (WSIs) is an important task in computational pathology. Some methods have been proposed to select a subset of patches as WSI representation for downstream tasks. While most of the computational pathology tasks are designed to classify or detect the presence of pathological lesions in each WSI, the confounding role and redundant nature of normal histology in tissue samples are generally overlooked in WSI representations. In this paper, we propose and validate the concept of an "atlas of normal tissue" solely using samples of WSIs obtained from normal tissue biopsies. Such atlases can be employed to eliminate normal fragments of tissue samples and hence increase the representativeness collection of patches. We tested our proposed method by establishing a normal atlas using 107 normal skin WSIs and demonstrated how established indexes and search engines like Yottixel can be improved. We used 553 WSIs of cutaneous squamous cell carcinoma (cSCC) to show the advantage. We also validated our method applied to an external dataset of 451 breast WSIs. The number of selected WSI patches was reduced by 30% to 50% after utilizing the proposed normal atlas while maintaining the same indexing and search performance in leave-one-patinet-out validation for both datasets. We show that the proposed normal atlas shows promise for unsupervised selection of the most representative patches of the abnormal/malignant WSI lesions.

Anirudh Choudhary, Mosbah Aouad, Krishnakant Saboo et al.

Squamous cell carcinoma (SCC) is the most common cancer subtype, with an increasing incidence and a significant impact on cancer-related mortality. SCC grading using whole slide images is inherently challenging due to the lack of a reliable protocol and substantial tissue heterogeneity. We propose RACR-MIL, the first weakly-supervised SCC grading approach achieving robust generalization across multiple anatomies (skin, head and neck, lung). RACR-MIL is an attention-based multiple-instance learning framework that enhances grade-relevant contextual representation learning and addresses tumor heterogeneity through two key innovations: (1) a hybrid WSI graph that captures both local tissue context and non-local phenotypical dependencies between tumor regions, and (2) a rank-ordering constraint in the attention mechanism that consistently prioritizes higher-grade tumor regions, aligning with pathologists diagnostic process. Our model achieves state-of-the-art performance across multiple SCC datasets, achieving 3-9% higher grading accuracy, resilience to class imbalance, and up to 16% improved tumor localization. In a pilot study, pathologists reported that RACR-MIL improved grading efficiency in 60% of cases, underscoring its potential as a clinically viable cancer diagnosis and grading assistant.

Riya Gupta, Yiwei Zong, Dennis H. Murphree

The rapid generation of whole-slide images (WSIs) in dermatopathology necessitates automated methods for efficient processing and accurate classification. This study evaluates the performance of two foundation models, UNI and Virchow2, as feature extractors for classifying WSIs into three diagnostic categories: melanocytic, basaloid, and squamous lesions. Patch-level embeddings were aggregated into slide-level features using a mean-aggregation strategy and subsequently used to train multiple machine learning classifiers, including logistic regression, gradient-boosted trees, and random forest models. Performance was assessed using precision, recall, true positive rate, false positive rate, and the area under the receiver operating characteristic curve (AUROC) on the test set. Results demonstrate that patch-level features extracted using Virchow2 outperformed those extracted via UNI across most slide-level classifiers, with logistic regression achieving the highest accuracy (90%) for Virchow2, though the difference was not statistically significant. The study also explored data augmentation techniques and image normalization to enhance model robustness and generalizability. The mean-aggregation approach provided reliable slide-level feature representations. All experimental results and metrics were tracked and visualized using WandB.ai, facilitating reproducibility and interpretability. This research highlights the potential of foundation models for automated WSI classification, providing a scalable and effective approach for dermatopathological diagnosis while paving the way for future advancements in slide-level representation learning.

Dennis H. Murphree, Che Ngufor

This manuscript describes our participation in the International Skin Imaging Collaboration's 2017 Skin Lesion Analysis Towards Melanoma Detection competition. We participated in Part 3: Lesion Classification. The two stated goals of this binary image classification challenge were to distinguish between (a) melanoma and (b) nevus and seborrheic keratosis, followed by distinguishing between (a) seborrheic keratosis and (b) nevus and melanoma. We chose a deep neural network approach with a transfer learning strategy, using a pre-trained Inception V3 network as both a feature extractor to provide input for a multi-layer perceptron as well as fine-tuning an augmented Inception network. This approach yielded validation set AUC's of 0.84 on the second task and 0.76 on the first task, for an average AUC of 0.80. We joined the competition unfortunately late, and we look forward to improving on these results.