arXiv subjects

Dennis Murphree

Publications and source records attributed to Dennis Murphree.

3 recordsLinked to original sources

arXiv2023

Creating an Atlas of Normal Tissue for Pruning WSI Patching Through Anomaly Detection

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.

eess.IV↗

arXiv2023

When is a Foundation Model a Foundation Model

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.

cs.IR↗

arXiv2023

RACR-MIL: Rank-aware contextual reasoning for weakly supervised grading of squamous cell carcinoma using whole slide images

Squamous cell carcinoma (SCC) is one of 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 standardized grading protocol and substantial tissue heterogeneity. We propose RACR-MIL, a weakly-supervised SCC grading approach that achieves robust generalization across multiple anatomies (skin, head & neck, lung). RACR-MIL is an attention-based multiple-instance learning framework that introduces two key innovations for learning grade-specific contextual representations: (1) a hybrid WSI graph that captures both local tissue context and non-local phenotypic dependencies between tumor regions, and (2) rank-ordering constraints on the attention mechanism that encourage consistent prioritization of higher-grade tumor regions and improve region-level grade confidence, aligning with pathologist's diagnostic process. Our model achieves state-of-the-art performance across multiple SCC datasets, achieving 3-9% improvements over existing methods and up to 10% improvement in 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.

cs.CV↗