Goto

Collaborating Authors

 histopathology image





SENCA-st: Integrating Spatial Transcriptomics and Histopathology with Cross Attention Shared Encoder for Region Identification in Cancer Pathology

Liyanaarachchi, Shanaka, Wijethunga, Chathurya, Ahamed, Shihab Aaqil, Absar, Akthas, Rodrigo, Ranga

arXiv.org Artificial Intelligence

Spatial transcriptomics is an emerging field that enables the identification of functional regions based on the spatial distribution of gene expression. Integrating this functional information present in transcriptomic data with structural data from histopathology images is an active research area with applications in identifying tumor substructures associated with cancer drug resistance. Current histopathology-spatial-transcriptomic region segmentation methods suffer due to either making spatial transcriptomics prominent by using histopathology features just to assist processing spatial transcriptomics data or using vanilla contrastive learning that make histopathology images prominent due to only promoting common features losing functional information. In both extremes, the model gets either lost in the noise of spatial transcriptomics or overly smoothed, losing essential information. Thus, we propose our novel architecture SENCA-st (Shared Encoder with Neighborhood Cross Attention) that preserves the features of both modalities. More importantly, it emphasizes regions that are structurally similar in histopathology but functionally different on spatial transcriptomics using cross-attention. We demonstrate the superior performance of our model that surpasses state-of-the-art methods in detecting tumor heterogeneity and tumor micro-environment regions, a clinically crucial aspect.





Towards Human-AI Collaboration System for the Detection of Invasive Ductal Carcinoma in Histopathology Images

Han, Shuo, Eldaly, Ahmed Karam, Oyelere, Solomon Sunday

arXiv.org Artificial Intelligence

Invasive ductal carcinoma (IDC) is the most prevalent form of breast cancer, and early, accurate diagnosis is critical to improving patient survival rates by guiding treatment decisions. Combining medical expertise with artificial intelligence (AI) holds significant promise for enhancing the precision and efficiency of IDC detection. In this work, we propose a human-in-the-loop (HITL) deep learning system designed to detect IDC in histopathology images. The system begins with an initial diagnosis provided by a high-performance EfficientNetV2S model, offering feedback from AI to the human expert. Medical professionals then review the AI-generated results, correct any misclassified images, and integrate the revised labels into the training dataset, forming a feedback loop from the human back to the AI. This iterative process refines the model's performance over time. The EfficientNetV2S model itself achieves state-of-the-art performance compared to existing methods in the literature, with an overall accuracy of 93.65\%. Incorporating the human-in-the-loop system further improves the model's accuracy using four experimental groups with misclassified images. These results demonstrate the potential of this collaborative approach to enhance AI performance in diagnostic systems. This work contributes to advancing automated, efficient, and highly accurate methods for IDC detection through human-AI collaboration, offering a promising direction for future AI-assisted medical diagnostics.


NuSeC: A Dataset for Nuclei Segmentation in Breast Cancer Histopathology Images

Samet, Refik, Nemati, Nooshin, Hancer, Emrah, Sak, Serpil, Kirmizi, Bilge Ayca

arXiv.org Artificial Intelligence

Prof. Dr. Bilge Ayca Kirmizi, akarabork@yahoo.com 1 Introduction Breast cancer is the most frequently diagnosed form of cancer and is the second leading cause of death caused by cancer in women. In order to diagnose breast cancer type, stage, and grade accurately, examination of tissue biopsies and operation specimens is necessary. The biopsy specimens must be fixed embedded in paraffin blocks, mounted on glass slides and stained. Hematoxylin and Eosin (H&E), is a routine stain used in pathology laboratories all over the globe, which gives a good contrast of a tissue section and is commonly used to identify nuclei and cytoplasm [1]. Nevertheless, histopathological examination of the prapared slides involves laborious, time - consuming processes that are limited by specimen quality and pathologist experience.


DLiPath: A Benchmark for the Comprehensive Assessment of Donor Liver Based on Histopathological Image Dataset

Pan, Liangrui, Li, Xingchen, Chen, Zhongyi, Chu, Ling, Peng, Shaoliang

arXiv.org Artificial Intelligence

Pathologists comprehensive evaluation of donor liver biopsies provides crucial information for accepting or discarding potential grafts. However, rapidly and accurately obtaining these assessments intraoperatively poses a significant challenge for pathologists. Features in donor liver biopsies, such as portal tract fibrosis, total steatosis, macrovesicular steatosis, and hepatocellular ballooning are correlated with transplant outcomes, yet quantifying these indicators suffers from substantial inter- and intra-observer variability. To address this, we introduce DLiPath, the first benchmark for comprehensive donor liver assessment based on a histopathology image dataset. We collected and publicly released 636 whole slide images from 304 donor liver patients at the Department of Pathology, the Third Xiangya Hospital, with expert annotations for key pathological features (including cholestasis, portal tract fibrosis, portal inflammation, total steatosis, macrovesicular steatosis, and hepatocellular ballooning). We selected nine state-of-the-art multiple-instance learning (MIL) models based on the DLiPath dataset as baselines for extensive comparative analysis. The experimental results demonstrate that several MIL models achieve high accuracy across donor liver assessment indicators on DLiPath, charting a clear course for future automated and intelligent donor liver assessment research. Data and code are available at https://github.com/panliangrui/ACM_MM_2025.