Sheida Nabavi

Mohammad Mahdi Behzadi, Mohammad Madani, Hanzhang Wang et al.

Prostate cancer is the most common cancer in men worldwide and the second leading cause of cancer death in the United States. One of the prognostic features in prostate cancer is the Gleason grading of histopathology images. The Gleason grade is assigned based on tumor architecture on Hematoxylin and Eosin (H&E) stained whole slide images (WSI) by the pathologists. This process is time-consuming and has known interobserver variability. In the past few years, deep learning algorithms have been used to analyze histopathology images, delivering promising results for grading prostate cancer. However, most of the algorithms rely on the fully annotated datasets which are expensive to generate. In this work, we proposed a novel weakly-supervised algorithm to classify prostate cancer grades. The proposed algorithm consists of three steps: (1) extracting discriminative areas in a histopathology image by employing the Multiple Instance Learning (MIL) algorithm based on Transformers, (2) representing the image by constructing a graph using the discriminative patches, and (3) classifying the image into its Gleason grades by developing a Graph Convolutional Neural Network (GCN) based on the gated attention mechanism. We evaluated our algorithm using publicly available datasets, including TCGAPRAD, PANDA, and Gleason 2019 challenge datasets. We also cross validated the algorithm on an independent dataset. Results show that the proposed model achieved state-of-the-art performance in the Gleason grading task in terms of accuracy, F1 score, and cohen-kappa. The code is available at https://github.com/NabaviLab/Prostate-Cancer.

Bingjun Li, Sheida Nabavi

The recent development of high-throughput sequencing creates a large collection of multi-omics data, which enables researchers to better investigate cancer molecular profiles and cancer taxonomy based on molecular subtypes. Integrating multi-omics data has been proven to be effective for building more precise classification models. Current multi-omics integrative models mainly use early fusion by concatenation or late fusion based on deep neural networks. Due to the nature of biological systems, graphs are a better representation of bio-medical data. Although few graph neural network (GNN) based multi-omics integrative methods have been proposed, they suffer from three common disadvantages. One is most of them use only one type of connection, either inter-omics or intra-omic connection; second, they only consider one kind of GNN layer, either graph convolution network (GCN) or graph attention network (GAT); and third, most of these methods lack testing on a more complex cancer classification task. We propose a novel end-to-end multi-omics GNN framework for accurate and robust cancer subtype classification. The proposed model utilizes multi-omics data in the form of heterogeneous multi-layer graphs that combines both inter-omics and intra-omic connections from established biological knowledge. The proposed model incorporates learned graph features and global genome features for accurate classification. We test the proposed model on TCGA Pan-cancer dataset and TCGA breast cancer dataset for molecular subtype and cancer subtype classification, respectively. The proposed model outperforms four current state-of-the-art baseline models in multiple evaluation metrics. The comparative analysis of GAT-based models and GCN-based models reveals that GAT-based models are preferred for smaller graphs with less information and GCN-based models are preferred for larger graphs with extra information.

Masum Shah Junayed, John Derek Van Vessem, Qian Wan et al.

Prostate cancer grading from whole-slide images (WSIs) remains a challenging task due to the large-scale nature of WSIs, the presence of heterogeneous tissue structures, and difficulty of selecting diagnostically relevant regions. Existing approaches often rely on random or static patch selection, leading to the inclusion of redundant or non-informative regions that degrade performance. To address this, we propose a Graph Laplacian Attention-Based Transformer (GLAT) integrated with an Iterative Refinement Module (IRM) to enhance both feature learning and spatial consistency. The IRM iteratively refines patch selection by leveraging a pretrained ResNet50 for local feature extraction and a foundation model in no-gradient mode for importance scoring, ensuring only the most relevant tissue regions are preserved. The GLAT models tissue-level connectivity by constructing a graph where patches serve as nodes, ensuring spatial consistency through graph Laplacian constraints and refining feature representations via a learnable filtering mechanism that enhances discriminative histological structures. Additionally, a convex aggregation mechanism dynamically adjusts patch importance to generate a robust WSI-level representation. Extensive experiments on five public and one private dataset demonstrate that our model outperforms state-of-the-art methods, achieving higher performance and spatial consistency while maintaining computational efficiency.

Josué Martínez-Martínez, Olivia Brown, Mostafa Karami et al.

Deep neural networks are increasingly being used to detect and diagnose medical conditions using medical imaging. Despite their utility, these models are highly vulnerable to adversarial attacks and distribution shifts, which can affect diagnostic reliability and undermine trust among healthcare professionals. In this study, we propose a robust training algorithm with data augmentation (RTDA) to mitigate these vulnerabilities in medical image classification. We benchmark classifier robustness against adversarial perturbations and natural variations of RTDA and six competing baseline techniques, including adversarial training and data augmentation approaches in isolation and combination, using experimental data sets with three different imaging technologies (mammograms, X-rays, and ultrasound). We demonstrate that RTDA achieves superior robustness against adversarial attacks and improved generalization performance in the presence of distribution shift in each image classification task while maintaining high clean accuracy.

Bingjun Li, Mostafa Karami, Masum Shah Junayed et al.

Understanding the intricate cellular environment within biological tissues is crucial for uncovering insights into complex biological functions. While single-cell RNA sequencing has significantly enhanced our understanding of cellular states, it lacks the spatial context necessary to fully comprehend the cellular environment. Spatial transcriptomics (ST) addresses this limitation by enabling transcriptome-wide gene expression profiling while preserving spatial context. One of the principal challenges in ST data analysis is spatial clustering, which reveals spatial domains based on the spots within a tissue. Modern ST sequencing procedures typically include a high-resolution histology image, which has been shown in previous studies to be closely connected to gene expression profiles. However, current spatial clustering methods often fail to fully integrate high-resolution histology image features with gene expression data, limiting their ability to capture critical spatial and cellular interactions. In this study, we propose the spatial transcriptomics multi-modal clustering (stMMC) model, a novel contrastive learning-based deep learning approach that integrates gene expression data with histology image features through a multi-modal parallel graph autoencoder. We tested stMMC against four state-of-the-art baseline models: Leiden, GraphST, SpaGCN, and stLearn on two public ST datasets with 13 sample slices in total. The experiments demonstrated that stMMC outperforms all the baseline models in terms of ARI and NMI. An ablation study further validated the contributions of contrastive learning and the incorporation of histology image features.

Jun Bai, Annie Jin, Madison Adams et al.

Breast cancer continues to be a significant cause of mortality among women globally. Timely identification and precise diagnosis of breast abnormalities are critical for enhancing patient prognosis. In this study, we focus on improving the early detection and accurate diagnosis of breast abnormalities, which is crucial for improving patient outcomes and reducing the mortality rate of breast cancer. To address the limitations of traditional screening methods, a novel unsupervised feature correlation network was developed to predict maps indicating breast abnormal variations using longitudinal 2D mammograms. The proposed model utilizes the reconstruction process of current year and prior year mammograms to extract tissue from different areas and analyze the differences between them to identify abnormal variations that may indicate the presence of cancer. The model is equipped with a feature correlation module, an attention suppression gate, and a breast abnormality detection module that work together to improve the accuracy of the prediction. The proposed model not only provides breast abnormal variation maps, but also distinguishes between normal and cancer mammograms, making it more advanced compared to the state-of the-art baseline models. The results of the study show that the proposed model outperforms the baseline models in terms of Accuracy, Sensitivity, Specificity, Dice score, and cancer detection rate.