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Understanding how deep learning models predict oncology patient risk can provide critical insights into disease progression, support clinical decision-making, and pave the way for trustworthy and data-driven precision medicine. Building on…

Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence,…

Deep learning based approaches to Computer Aided Diagnosis (CAD) typically pose the problem as an image classification (Normal or Abnormal) problem. These systems achieve high to very high accuracy in specific disease detection for which…

Graph Neural Networks (GNNs) achieve outstanding performance across graph-based tasks but remain difficult to interpret. In this paper, we revisit foundational assumptions underlying model-level explanation methods for GNNs, namely: (1)…

Graph Neural Networks (GNNs) have shown remarkable success in molecular tasks, yet their interpretability remains challenging. Traditional model-level explanation methods like XGNN and GNNInterpreter often fail to identify valid…

Deep neural networks (DNNs) achieve state-of-the-art performance on many tasks, but this often requires increasingly larger model sizes, which in turn leads to more complex internal representations. Explainability techniques (XAI) have made…

Graphical model estimation from multi-omics data requires a balance between statistical estimation performance and computational scalability. We introduce a novel pseudolikelihood-based graphical model framework that reparameterizes the…

Graph Transformers (GTs) have emerged as powerful architectures for graph-structured data, yet remain constrained by rigid designs and lack quantifiable interpretability. Current state-of-the-art GTs commit to fixed GNN types across all…

Malignant lymphoma subtype classification directly impacts treatment strategies and patient outcomes, necessitating classification models that achieve both high accuracy and sufficient explainability. This study proposes a novel explainable…

The exploration of Graph Neural Networks (GNNs) for processing graph-structured data has expanded, particularly their potential for causal analysis due to their universal approximation capabilities. Anticipated to significantly enhance…

Artificial intelligence methods including deep neural networks (DNN) can provide rapid molecular classification of tumors from routine histology with accuracy that matches or exceeds human pathologists. Discerning how neural networks make…

Cancer diagnosis, prognosis, and therapy response predictions from tissue specimens highly depend on the phenotype and topological distribution of constituting histological entities. Thus, adequate tissue representations for encoding…

Explainability is crucial for the application of black-box Graph Neural Networks (GNNs) in critical fields such as healthcare, finance, cybersecurity, and more. Various feature attribution methods, especially the perturbation-based methods,…

Graph neural networks (GNNs) have witnessed an unprecedented proliferation in tackling several problems in computer vision, computer-aided diagnosis, and related fields. While prior studies have focused on boosting the model accuracy,…

Pathologic analysis of surgical excision specimens for breast carcinoma is important to evaluate the completeness of surgical excision and has implications for future treatment. This analysis is performed manually by pathologists reviewing…

Graph Neural Networks (GNNs) have become a powerful tool for modeling and analyzing data with graph structures. The wide adoption in numerous applications underscores the value of these models. However, the complexity of these methods often…

Control Flow Graphs and Function Call Graphs have become pivotal in providing a detailed understanding of program execution and effectively characterizing the behavior of malware. These graph-based representations, when combined with Graph…

The accurate automatic segmentation of gliomas and its intra-tumoral structures is important not only for treatment planning but also for follow-up evaluations. Several methods based on 2D and 3D Deep Neural Networks (DNN) have been…

Explanations in a recommender system assist users in making informed decisions among a set of recommended items. Great research attention has been devoted to generating natural language explanations to depict how the recommendations are…

The heterogeneity of breast cancer presents considerable challenges for its early detection, prognosis, and treatment selection. Convolutional neural networks often neglect the spatial relationships within histopathological images, which…