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Digital Pathology is a cornerstone in the diagnosis and treatment of diseases. A key task in this field is the identification and segmentation of cells in hematoxylin and eosin-stained images. Existing methods for cell segmentation often…

The integration of deep learning based systems in clinical practice is often impeded by challenges rooted in limited and heterogeneous medical datasets. In addition, the field has increasingly prioritized marginal performance gains on a…

In digital pathology, whole slide images (WSIs) are widely used for applications such as cancer diagnosis and prognosis prediction. Visual transformer models have recently emerged as a promising method for encoding large regions of WSIs…

The recent surge of foundation models in computer vision and natural language processing opens up perspectives in utilizing multi-modal clinical data to train large models with strong generalizability. Yet pathological image datasets often…

Accurate segmentation of carotid artery structures in histopathological images is vital for cardiovascular disease research. This study systematically evaluates ten deep learning segmentation models including classical architectures, modern…

Semantic segmentation has a broad range of applications in a variety of domains including land coverage analysis, autonomous driving, and medical image analysis. Convolutional neural networks (CNN) and Vision Transformers (ViTs) provide the…

In this thesis, we study the problem of feature learning on heterogeneous knowledge graphs. These features can be used to perform tasks such as link prediction, classification and clustering on graphs. Knowledge graphs provide rich…

Medical image segmentation plays a crucial role in various healthcare applications, enabling accurate diagnosis, treatment planning, and disease monitoring. Traditionally, convolutional neural networks (CNNs) dominated this domain,…

Multiple instance learning (MIL) is the dominant framework for whole-slide image analysis in computational pathology, typically combining a frozen patch encoder, a projection layer, and a slide-level aggregator. While encoders and…

Colon cancer also known as Colorectal cancer, is one of the most malignant types of cancer worldwide. Early-stage detection of colon cancer is highly crucial to prevent its deterioration. This research presents a hybrid multi-scale deep…

The Encoder-Decoder architecture is a main stream deep learning model for biomedical image segmentation. The encoder fully compresses the input and generates encoded features, and the decoder then produces dense predictions using encoded…

Histopathology remains the gold standard for cancer diagnosis because it provides detailed cellular-level assessment of tissue morphology. However, manual histopathological examination is time-consuming, labour-intensive, and subject to…

Vision transformers (ViTs) that model an image as a sequence of partitioned patches have shown notable performance in diverse vision tasks. Because partitioning patches eliminates the image structure, to reflect the order of patches, ViTs…

In biomedical imaging, deep learning-based methods are state-of-the-art for every modality (virtual slides, MRI, etc.) In histopathology, these methods can be used to detect certain biomarkers or classify lesions. However, such techniques…

Image segmentation is often ambiguous at the level of individual image patches and requires contextual information to reach label consensus. In this paper we introduce Segmenter, a transformer model for semantic segmentation. In contrast to…

Vision foundation models trained on discretely sampled images achieve strong performance on classification benchmarks, yet whether their representations encode the continuous processes underlying their training data remains unclear. This…

Large vision foundation models have been widely adopted for retinal disease classification without systematic evidence justifying their parameter requirements. In the present work we address two critical questions: First, are large…

Purpose: Accurate identification of hepatocystic anatomy is critical to preventing surgical complications during laparoscopic cholecystectomy. Deep learning models often struggle with occlusions, long-range dependencies, and capturing the…

Vision Transformers (ViT) have recently brought a new wave of research in the field of computer vision. These models have performed particularly well in image classification and segmentation. Research on semantic and instance segmentation…

Recent studies have demonstrated the superiority of deep learning in medical image analysis, especially in cell instance segmentation, a fundamental step for many biological studies. However, the excellent performance of the neural networks…