Related papers: Phylogenetic quantification of intra-tumour hetero…
Intratumor heterogeneity is often manifested by vascular compartments with distinct pharmacokinetics that cannot be resolved directly by in vivo dynamic imaging. We developed tissue-specific compartment modeling (TSCM), an unsupervised…
Ovarian cancer remains one of the most lethal gynecological malignancies, largely due to late diagnosis and extensive heterogeneity across subtypes. Current diagnostic methods are limited in their ability to reveal underlying genomic…
The reconstruction of phylogenetic trees from mixed populations has become important in the study of cancer evolution, as sequencing is often performed on bulk tumor tissue containing mixed populations of cells. Recent work has shown how to…
Explicit accounting for copy number alterations can dramatically improve mutation frequency estimates, leading to more accurate phylogeny reconstructions and subclone characterizations.
Cancer is one of the most feared diseases in the world it has increased disturbingly and breast cancer occurs in one out of eight women, the prediction of malignancies plays essential roles not only in revealing human genome, but also in…
The overexpression of the human epidermal growth factor receptor 2 (HER2) in breast cells is a key driver of HER2-positive breast cancer, a highly aggressive subtype requiring precise diagnosis and targeted therapy. Immunohistochemistry…
Cancer results from genetic alterations that disturb the normal cooperative behavior of cells. Recent high-throughput genomic studies of cancer cells have shown that the mutational landscape of cancer is complex and that individual cancers…
We pursue a computational analysis of the biomedical problem on the identification of the cancerous tumor at an early stage of development based on the Electrical Impedance Tomography (EIT) and optimal control of elliptic partial…
Immunohistochemical (IHC) staining provides crucial molecular characterization of tissue samples and plays an indispensable role in the clinical examination and diagnosis of cancers. However, compared with the commonly used Hematoxylin and…
Breast cancer, the most common malignancy among women, requires precise detection and classification for effective treatment. Immunohistochemistry (IHC) biomarkers like HER2, ER, and PR are critical for identifying breast cancer subtypes.…
We consider the phylogenetic tree reconstruction problem with insertions and deletions (indels). Phylogenetic algorithms proceed under a model where sequences evolve down the model tree, and given sequences at the leaves, the problem is to…
Histopathology remains the gold standard for cancer diagnosis and prognosis. With the advent of transcriptome profiling, multi-modal learning combining transcriptomics with histology offers more comprehensive information. However, existing…
Despite advancements in methodologies, immunohistochemistry (IHC) remains the most utilized ancillary test for histopathologic and companion diagnostics in targeted therapies. However, objective IHC assessment poses challenges. Artificial…
We develop a feature allocation model for inference on genetic tumor variation using next-generation sequencing data. Specifically, we record single nucleotide variants (SNVs) based on short reads mapped to human reference genome and…
We present an individual-based model for the coevolutionary dynamics between CD8+ cytotoxic T lymphocytes (CTLs) and tumour cells. In this model, every cell is viewed as an individual agent whose phenotypic state is modelled by a discrete…
This paper presents a novel approach to accurately classify the hallmarks of cancer, which is a crucial task in cancer research. Our proposed method utilizes the Bidirectional Encoder Representations from Transformers (BERT) architecture,…
Breast cancer remains a critical global health challenge, necessitating early and accurate detection for effective treatment. This paper introduces a methodology that combines automated image augmentation selection (RandAugment) with search…
Resistance to chemotherapies, particularly to anticancer treatments, is an increasing medical concern. Among the many mechanisms at work in cancers, one of the most important is the selection of tumor cells expressing resistance genes or…
Foundation models (FMs) have demonstrated strong performance across diverse pathology tasks. While there are similarities in the pre-training objectives of FMs, there is still limited understanding of their complementarity, redundancy in…
The density of mitotic figures within tumor tissue is known to be highly correlated with tumor proliferation and thus is an important marker in tumor grading. Recognition of mitotic figures by pathologists is known to be subject to a strong…