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We propose a novel computational framework leveraging hypergraph theory to analyse cancer stem cell markers (CSCMs) across multiple organs. Hypergraphs provide a robust representation of CSCM co-expression patterns, capturing their complex…
Histopathological images are widely used for the analysis of diseased (tumor) tissues and patient treatment selection. While the majority of microscopy image processing was previously done manually by pathologists, recent advances in…
Camouflaged object detection (COD) aims to identify objects in images that are well hidden in the environment due to their high similarity to the background in terms of texture and color. However, existing most boundary-guided camouflage…
We investigate the design of an entire mobile imaging system for early detection of melanoma. Different from previous work, we focus on smartphone-captured visible light images. Our design addresses two major challenges. First, images…
The diagnosis of cancer is mainly performed by visual analysis of the pathologists, through examining the morphology of the tissue slices and the spatial arrangement of the cells. If the microscopic image of a specimen is not stained, it…
High-throughput omics profiling advancements have greatly enhanced cancer patient stratification. However, incomplete data in multi-omics integration presents a significant challenge, as traditional methods like sample exclusion or…
This research introduces a sophisticated transfer learning model based on Google's MobileNetV2 for breast cancer tumor classification into normal, benign, and malignant categories, utilizing a dataset of 1576 ultrasound images (265 normal,…
Breast cancer is the most common cancer among women worldwide. The human epidermal growth factor receptor 2 (HER2) with immunohistochemical (IHC) is widely used for pathological evaluation to provide the appropriate therapy for patients…
Motivation: The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is…
The genomic profile underlying an individual tumor can be highly informative in the creation of a personalized cancer treatment strategy for a given patient; a practice known as precision oncology. This involves next generation sequencing…
A central goal in cancer genomics is to identify the somatic alterations that underpin tumor initiation and progression. This task is challenging as the mutational profiles of cancer genomes exhibit vast heterogeneity, with many alterations…
Skin cancer is a highly dangerous type of cancer that requires an accurate diagnosis from experienced physicians. To help physicians diagnose skin cancer more efficiently, a computer-aided diagnosis (CAD) system can be very helpful. In this…
Sequence alignment data is often ordered by coordinate (id of the reference sequence plus position on the sequence where the fragment was mapped) when stored in BAM files, as this simplifies the extraction of variants between the mapped…
At present it is still quite difficult to match the vast knowledge on the behavior of individual tumor cells with macroscopic measurements on clinical tumors. On the modeling side, we already know how to deal with many molecular pathways…
Motivation: Manual curation of genome-scale reconstructions is laborious, yet existing automated curation tools typically do not take species-specific experimental data and manually refined genome annotations into account. Results: We…
In cancer research, high-throughput profiling has been extensively conducted. In recent studies, the integrative analysis of data on multiple cancer patient groups/subgroups has been conducted. Such analysis has the potential to reveal the…
This work introduces a new software package `Sesame' for the numerical computation of classical semiconductor equations. It supports 1 and 2-dimensional systems and provides tools to easily implement extended defects such as grain…
We describe a software toolbox for the configuration of deep neural networks in the domain of skin cancer classification. The implemented software architecture allows developers to quickly set up new convolutional neural network (CNN)…
When investigating a malicious file, searching for related files is a common task that malware analysts must perform. Given that production malware corpora may contain over a billion files and consume petabytes of storage, many feature…
Genomic aberrations, such as somatic copy number alterations, are frequently observed in tumor tissue. Recurrent aberrations, occurring in the same region across multiple subjects, are of interest because they may highlight genes associated…