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PURPOSE: Deep learning methods for classifying prostate cancer (PCa) in ultrasound images typically employ convolutional networks (CNNs) to detect cancer in small regions of interest (ROI) along a needle trace region. However, this approach…

Cancer is an epidemic worldwide. At present one in four persons has cancer and this statistic will change to one in a two person in the near future. It is now known that war against cancer is the early, curable detection and treatment.…

Determining the primary site of origin for metastatic tumors is one of the open problems in cancer care because the efficacy of treatment often depends on the cancer tissue of origin. Classification methods that can leverage tumor genomic…

Magnetic Resonance Imaging (MRI) is widely used for screening and staging prostate cancer. However, many prostate cancers have subtle features which are not easily identifiable on MRI, resulting in missed diagnoses and alarming variability…

We present a new method for exploring cancer gene expression data based on tools from algebraic topology. Our method selects a small relevant subset from tens of thousands of genes while simultaneously identifying nontrivial higher order…

DNA Methylation has been the most extensively studied epigenetic mark. Usually a change in the genotype, DNA sequence, leads to a change in the phenotype, observable characteristics of the individual. But DNA methylation, which happens in…

As Deep Convolutional Neural Networks (DCNNs) have shown robust performance and results in medical image analysis, a number of deep-learning-based tumor detection methods were developed in recent years. Nowadays, the automatic detection of…

While deep learning approaches have shown remarkable performance in many imaging tasks, most of these methods rely on availability of large quantities of data. Medical image data, however, is scarce and fragmented. Generative Adversarial…

A tumor often consists of multiple cell subpopulations (clones). Current chemo-treatments often target one clone of a tumor. Although the drug kills that clone, other clones overtake it and the tumor reoccurs. Genome sequencing and…

Research on the localization of the genetic basis associated with diseases or traits has been widely conducted in the last a few decades. Scan methods have been developed for region-based analysis in whole-genome association studies,…

Segmentation of regions of interest (ROIs) for identifying abnormalities is a leading problem in medical imaging. Using machine learning for this problem generally requires manually annotated ground-truth segmentations, demanding extensive…

Signet ring cell carcinoma is a type of rare adenocarcinoma with poor prognosis. Early detection leads to huge improvement of patients' survival rate. However, pathologists can only visually detect signet ring cells under the microscope.…

Motivation: Standard genome-wide association studies in cancer genomics rely on statistical significance with multiple testing correction, but systematically fail in underpowered cohorts. In TCGA breast cancer (n=967, 133 deaths), low event…

Cancer ranks as one of the deadliest diseases worldwide. The high mortality rate associated with cancer is partially due to the lack of reliable early detection methods and/or inaccurate diagnostic tools such as certain protein biomarkers.…

The spread of metastases is a crucial process in which some questions remain unanswered. In this work, we focus on tumor cells circulating in the bloodstream, the so-called Circulating Tumor Cells (CTCs). Our aim is to characterize their…

The annotated medical images are usually expensive to be collected. This paper proposes a deep learning method on small data to classify Common Imaging Signs of Lung diseases (CISL) in computed tomography (CT) images. We explore both the…

Several machine learning techniques for accurate detection of skin cancer from medical images have been reported. Many of these techniques are based on pre-trained convolutional neural networks (CNNs), which enable training the models based…

Advancing the discovery of prognostic cancer biomarkers is crucial for comprehending disease mechanisms, refining treatment plans, and improving patient outcomes. This study introduces Weighted Gene Topological Data Analysis (WGTDA), an…

The past years have seen a considerable increase in cancer cases. However, a cancer diagnosis is often complex and depends on the types of images provided for analysis. It requires highly skilled practitioners but is often time-consuming…

Non-small cell lung cancer (NSCLC) is a serious disease and has a high recurrence rate after the surgery. Recently, many machine learning methods have been proposed for recurrence prediction. The methods using gene data have high prediction…