Related papers: A Weighted Exact Test for Mutually Exclusive Mutat…
Mutational signature analysis has emerged as a powerful method for uncovering the underlying biological processes driving cancer development. However, the signature extraction process, typically performed using non-negative matrix…
Plausibility is a formalization of exact tests for parametric models and generalizes procedures such as Fisher's exact test. The resulting tests are based on cumulative probabilities of the probability density function and evaluate…
Somatic mutations, or alterations in DNA of a somatic cell, are key markers of cancer. In recent years, mutational signature analysis has become a prominent field of study within cancer research, commonly with Nonnegative Matrix…
Multi-gene panel testing allows efficient detection of pathogenic variants in cancer susceptibility genes including moderate-risk genes such as ATM and PALB2. A growing number of studies examine the risk of breast cancer (BC) conferred by…
Quantum machine learning integrates the strengths of quantum computing and machine learning, enabling models to learn complex features using fewer parameters than their classical counterparts. Due to the increasing complexity of quantum…
Motivation: A branching processes model yields an unevenly stochastically distributed dataset that consists of sparse and dense regions. This work addresses the problem of precisely evaluating parameters for such a model. Applying a…
The goal of cancer genome sequencing projects is to determine the genetic alterations that cause common cancers. Many malignancies arise during the clonal expansion of a benign tumor which motivates the study of recurrent selective sweeps…
Synthetic lethality refers to a combination of two or more genetic events (typically affecting different genes) in which the co-occurrence of the events results in cell or organismal lethality, but the cell or organism remains viable when…
Single-cell technologies have revolutionized biomedical research by enabling scalable measurement of the genome, transcriptome, and proteome of multiple systems at single-cell resolution. Now widely applied to cancer models, these assays…
There is multiple databases contain datasets of TP53 gene and its tumor protein P53 which believed to be involved in over 50% of human cancers cases, these databases are rich as datasets covered all mutations caused diseases (cancers), but…
Molecular testing of tumor samples for targetable biomarkers is restricted by a lack of standardization, turnaround-time, cost, and tissue availability across cancer types. Additionally, targetable alterations of low prevalence may not be…
Machine Translation Quality Estimation is a notoriously difficult task, which lessens its usefulness in real-world translation environments. Such scenarios can be improved if quality predictions are accompanied by a measure of uncertainty.…
Cancer pathology is unique to a given individual, and developing personalized diagnostic and treatment protocols are a primary concern. Mathematical modeling and simulation is a promising approach to personalized cancer medicine. Yet, the…
Cancer progression is driven by a small number of genetic alterations accumulating in a neoplasm. These few driver alterations reside in a cancer genome alongside tens of thousands of other mutations that are widely believed to have no role…
Certain cancer types, notably pancreatic cancer, are difficult to detect at an early stage, motivating robust biomarker-based screening. Liquid biopsies enable non-invasive monitoring of circulating biomarkers, but typical machine learning…
Survival models are used in various fields, such as the development of cancer treatment protocols. Although many statistical and machine learning models have been proposed to achieve accurate survival predictions, little attention has been…
A number of biomedical problems require performing many hypothesis tests, with an attendant need to apply stringent thresholds. Often the data take the form of a series of predictor vectors, each of which must be compared with a single…
In the search for genetic factors that are associated with complex heritable human traits, considerable attention is now being focused on rare variants that individually have small effects. In response, numerous recent papers have proposed…
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…
In a variety of application areas, there is interest in assessing evidence of differences in the intensity of event realizations between groups. For example, in cancer genomic studies collecting data on rare variants, the focus is on…