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Identifying genes underlying cancer development is critical to cancer biology and has important implications across prevention, diagnosis and treatment. Cancer sequencing studies aim at discovering genes with high frequencies of somatic…
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…
With recent advancements in the development of artificial intelligence applications using theories and algorithms in machine learning, many accurate models can be created to train and predict on given datasets. With the realization of the…
Imaging in clinical oncology trials provides a wealth of information that contributes to the drug development process, especially in early phase studies. This paper focuses on kinetic modeling in DCE-MRI, inspired by mixed-effects models…
Graphical models are commonly used to discover associations within gene or protein networks for complex diseases such as cancer. Most existing methods estimate a single graph for a population, while in many cases, researchers are interested…
An important task in drug development is to identify patients, which respond better or worse to an experimental treatment. Identifying predictive covariates, which influence the treatment effect and can be used to define subgroups of…
The emerging field of precision oncology relies on the accurate pinpointing of alterations in the molecular profile of a tumor to provide personalized targeted treatments. Current methodologies in the field commonly include the application…
Cancers are complex adaptive diseases regulated by the nonlinear feedback systems between genetic instabilities, environmental signals, cellular protein flows, and gene regulatory networks. Understanding the cybernetics of cancer requires…
Quantifying the dynamics of tumor burden reveals useful information about cancer evolution concerning treatment effects and drug resistance, which play a crucial role in advancing model-informed drug developments (MIDD) towards personalized…
Determining the extent to which a patient is benefiting from cancer therapy is challenging. Criteria for quantifying the extent of "tumor response" observed within a few cycles of treatment have been established for various types of solid…
Bayes linear kinematics and Bayes linear Bayes graphical models provide an extension of Bayes linear methods so that full conditional updates may be combined with Bayes linear belief adjustment. In this paper we investigate the application…
In a mathematical model of interacting biological organisms, where external interventions may alter behavior over time, traditional models that assume fixed parameters usually do not capture the evolving dynamics. In oncology, this is…
High-dimensional variable selection, with many more covariates than observations, is widely documented in standard regression models, but there are still few tools to address it in non-linear mixed-effects models where data are collected…
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…
Gene and protein networks are very important to model complex large-scale systems in molecular biology. Inferring or reverseengineering such networks can be defined as the process of identifying gene/protein interactions from experimental…
In this article, we present a Bayesian hierarchical model for predicting a latent health state from longitudinal clinical measurements. Model development is motivated by the need to integrate multiple sources of data to improve clinical…
Convolutional neural networks (CNNs) provide flexible function approximations for a wide variety of applications when the input variables are in the form of images or spatial data. Although CNNs often outperform traditional statistical…
Predicting cancer-associated clinical events is challenging in oncology. In Multiple Myeloma (MM), a cancer of plasma cells, disease progression is determined by changes in biomarkers, such as serum concentration of the paraprotein secreted…
Targeted therapies on the basis of genomic aberrations analysis of the tumor have shown promising results in cancer prognosis and treatment. Regardless of tumor type, trials that match patients to targeted therapies for their particular…
We propose a general Bayesian network model for application in a wide class of problems of therapy monitoring. We discuss the use of stochastic simulation as a computational approach to inference on the proposed class of models. As an…