Related papers: Bayesian Cox model with graph-structured variable …

Cancer is a highly heterogeneous disease with significant variability in molecular features and clinical outcomes, making diagnosis and treatment challenging. In recent years, high-throughput omic technologies have facilitated the discovery…

Bayesian nonparametric mixtures and random partition models are powerful tools for probabilistic clustering. However, standard independent mixture models can be restrictive in some applications such as inference on cell lineage due to the…

We propose the molecular omics network (MOOMIN) a multimodal graph neural network used by AstraZeneca oncologists to predict the synergy of drug combinations for cancer treatment. Our model learns drug representations at multiple scales…

We consider the problem of learning a conditional Gaussian graphical model in the presence of latent variables. Building on recent advances in this field, we suggest a method that decomposes the parameters of a conditional Markov random…

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…

Glioblastoma is profoundly heterogeneous in microstructure and vasculature, which may lead to tumor regional diversity and distinct treatment response. Although successful in tumor sub-region segmentation and survival prediction, radiomics…

McCullagh and Yang (2006) suggest a family of classification algorithms based on Cox processes. We further investigate the log Gaussian variant which has a number of appealing properties. Conditioned on the covariates, the distribution over…

Several statistical models used in genome-wide prediction assume independence of marker allele substitution effects, but it is known that these effects might be correlated. In statistics, graphical models have been identified as a useful…

Variable selection has played a critical role in modern statistical learning and scientific discoveries. Numerous regularization and Bayesian variable selection methods have been developed in the past two decades for variable selection, but…

Graphical models or networks describe the statistical dependence among multiple variables and are widely used in biology (e.g., gene regulatory networks). Under appropriate assumptions, directed edges may represent causal relationships. A…

High dimensional and heterogeneous count data are collected in various applied fields. In this paper, we look closely at high-resolution sequencing data on the microbiome, which have enabled researchers to study the genomes of entire…

The problem of joint estimation of multiple graphical models from high dimensional data has been studied in the statistics and machine learning literature, due to its importance in diverse fields including molecular biology, neuroscience…

Time-to-event endpoints are frequently used as outcomes in oncology and other disease areas where the outcome of interest may not be observed within a predetermined period. Although many analytical methods address the challenges of…

Multi-gene panel testing allows many cancer susceptibility genes to be tested quickly at a lower cost making such testing accessible to a broader population. Thus, more patients carrying pathogenic germline mutations in various…

The idea of "stratified medicine" is an important driver of methodological research on the identification of predictive biomarkers. Most methods proposed so far for this purpose have been developed for the use on randomized data only.…

In many applications, data often arise from multiple groups that may share similar characteristics. A joint estimation method that models several groups simultaneously can be more efficient than estimating parameters in each group…

In this paper, we develop a graphical modeling framework for the inference of networks across multiple sample groups and data types. In medical studies, this setting arises whenever a set of subjects, which may be heterogeneous due to…

This work proposes a unified framework to leverage biological information in network propagation-based gene prioritization algorithms. Preliminary results on breast cancer data show significant improvements over state-of-the-art baselines,…

In healthcare, it is essential to explain the decision-making process of machine learning models to establish the trustworthiness of clinicians. This paper introduces BI-RADS-Net, a novel explainable deep learning approach for cancer…

We study the variable selection problem in survival analysis to identify the most important factors affecting survival time. Our method incorporates prior knowledge of mutual correlations among variables, represented through a graph. We…