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Several brain disorders can be detected by observing alterations in the brain's structural and functional connectivities. Neurological findings suggest that early diagnosis of brain disorders, such as mild cognitive impairment (MCI), can…

Heterogeneity is a fundamental characteristic of cancer. To accommodate heterogeneity, subgroup identification has been extensively studied and broadly categorized into unsupervised and supervised analysis. Compared to unsupervised…

Multi-output Gaussian process (MOGP) regression allows modelling dependencies among multiple correlated response variables. Similarly to standard Gaussian processes, MOGPs are sensitive to model misspecification and outliers, which can…

Gaussian graphical models provide a powerful framework to reveal the conditional dependency structure between multivariate variables. The process of uncovering the conditional dependency network is known as structure learning. Bayesian…

In Oncology, trials evaluating drug combinations are becoming more common. While combination therapies bring the potential for greater efficacy, they also create unique challenges for ensuring drug safety. In Phase-I dose escalation trials…

We address the problem of Bayesian structure learning for domains with hundreds of variables by employing non-parametric bootstrap, recursively. We propose a method that covers both model averaging and model selection in the same framework.…

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…

Motivated by the need to study the molecular mechanism underlying Type 1 Diabetes (T1D) with the gene expression data collected from both the patients and healthy controls at multiple time points, we propose an innovative method for jointly…

In heterogeneous disease settings, accounting for intrinsic sample variability is crucial for obtaining reliable and interpretable omic network estimates. However, most graphical model analyses of biomedical data assume homogeneous…

In genome-wide prediction, independence of marker allele substitution effects is typically assumed; however, since early stages of this technology it has been known that nature points to correlated effects. In statistics, graphical models…

The Gaussian graphical model is a widely used tool for learning gene regulatory networks with high-dimensional gene expression data. Most existing methods for Gaussian graphical models assume that the data are homogeneous, i.e., all samples…

In statistics and machine learning, detecting dependencies in datasets is a central challenge. We propose a novel neural network model for supervised graph structure learning, i.e., the process of learning a mapping between observational…

Bayesian networks are a widely-used class of probabilistic graphical models capable of representing symmetric conditional independence between variables of interest using the topology of the underlying graph. For categorical variables, they…

Structural learning of directed acyclic graphs (DAGs) or Bayesian networks has been studied extensively under the assumption that data are independent. We propose a new Gaussian DAG model for dependent data which assumes the observations…

Bayesian methods for learning Gaussian graphical models offer a principled framework for quantifying model uncertainty and incorporating prior knowledge. However, their scalability is constrained by the computational cost of jointly…

Introduction: To leverage functionality and clinical relevance into understanding systems biology, one needs to understand the pathway of the genetic effects on risk factors/disease through intermediate molecular levels, such as…

The increasing availability of high-dimensional, longitudinal measures of gene expression can facilitate understanding of biological mechanisms, as required for precision medicine. Biological knowledge suggests that it may be best to…

Graphical models provide a powerful methodology for learning the conditional independence structure in multivariate data. Inference is often focused on estimating individual edges in the latent graph. Nonetheless, there is increasing…

The adaptive processing of structured data is a long-standing research topic in machine learning that investigates how to automatically learn a mapping from a structured input to outputs of various nature. Recently, there has been an…

Many popular models from the networks literature can be viewed through a common lens of contingency tables on network dyads, resulting in \emph{log-linear ERGMs}: exponential family models for random graphs whose sufficient statistics are…