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We present the nested Chinese restaurant process (nCRP), a stochastic process which assigns probability distributions to infinitely-deep, infinitely-branching trees. We show how this stochastic process can be used as a prior distribution in…

We present TreeClone, a latent feature allocation model to reconstruct tumor subclones subject to phylogenetic evolution that mimics tumor evolution. Similar to most current methods, we consider data from next-generation sequencing of tumor…

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…

Cancer radiomics is an emerging discipline promising to elucidate lesion phenotypes and tumor heterogeneity through patterns of enhancement, texture, morphology, and shape. The prevailing technique for image texture analysis relies on the…

Revealing the clonal composition of a single tumor is essential for identifying cell subpopulations with metastatic potential in primary tumors or with resistance to therapies in metastatic tumors. Sequencing technologies provide an…

In Bayesian phylogenetics, our goal is to estimate the posterior distribution over phylogenetic trees. Markov chain Monte Carlo methods are widely used to approximate the phylogenetic posterior distributions. For large-scale sequence data,…

A method was developed for Bayesian inference of species phylogeny using the multi-species coalescent model. To improve the mixing properties of the Markov chain Monte Carlo (MCMC) algorithm that traverses the space of species trees, we…

Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…

This paper focuses on the problem of hierarchical non-overlapping clustering of a dataset. In such a clustering, each data item is associated with exactly one leaf node and each internal node is associated with all the data items stored in…

The distance dependent Chinese Restaurant Process (ddCRP) provides a flexible prior distribution for clustering observations, incorporating covariate information through pairwise distances and accommodating a rich variety of cluster…

In order to gain an understanding of the effectiveness of phylogenetic Markov chain Monte Carlo (MCMC), it is important to understand how quickly the empirical distribution of the MCMC converges to the posterior distribution. In this paper…

Tumor cell populations can be thought of as being composed of homogeneous cell subpopulations, with each subpopulation being characterized by overlapping sets of single nucleotide variants (SNVs). Such subpopulations are known as subclones…

The tree-structured stick-breaking process (TS-SBP) mixture model is a non-parametric Bayesian model that can represent tree-like hierarchical structures among the mixture components. For TS-SBP mixture models, only a Markov chain Monte…

This paper studies a Markov chain for phylogenetic reconstruction which uses a popular transition between tree topologies known as subtree pruning-and-regrafting (SPR). We analyze the Markov chain in the simpler setting that the generating…

Accurate identification of synergistic treatment combinations and their underlying biological mechanisms is critical across many disease domains, especially cancer. In translational oncology research, preclinical systems such as…

Medical image segmentation faces a fundamental challenge in continual learning: data arrives sequentially from heterogeneous sources, yet effective continual learning requires discovering which tasks share sufficient structure to benefit…

We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…

There is a keen interest in characterizing variation in the microbiome across cancer patients, given increasing evidence of its important role in determining treatment outcomes. Here our goal is to discover subgroups of patients with…

X-ray computed tomography (CT) reveals the materials' internal structures non-destructively from a tilt series of projected images. Filtered back projection (FBP) is a widely-adopted reconstruction algorithm in CT owing to its small…

High-throughput sequencing allows the detection and quantification of frequencies of somatic single nucleotide variants (SNV) in heterogeneous tumor cell populations. In some cases, the evolutionary history and population frequency of the…