Reconstructing probabilistic trees of cellular differentiation from single-cell RNA-seq data

Abstract

Until recently, transcriptomics was limited to bulk RNA sequencing, obscuring the underlying expression patterns of individual cells in favor of a global average. Thanks to technological advances, we can now profile gene expression across thousands or millions of individual cells in parallel. This new type of data has led to the intriguing discovery that individual cell profiles can reflect the imprint of time or dynamic processes. However, synthesizing this information to reconstruct dynamic biological phenomena from data that are noisy, heterogenous, and sparse-and from processes that may unfold asynchronously-poses a complex computational and statistical challenge. Here, we develop a full generative model for probabilistically reconstructing trees of cellular differentiation from single-cell RNA-seq data. Specifically, we extend the framework of the classical Dirichlet diffusion tree to simultaneously infer branch topology and latent cell states along continuous trajectories over the full tree. In tandem, we construct a novel Markov chain Monte Carlo sampler that interleaves Metropolis-Hastings and message passing to leverage model structure for efficient inference. Finally, we demonstrate that these techniques can recover latent trajectories from simulated single-cell transcriptomes. While this work is motivated by cellular differentiation, we derive a tractable model that provides flexible densities for any data (coupled with an appropriate noise model) that arise from continuous evolution along a latent nonparametric tree.

Nonparametric Bayesian multi-armed bandits for single cell experiment design

“…As cell types arise through cellular differentiation [Rizvi et al, 2017], they organize themselves in suitable hierarchies or developmental landscapes [Waddington et al, 1957]. Hierarchical structures can be imposed on the cell types through Bayesian nonparametric priors, as was done for cell trajectory reconstruction and Bayesian inference on developmental lineages [Heaukulani et al, 2014, Shiffman et al, 2018.…”