Factorial state-space modelling for kinetic clustering and lineage inference

Single-cell RNA sequencing (scRNAseq) protocols measure the abundance of expressed transcripts for single cells. Gene expression profiles of cells (cell-states) represent the functional properties of the cell and are used to cluster cell-states that have a common functional identity (cell-type). Standard clustering methods for scRNAseq data perform hard clustering based on KNN graphs. This approach implicitly assumes that variation among cell-states within a cluster does not correspond to changes in functional properties. Differentiation is a directed process of transitions between cell-types via gradual changes in cell-states over the course of the process. We propose a latent state-space Markov model that utilises cell-state transitions derived from RNA velocity to model differentiation as a sequence of latent state transitions and to perform soft kinetic clustering of cell-states that accommodates the transitional nature of cells in a differentiation process. We applied this model to the differentiation of Radial-glia cells into mature neurons and demonstrate the utility of our method in discriminating between functional and transitional cell-states.