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Bioinformatics. 2018 Aug 28. doi: 10.1093/bioinformatics/bty702. [Epub ahead of print]

Parallel Clustering of Single Cell Transcriptomic Data with Split-Merge Sampling on Dirichlet Process Mixtures.

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Department of Computer Science, University of California, Irvine, CA, United States.
Systems Biology and Bioinformatics Laboratory (SysBioLab), University of Algarve, Faro, Algarve, Portugal.



With the development of droplet based systems, massive single cell transcriptome data has become available, which enables analysis of cellular and molecular processes at single cell resolution and is instrumental to understanding many biological processes. While state-of-the-art clustering methods have been applied to the data, they face challenges in the following aspects: (1) the clustering quality still needs to be improved; (2) most models need prior knowledge on number of clusters, which is not always available; (3) there is a demand for faster computational speed.


We propose to tackle these challenges with Parallelized Split Merge Sampling on Dirichlet Process Mixture Model (the Para-DPMM model). Unlike classic DPMM methods that perform sampling on each single data point, the split merge mechanism samples on the cluster level, which significantly improves convergence and optimality of the result. The model is highly parallelized and can utilize the computing power of high performance computing (HPC) clusters, enabling massive inference on huge datasets. Experiment results show the model outperforms current widely used models in both clustering quality and computational speed.


Source code is publicly available on

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