Visualizing hierarchies in scRNA-seq data using a density tree-biased autoencoder

Quentin Garrido (1, 2) , Sebastian Damrich (2) , Alexander Jäger (2) , Dario Cerletti (2, 3) , Manfred Claassen (4) , Laurent Najman (1) , Fred Hamprecht (2)

1 LIGM - Laboratoire d'Informatique Gaspard-Monge
2 HCI - Heidelberg Collaboratory for Image Processing
3 ETH Zürich - Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich]
4 Universitätsklinikum Tübingen - University Hospital of Tübingen

Single cell RNA sequencing (scRNA-seq) data makes studying the development of cells possible at unparalleled resolution. Given that many cellular differentiation pro- cesses are hierarchical, their scRNA-seq data is expected to be approximately tree-shaped in gene expression space. Inference and representation of this tree-structure in two dimensions is highly desirable for biological interpretation and exploratory analysis. Our two contributions are an approach for identifying a meaningful tree structure from high-dimensional scRNA-seq data, and a visualization method respecting the tree-structure. We extract the tree structure by means of a density based minimum spanning tree on a vector quantization of the data and show that it captures biological information well. We then introduce DTAE, a tree-biased autoencoder that emphasizes the tree structure of the data in low dimensional space. We com- pare to other dimension reduction methods and demonstrate the success of our method experimentally. Our implementation relying on PyTorch and Higra is available at github.com/hci-unihd/DTAE.

Domaines: Bio-informatique [q-bio.QM]; Réseau de neurones [cs.NE]

Quentin Garrido, Sebastian Damrich, Alexander Jäger, Dario Cerletti, Manfred Claassen, et al.. Visualizing hierarchies in scRNA-seq data using a density tree-biased autoencoder. 2021. ⟨hal-03136103v1⟩