sysbio-curie.github.io

ElPiGraph

ElPiGraph (Elastic Principal Graph) is a method for approximating datasets with complex topologies.

This directory contains codes, example datasets, and analyses centered on the application of ElPiGraph to different types of data.

ElPiGraph implementations (from most to least complete)

ElPiGraph.R - implementation of ElPiGraph in R (most complete functionality and multi-core support)

ElPiGraph.P - implementation of ElPiGraph in Python (Equivalent to R version, multi-core and GPU support. Missing some of the plotting functionalities)

ElPiGraph.M - implementation of ElPiGraph in MATLAB (Less options than Python and R version)

ElPiGraph.Java - implementation of ElPiGraph as part of the VDAO engine

ElPiGraph.Scala - implementation of ElPiGraph in Scala

Notebooks (containing code and figures)

Branching pseudotime reconstruction from Nestorowa et la. with MLLE

Branching pseudotime reconstruction from Nestorowa et la. with PCA

Linear pseudotime reconstruction from Schlitzer et la. with MLLE and PCA

Figures

3D Force directed layout derived for xenopus stage 22 embryos - Interactive figure (see Albergante et al, 2018 for details)

3D Force directed layout with the fitted consensus graph for xenopus stage 22 embryos - Interactive figure (see Albergante et al, 2018 for details)

References

Albergante et al, Robust and scalable learning of data manifolds with complex topologies via ElPiGraph, 2018, preprint

Gorban A, Sumner N, Zinovyev A. Topological grammars for data approximation. 2007. Applied Mathematics Letters 20(4), 382-386

Gorban A.N, Zinovyev A. Principal manifolds and graphs in practice: from molecular biology to dynamical systems. 2010. Int J Neural Syst 20(3):219-32

Chen H, Albergante L, Hsu JY, Lareau CA, Lo Bosco G, Guan J, Zhou S, Gorban AN, Bauer DE, Aryee MJ, Langenau DM, Zinovyev A, Buenrostro JD, Yuan G-C, Pinello L. Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data with STREAM. 2019. Nature Communications 10:1903.

Gorban A, Mirkes E, Zinovyev A. Robust principal graphs for data approximation. Archives of Data Science 2(1):1:16, 2017.

Zinovyev A. and Mirkes E. Data complexity measured by principal graphs. 2013. Computers and Mathematics with Applications 65:1471-1482.

Contact

Jonathan Bac

Luca Albergante

Andrei Zinovyev