We present ElPiGraph, a method for approximating data distributions having non-trivial topological features such as the existence of excluded regionsor branching structures. Unlike many existing methods, ElPiGraph is not based on the construction of a k-nearest neighbour graph, a procedure that can perform poorly in the case of multidimensional and noisy data. Instead, ElPiGraphconstructs elastic principal graphs in a more robust way by minimizing elastic energy, applying graph grammars and explicitly controlling topological complexity. Using trimmed approximation error function makes ElPiGraph extremely robust to the presence of background noise without decreasing computational performance and allows it to deal with complex cases of manifold learning (for example, ElPiGraph can learn disconnected intersecting manifolds). Thanks to the quasi-quadratic nature of the elastic function, ElPiGraph performs almost as fast as a simple k-means clustering and, therefore, is much more scalable than alternative methods, and can work on large datasets containing millions of high dimensional points on a personal computer. The excellent performance of the method opens the possibility to apply resampling and to approximate complex data structures via principal graph ensembles which can be used to construct consensus principal graphs. ElPiGraph is currently implemented in five programming languages and accompanied by a graphical user interface, which makes it a versatile tool to deal with complex data in various fields from molecular biology, where it can be used to infer pseudo-time trajectories from single-cell RNASeq , to astronomy, where it can be used to approximate complex structures in the distribution of galaxies.
Large datasets represented by multidimensional data point clouds often possess non-trivial distributions with branching trajectories and excluded regions, with the recent single-cell transcriptomic studies of developing embryo being notable examples. Reducing the complexity and producing compact and interpretable representations of such data remains a challenging task. Most of the existing computational methods are based on exploring the local data point neighbourhood relations, a step that can perform poorly in the case of multidimensional and noisy data. Here we present ElPiGraph, a scalable and robust method for approximation of datasets with complex structures which does not require computing the complete data distance matrix or the data point neighbourhood graph. This method is able to withstand high levels of noise and is capable of approximating complex topologies via principal graph ensembles that can be combined into a consensus principal graph. ElPiGraph deals efficiently with large and complex datasets in various fields from biology, where it can be used to infer gene dynamics from single-cell RNA-Seq , to astronomy, where it can be used to explore complex structures in the distribution of galaxies.
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We present ElPiGraph, a method for approximating data distributions having
Large datasets represented by multidimensional data point clouds often possess
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topological features such as the existence of excluded regionsor branching structures. Unlike many existing methods, ElPiGraph is not based on the construction of a k-nearest neighbour graph, a procedure
distributions with branching trajectories and excluded regions, with the recent single-cell transcriptomic studies of developing embryo being notable examples. Reducing the complexity and producing compact and interpretable representations of such data remains a challenging task. Most of the existing computational methods are based on exploring the local data point neighbourhood relations, a step
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Instead, ElPiGraphconstructs elastic principal graphs in a more robust way by minimizing elastic energy, applying graph grammars and explicitly controlling topological complexity. Using trimmed approximation error function makes ElPiGraph extremely robust to the presence of background noise without decreasing computational performance and allows it to deal with complex cases of manifold learning (for example, ElPiGraph can learn disconnected intersecting manifolds). Thanks to the quasi-quadratic nature of the elastic function, ElPiGraph performs almost as fast as a simple k-means clustering and, therefore, is much more scalable than alternative methods, and can work on large datasets containing millions of high dimensional points on a personal computer. The excellent performance of the method opens the possibility to apply resampling and to approximate complex data structures
Here we present ElPiGraph, a scalable and robust method for approximation of datasets with complex structures which does not require computing the complete data distance matrix or the data point neighbourhood graph. This method is able to withstand high levels of noise and is capable of approximating complex topologies
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which can be used to construct consensus principal graphs. ElPiGraph is currently implemented in five programming languages and accompanied by a graphical user interface, which makes it a versatile tool to deal with complex data
that can be combined into a consensus principal graph. ElPiGraph deals efficiently with large and complex datasets
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molecular
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pseudo-time trajectories
gene dynamics
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RNASeq
RNA-Seq
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approximate
explore