On efficient implementation of an approximation algorithm for the Steiner tree problem

Given a complete graph [Formula: see text], with nonnegative edge costs, two subsets [Formula: see text] and [Formula: see text], a partition [Formula: see text] of [Formula: see text], [Formula: see text], [Formula: see text] and [Formula: see text] of [Formula: see text], [Formula: see text], a clustered Steiner tree is a tree [Formula: see text] of [Formula: see text] that spans all vertices in [Formula: see text] such that [Formula: see text] can be cut into [Formula: see text] subtrees [Formula: see text] by removing [Formula: see text] edges and each subtree [Formula: see text] spans all vertices in [Formula: see text], [Formula: see text]. The cost of a clustered Steiner tree is defined to be the sum of the costs of all its edges. A clustered selected-internal Steiner tree of [Formula: see text] is a clustered Steiner tree for [Formula: see text] if all vertices in [Formula: see text] are internal vertices of [Formula: see text]. The clustered selected-internal Steiner tree problem is concerned with the determination of a clustered selected-internal Steiner tree [Formula: see text] for [Formula: see text] and [Formula: see text] in [Formula: see text] with minimum cost. In this paper, we present the first known approximation algorithm with performance ratio [Formula: see text] for the clustered selected-internal Steiner tree problem, where [Formula: see text] is the best-known performance ratio for the Steiner tree problem.

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Scelestial: fast and accurate single-cell lineage tree inference based on a Steiner tree approximation algorithm

10.1101/2021.05.24.445405 ◽

2021 ◽

Author(s):

Mohammad-Hadi Foroughmand-Araabi ◽

Sama Goliaei ◽

Alice Carolyn McHardy

Keyword(s):

Approximation Algorithm ◽

Single Cell ◽

Steiner Tree ◽

Missing Values ◽

Cell Lineage ◽

Error Rates ◽

Steiner Tree Problem ◽

Tree Reconstruction ◽

Tree Inference ◽

Lineage Tree

Single-cell genome sequencing provides a highly granular view of biological systems but is affected by high error rates, allelic amplification bias, and uneven genome coverage. This creates a need for data-specific computational methods, for purposes such as for cell lineage tree inference. The objective of cell lineage tree reconstruction is to infer the evolutionary process that generated a set of observed cell genomes. Lineage trees may enable a better understanding of tumor formation and growth, as well as of organ development for healthy body cells. We describe a method, Scelestial, for lineage tree reconstruction from single-cell data, which is based on an approximation algorithm for the Steiner tree problem and is a generalization of the neighbor-joining method. We adapt the algorithm to efficiently select a limited subset of potential sequences as internal nodes, in the presence of missing values, and to minimize cost by lineage tree-based missing value imputation. In a comparison against seven state-of-the-art single-cell lineage tree reconstruction algorithms - BitPhylogeny, OncoNEM, SCITE, SiFit, SASC, SCIPhI, and SiCloneFit - on simulated and real single-cell tumor samples, Scelestial performed best at reconstructing trees in terms of accuracy and run time. Scelestial has been implemented in C++. It is also available as an R package named RScelestial.

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