A divide and conquer matheuristic algorithm for the Prize-collecting Steiner Tree Problem

•Application of Steiner tree problems to genomics.•Mathematical programming based heuristic exploiting domain characteristics.•Approach able to handle large instances effectively.

The Prize-collecting Steiner Tree Problem (PCSTP) is a well-known problem in graph theory and combinatorial optimization. It has been successfully applied to solve real problems such as fiber-optic and gas distribution networks design. In this work, we concentrate on its application in biology to perform a functional analysis of genes. It is common to analyze large networks in genomics to infer a hidden knowledge. Due to the NP-hard characteristics of the PCSTP, it is computationally costly, if possible, to achieve exact solutions for such huge instances. Therefore, there is a need for fast and efficient matheuristic algorithms to explore and understand the concealed information in huge biological graphs. In this study, we propose a matheuristic method based on clustering algorithm. The main target of the method is to scale up the applicability of the currently available exact methods to large graph instances, without loosing too much on solution quality. The proposed matheuristic method is composed of a preprocessing procedures, a heuristic clustering algorithm and an exact solver for the PCSTP, applied on sub-graphs. We examine the performance of the proposed method on real-world benchmark instances from biology, and compare its results with those of the exact solver alone, without the heuristic clustering. We obtain solutions in shorter execution time and with negligible optimality gaps. This enables analyzing very large biological networks with the currently available exact solvers.