Data and source code for optimal contribution problem from tree breeding

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Contact address : Makoto.Yamashita at is.titech.ac.jp

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This page provides data and source code for optimal contribution problem arising from tree breeding. Please download from here.
Download ocp01.zip

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The zipped file contains

• SDPrelaxation.pdf [explains the original problem and how to derive an SDP relaxation]
• sp_mat_000200.mat, sp_mat_010100.mat [includes data for the sizes Z = 200 and 10100]
• OCP01.m [generates SDP relaxation and solves the SDP in the following steps]
  1. Load data (sp_mat_000200 or sp_mat_010100)
  2. Set Parameters
  3. Generate SDP relaxation
  4. Solve SDP by sdpa, sdpt3 or sedumi
  5. Revert SDP solution to the original problem

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For the details on the matrix A, please refer to
Makoto Yamashita, Tim J Mullin, and Sena Safarina. An efficient second-order cone programming approach for optimal selection in tree breeding. arXiv preprint arXiv:1506.04487, 2015.

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The above file is still under development, and there is a possibilty that it has some bugs. In addition, the generated SDP problems do not have interior-points and this causes numerical difficulty. For example, the objective value obtained by SDPT-3 for the parameters Z = 10100 and theta = 0.0701/2 was $g^T x$ = 21.212330, but this value should be at least 46.568. SDPA also gave an incorrect objective value.

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2016/Sep/20