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In this study, we address the mate selection problem in the hybridization stage of a breeding pipeline, which constitutes the multi-objective breeding goal key to the performance of a variety development program. The solution framework we formulate seeks to ensure that individuals with the most desirable genomic characteristics are selected to cross in order to maximize the likelihood of the inheritance of desirable genetic materials to the progeny. Unlike approaches that use phenotypic values for parental selection and evaluate individuals separately, we use a criterion that relies on the genetic architecture of traits and evaluates combinations of genomic information of the pairs of individuals. We introduce the expected cross value(ECV) criterion that measures the expected number of desirable alleles for gametes produced by pairs of individuals sampled from a population of potential parents. We use the ECV criterion to develop an integer linear programming formulation for the parental selection problem. The formulation is capable of controlling the inbreeding level between selected mates. We evaluate the approach or two applications: (i) improving multiple target traits simultaneously, and (ii) finding a multi-parental solution to design crossing blocks. We evaluate the performance of the ECV criterion using a simulation study. Finally, we discuss how the ECV criterion and the proposed integer linear programming techniques can be applied to improve breeding efficiency while maintaining genetic diversity in a breeding program.

A k-club is a subset of vertices of a graph that induces a subgraph of diameter at most k, where k is a positive integer. By definition, 1-clubs are cliques [...]

This paper introduces and studies the maximum k-plex problem, which arises in social network analysis and has wider applicability in several important areas employing graph-based data mining. After establishing NP-completeness [...]

In this paper we characterize the local maxima of a continuous global optimization formulation for finding the independence number of a graph. Classical Karush-Kuhn-Tucker conditions and simple combinatorial arguments are found sufficient to deduce several interesting properties of the local and global maxima. These properties can be utilized in developing new approaches to the maximum independent set problem.In this paper we characterize the local maxima of a continuous global optimization formulation for finding the independence number of a graph. Classical Karush-Kuhn-Tucker conditions and simple combinatorial arguments are found sufficient to deduce several interesting properties of the local and global maxima. These properties can be utilized in developing new approaches to the maximum independent set problem.

Abstract This paper proposes clique relaxations to identify clusters in biological networks. In particular, the maximum n-clique and maximum n-club problems on an arbitrary graph are introduced and their recognition versions are shown to be NP-complete. In addition, integer programming formulations are proposed and the results of sample numerical experiments performed on biological networks are reported.