SOME EXPERIENCES WITH SOLVING SEMIDEFINITE PROGRAMMING RELAXATIONS OF BINARY QUADRATIC OPTIMIZATION MODELS IN COMPUTATIONAL BIOLOGY

We present two recent integer programming models in molecular biology and study practical reformulations to compute solutions to some of these problems. In extension of previously tested linearization techniques, we formulate corresponding semidefinite relaxations and discuss practical rounding strategies to find good feasible approximate solutions. Our computational results highlight the possible advantages and remaining challenges of this approach especially on large-scale problems.