Integer Linear Programming for Sequence Problems: A general approach to reduce the problem size

Sequence problems belong to the most challenging interdisciplinary topics of the actuality. They are ubiquitous in science and daily life and occur, for example, in form of DNA sequences encoding all information of an organism, as a text (natural or formal) or in form of a computer program. Therefore, sequence problems occur in many variations in computational biology (drug development), coding theory, data compression, quantitative and computational linguistics (e.g. machine translation). In recent years appeared some proposals to formulate sequence problems like the closest string problem (CSP) and the farthest string problem (FSP) as an Integer Linear Programming Problem (ILPP). In the present talk we present a general novel approach to reduce the size of the ILPP by grouping isomorphous columns of the string matrix together. The approach is of practical use, since the solution of sequence problems is very time consuming, in particular when the sequences are long.

Efficient Hill Climber for Constrained Pseudo-Boolean Optimization Problems

Efficient hill climbers have been recently proposed for single- and multi-objective pseudo-Boolean optimization problems. For $k$-bounded pseudo-Boolean functions where each variable appears in at most a constant number of subfunctions, it has been theoretically proven that the neighborhood of a solution can be explored in constant time. These hill climbers, combined with a high-level exploration strategy, have shown to improve state of the art methods in experimental studies and open the door to the so-called Gray Box Optimization, where part, but not all, of the details of the objective functions are used to better explore the search space. One important limitation of all the previous proposals is that they can only be applied to unconstrained pseudo-Boolean optimization problems. In this work, we address the constrained case for multi-objective $k$-bounded pseudo-Boolean optimization problems. We find that adding constraints to the pseudo-Boolean problem has a linear computational cost in the hill climber.