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The topic of this thesis is the examination of an optimization model
which stems from the clustering process of non-reversible markov processes.
We introduce the cycle clustering problem und formulate it as a mixed
integer program (MIP).
We prove that this problem is N P-hard and discuss polytopal aspects
such as facets and dimension. The focus of this thesis is the development of
solving methods for this clustering problem. We develop problem specific
primal heuristics, as well as separation methods and an approximation
algorithm. These techniques are implemented in practice as an application
for the MIP solver SCIP.
Our computational experiments show that these solving methods result
in an average speedup of ×4 compared to generic solvers and that our
application is able to solve more instances to optimality within the given
time limit of one hour.
This article describes new features and enhanced algorithms made available in version 5.0 of the SCIP Optimization Suite. In its central component, the constraint integer programming solver SCIP, remarkable performance improvements have been achieved for solving mixed-integer linear and nonlinear programs. On MIPs, SCIP 5.0 is about 41 % faster than SCIP 4.0 and over twice as fast on instances that take at least 100 seconds to solve. For MINLP, SCIP 5.0 is about 17 % faster overall and 23 % faster on instances that take at least 100 seconds to solve. This boost is due to algorithmic advances in several parts of the solver such as cutting plane generation and management, a new adaptive coordination of large neighborhood search heuristics, symmetry handling, and strengthened McCormick relaxations for bilinear terms in MINLPs. Besides discussing the theoretical background and the implementational aspects of these developments, the report describes recent additions for the other software packages connected to SCIP, in particular for the LP solver SoPlex, the Steiner tree solver SCIP-Jack, the MISDP solver SCIP-SDP, and the parallelization framework UG.