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In this paper, we present a new, optimization-based method to exhibit cyclic behavior in non-reversible stochastic processes. While our method is general, it is strongly motivated by discrete simulations of ordinary differential equations representing non-reversible biological processes, in particular molecular simulations. Here, the discrete time steps of the simulation are often very small compared to the time scale of interest, i.e., of the whole process. In this setting, the detection of a global cyclic behavior of the process becomes difficult because transitions between individual states may appear almost reversible on the small time scale of the simulation. We address this difficulty using a mixed-integer programming model that allows us to compute a cycle of clusters with maximum net flow, i.e., large forward and small backward probability. For a synthetic genetic regulatory network consisting of a ring-oscillator with three genes, we show that this approach can detect the most productive overall cycle, outperforming classical spectral analysis methods. Our method applies to general non-equilibrium steady state systems such as catalytic reactions, for which the objective value computes the effectiveness of the catalyst.

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.

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.

The last milestone achievement for the roundoff-error-free solution of general
mixed integer programs over the rational numbers was a hybrid-precision
branch-and-bound algorithm published by Cook, Koch, Steffy, and Wolter in 2013.
We describe a substantial revision and extension of this framework that
integrates symbolic presolving, features an exact repair step for solutions from
primal heuristics, employs a faster rational LP solver based on LP iterative
refinement, and is able to produce independently verifiable certificates of
optimality.
We study the significantly improved performance and give insights into the
computational behavior of the new algorithmic components.
On the MIPLIB 2017 benchmark set, we observe an average speedup of
6.6x over the original framework and 2.8
times as many instances solved within a time limit of two hours.

The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. This paper discusses enhancements and extensions contained in version 6.0 of the SCIP Optimization Suite. Besides performance improvements of the MIP and MINLP core achieved by new primal heuristics and a new selection criterion for cutting planes, one focus of this release are decomposition algorithms. Both SCIP and the automatic decomposition solver GCG now include advanced functionality for performing Benders’ decomposition in a generic framework. GCG’s detection loop for structured matrices and the coordination of pricing routines for Dantzig-Wolfe decomposition has been significantly revised for greater flexibility. Two SCIP extensions have been added
to solve the recursive circle packing problem by a problem-specific column generation scheme and to demonstrate the use of the new Benders’ framework for stochastic capacitated facility location. Last, not least, the report presents updates and additions to the other components and extensions of the SCIP Optimization Suite: the LP solver SoPlex, the modeling language Zimpl, the parallelization framework UG, the Steiner tree solver SCIP-Jack, and the mixed-integer semidefinite programming solver SCIP-SDP.

We establish a general computational framework for Chvátal’s conjecture based on exact rational integer programming. As a result we prove Chvátal’s conjecture holds for all downsets whose union of sets contains seven elements or less. The computational proof relies on an exact branch-and-bound certificate that allows for elementary verification and is independent of the integer programming solver used.

We describe a general and safe computational framework that provides integer programming results with the degree of certainty that is required for machine-assisted proofs of mathematical theorems.
At its core, the framework relies on a rational branch-and-bound certificate produced by an exact integer programming solver, SCIP, in order to circumvent floating-point roundoff errors present in most state-of-the-art solvers for mixed-integer programs.
The resulting certificates are self-contained and checker software exists that can verify their correctness independently of the integer programming solver used to produce the certificate.
This acts as a safeguard against programming errors that may be present in complex solver software.
The viability of this approach is tested by applying it to finite cases of Chvátal's conjecture, a long-standing open question in extremal combinatorics.
We take particular care to verify also the correctness of the input for this specific problem, using the Coq formal proof assistant.
As a result we are able to provide a first machine-assisted proof that
Chvátal's conjecture holds for all downsets whose union of sets contains seven elements or less.

The last milestone achievement for the roundoff-error-free solution of general mixed integer programs over the rational numbers was a hybrid-precision branch-and-bound algorithm published by Cook, Koch, Steffy, and Wolter in 2013. We describe a substantial revision and extension of this framework that integrates symbolic presolving, features an exact repair step for solutions from primal heuristics, employs a faster rational LP solver based on LP iterative refinement, and is able to produce independently verifiable certificates of optimality. We study the significantly improved performance and give insights into the computational behavior of the new algorithmic components. On the MIPLIB 2017 benchmark set, we observe an average speedup of 10.7x over the original framework and 2.9 times as many instances solved within a time limit of two hours.