TY - GEN A1 - Witzig, Jakob A1 - Beckenbach, Isabel A1 - Eifler, Leon A1 - Fackeldey, Konstantin A1 - Gleixner, Ambros A1 - Grever, Andreas A1 - Weber, Marcus T1 - Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes N2 - 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. T3 - ZIB-Report - 16-39 KW - Non-reversible Markov Processes KW - NESS KW - Mixed-Integer Programming KW - Markov State Models Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-60353 SN - 1438-0064 ER - TY - THES A1 - Eifler, Leon T1 - Mixed-Integer Programming for Clustering in Non-reversible Markov Processes N2 - 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. KW - Markov State Models KW - NESS KW - Non-reversible Markov Processes KW - Mixed-Integer Programming Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66486 ER - TY - GEN A1 - Gleixner, Ambros A1 - Eifler, Leon A1 - Gally, Tristan A1 - Gamrath, Gerald A1 - Gemander, Patrick A1 - Gottwald, Robert Lion A1 - Hendel, Gregor A1 - Hojny, Christopher A1 - Koch, Thorsten A1 - Miltenberger, Matthias A1 - Müller, Benjamin A1 - Pfetsch, Marc A1 - Puchert, Christian A1 - Rehfeldt, Daniel A1 - Schlösser, Franziska A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Viernickel, Jan Merlin A1 - Vigerske, Stefan A1 - Weninger, Dieter A1 - Witt, Jonas T. A1 - Witzig, Jakob T1 - The SCIP Optimization Suite 5.0 N2 - 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. T3 - ZIB-Report - 17-61 KW - constraint integer programming KW - linear programming KW - mixed-integer linear programming KW - mixed-integer nonlinear programming KW - optimization solver KW - branch-and-cut KW - branch-and-price KW - column generation framework KW - parallelization KW - mixed-integer semidefinite programming KW - Steiner tree optimization Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-66297 SN - 1438-0064 ER - TY - GEN A1 - Eifler, Leon A1 - Gleixner, Ambros A1 - Pulaj, Jonad T1 - Chvátal’s Conjecture Holds for Ground Sets of Seven Elements N2 - 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. T3 - ZIB-Report - 18-49 KW - extremal combinatorics KW - exact rational integer programming Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-70240 SN - 1438-0064 ER - TY - JOUR A1 - Witzig, Jakob A1 - Beckenbach, Isabel A1 - Eifler, Leon A1 - Fackeldey, Konstantin A1 - Gleixner, Ambros A1 - Grever, Andreas A1 - Weber, Marcus T1 - Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes JF - Multiscale Modeling and Simulation N2 - 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. KW - Markov State Models KW - NESS KW - Non-reversible Markov Processes KW - Mixed-Integer Programming Y1 - 2018 U6 - https://doi.org/10.1137/16M1091162 SN - 1438-0064 VL - 16 IS - 1 SP - 248 EP - 265 ER - TY - GEN A1 - Gleixner, Ambros A1 - Bastubbe, Michael A1 - Eifler, Leon A1 - Gally, Tristan A1 - Gamrath, Gerald A1 - Gottwald, Robert Lion A1 - Hendel, Gregor A1 - Hojny, Christopher A1 - Koch, Thorsten A1 - Lübbecke, Marco A1 - Maher, Stephen J. A1 - Miltenberger, Matthias A1 - Müller, Benjamin A1 - Pfetsch, Marc A1 - Puchert, Christian A1 - Rehfeldt, Daniel A1 - Schlösser, Franziska A1 - Schubert, Christoph A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Viernickel, Jan Merlin A1 - Walter, Matthias A1 - Wegscheider, Fabian A1 - Witt, Jonas T. A1 - Witzig, Jakob T1 - The SCIP Optimization Suite 6.0 N2 - 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. T3 - ZIB-Report - 18-26 KW - constraint integer programming KW - linear programming KW - mixed-integer linear programming KW - mixed-integer nonlinear programming KW - optimization solver KW - branch-and-cut KW - branch-and-price KW - column generation framework KW - parallelization KW - mixed-integer semidefinite programming KW - Steiner tree optimization Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-69361 SN - 1438-0064 ER - TY - GEN A1 - Gamrath, Gerald A1 - Anderson, Daniel A1 - Bestuzheva, Ksenia A1 - Chen, Wei-Kun A1 - Eifler, Leon A1 - Gasse, Maxime A1 - Gemander, Patrick A1 - Gleixner, Ambros A1 - Gottwald, Leona A1 - Halbig, Katrin A1 - Hendel, Gregor A1 - Hojny, Christopher A1 - Koch, Thorsten A1 - Le Bodic, Pierre A1 - Maher, Stephen J. A1 - Matter, Frederic A1 - Miltenberger, Matthias A1 - Mühmer, Erik A1 - Müller, Benjamin A1 - Pfetsch, Marc A1 - Schlösser, Franziska A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Tawfik, Christine A1 - Vigerske, Stefan A1 - Wegscheider, Fabian A1 - Weninger, Dieter A1 - Witzig, Jakob T1 - The SCIP Optimization Suite 7.0 N2 - The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming frame- work SCIP. This paper discusses enhancements and extensions contained in version 7.0 of the SCIP Optimization Suite. The new version features the parallel presolving library PaPILO as a new addition to the suite. PaPILO 1.0 simplifies mixed-integer linear op- timization problems and can be used stand-alone or integrated into SCIP via a presolver plugin. SCIP 7.0 provides additional support for decomposition algorithms. Besides im- provements in the Benders’ decomposition solver of SCIP, user-defined decomposition structures can be read, which are used by the automated Benders’ decomposition solver and two primal heuristics. Additionally, SCIP 7.0 comes with a tree size estimation that is used to predict the completion of the overall solving process and potentially trigger restarts. Moreover, substantial performance improvements of the MIP core were achieved by new developments in presolving, primal heuristics, branching rules, conflict analysis, and symmetry handling. Last, not least, the report presents updates to other components and extensions of the SCIP Optimization Suite, in particular, the LP solver SoPlex and the mixed-integer semidefinite programming solver SCIP-SDP. T3 - ZIB-Report - 20-10 Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78023 SN - 1438-0064 ER - TY - GEN A1 - Eifler, Leon A1 - Gleixner, Ambros A1 - Pulaj, Jonad T1 - A Safe Computational Framework for Integer Programming applied to Chvátal's Conjecture N2 - 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. T3 - ZIB-Report - 21-35 KW - exact rational mixed integer programming KW - extremal combinatorics Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-84444 SN - 1438-0064 ER - TY - JOUR A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - A Computational Status Update for Exact Rational Mixed Integer Programming JF - Integer Programming and Combinatorial Optimization: 22th International Conference, IPCO 2021 N2 - 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. Y1 - 2021 U6 - https://doi.org/10.1007/978-3-030-73879-2_12 ER - TY - GEN A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - A Computational Status Update for Exact Rational Mixed Integer Programming N2 - 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. T3 - ZIB-Report - 21-04 Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-81298 SN - 1438-0064 ER -