@misc{Eifler, type = {Master Thesis}, author = {Eifler, Leon}, title = {Mixed-Integer Programming for Clustering in Non-reversible Markov Processes}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-66486}, pages = {74}, abstract = {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.}, language = {en} } @misc{EiflerGleixnerPulaj, author = {Eifler, Leon and Gleixner, Ambros and Pulaj, Jonad}, title = {Chv{\´a}tal's Conjecture Holds for Ground Sets of Seven Elements}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-70240}, abstract = {We establish a general computational framework for Chv{\´a}tal's conjecture based on exact rational integer programming. As a result we prove Chv{\´a}tal'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.}, language = {en} } @misc{WitzigBeckenbachEifleretal., author = {Witzig, Jakob and Beckenbach, Isabel and Eifler, Leon and Fackeldey, Konstantin and Gleixner, Ambros and Grever, Andreas and Weber, Marcus}, title = {Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes}, issn = {1438-0064}, doi = {10.1137/16M1091162}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-60353}, abstract = {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.}, language = {en} } @article{WitzigBeckenbachEifleretal., author = {Witzig, Jakob and Beckenbach, Isabel and Eifler, Leon and Fackeldey, Konstantin and Gleixner, Ambros and Grever, Andreas and Weber, Marcus}, title = {Mixed-Integer Programming for Cycle Detection in Non-reversible Markov Processes}, series = {Multiscale Modeling and Simulation}, volume = {16}, journal = {Multiscale Modeling and Simulation}, number = {1}, issn = {1438-0064}, doi = {10.1137/16M1091162}, pages = {248 -- 265}, abstract = {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.}, language = {en} } @misc{EiflerGleixner, author = {Eifler, Leon and Gleixner, Ambros}, title = {Safe and Verified Gomory Mixed Integer Cuts in a Rational MIP Framework}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-90159}, abstract = {This paper is concerned with the exact solution of mixed-integer programs (MIPs) over the rational numbers, i.e., without any roundoff errors and error tolerances. Here, one computational bottleneck that should be avoided whenever possible is to employ large-scale symbolic computations. Instead it is often possible to use safe directed rounding methods, e.g., to generate provably correct dual bounds. In this work, we continue to leverage this paradigm and extend an exact branch-and-bound framework by separation routines for safe cutting planes, based on the approach first introduced by Cook, Dash, Fukasawa, and Goycoolea in 2009. Constraints are aggregated safely using approximate dual multipliers from an LP solve, followed by mixed-integer rounding to generate provably valid, although slightly weaker inequalities. We generalize this approach to problem data that is not representable in floating-point arithmetic, add routines for controlling the encoding length of the resulting cutting planes, and show how these cutting planes can be verified according to the VIPR certificate standard. Furthermore, we analyze the performance impact of these cutting planes in the context of an exact MIP framework, showing that we can solve 21.5\% more instances and reduce solving times by 26.8\% on the MIPLIB 2017 benchmark test set.}, language = {en} } @misc{EiflerGleixnerPulaj, author = {Eifler, Leon and Gleixner, Ambros and Pulaj, Jonad}, title = {A Safe Computational Framework for Integer Programming applied to Chv{\´a}tal's Conjecture}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-84444}, abstract = {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 Chv{\´a}tal'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 Chv{\´a}tal's conjecture holds for all downsets whose union of sets contains seven elements or less.}, language = {en} } @article{EiflerGleixnerPulaj, author = {Eifler, Leon and Gleixner, Ambros and Pulaj, Jonad}, title = {A Safe Computational Framework for Integer Programming applied to Chv{\´a}tal's Conjecture}, series = {ACM Transactions on Mathematical Software}, volume = {48}, journal = {ACM Transactions on Mathematical Software}, number = {2}, doi = {10.1145/3485630}, abstract = {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 Chv{\´a}tal'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 Chv{\´a}tal's conjecture holds for all downsets whose union of sets contains seven elements or less.}, language = {en} } @article{EiflerGleixner, author = {Eifler, Leon and Gleixner, Ambros}, title = {Safe and Verified Gomory Mixed Integer Cuts in a Rational MIP Framework}, series = {SIAM Journal on Optimization}, journal = {SIAM Journal on Optimization}, abstract = {This paper is concerned with the exact solution of mixed-integer programs (MIPs) over the rational numbers, i.e., without any roundoff errors and error tolerances. Here, one computational bottleneck that should be avoided whenever possible is to employ large-scale symbolic computations. Instead it is often possible to use safe directed rounding methods, e.g., to generate provably correct dual bounds. In this work, we continue to leverage this paradigm and extend an exact branch-and-bound framework by separation routines for safe cutting planes, based on the approach first introduced by Cook, Dash, Fukasawa, and Goycoolea in 2009. Constraints are aggregated safely using approximate dual multipliers from an LP solve, followed by mixed-integer rounding to generate provably valid, although slightly weaker inequalities. We generalize this approach to problem data that is not representable in floating-point arithmetic, add routines for controlling the encoding length of the resulting cutting planes, and show how these cutting planes can be verified according to the VIPR certificate standard. Furthermore, we analyze the performance impact of these cutting planes in the context of an exact MIP framework, showing that we can solve 21.5\% more instances and reduce solving times by 26.8\% on the MIPLIB 2017 benchmark test set.}, language = {en} } @article{EiflerGleixner, author = {Eifler, Leon and Gleixner, Ambros}, title = {A Computational Status Update for Exact Rational Mixed Integer Programming}, series = {Integer Programming and Combinatorial Optimization: 22th International Conference, IPCO 2021}, journal = {Integer Programming and Combinatorial Optimization: 22th International Conference, IPCO 2021}, doi = {10.1007/978-3-030-73879-2_12}, abstract = {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.}, language = {en} } @article{EiflerGleixner, author = {Eifler, Leon and Gleixner, Ambros}, title = {A computational status update for exact rational mixed integer programming}, series = {Mathematical Programming}, journal = {Mathematical Programming}, publisher = {Springer}, doi = {10.1007/s10107-021-01749-5}, abstract = {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.}, language = {en} }