@misc{WitzigBeckenbachEifleretal.2016, 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}, year = {2016}, 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.2018, 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}, volume = {16}, journal = {Multiscale Modeling and Simulation}, number = {1}, issn = {1438-0064}, doi = {10.1137/16M1091162}, pages = {248 -- 265}, year = {2018}, 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{Beckenbach2017, author = {Beckenbach, Isabel}, title = {A Hypergraph Network Simplex Algorithm}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-64539}, year = {2017}, abstract = {We describe a network simplex algorithm for the minimum cost flow problem on graph-based hypergraphs which are directed hypergraphs of a particular form occurring in railway rotation planning. The algorithm is based on work of Cambini, Gallo, and Scutell{\`a} who developed a hypergraphic generalization of the network simplex algorithm. Their main theoretical result is the characterization of basis matrices. We give a similar characterization for graph-based hypergraphs and show that some operations of the simplex algorithm can be done combinatorially by exploiting the underlying digraph structure.}, language = {en} } @article{BeckenbachScheidweiler2017, author = {Beckenbach, Isabel and Scheidweiler, Robert}, title = {Perfect f-Matchings and f-Factors in Hypergraphs - A Combinatorial Approach}, volume = {340}, journal = {Discrete Mathematics}, number = {10}, doi = {10.1016/j.disc.2017.05.005}, pages = {2499 -- 2506}, year = {2017}, abstract = {We prove characterizations of the existence of perfect f-matchings in uniform mengerian and perfect hypergraphs. Moreover, we investigate the f-factor problem in balanced hypergraphs. For uniform balanced hypergraphs we prove two existence theorems with purely combinatorial arguments, whereas for non-uniform balanced hypergraphs we show that the f-factor problem is NP-hard.}, language = {de} } @misc{BeckenbachBorndoerfer2014, author = {Beckenbach, Isabel and Bornd{\"o}rfer, Ralf}, title = {An Approximation Result for Matchings in Partitioned Hypergraphs}, doi = {10.1007/978-3-319-28697-6_5}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-51083}, year = {2014}, abstract = {We investigate the matching and perfect matching polytopes of hypergraphs having a special structure, which we call partitioned hypergraphs. We show that the integrality gap of the standard LP-relaxation is at most \$2\sqrt{d}\$ for partitioned hypergraphs with parts of size \$\leq d\$. Furthermore, we show that this bound cannot be improved to \$\mathcal{O}(d^{0.5-\epsilon})\$.}, language = {en} } @misc{BeckenbachBorndoerfer2015, author = {Beckenbach, Isabel and Bornd{\"o}rfer, Ralf}, title = {A Hall Condition for Normal Hypergraphs}, issn = {1438-0064}, doi = {10.1016/j.disc.2018.06.013}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-56175}, year = {2015}, abstract = {Conforti, Cornu{\´e}jols, Kapoor, and Vusković gave a Hall-type condition for the non-existence of a perfect matching in a balanced hypergraph. We generalize this result to the class of normal hypergraphs.}, language = {en} } @article{Beckenbach2020, author = {Beckenbach, Isabel}, title = {Von Graphen zu Hypergraphen}, journal = {OR News}, number = {70}, issn = {1437-2045}, year = {2020}, language = {en} }