@article{TrepteSeckerKostovaetal.2023, author = {Trepte, Philipp and Secker, Christopher and Kostova, Simona and Maseko, Sibusiso B. and Gang Choi, Soon and Blavier, Jeremy and Minia, Igor and Silva Ramos, Eduardo and Cassonnet, Patricia and Golusik, Sabrina and Zenkner, Martina and Beetz, Stephanie and Liebich, Mara J. and Scharek, Nadine and Sch{\"u}tz, Anja and Sperling, Marcel and Lisurek, Michael and Wang, Yang and Spirohn, Kerstin and Hao, Tong and Calderwood, Michael A. and Hill, David E. and Landthaler, Markus and Olivet, Julien and Twizere, Jean-Claude and Vidal, Marc and Wanker, Erich E.}, title = {AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor}, journal = {bioRxiv}, doi = {10.1101/2023.06.14.544560}, year = {2023}, language = {en} } @misc{LindnerLiebchen2020, author = {Lindner, Niels and Liebchen, Christian}, title = {Determining all integer vertices of the PESP polytope by flipping arcs}, issn = {1438-0064}, doi = {10.4230/OASIcs.ATMOS.2020.5}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-78793}, year = {2020}, abstract = {We investigate polyhedral aspects of the Periodic Event Scheduling Problem (PESP), the mathematical basis for periodic timetabling problems in public transport. Flipping the orientation of arcs, we obtain a new class of valid inequalities, the flip inequalities, comprising both the known cycle and change-cycle inequalities. For a point of the LP relaxation, a violated flip inequality can be found in pseudo-polynomial time, and even in linear time for a spanning tree solution. Our main result is that the integer vertices of the polytope described by the flip inequalities are exactly the vertices of the PESP polytope, i.e., the convex hull of all feasible periodic slacks with corresponding modulo parameters. Moreover, we show that this flip polytope equals the PESP polytope in some special cases. On the computational side, we devise several heuristic approaches concerning the separation of cutting planes from flip inequalities. These produce better dual bounds for the smallest and largest instance of the benchmarking library PESPlib.}, language = {en} } @article{BorndoerferDaneckerWeiser2021, author = {Bornd{\"o}rfer, Ralf and Danecker, Fabian and Weiser, Martin}, title = {A Discrete-Continuous Algorithm for Free Flight Planning}, volume = {14}, journal = {Algorithms}, number = {1}, publisher = {MDPI}, issn = {1438-0064}, doi = {10.3390/a14010004}, pages = {4}, year = {2021}, abstract = {We propose a hybrid discrete-continuous algorithm for flight planning in free flight airspaces. In a first step, our DisCOptER method discrete-continuous optimization for enhanced resolution) computes a globally optimal approximate flight path on a discretization of the problem using the A* method. This route initializes a Newton method that converges rapidly to the smooth optimum in a second step. The correctness, accuracy, and complexity of the method are goverened by the choice of the crossover point that determines the coarseness of the discretization. We analyze the optimal choice of the crossover point and demonstrate the asymtotic superority of DisCOptER over a purely discrete approach.}, language = {en} } @misc{BorndoerferDaneckerWeiser2020, author = {Bornd{\"o}rfer, Ralf and Danecker, Fabian and Weiser, Martin}, title = {A Discrete-Continuous Algorithm for Free Flight Planning}, issn = {1438-0064}, doi = {10.3390/a14010004}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-81343}, year = {2020}, abstract = {We propose a hybrid discrete-continuous algorithm for flight planning in free flight airspaces. In a first step, our DisCOptER method discrete-continuous optimization for enhanced resolution) computes a globally optimal approximate flight path on a discretization of the problem using the A* method. This route initializes a Newton method that converges rapidly to the smooth optimum in a second step. The correctness, accuracy, and complexity of the method are goverened by the choice of the crossover point that determines the coarseness of the discretization. We analyze the optimal choice of the crossover point and demonstrate the asymtotic superority of DisCOptER over a purely discrete approach.}, language = {en} } @misc{KempkeMaherRehfeldtetal.2026, author = {Kempke, Nils-Christian and Maher, Stephen John and Rehfeldt, Daniel and Gleixner, Ambros and Koch, Thorsten and Uslu, Svenja}, title = {Distributed Parallel Structure-Aware Presolving for Arrowhead Linear Programs}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-103034}, year = {2026}, abstract = {We present a structure-aware parallel presolve framework specialized to arrowhead linear programs (AHLPs) and designed for high-performance computing (HPC) environments, integrated into the parallel interior point solver PIPS-IPM++. Large-scale LPs arising from automated model generation frequently contain redundancies and numerical pathologies that necessitate effective presolve, yet existing presolve techniques are primarily serial or structure-agnostic and can become time-consuming in parallel solution workflows. Within PIPS-IPM++, AHLPs are stored in distributed memory, and our presolve builds on this to apply a highly parallel, distributed presolve across compute nodes while keeping communication overhead low and preserving the underlying arrowhead structure. We demonstrate the scalability and effectiveness of our approach on a diverse set of AHLPs and compare it against state-of-the-art presolve implementations, including PaPILO and the presolve implemented within Gurobi. Even on a single machine, our presolve significantly outperforms PaPILO by a factor of 18 and Gurobi's presolve by a factor of 6 in terms of shifted geometric mean runtime, while reducing the problems by a similar amount to PaPILO. Using a distributed compute environment, we outperform Gurobi's presolve by a factor of 13.}, language = {en} }