@misc{Shinano2021, author = {Shinano, Yuji}, title = {UG - Ubiquity Generator Framework v1.0.0beta}, doi = {10.12752/8521}, year = {2021}, abstract = {UG is a generic framework to parallelize branch-and-bound based solvers (e.g., MIP, MINLP, ExactIP) in a distributed or shared memory computing environment. It exploits the powerful performance of state-of-the-art "base solvers", such as SCIP, CPLEX, etc. without the need for base solver parallelization. UG framework, ParaSCIP(ug[SCIP,MPI]) and FiberSCIP (ug[SCIP,Pthreads]) are available as a beta version. v1.0.0: new documentation and cmake, generalization of ug framework, implementation of selfsplitrampup for fiber- and parascip, better memory and time limit handling.}, language = {en} } @inproceedings{SofranacGleixnerPokutta2021, author = {Sofranac, Boro and Gleixner, Ambros and Pokutta, Sebastian}, title = {An Algorithm-Independent Measure of Progress for Linear Constraint Propagation}, volume = {210}, booktitle = {27th International Conference on Principles and Practice of Constraint Programming (CP 2021)}, doi = {10.4230/LIPIcs.CP.2021.52}, pages = {52:1 -- 52:17}, year = {2021}, abstract = {Propagation of linear constraints has become a crucial sub-routine in modern Mixed-Integer Programming (MIP) solvers. In practice, iterative algorithms with tolerance-based stopping criteria are used to avoid problems with slow or infinite convergence. However, these heuristic stopping criteria can pose difficulties for fairly comparing the efficiency of different implementations of iterative propagation algorithms in a real-world setting. Most significantly, the presence of unbounded variable domains in the problem formulation makes it difficult to quantify the relative size of reductions performed on them. In this work, we develop a method to measure -- independently of the algorithmic design -- the progress that a given iterative propagation procedure has made at a given point in time during its execution. Our measure makes it possible to study and better compare the behavior of bounds propagation algorithms for linear constraints. We apply the new measure to answer two questions of practical relevance: (i) We investigate to what extent heuristic stopping criteria can lead to premature termination on real-world MIP instances. (ii) We compare a GPU-parallel propagation algorithm against a sequential state-of-the-art implementation and show that the parallel version is even more competitive in a real-world setting than originally reported.}, language = {en} } @misc{KempkeRehfeldtKoch2024, author = {Kempke, Nils-Christian and Rehfeldt, Daniel and Koch, Thorsten}, title = {A Massively Parallel Interior-Point-Method for Arrowhead Linear Programs}, issn = {1438-0064}, arxiv = {http://arxiv.org/abs/2412.07731}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-98829}, year = {2024}, abstract = {In practice, non-specialized interior point algorithms often cannot utilize the massively parallel compute resources offered by modern many- and multi-core compute platforms. However, efficient distributed solution techniques are required, especially for large-scale linear programs. This article describes a new decomposition technique for systems of linear equations implemented in the parallel interior-point solver PIPS-IPM++. The algorithm exploits a matrix structure commonly found in optimization problems: a doubly-bordered block-diagonal or arrowhead structure. This structure is preserved in the linear KKT systems solved during each iteration of the interior-point method. We present a hierarchical Schur complement decomposition that distributes and solves the linear optimization problem; it is designed for high-performance architectures and scales well with the availability of additional computing resources. The decomposition approach uses the border constraints' locality to decouple the factorization process. Our approach is motivated by large-scale unit-commitment problems. We demonstrate the performance of our method on a set of mid-to large-scale instances, some of which have more than 10^9 nonzeros in their constraint matrix.}, language = {en} } @article{VanBulckGoossensClarneretal.2024, author = {Van Bulck, David and Goossens, Dries and Clarner, Jan-Patrick and Dimitsas, Angelos and Fonseca, Georg H. G. and Lamas-Fernandez, Carlos and Lester, Martin Mariusz and Pedersen, Jaap and Phillips, Antony E. and Rosati, Roberto Maria}, title = {Which algorithm to select in sports timetabling?}, volume = {318}, journal = {European Journal of Operational Research}, number = {2}, arxiv = {http://arxiv.org/abs/2309.03229}, doi = {10.1016/j.ejor.2024.06.005}, pages = {575 -- 591}, year = {2024}, abstract = {Any sports competition needs a timetable, specifying when and where teams meet each other. The recent International Timetabling Competition (ITC2021) on sports timetabling showed that, although it is possible to develop general algorithms, the performance of each algorithm varies considerably over the problem instances. This paper provides a problem type analysis for sports timetabling, resulting in powerful insights into the strengths and weaknesses of eight state-of-the-art algorithms. Based on machine learning techniques, we propose an algorithm selection system that predicts which algorithm is likely to perform best based on the type of competition and constraints being used (i.e., the problem type) in a given sports timetabling problem instance. Furthermore, we visualize how the problem type relates to algorithm performance, providing insights and possibilities to further enhance several algorithms. Finally, we assess the empirical hardness of the instances. Our results are based on large computational experiments involving about 50 years of CPU time on more than 500 newly generated problem instances.}, language = {en} } @inproceedings{PedersenHoppmannBaumZitteletal.2022, author = {Pedersen, Jaap and Hoppmann-Baum, Kai and Zittel, Janina and Koch, Thorsten}, title = {Blending hydrogen into natural gas: An assessment of the capacity of the German gas grid}, booktitle = {Operations Research Proceedings 2021}, doi = {https://doi.org/10.1007/978-3-031-08623-6_28}, pages = {182 -- 187}, year = {2022}, abstract = {In the transition towards a pure hydrogen infrastructure, repurposing the existing natural gas infrastructure is considered. In this study, the maximal technically feasible injection of hydrogen into the existing German natural gas transmission network is analysed with respect to regulatory limits regarding the gas quality. We propose a transient tracking model based on the general pooling problem including linepack. The analysis is conducted using real-world hourly gas flow data on a network of about 10,000 km length.}, language = {en} } @article{Hennings2021, author = {Hennings, Felix}, title = {Large-scale empirical study on the momentum equation's inertia term}, volume = {95}, journal = {Journal of Natural Gas Science and Engineering}, publisher = {Elsevier}, doi = {10.1016/j.jngse.2021.104153}, year = {2021}, abstract = {A common approach to reduce the Euler equations' complexity for the simulation and optimization of gas networks is to neglect small terms that contribute little to the overall equations. An example is the inertia term of the momentum equation, which is said to be of negligible size under real-world operating conditions. However, this justification has always only been based on experience or single sets of artificial data points. This study closes this gap by presenting a large-scale empirical evaluation of the absolute and relative size of the inertia term when operating a real-world gas network. Our data consists of three years of fine-granular state data of one of the largest gas networks in Europe, featuring over 6,000 pipes with a total length of over 10,000 km. We found that there are only 120 events in which a subnetwork consisting of multiple pipes has an inertia term of high significance for more than three minutes. On average, such an event occurs less often than once every ten days. Therefore, we conclude that the inertia term is indeed negligible for real-world transient gas network control problems.}, language = {en} } @article{HoppmannBaum2021, author = {Hoppmann-Baum, Kai}, title = {On the Complexity of Computing Maximum and Minimum Min-Cost-Flows}, journal = {Networks}, doi = {10.1002/net.22060}, year = {2021}, abstract = {Consider a flow network, i.e., a directed graph where each arc has a nonnegative capacity value and an associated length, together with nonempty supply intervals for the sources and nonempty demand intervals for the sinks. The Maximum Min-Cost-Flow Problem (MaxMCF) is to find fixed supply and demand values within these intervals such that the optimal objective value of the induced Min-Cost-Flow Problem (MCF) is maximized. In this paper, we show that MaxMCF as well as its uncapacitated variant, the Maximum Transportation Problem (MaxTP), are NP-hard. Further, we prove that MaxMCF is APX-hard if a connectedness-condition regarding the sources and the sinks of the flow network is dropped. Finally, we show how the Minimum Min-Cost-Flow Problem (MinMCF) can be solved in polynomial time.}, language = {en} } @misc{Hennings2021, author = {Hennings, Felix}, title = {Large-scale empirical study on the momentum equation's inertia term}, issn = {1438-0064}, doi = {10.1016/j.jngse.2021.104153}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-81881}, year = {2021}, abstract = {A common approach to reduce the Euler equations' complexity for the simulation and optimization of gas networks is to neglect small terms that contribute little to the overall equations. An example is the inertia term of the momentum equation since it is said to be of negligible size under real-world operating conditions. However, this justification has always only been based on experience or single sets of artificial data points. This study closes this gap by presenting a large-scale empirical evaluation of the absolute and relative size of the inertia term when operating a real-world gas network. Our data consists of three years of fine-granular state data of one of the largest gas networks in Europe, featuring over 6,000 pipes with a total length of over 10,000 km. We found that there are only 120 events in which a subnetwork consisting of multiple pipes has an inertia term of high significance for more than three minutes. On average, such an event occurs less often than once every ten days. Therefore, we conclude that the inertia term is indeed negligible for real-world transient gas network control problems.}, language = {en} } @article{AndersonTurnerKoch2022, author = {Anderson, Lovis and Turner, Mark and Koch, Thorsten}, title = {Generative deep learning for decision making in gas networks}, volume = {95}, journal = {Mathematical Methods of Operations Research}, publisher = {Springer Nature}, doi = {10.1007/s00186-022-00777-x}, pages = {503 -- 532}, year = {2022}, abstract = {A decision support system relies on frequent re-solving of similar problem instances. While the general structure remains the same in corresponding applications, the input parameters are updated on a regular basis. We propose a generative neural network design for learning integer decision variables of mixed-integer linear programming (MILP) formulations of these problems. We utilise a deep neural network discriminator and a MILP solver as our oracle to train our generative neural network. In this article, we present the results of our design applied to the transient gas optimisation problem. With the trained network we produce a feasible solution in 2.5s, use it as a warm-start solution, and thereby decrease global optimal solution solve time by 60.5\%.}, language = {en} } @inproceedings{SofranacGleixnerPokutta2020, author = {Sofranac, Boro and Gleixner, Ambros and Pokutta, Sebastian}, title = {Accelerating Domain Propagation: an Efficient GPU-Parallel Algorithm over Sparse Matrices}, booktitle = {2020 IEEE/ACM 10th Workshop on Irregular Applications: Architectures and Algorithms (IA3)}, arxiv = {http://arxiv.org/abs/2009.07785}, doi = {10.1109/IA351965.2020.00007}, pages = {1 -- 11}, year = {2020}, abstract = {Fast domain propagation of linear constraints has become a crucial component of today's best algorithms and solvers for mixed integer programming and pseudo-boolean optimization to achieve peak solving performance. Irregularities in the form of dynamic algorithmic behaviour, dependency structures, and sparsity patterns in the input data make efficient implementations of domain propagation on GPUs and, more generally, on parallel architectures challenging. This is one of the main reasons why domain propagation in state-of-the-art solvers is single thread only. In this paper, we present a new algorithm for domain propagation which (a) avoids these problems and allows for an efficient implementation on GPUs, and is (b) capable of running propagation rounds entirely on the GPU, without any need for synchronization or communication with the CPU. We present extensive computational results which demonstrate the effectiveness of our approach and show that ample speedups are possible on practically relevant problems: on state-of-the-art GPUs, our geometric mean speed-up for reasonably-large instances is around 10x to 20x and can be as high as 195x on favorably-large instances.}, language = {en} } @misc{HenningsPetkovicStreubel2021, author = {Hennings, Felix and Petkovic, Milena and Streubel, Tom}, title = {On the Numerical Treatment of Interlaced Target Values - Modeling, Optimization and Simulation of Regulating Valves in Gas Networks}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-85359}, year = {2021}, abstract = {Due to the current and foreseeable shifts in energy production, the trading and transport operations of gas will become more dynamic, volatile, and hence also less predictable. Therefore, computer-aided support in terms of rapid simulation and control optimization will further broaden its importance for gas network dispatching. In this paper, we aim to contribute and openly publish two new mathematical models for regulators, also referred to as control valves, which together with compressors make up the most complex and involved types of active elements in gas network infrastructures. They provide full direct control over gas networks but are in turn controlled via target values, also known as set-point values, themselves. Our models incorporate up to six dynamical target values to define desired transient states for the elements' local vicinity within the network. That is, each pair of every two target values defines a bounding box for the inlet pressure, outlet pressure as well as the passing mass flow of gas. In the proposed models, those target values are prioritized differently and are constantly in competition with each other, which can only be resolved dynamically at run-time of either a simulation or optimization process. Besides careful derivation, we compare simulation and optimization results with predictions of the commercial simulation tool SIMONE.}, language = {en} } @article{ŠofranacGleixnerPokutta2022, author = {Šofranac, Boro and Gleixner, Ambros and Pokutta, Sebastian}, title = {Accelerating domain propagation: An efficient GPU-parallel algorithm over sparse matrices}, volume = {109}, journal = {Parallel Computing}, doi = {10.1016/j.parco.2021.102874}, pages = {102874}, year = {2022}, abstract = {• Currently, domain propagation in state-of-the-art MIP solvers is single thread only. • The paper presents a novel, efficient GPU algorithm to perform domain propagation. • Challenges are dynamic algorithmic behavior, dependency structures, sparsity patterns. • The algorithm is capable of running entirely on the GPU with no CPU involvement. • We achieve speed-ups of around 10x to 20x, up to 180x on favorably-large instances.}, language = {en} } @article{PedersenSpreckelsenGotzesetal.2023, author = {Pedersen, Jaap and Spreckelsen, Klaus and Gotzes, Uwe and Zittel, Janina and Koch, Thorsten}, title = {Beimischung von Wasserstoff zum Erdgas: Eine Kapazit{\"a}tsstudie des deutschen Gasnetzes}, journal = {gwf Gas + Energie}, edition = {06/2023}, publisher = {Vulkan Verlag}, year = {2023}, abstract = {Die europaische Gasinfrastruktur wird disruptiv in ein zukunftiges dekarbonisiertes Energiesystem ver{\"a}ndert; ein Prozess, der angesichts der j{\"u}ngsten politischen Situation beschleunigt werden muss. Mit einem wachsenden Wasserstoffmarkt wird der pipelinebasierte Transport unter Nutzung der bestehenden Erdgasinfrastruktur wirtschaftlich sinnvoll, tr{\"a}gt zur Erh{\"o}hung der {\"o}ffentlichen Akzeptanz bei und beschleunigt den Umstellungsprozess. In diesem Beitrag wird die maximal technisch machbare Einspeisung von Wasserstoff in das bestehende deutsche Erdgastransportnetz hinsichtlich regulatorischer Grenzwerte der Gasqualit{\"a}t analysiert. Die Analyse erfolgt auf Basis eines transienten Tracking-Modells, das auf dem allgemeinen Pooling-Problem einschließlich Linepack aufbaut. Es zeigt sich, dass das Gasnetz auch bei strengen Grenzwerten gen ̈ugend Kapazit{\"a}t bietet, um f{\"u}r einen großen Teil der bis 2030 geplanten Erzeugungskapazit{\"a}t f{\"u}r gr{\"u}nen Wasserstoff als garantierter Abnehmer zu dienen.}, language = {de} } @article{LeKoch2023, author = {Le, Thi Thai and Koch, Thorsten}, title = {Effect of inertia force on the interface stability of a tangential-velocity discontinuity in porous media}, volume = {169}, journal = {International Journal of Multiphase Flow}, doi = {10.1016/j.ijmultiphaseflow.2023.104612}, year = {2023}, abstract = {The present study investigates the stability of a tangential-velocity discontinuity in porous media during the withdrawing and injecting processes of natural gases from and into an underground gas storage. The focus is placed on analyzing the impact of inertia forces on the interface stability using the Forchheimer equations. Other publications have relied primarily on Darcy's law to describe flow stability in porous media. However, Darcy's law only adequately describes flows in which viscous forces dominate over inertia forces. As the flow rate increases, the significance of inertia forces becomes more pronounced, and Darcy's law becomes insufficient for considering such flows. Our findings indicate that even a slight consideration of the inertia effect leads to permanent destabilization of the discontinuity interface, regardless of the fluid viscosity or the Mach number. In contrast, when the inertia effect is neglected, the interface is stabilized across the entire Mach number range if the fluid viscosity is strong enough.}, language = {en} } @phdthesis{HoppmannBaum2022, author = {Hoppmann-Baum, Kai}, title = {Mathematical programming for stable control and safe operation of gas transport networks}, publisher = {TU Berlin}, doi = {10.14279/depositonce-15837}, year = {2022}, abstract = {The fight against climate change makes extreme but inevitable changes in the energy sector necessary. These in turn lead to novel and complex challenges for the transmission system operators (TSOs) of gas transport networks. In this thesis, we consider four different planning problems emerging from real-world operations and present mathematical programming models and solution approaches for all of them. Due to regulatory requirements and side effects of renewable energy production, controlling today's gas networks with their involved topologies is becoming increasingly difficult. Based on the network station modeling concept for approximating the technical capabilities of complex subnetworks, e.g., compressor stations, we introduce a tri-level MIP model to determine important global control decisions. Its goal is to avoid changes in the network elements' settings while deviations from future inflow pressures as well as supplies and demands are minimized. A sequential linear programming inspired post-processing routine is run to derive physically accurate solutions w.r.t. the transient gas flow in pipelines. Computational experiments based on real-world data show that meaningful solutions are quickly and reliably determined. Therefore, the algorithmic approach is used within KOMPASS, a decision support system for the transient network control that we developed together with the Open Grid Europe GmbH (OGE), one of Europe's largest natural gas TSOs. Anticipating future use cases, we adapt the aforementioned algorithmic approach for hydrogen transport. We investigate whether the natural gas infrastructure can be repurposed and how the network control changes when energy-equivalent amounts of hydrogen are transported. Besides proving the need for purpose-built compressors, we observe that, due to the reduced linepack, the network control becomes more dynamic, compression energy increases by 440\% on average, and stricter regulatory rules regarding the balancing of supply and demand become necessary. Extreme load flows expose the technical limits of gas networks and are therefore of great importance to the TSOs. In this context, we introduce the Maximum Transportation Problem and the Maximum Potential Transport Moment Problem to determine severe transport scenarios. Both can be modeled as linear bilevel programs where the leader selects supplies and demands, maximizing the follower's transport effort. To solve them, we identify solution-equivalent instances with acyclic networks, provide variable bounds regarding their KKT reformulations, apply the big-M technique, and solve the resulting MIPs. A case study shows that the obtained scenarios exceed the maximum severity values of a provided test set by at least 23\%. OGE's transmission system is 11,540km long. Monitoring it is crucial for safe operations. To this end, we discuss the idea of using uncrewed aerial vehicles and introduce the Length-Constrained Cycle Partition Problem to optimize their routing. Its goal is to find a smallest cycle partition satisfying vertex-induced length requirements. Besides a greedy-style heuristic, we propose two MIP models. Combining them with symmetry-breaking constraints as well as valid inequalities and lower bounds from conflict hypergraphs yields a highly performant solution algorithm for this class of problems.}, language = {en} } @misc{PedersenWeinandSyranidouetal.2023, author = {Pedersen, Jaap and Weinand, Jann Michael and Syranidou, Chloi and Rehfeldt, Daniel}, title = {An efficient solver for multi-objective onshore wind farm siting and network integration}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-90590}, year = {2023}, abstract = {Existing planning approaches for onshore wind farm siting and network integration often do not meet minimum cost solutions or social and environmental considerations. In this paper, we develop an approach for the multi-objective optimization of turbine locations and their network connection using a Quota Steiner tree problem. Applying a novel transformation on a known directed cut formulation, reduction techniques, and heuristics, we design an exact solver that makes large problem instances solvable and outperforms generic MIP solvers. Although our case studies in selected regions of Germany show large trade-offs between the objective criteria of cost and landscape impact, small burdens on one criterion can significantly improve the other criteria. In addition, we demonstrate that contrary to many approaches for exclusive turbine siting, network integration must be simultaneously optimized in order to avoid excessive costs or landscape impacts in the course of a wind farm project. Our novel problem formulation and the developed solver can assist planners in decision making and help optimize wind farms in large regions in the future.}, language = {en} } @phdthesis{Hennings2023, author = {Hennings, Felix}, title = {Modeling and solving real-world transient gas network transport problems using mathematical programming}, year = {2023}, abstract = {This thesis considers the transient gas network control optimization problem for on-shore pipeline-based transmission networks with numerous gas routing options. As input, the problem is given the network's topology, its initial state, and future demands at the boundaries of the network, which prescribe the gas flow exchange and potentially the pressure values. The task is to find a set of future control measures for all the active, i.e., controllable, elements in the network that minimizes a combination of different penalty functions. The problem is examined in the context of a decision support tool for gas network dispatchers. This results in detailed models featuring a diverse set of constraints, large and challenging real-world instances, and demanding time limit requirements. All these factors further complicate the problem, which is already difficult to solve in theory due to the inherent combination of non-linear and combinatorial aspects. Our contributions concern different steps of the process of solving the problem. Regarding the model formulation, we investigate the validity of two common approximations of the gas flow description in transport pipes: neglecting the inertia term and assuming a friction term that linearly depends on the gas flow and the pressure. For both, we examine if they can be applied under real-world conditions by evaluating a large amount of historical state data of the network of our project partner, the gas network operator Open Grid Europe. While we can confirm that it is reasonable to ignore the influence of the inertia term, the friction term linearization leads to significant errors and, as a consequence, cannot be used for describing the general gas flow behavior in transport pipes. As another topic of this thesis, we introduce the target value concept as a more realistic approach to express control actions of dispatchers regarding regulators and compressor stations. Here, we derive the mechanisms defined for target values based on the gas flow principles in pipes and develop a mixed-integer programming model capturing their behavior. The accuracy of this model is demonstrated in comparison to a target-value-based industry-standard simulator. Furthermore, we present two heuristics for the transient gas network control optimization problem featuring target values that are based on approximative models for the target-value-based control and determine the final decisions in a post-processing step. To compare the performance of the two heuristics with the approach of directly solving the corresponding model, we evaluate them on a set of artificially created test instances. Finally, we develop problem-specific algorithms for two variants of the described problem. One considers the control optimization for a single network station, which represents a local operation site featuring a large number of active elements. The used transient model is very detailed and includes a sophisticated representation of the compressor stations. Based on the shortness of the pipes in the station, the corresponding algorithm finds valid solutions by solving a series of stationary model variants as well as a transient rolling horizon approach. As the second variant, we consider the problem on the entire network but assume an approximative model representing the control capabilities of network stations. Aside from a new description of the compression capabilities, we introduce an algorithm that uses a combination of sequential mixed-integer programming, two heuristics based on reduced time horizons, and a specialized dynamic branch-and-bound node limit to determine promising values for the binary variables of the model. Complete solutions for the problem are obtained by fixing the binary values and solving the remaining non-linear program. Both algorithms are investigated in extensive empirical studies based on real-world instances of the corresponding model variants.}, language = {en} } @article{HenningsPetkovicStreubel2024, author = {Hennings, Felix and Petkovic, Milena and Streubel, Tom}, title = {On the Numerical Treatment of Interlaced Target Values - Modeling, Optimization and Simulation of Regulating Valves in Gas Networks}, volume = {25}, journal = {Optimization and Engineering}, publisher = {Springer Nature}, doi = {10.1007/s11081-023-09812-0}, pages = {491 -- 527}, year = {2024}, abstract = {Due to the current and foreseeable shifts towards carbon dioxide neutral energy production, which will likely result in balancing fluctuating renewable energy generation by transforming power-to-gas-to-power as well as building a large-scale hydrogen transport infrastructure, the trading and transport operations of gas will become more dynamic, volatile, and hence also less predictable. Therefore, computer-aided support in terms of rapid simulation and control optimization will further broaden its importance for gas network dispatching. In this paper, we aim to contribute and openly publish two new mathematical models for regulators, also referred to as control valves, which together with compressors make up the most complex and involved types of active elements in gas network infrastructures. They provide direct control over gas networks but are in turn controlled via target values, also known as set-point values, themselves. Our models incorporate up to six dynamical target values to define desired transient states for the elements' local vicinity within the network. That is, each pair of every two target values defines a bounding box for the inlet pressure, outlet pressure as well as the passing mass flow of gas. In the proposed models, those target values are prioritized differently and are constantly in competition with each other, which can only be resolved dynamically at run-time of either a simulation or optimization process. Besides careful derivation, we compare simulation and optimization results with predictions of the widely adopted commercial simulation tool SIMONE, serving as our substitute for actual real-world transport operations.}, language = {en} } @misc{PrauseHoppmannBaumDefournyetal.2020, author = {Prause, Felix and Hoppmann-Baum, Kai and Defourny, Boris and Koch, Thorsten}, title = {The Maximum Diversity Assortment Selection Problem}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-81039}, year = {2020}, abstract = {In this paper, we introduce the Maximum Diversity Assortment Selection Problem (MADASS), which is a generalization of the 2-dimensional Cutting Stock Problem (2CSP). Given a set of rectangles and a rectangular container, the goal of 2CSP is to determine a subset of rectangles that can be placed in the container without overlapping, i.e., a feasible assortment, such that a maximum area is covered. In MADASS, we need to determine a set of feasible assortments, each of them covering a certain minimum threshold of the container, such that the diversity among them is maximized. Thereby, diversity is defined as minimum or average normalized Hamming-Distance of all assortment pairs. The MADASS Problem was used in the 11th AIMMS-MOPTA Competition in 2019. The methods we describe in this article and the computational results won the contest. In the following, we give a definition of the problem, introduce a mathematical model and solution approaches, determine upper bounds on the diversity, and conclude with computational experiments conducted on test instances derived from the 2CSP literature.}, language = {en} } @misc{AndersonTurnerKoch2020, author = {Anderson, Lovis and Turner, Mark and Koch, Thorsten}, title = {Generative deep learning for decision making in gas networks}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-81103}, year = {2020}, abstract = {A decision support system relies on frequent re-solving of similar problem instances. While the general structure remains the same in corresponding applications, the input parameters are updated on a regular basis. We propose a generative neural network design for learning integer decision variables of mixed-integer linear programming (MILP) formulations of these problems. We utilise a deep neural network discriminator and a MILP solver as our oracle to train our generative neural network. In this article, we present the results of our design applied to the transient gas optimisation problem. With the trained network we produce a feasible solution in 2.5s, use it as a warm-start solution, and thereby decrease global optimal solution solve time by 60.5\%.}, language = {en} } @article{HoppmannBaumHenningsZitteletal.2021, author = {Hoppmann-Baum, Kai and Hennings, Felix and Zittel, Janina and Gotzes, Uwe and Spreckelsen, Eva-Maria and Spreckelsen, Klaus and Koch, Thorsten}, title = {An Optimization Approach for the Transient Control of Hydrogen Transport Networks}, journal = {Mathematical Methods of Operations Research}, number = {Special Issue on Energy Networks}, year = {2021}, language = {en} } @misc{HoppmannBaumMexiBurdakovetal.2020, author = {Hoppmann-Baum, Kai and Mexi, Gioni and Burdakov, Oleg and Casselgren, Carl Johan and Koch, Thorsten}, title = {Length-Constrained Cycle Partition with an Application to UAV Routing}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-80489}, year = {2020}, abstract = {In this article, we discuss the Length-Constrained Cycle Partition Problem (LCCP). Besides edge weights, the undirected graph in LCCP features an individual critical weight value for each vertex. A cycle partition, i.e., a vertex disjoint cycle cover, is a feasible solution if the length of each cycle is not greater than the critical weight of each of the vertices in the cycle. The goal is to find a feasible partition with the minimum number of cycles. In this article, we discuss theoretical properties, preprocessing techniques, and two mixed-integer programming models (MIP) for LCCP both inspired by formulations for the closely related Travelling Salesperson Problem (TSP). Further, we introduce conflict hypergraphs, whose cliques yield valid constraints for the MIP models. We conclude with a report on computational experiments conducted on (A)TSPLIB-based instances. As an example, we use a routing problem in which a fleet of uncrewed aerial vehicles (UAVs) patrols a set of areas.}, language = {en} } @article{GotzesHoppmannBaum2020, author = {Gotzes, Uwe and Hoppmann-Baum, Kai}, title = {Bounding the final rank during a round robin tournament with integer programming}, volume = {1866-1505}, journal = {Operational Research}, doi = {https://doi.org/10.1007/s12351-020-00546-w}, year = {2020}, abstract = {This article is mainly motivated by the urge to answer two kinds of questions regarding the Bundesliga, which is Germany's primary football (soccer) division having the highest average stadium attendance worldwide: "At any point in the season, what is the lowest final rank a certain team can achieve?" and "At any point in the season, what is the highest final rank a certain team can achieve?". Although we focus on the Bundesliga in particular, the integer programming formulations we introduce to answer these questions can easily be adapted to a variety of other league systems and tournaments.}, language = {en} } @article{KochSchmidtHilleretal.2020, author = {Koch, Thorsten and Schmidt, Martin and Hiller, Benjamin and Pfetsch, Marc and Geißler, Bj{\"o}rn and Henrion, Ren{\´e} and Joormann, Imke and Martin, Alexander and Morsi, Antonio and R{\"o}misch, Werner and Schewe, Lars and Schultz, R{\"u}diger}, title = {Capacity Evaluation for Large-Scale Gas Networks}, volume = {35}, journal = {German Success Stories in Industrial Mathematics}, isbn = {978-3-030-81454-0}, doi = {10.1007/978-3-030-81455-7}, pages = {23 -- 28}, year = {2020}, language = {en} } @article{ChenZakiyevaZhuetal.2020, author = {Chen, Ying and Zakiyeva, Nazgul and Zhu, Bangzhu and Koch, Thorsten}, title = {Modeling and Forecasting the Dynamics of the Natural Gas Transmission Network in Germany with the Demand and Supply Balance Constraint}, journal = {Applied Energy}, number = {278}, doi = {10.1016/j.apenergy.2020.115597}, year = {2020}, language = {en} } @article{KochChenLimetal.2020, author = {Koch, Thorsten and Chen, Ying and Lim, Kian Guan and Xu, Xiaofei and Zakiyeva, Nazgul}, title = {A review study of functional autoregressive models with application to energy forecasting}, journal = {WIREs Computational Statistics}, doi = {10.1002/wics.1525}, year = {2020}, language = {en} } @incollection{KochRehfeldtShinano2020, author = {Koch, Thorsten and Rehfeldt, Daniel and Shinano, Yuji}, title = {An exact high performance solver for Steiner tree problems in graphs and related problems}, booktitle = {Modeling, Simulation and Optimization of Complex Processes HPSC 2018}, publisher = {Springer}, year = {2020}, language = {en} } @misc{HoppmannBaumHenningsZitteletal.2020, author = {Hoppmann-Baum, Kai and Hennings, Felix and Zittel, Janina and Gotzes, Uwe and Spreckelsen, Eva-Maria and Spreckelsen, Klaus and Koch, Thorsten}, title = {From Natural Gas towards Hydrogen - A Feasibility Study on Current Transport Network Infrastructure and its Technical Control}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-79901}, year = {2020}, abstract = {This study examines the usability of a real-world, large-scale natural gas transport infrastructure for hydrogen transport. We investigate whether a converted network can transport the amounts of hydrogen necessary to satisfy current energy demands. After introducing an optimization model for the robust transient control of hydrogen networks, we conduct computational experiments based on real-world demand scenarios. Using a representative network, we demonstrate that replacing each turbo compressor unit by four parallel hydrogen compressors, each of them comprising multiple serial compression stages, and imposing stricter rules regarding the balancing of in- and outflow suffices to realize transport in a majority of scenarios. However, due to the reduced linepack there is an increased need for technical and non-technical measures leading to a more dynamic network control. Furthermore, the amount of energy needed for compression increases by 364\% on average.}, language = {en} } @article{HoppmannBaumHenningsLenzetal.2021, author = {Hoppmann-Baum, Kai and Hennings, Felix and Lenz, Ralf and Gotzes, Uwe and Heinecke, Nina and Spreckelsen, Klaus and Koch, Thorsten}, title = {Optimal Operation of Transient Gas Transport Networks}, volume = {22}, journal = {Optimization and Engineering}, doi = {10.1007/s11081-020-09584-x}, pages = {735 -- 781}, year = {2021}, abstract = {In this paper, we describe an algorithmic framework for the optimal operation of transient gas transport networks consisting of a hierarchical MILP formulation together with a sequential linear programming inspired post-processing routine. Its implementation is part of the KOMPASS decision support system, which is currently used in an industrial setting. Real-world gas transport networks are controlled by operating complex pipeline intersection areas, which comprise multiple compressor units, regulators, and valves. In the following, we introduce the concept of network stations to model them. Thereby, we represent the technical capabilities of a station by hand-tailored artificial arcs and add them to network. Furthermore, we choose from a predefined set of flow directions for each network station and time step, which determines where the gas enters and leaves the station. Additionally, we have to select a supported simple state, which consists of two subsets of artificial arcs: Arcs that must and arcs that cannot be used. The goal is to determine a stable control of the network satisfying all supplies and demands. The pipeline intersections, that are represented by the network stations, were initially built centuries ago. Subsequently, due to updates, changes, and extensions, they evolved into highly complex and involved topologies. To extract their basic properties and to model them using computer-readable and optimizable descriptions took several years of effort. To support the dispatchers in controlling the network, we need to compute a continuously updated list of recommended measures. Our motivation for the model presented here is to make fast decisions on important transient global control parameters, i.e., how to route the flow and where to compress the gas. Detailed continuous and discrete technical control measures realizing them, which take all hardware details into account, are determined in a subsequent step. In this paper, we present computational results from the KOMPASS project using detailed real-world data.}, language = {en} } @incollection{HoppmannBaumMexiBurdakovetal.2020, author = {Hoppmann-Baum, Kai and Mexi, Gioni and Burdakov, Oleg and Casselgren, Carl Johan and Koch, Thorsten}, title = {Minimum Cycle Partition with Length Requirements}, volume = {12296}, booktitle = {Integration of Constraint Programming, Artificial Intelligence, and Operations Research}, editor = {Hebrard, Emmanuel and Musliu, Nysret}, publisher = {Springer International Publishing}, address = {Cham}, isbn = {978-3-030-58941-7}, doi = {10.1007/978-3-030-58942-4_18}, pages = {273 -- 282}, year = {2020}, abstract = {In this article we introduce a Minimum Cycle Partition Problem with Length Requirements (CPLR). This generalization of the Travelling Salesman Problem (TSP) originates from routing Unmanned Aerial Vehicles (UAVs). Apart from nonnegative edge weights, CPLR has an individual critical weight value associated with each vertex. A cycle partition, i.e., a vertex disjoint cycle cover, is regarded as a feasible solution if the length of each cycle, which is the sum of the weights of its edges, is not greater than the critical weight of each of its vertices. The goal is to find a feasible partition, which minimizes the number of cycles. In this article, a heuristic algorithm is presented together with a Mixed Integer Programming (MIP) formulation of CPLR. We furthermore introduce a conflict graph, whose cliques yield valid constraints for the MIP model. Finally, we report on computational experiments conducted on TSPLIB-based test instances.}, language = {en} } @article{RaminBestuzhevaGargaloetal.2021, author = {Ramin, Elham and Bestuzheva, Ksenia and Gargalo, Carina and Ramin, Danial and Schneider, Carina and Ramin, Pedram and Flores-Alsina, Xavier and Andersen, Maj M. and Gernaey, Krist V.}, title = {Incremental design of water symbiosis networks with prior knowledge: The case of an industrial park in Kenya}, volume = {751}, journal = {Science of the Total Environment}, doi = {https://doi.org/10.1016/j.scitotenv.2020.141706}, year = {2021}, abstract = {Industrial parks have a high potential for recycling and reusing resources such as water across companies by creating symbiosis networks. In this study, we introduce a mathematical optimization framework for the design of water network integration in industrial parks formulated as a large-scale standard mixed-integer non-linear programming (MINLP) problem. The novelty of our approach relies on i) developing a multi-level incremental optimization framework for water network synthesis, ii) including prior knowledge of demand growth and projected water scarcity to evaluate the significance of water-saving solutions, iii) incorporating a comprehensive formulation of water network synthesis problem including multiple pollutants and different treatment units and iv) performing a multi-objective optimization of the network including freshwater savings and relative cost of the network. The significance of the proposed optimization framework is illustrated by applying it to an existing industrial park in a water-scarce region in Kenya. Firstly, we illustrated the benefits of including prior knowledge to prevent an over-design of the network at the early stages. In the case study, we achieved a more flexible and expandable water network with 36\% lower unit cost at the early stage and 15\% lower unit cost at later stages for the overall maximum freshwater savings of 25\%. Secondly, multi-objective analysis suggests an optimum freshwater savings of 14\% to reduce the unit cost of network by half. Moreover, the significance of symbiosis networks is highlighted by showing that intra-company connections can only achieve a maximum freshwater savings of 17\% with significantly higher unit cost (+45\%). Finally, we showed that the values of symbiosis connectivity index in the Pareto front correspond to higher freshwater savings, indicating the significant role of the symbiosis network in the industrial park under study. This is the first study, where all the above elements have been taken into account simultaneously for the design of a water reuse network.}, language = {en} } @book{HadjidimitriouFrangioniLodietal.2020, author = {Hadjidimitriou, Natalia Selini and Frangioni, Antonio and Lodi, Andrea and Koch, Thorsten}, title = {Mathematical Optimization for Efficient and Robust Energy Networks}, volume = {4}, editor = {Hadjidimitriou, Natalia Selini and Frangioni, Antonio and Lodi, Andrea and Koch, Thorsten}, publisher = {Springer}, isbn = {978-3-030-57441-3}, doi = {10.1007/978-3-030-57442-0}, year = {2020}, language = {en} } @misc{HenningsHoppmannBaumZittel2022, author = {Hennings, Felix and Hoppmann-Baum, Kai and Zittel, Janina}, title = {Optimizing transient gas network control for challenging real-world instances using MIP-based heuristics}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-86842}, year = {2022}, abstract = {Optimizing the transient control of gas networks is a highly challenging task. The corresponding model incorporates the combinatorial complexity of determining the settings for the many active elements as well as the non-linear and non-convex nature of the physical and technical principles of gas transport. In this paper, we present the latest improvements of our ongoing work to solve this problem for real-world, large-scale problem instances: By adjusting our mixed-integer non-linear programming model regarding the gas compression capabilities in the network, we reflect the technical limits of the underlying units more accurately while maintaining a similar overall model size. In addition, we introduce a new algorithmic approach that is based on splitting the complexity of the problem by first finding assignments for discrete variables and then determining the continuous variables as locally optimal solution of the corresponding non-linear program. For the first task, we design multiple different heuristics based on concepts for general time-expanded optimization problems that find solutions by solving a sequence of sub-problems defined on reduced time horizons. To demonstrate the competitiveness of our approach, we test our algorithm on particularly challenging historic demand scenarios. The results show that high-quality solutions are obtained reliably within short solving times, making the algorithm well-suited to be applied at the core of time-critical industrial applications.}, language = {en} } @misc{PedersenLeKochetal.2022, author = {Pedersen, Jaap and Le, Thi Thai and Koch, Thorsten and Zittel, Janina}, title = {Optimal discrete pipe sizing for tree-shaped CO2 networks}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-87574}, year = {2022}, abstract = {While energy-intensive industries like the steel industry plan to switch to renewable energy sources, other industries, such as the cement industry, have to rely on carbon capture storage and utilization technologies to reduce the inevitable carbon dioxide (CO2) emissions of their production processes. In this context, we investigate the problem of finding optimal pipeline diameters from a discrete set of diameters for a tree-shaped network transporting captured CO2 from multiple sources to a single sink. The general problem of optimizing arc capacities in potential-based fluid networks is a challenging mixed-integer nonlinear program. Additionally, the behaviour of CO2 is highly sensitive and nonlinear regarding temperature and pressure changes. We propose an iterative algorithm splitting the problem into two parts: a) the pipe-sizing problem under a fixed supply scenario and temperature distribution and b) the thermophysical modelling including mixing effects, the Joule-Thomson effect, and heat exchange with the surrounding environment. We show the effectiveness of our approach by applying our algorithm to a real-world network planning problem for a CO2 network in Western Germany.}, language = {en} } @article{HoppmannBaumBurdakovMexietal.2022, author = {Hoppmann-Baum, Kai and Burdakov, Oleg and Mexi, Gioni and Casselgren, Carl Johan and Koch, Thorsten}, title = {Length-Constrained Cycle Partition with an Application to UAV Routing}, journal = {Optimization Methods and Software}, doi = {10.1080/10556788.2022.2053972}, year = {2022}, abstract = {This article discusses the Length-Constrained Cycle Partition Problem (LCCP), which constitutes a new generalization of the Travelling Salesperson Problem (TSP). Apart from nonnegative edge weights, the undirected graph in LCCP features a nonnegative critical length parameter for each vertex. A cycle partition, i.e., a vertex-disjoint cycle cover, is a feasible solution for LCCP if the length of each cycle is not greater than the critical length of each vertex contained in it. The goal is to find a feasible partition having a minimum number of cycles. Besides analyzing theoretical properties and developing preprocessing techniques, we propose an elaborate heuristic algorithm that produces solutions of good quality even for large-size instances. Moreover, we present two exact mixed-integer programming formulations (MIPs) for LCCP, which are inspired by well-known modeling approaches for TSP. Further, we introduce the concept of conflict hypergraphs, whose cliques yield valid constraints for the MIP models. We conclude with a discussion on computational experiments that we conducted using (A)TSPLIB-based problem instances. As a motivating example application, we describe a routing problem where a fleet of uncrewed aerial vehicles (UAVs) must patrol a given set of areas.}, language = {en} } @misc{Shinano2020, author = {Shinano, Yuji}, title = {UG - Ubiquity Generator Framework v0.9.1}, doi = {10.12752/8508}, year = {2020}, abstract = {UG is a generic framework to parallelize branch-and-bound based solvers (e.g., MIP, MINLP, ExactIP) in a distributed or shared memory computing environment. It exploits the powerful performance of state-of-the-art "base solvers", such as SCIP, CPLEX, etc. without the need for base solver parallelization. UG framework, ParaSCIP(ug[SCIP,MPI]) and FiberSCIP (ug[SCIP,Pthreads]) are available as a beta version. For MIP solving, ParaSCIP and FiberSCIP are well debugged and should be stable. For MINLP solving, they are relatively stable, but not as thoroughly debugged. This release version should handle branch-and-cut approaches where subproblems are defined by variable bounds and also by constrains for ug[SCIP,*] ParaSCIP and FiberSCIP). Therefore, problem classes other than MIP or MINLP can be handled, but they have not been tested yet. v0.9.1: Update orbitope cip files.}, language = {en} } @inproceedings{CriadoMartinezRubioPokutta2022, author = {Criado, Francisco and Mart{\´i}nez-Rubio, David and Pokutta, Sebastian}, title = {Fast Algorithms for Packing Proportional Fairness and its Dual}, volume = {36}, booktitle = {Proceedings of the Conference on Neural Information Processing Systems}, year = {2022}, abstract = {The proportional fair resource allocation problem is a major problem studied in flow control of networks, operations research, and economic theory, where it has found numerous applications. This problem, defined as the constrained maximization of sum_i log x_i, is known as the packing proportional fairness problem when the feasible set is defined by positive linear constraints and x ∈ R≥0. In this work, we present a distributed accelerated first-order method for this problem which improves upon previous approaches. We also design an algorithm for the optimization of its dual problem. Both algorithms are width-independent.}, language = {en} } @article{Kerdreuxd'AspremontPokutta2021, author = {Kerdreux, Thomas and d'Aspremont, Alexandre and Pokutta, Sebastian}, title = {Local and Global Uniform Convexity Conditions}, year = {2021}, abstract = {We review various characterizations of uniform convexity and smoothness on norm balls in finite-dimensional spaces and connect results stemming from the geometry of Banach spaces with scaling inequalities used in analysing the convergence of optimization methods. In particular, we establish local versions of these conditions to provide sharper insights on a recent body of complexity results in learning theory, online learning, or offline optimization, which rely on the strong convexity of the feasible set. While they have a significant impact on complexity, these strong convexity or uniform convexity properties of feasible sets are not exploited as thoroughly as their functional counterparts, and this work is an effort to correct this imbalance. We conclude with some practical examples in optimization and machine learning where leveraging these conditions and localized assumptions lead to new complexity results.}, language = {en} } @article{SchimunekSeidlElezetal.2024, author = {Schimunek, Johannes and Seidl, Philipp and Elez, Katarina and Hempel, Tim and Le, Tuan and No{\´e}, Frank and Olsson, Simon and Raich, Llu{\´i}s and Winter, Robin and Gokcan, Hatice and Gusev, Filipp and Gutkin, Evgeny M. and Isayev, Olexandr and Kurnikova, Maria G. and Narangoda, Chamali H. and Zubatyuk, Roman and Bosko, Ivan P. and Furs, Konstantin V. and Karpenko, Anna D. and Kornoushenko, Yury V. and Shuldau, Mikita and Yushkevich, Artsemi and Benabderrahmane, Mohammed B. and Bousquet-Melou, Patrick and Bureau, Ronan and Charton, Beatrice and Cirou, Bertrand C. and Gil, G{\´e}rard and Allen, William J. and Sirimulla, Suman and Watowich, Stanley and Antonopoulos, Nick and Epitropakis, Nikolaos and Krasoulis, Agamemnon and Itsikalis, Vassilis and Theodorakis, Stavros and Kozlovskii, Igor and Maliutin, Anton and Medvedev, Alexander and Popov, Petr and Zaretckii, Mark and Eghbal-Zadeh, Hamid and Halmich, Christina and Hochreiter, Sepp and Mayr, Andreas and Ruch, Peter and Widrich, Michael and Berenger, Francois and Kumar, Ashutosh and Yamanishi, Yoshihiro and Zhang, Kam Y. J. and Bengio, Emmanuel and Bengio, Yoshua and Jain, Moksh J. and Korablyov, Maksym and Liu, Cheng-Hao and Marcou, Gilles and Glaab, Enrico and Barnsley, Kelly and Iyengar, Suhasini M. and Ondrechen, Mary Jo and Haupt, V. Joachim and Kaiser, Florian and Schroeder, Michael and Pugliese, Luisa and Albani, Simone and Athanasiou, Christina and Beccari, Andrea and Carloni, Paolo and D'Arrigo, Giulia and Gianquinto, Eleonora and Goßen, Jonas and Hanke, Anton and Joseph, Benjamin P. and Kokh, Daria B. and Kovachka, Sandra and Manelfi, Candida and Mukherjee, Goutam and Mu{\~n}iz-Chicharro, Abraham and Musiani, Francesco and Nunes-Alves, Ariane and Paiardi, Giulia and Rossetti, Giulia and Sadiq, S. Kashif and Spyrakis, Francesca and Talarico, Carmine and Tsengenes, Alexandros and Wade, Rebecca C. and Copeland, Conner and Gaiser, Jeremiah and Olson, Daniel R. and Roy, Amitava and Venkatraman, Vishwesh and Wheeler, Travis J. and Arthanari, Haribabu and Blaschitz, Klara and Cespugli, Marco and Durmaz, Vedat and Fackeldey, Konstantin and Fischer, Patrick D. and Gorgulla, Christoph and Gruber, Christian and Gruber, Karl and Hetmann, Michael and Kinney, Jamie E. and Padmanabha Das, Krishna M. and Pandita, Shreya and Singh, Amit and Steinkellner, Georg and Tesseyre, Guilhem and Wagner, Gerhard and Wang, Zi-Fu and Yust, Ryan J. and Druzhilovskiy, Dmitry S. and Filimonov, Dmitry A. and Pogodin, Pavel V. and Poroikov, Vladimir and Rudik, Anastassia V. and Stolbov, Leonid A. and Veselovsky, Alexander V. and De Rosa, Maria and De Simone, Giada and Gulotta, Maria R. and Lombino, Jessica and Mekni, Nedra and Perricone, Ugo and Casini, Arturo and Embree, Amanda and Gordon, D. Benjamin and Lei, David and Pratt, Katelin and Voigt, Christopher A. and Chen, Kuang-Yu and Jacob, Yves and Krischuns, Tim and Lafaye, Pierre and Zettor, Agn{\`e}s and Rodr{\´i}guez, M. Luis and White, Kris M. and Fearon, Daren and Von Delft, Frank and Walsh, Martin A. and Horvath, Dragos and Brooks III, Charles L. and Falsafi, Babak and Ford, Bryan and Garc{\´i}a-Sastre, Adolfo and Yup Lee, Sang and Naffakh, Nadia and Varnek, Alexandre and Klambauer, G{\"u}nter and Hermans, Thomas M.}, title = {A community effort in SARS-CoV-2 drug discovery}, volume = {43}, journal = {Molecular Informatics}, number = {1}, doi = {https://doi.org/10.1002/minf.202300262}, pages = {e202300262}, year = {2024}, language = {en} } @article{GorgullaNigamKoopetal.2023, author = {Gorgulla, Christoph and Nigam, AkshatKumar and Koop, Matt and Selim {\c{C}}{\i}naroğlu, S{\"u}leyman and Secker, Christopher and Haddadnia, Mohammad and Kumar, Abhishek and Malets, Yehor and Hasson, Alexander and Li, Minkai and Tang, Ming and Levin-Konigsberg, Roni and Radchenko, Dmitry and Kumar, Aditya and Gehev, Minko and Aquilanti, Pierre-Yves and Gabb, Henry and Alhossary, Amr and Wagner, Gerhard and Aspuru-Guzik, Al{\´a}n and Moroz, Yurii S. and Fackeldey, Konstantin and Arthanari, Haribabu}, title = {VirtualFlow 2.0 - The Next Generation Drug Discovery Platform Enabling Adaptive Screens of 69 Billion Molecules}, journal = {bioRxiv}, doi = {10.1101/2023.04.25.537981}, year = {2023}, language = {en} } @article{RaharinirinaSunkaravonKleistetal.2024, author = {Raharinirina, Nomenjanahary Alexia and Sunkara, Vikram and von Kleist, Max and Fackeldey, Konstantin and Weber, Marcus}, title = {Multi-Input data ASsembly for joint Analysis (MIASA): A framework for the joint analysis of disjoint sets of variables}, volume = {19}, journal = {PLOS ONE}, number = {5}, publisher = {Public Library of Science}, doi = {10.1371/journal.pone.0302425}, pages = {26}, year = {2024}, language = {en} } @article{TrepteSeckerOlivetetal.2024, author = {Trepte, Philipp and Secker, Christopher and Olivet, Julien and Blavier, Jeremy and Kostova, Simona and Maseko, Sibusiso B 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 Choi, Soon Gang 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}, volume = {20}, journal = {Molecular Systems Biology}, number = {4}, publisher = {Springer Science and Business Media LLC}, issn = {1744-4292}, doi = {https://doi.org/10.1038/s44320-024-00019-8}, pages = {428 -- 457}, year = {2024}, abstract = {Protein-protein interactions (PPIs) offer great opportunities to expand the druggable proteome and therapeutically tackle various diseases, but remain challenging targets for drug discovery. Here, we provide a comprehensive pipeline that combines experimental and computational tools to identify and validate PPI targets and perform early-stage drug discovery. We have developed a machine learning approach that prioritizes interactions by analyzing quantitative data from binary PPI assays or AlphaFold-Multimer predictions. Using the quantitative assay LuTHy together with our machine learning algorithm, we identified high-confidence interactions among SARS-CoV-2 proteins for which we predicted three-dimensional structures using AlphaFold-Multimer. We employed VirtualFlow to target the contact interface of the NSP10-NSP16 SARS-CoV-2 methyltransferase complex by ultra-large virtual drug screening. Thereby, we identified a compound that binds to NSP10 and inhibits its interaction with NSP16, while also disrupting the methyltransferase activity of the complex, and SARS-CoV-2 replication. Overall, this pipeline will help to prioritize PPI targets to accelerate the discovery of early-stage drug candidates targeting protein complexes and pathways.}, language = {en} } @article{BaermannMartinPokuttaetal.2018, author = {B{\"a}rmann, Andreas and Martin, Alexander and Pokutta, Sebastian and Schneider, Oskar}, title = {An Online-Learning Approach to Inverse Optimization}, year = {2018}, language = {en} } @article{BienenstockMunozPokutta2018, author = {Bienenstock, Daniel and Mu{\~n}oz, Gonzalo and Pokutta, Sebastian}, title = {Principled Deep Neural Network Training through Linear Programming}, year = {2018}, abstract = {Deep Learning has received significant attention due to its impressive performance in many state-of-the-art learning tasks. Unfortunately, while very powerful, Deep Learning is not well understood theoretically and in particular only recently results for the complexity of training deep neural networks have been obtained. In this work we show that large classes of deep neural networks with various architectures (e.g., DNNs, CNNs, Binary Neural Networks, and ResNets), activation functions (e.g., ReLUs and leaky ReLUs), and loss functions (e.g., Hinge loss, Euclidean loss, etc) can be trained to near optimality with desired target accuracy using linear programming in time that is exponential in the input data and parameter space dimension and polynomial in the size of the data set; improvements of the dependence in the input dimension are known to be unlikely assuming P≠NP, and improving the dependence on the parameter space dimension remains open. In particular, we obtain polynomial time algorithms for training for a given fixed network architecture. Our work applies more broadly to empirical risk minimization problems which allows us to generalize various previous results and obtain new complexity results for previously unstudied architectures in the proper learning setting.}, language = {en} } @inproceedings{Kerdreuxd'AspremontPokutta2020, author = {Kerdreux, Thomas and d'Aspremont, Alexandre and Pokutta, Sebastian}, title = {Projection-Free Optimization on Uniformly Convex Sets}, booktitle = {To Appear in Proceedings of AISTATS}, year = {2020}, language = {en} } @article{SeckerFackeldeyWeberetal.2023, author = {Secker, Christopher and Fackeldey, Konstantin and Weber, Marcus and Ray, Sourav and Gorgulla, Christoph and Sch{\"u}tte, Christof}, title = {Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists}, volume = {15}, journal = {Journal of Cheminformatics}, doi = {10.1186/s13321-023-00746-4}, year = {2023}, abstract = {Opioids are essential pharmaceuticals due to their analgesic properties, however, lethal side effects, addiction, and opioid tolerance are extremely challenging. The development of novel molecules targeting the μ-opioid receptor (MOR) in inflamed, but not in healthy tissue, could significantly reduce these unwanted effects. Finding such novel molecules can be achieved by maximizing the binding affinity to the MOR at acidic pH while minimizing it at neutral pH, thus combining two conflicting objectives. Here, this multi-objective optimal affinity approach is presented, together with a virtual drug discovery pipeline for its practical implementation. When applied to finding pH-specific drug candidates, it combines protonation state-dependent structure and ligand preparation with high-throughput virtual screening. We employ this pipeline to characterize a set of MOR agonists identifying a morphine-like opioid derivative with higher predicted binding affinities to the MOR at low pH compared to neutral pH. Our results also confirm existing experimental evidence that NFEPP, a previously described fentanyl derivative with reduced side effects, and recently reported β-fluorofentanyls and -morphines show an increased specificity for the MOR at acidic pH when compared to fentanyl and morphine. We further applied our approach to screen a >50K ligand library identifying novel molecules with pH-specific predicted binding affinities to the MOR. The presented differential docking pipeline can be applied to perform multi-objective affinity optimization to identify safer and more specific drug candidates at large scale.}, language = {en} } @misc{LenzSerrano2021, author = {Lenz, Ralf and Serrano, Felipe}, title = {Tight Convex Relaxations for the Expansion Planning Problem}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-81459}, year = {2021}, abstract = {Secure energy transport is considered as highly relevant for the basic infrastructure of nowadays society and economy. To satisfy increasing demands and to handle more diverse transport situations, operators of energy networks regularly expand the capacity of their network by building new network elements, known as the expansion planning problem. A key constraint function in expansion planning problems is a nonlinear and nonconvex potential loss function. In order to improve the algorithmic performance of state-of-the-art MINLP solvers, this paper presents an algebraic description for the convex envelope of this function. Through a thorough computational study, we show that this tighter relaxation tremendously improve the performance of the MINLP solver SCIP on a large test set of practically relevant instances for the expansion planning problem. In particular, the results show that our achievements lead to an improvement of the solver performance for a development version by up to 58\%.}, language = {en} } @article{PokuttaSpiegelZimmer2020, author = {Pokutta, Sebastian and Spiegel, Christoph and Zimmer, Max}, title = {Deep Neural Network Training with Frank-Wolfe}, arxiv = {http://arxiv.org/abs/2010.07243}, year = {2020}, abstract = {This paper studies the empirical efficacy and benefits of using projection-free first-order methods in the form of Conditional Gradients, a.k.a. Frank-Wolfe methods, for training Neural Networks with constrained parameters. We draw comparisons both to current state-of-the-art stochastic Gradient Descent methods as well as across different variants of stochastic Conditional Gradients. In particular, we show the general feasibility of training Neural Networks whose parameters are constrained by a convex feasible region using Frank-Wolfe algorithms and compare different stochastic variants. We then show that, by choosing an appropriate region, one can achieve performance exceeding that of unconstrained stochastic Gradient Descent and matching state-of-the-art results relying on L2-regularization. Lastly, we also demonstrate that, besides impacting performance, the particular choice of constraints can have a drastic impact on the learned representations.}, language = {en} } @article{CryilleWSpiegelPokutta2020, author = {Cryille W., Combettes and Spiegel, Christoph and Pokutta, Sebastian}, title = {Projection-Free Adaptive Gradients for Large-Scale Optimization}, arxiv = {http://arxiv.org/abs/2009.14114}, year = {2020}, abstract = {The complexity in large-scale optimization can lie in both handling the objective function and handling the constraint set. In this respect, stochastic Frank-Wolfe algorithms occupy a unique position as they alleviate both computational burdens, by querying only approximate first-order information from the objective and by maintaining feasibility of the iterates without using projections. In this paper, we improve the quality of their first-order information by blending in adaptive gradients. We derive convergence rates and demonstrate the computational advantage of our method over the state-of-the-art stochastic Frank-Wolfe algorithms on both convex and nonconvex objectives. The experiments further show that our method can improve the performance of adaptive gradient algorithms for constrained optimization.}, language = {en} } @misc{Pedersen2020, type = {Master Thesis}, author = {Pedersen, Jaap}, title = {Multiperiod Optimal Power Flow Problem In Distribution System Planning}, pages = {61}, year = {2020}, abstract = {Growing demand, distributed generation, such as renewable energy sources (RES), and the increasing role of storage systems to mitigate the volatility of RES on a medium voltage level, push existing distribution grids to their limits. Therefore, necessary network expansion needs to be evaluated to guarantee a safe and reliable electricity supply in the future taking these challenges into account. This problem is formulated as an optimal power flow (OPF) problem which combines network expansion, volatile generation and storage systems, minimizing network expansion and generation costs. As storage systems introduce a temporal coupling into the system, a multiperiod OPF problem is needed and analysed in this thesis. To reduce complexity, the network expansion problem is represented in a continuous nonlinear programming formulation by using fundamental properties of electrical engeneering. This formulation is validated succesfully against a common mixed integer programming approach on a 30 and 57 bus network with respect to solution and computing time. As the OPF problem is, in general, a nonconvex, nonlinear problem and, thus, hard to solve, convex relaxations of the power flow equations have gained increasing interest. Sufficient conditions are represented which guarantee exactness of a second-order cone (SOC) relaxation of an operational OPF in radial networks. In this thesis, these conditions are enhanced for the network expansion planning problem. Additionally, nonconvexities introduced by the choice of network expansion variables are relaxed by using McCormick envelopes. These relaxations are then applied on the multiperiod OPF and compared to the original problem on a 30 and a 57 bus network. In particular, the computational time is decreased by an order up to 10^2 by the SOC relaxation while it provides either an exact solution or a sufficient lower bound on the original problem. Finally, a sensitivity study is performed on weights of network expansion costs showing strong dependency of both the solution of performed expansion and solution time on the chosen weights.}, language = {en} } @misc{BestuzhevaGleixnerVigerske2021, author = {Bestuzheva, Ksenia and Gleixner, Ambros and Vigerske, Stefan}, title = {A Computational Study of Perspective Cuts}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-81821}, year = {2021}, abstract = {The benefits of cutting planes based on the perspective function are well known for many specific classes of mixed-integer nonlinear programs with on/off structures. However, we are not aware of any empirical studies that evaluate their applicability and computational impact over large, heterogeneous test sets in general-purpose solvers. This paper provides a detailed computational study of perspective cuts within a linear programming based branch-and-cut solver for general mixed-integer nonlinear programs. Within this study, we extend the applicability of perspective cuts from convex to nonconvex nonlinearities. This generalization is achieved by applying a perspective strengthening to valid linear inequalities which separate solutions of linear relaxations. The resulting method can be applied to any constraint where all variables appearing in nonlinear terms are semi-continuous and depend on at least one common indicator variable. Our computational experiments show that adding perspective cuts for convex constraints yields a consistent improvement of performance, and adding perspective cuts for nonconvex constraints reduces branch-and-bound tree sizes and strengthens the root node relaxation, but has no significant impact on the overall mean time.}, language = {en} } @article{CsizmadiaBerthold2020, author = {Csizmadia, Zsolt and Berthold, Timo}, title = {The confined primal integral: a measure to benchmark heuristic MINLP solvers against global MINLP solvers}, journal = {Mathematical Programming}, doi = {10.1007/s10107-020-01547-5}, year = {2020}, abstract = {It is a challenging task to fairly compare local solvers and heuristics against each other and against global solvers. How does one weigh a faster termination time against a better quality of the found solution? In this paper, we introduce the confined primal integral, a new performance measure that rewards a balance of speed and solution quality. It emphasizes the early part of the solution process by using an exponential decay. Thereby, it avoids that the order of solvers can be inverted by choosing an arbitrarily large time limit. We provide a closed analytic formula to compute the confined primal integral a posteriori and an incremental update formula to compute it during the run of an algorithm. For the latter, we show that we can drop one of the main assumptions of the primal integral, namely the knowledge of a fixed reference solution to compare against. Furthermore, we prove that the confined primal integral is a transitive measure when comparing local solves with different final solution values. Finally, we present a computational experiment where we compare a local MINLP solver that uses certain classes of cutting planes against a solver that does not. Both versions show very different tendencies w.r.t. average running time and solution quality, and we use the confined primal integral to argue which of the two is the preferred setting.}, language = {en} } @article{WitzigBerthold2021, author = {Witzig, Jakob and Berthold, Timo}, title = {Conflict Analysis for MINLP}, volume = {33}, journal = {INFORMS Journal on Computing}, number = {2}, doi = {10.1287/ijoc.2020.1050}, pages = {421 -- 435}, year = {2021}, abstract = {The generalization of MIP techniques to deal with nonlinear, potentially non-convex, constraints have been a fruitful direction of research for computational MINLP in the last decade. In this paper, we follow that path in order to extend another essential subroutine of modern MIP solvers towards the case of nonlinear optimization: the analysis of infeasible subproblems for learning additional valid constraints. To this end, we derive two different strategies, geared towards two different solution approaches. These are using local dual proofs of infeasibility for LP-based branch-and-bound and the creation of nonlinear dual proofs for NLP-based branch-and-bound, respectively. We discuss implementation details of both approaches and present an extensive computational study, showing that both techniques can significantly enhance performance when solving MINLPs to global optimality.}, language = {en} } @article{GamrathBertholdSalvagnin2020, author = {Gamrath, Gerald and Berthold, Timo and Salvagnin, Domenico}, title = {An exploratory computational analysis of dual degeneracy in mixed-integer programming}, journal = {EURO Journal on Computational Optimization}, number = {8}, doi = {10.1007/s13675-020-00130-z}, pages = {241 -- 246}, year = {2020}, abstract = {Dual degeneracy, i.e., the presence of multiple optimal bases to a linear programming (LP) problem, heavily affects the solution process of mixed integer programming (MIP) solvers. Different optimal bases lead to different cuts being generated, different branching decisions being taken and different solutions being found by primal heuristics. Nevertheless, only a few methods have been published that either avoid or exploit dual degeneracy. The aim of the present paper is to conduct a thorough computational study on the presence of dual degeneracy for the instances of well-known public MIP instance collections. How many instances are affected by dual degeneracy? How degenerate are the affected models? How does branching affect degeneracy: Does it increase or decrease by fixing variables? Can we identify different types of degenerate MIPs? As a tool to answer these questions, we introduce a new measure for dual degeneracy: the variable-constraint ratio of the optimal face. It provides an estimate for the likelihood that a basic variable can be pivoted out of the basis. Furthermore, we study how the so-called cloud intervals—the projections of the optimal face of the LP relaxations onto the individual variables—evolve during tree search and the implications for reducing the set of branching candidates.}, language = {en} } @article{DevriendtGleixnerNordstroem2021, author = {Devriendt, Jo and Gleixner, Ambros and Nordstr{\"o}m, Jakob}, title = {Learn to Relax: Integrating 0-1 Integer Linear Programming with Pseudo-Boolean Conflict-Driven Search}, volume = {26}, journal = {Constraints}, doi = {10.1007/s10601-020-09318-x}, pages = {26 -- 55}, year = {2021}, abstract = {Conflict-driven pseudo-Boolean solvers optimize 0-1 integer linear programs by extending the conflict-driven clause learning (CDCL) paradigm from SAT solving. Though pseudo-Boolean solvers have the potential to be exponentially more efficient than CDCL solvers in theory, in practice they can sometimes get hopelessly stuck even when the linear programming (LP) relaxation is infeasible over the reals. Inspired by mixed integer programming (MIP), we address this problem by interleaving incremental LP solving with cut generation within the conflict-driven pseudo-Boolean search. This hybrid approach, which for the first time combines MIP techniques with full-blown conflict analysis operating directly on linear inequalities using the cutting planes method, significantly improves performance on a wide range of benchmarks, approaching a "best-of-both-worlds" scenario between SAT-style conflict-driven search and MIP-style branch-and-cut.}, language = {en} } @inproceedings{ShinanoTateiwaNakamuraetal.2020, author = {Shinano, Yuji and Tateiwa, N. and Nakamura, S. and Yoshida, A. and Yasuda, M. and Kaji, S. and Fujisawa, K.}, title = {Massive Parallelization for Finding Shortest Lattice Vectors Based on Ubiquity Generator Framework}, booktitle = {2020 SC20: International Conference for High Performance Computing, Networking, Storage and Analysis (SC)}, doi = {10.1109/SC41405.2020.00064}, pages = {834 -- 848}, year = {2020}, abstract = {Lattice-based cryptography has received attention as a next-generation encryption technique, because it is believed to be secure against attacks by classical and quantum computers. Its essential security depends on the hardness of solving the shortest vector problem (SVP). In the cryptography, to determine security levels, it is becoming significantly more important to estimate the hardness of the SVP by high-performance computing. In this study, we develop the world's first distributed and asynchronous parallel SVP solver, the MAssively Parallel solver for SVP (MAP-SVP). It can parallelize algorithms for solving the SVP by applying the Ubiquity Generator framework, which is a generic framework for branch-and-bound algorithms. The MAP-SVP is suitable for massive-scale parallelization, owing to its small memory footprint, low communication overhead, and rapid checkpoint and restart mechanisms. We demonstrate its performance and scalability of the MAP-SVP by using up to 100,032 cores to solve instances of the Darmstadt SVP Challenge.}, language = {en} } @article{YokoyamaShinanoWakayamaetal.2019, author = {Yokoyama, Ryohei and Shinano, Yuji and Wakayama, Yuki and Wakui, Tetsuya}, title = {Model reduction by time aggregation for optimal design of energy supply systems by an MILP hierarchical branch and bound method}, volume = {181}, journal = {Energy}, doi = {https://doi.org/10.1016/j.energy.2019.04.066}, pages = {782 -- 792}, year = {2019}, abstract = {Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems in consideration of multi-period operation. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. An original problem has been solved by dividing it into a relaxed optimal design problem at the upper level and optimal operation problems which are independent of one another at the lower level. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. In this paper, a method of reducing model by time aggregation is proposed as a novel strategy to search design candidates efficiently in the relaxed optimal design problem at the upper level. In addition, the previous strategies are modified in accordance with the novel strategy. This method is realized only by clustering periods and averaging energy demands for clustered periods, while it guarantees to derive the optimal solution. Thus, it may decrease the computation time at the upper level. Through a case study on the optimal design of a gas turbine cogeneration system, it is clarified how the model reduction is effective to enhance the computation efficiency in comparison and combination with the modified previous strategies.}, language = {en} } @inproceedings{PfetschPokutta2020, author = {Pfetsch, Marc and Pokutta, Sebastian}, title = {IPBoost - Non-Convex Boosting via Integer Programming}, booktitle = {Proceedings of ICML}, arxiv = {http://arxiv.org/abs/2002.04679}, year = {2020}, language = {en} } @inproceedings{PokuttaSinghTorrico2020, author = {Pokutta, Sebastian and Singh, M. and Torrico, A.}, title = {On the Unreasonable Effectiveness of the Greedy Algorithm: Greedy Adapts to Sharpness}, booktitle = {Proceedings of ICML}, arxiv = {http://arxiv.org/abs/2002.04063}, year = {2020}, language = {en} } @inproceedings{DiakonikolasCardereraPokutta2020, author = {Diakonikolas, Jelena and Carderera, Alejandro and Pokutta, Sebastian}, title = {Locally Accelerated Conditional Gradients}, booktitle = {Proceedings of AISTATS}, arxiv = {http://arxiv.org/abs/1906.07867}, year = {2020}, language = {en} } @article{FaenzaMunozPokutta2020, author = {Faenza, Yuri and Mu{\~n}oz, Gonzalo and Pokutta, Sebastian}, title = {New Limits of Treewidth-based tractability in Optimization}, volume = {191}, journal = {Mathematical Programming}, arxiv = {http://arxiv.org/abs/1807.02551}, doi = {10.1007/s10107-020-01563-5}, pages = {559 -- 594}, year = {2020}, language = {en} } @article{AnariHaghtalabNaoretal.2020, author = {Anari, N. and Haghtalab, N. and Naor, S. and Pokutta, Sebastian and Singh, M. and Torrico, A.}, title = {Structured Robust Submodular Maximization: Offline and Online Algorithms}, journal = {INFORMS Journal on Computing}, arxiv = {http://arxiv.org/abs/1710.04740}, year = {2020}, language = {en} } @inproceedings{CombettesPokutta2020, author = {Combettes, Cyrille W. and Pokutta, Sebastian}, title = {Boosting Frank-Wolfe by Chasing Gradients}, booktitle = {Proceedings of ICML}, arxiv = {http://arxiv.org/abs/2003.06369}, year = {2020}, language = {en} } @inproceedings{MortagyGuptaPokutta2020, author = {Mortagy, Hassan and Gupta, Swati and Pokutta, Sebastian}, title = {Walking in the Shadow: A New Perspective on Descent Directions for Constrained Minimization}, booktitle = {Proceedings of NeurIPS}, arxiv = {http://arxiv.org/abs/2006.08426}, year = {2020}, language = {en} } @inproceedings{Pokutta2020, author = {Pokutta, Sebastian}, title = {Restarting Algorithms: Sometimes there is Free Lunch}, booktitle = {Proceedings of CPAIOR}, arxiv = {http://arxiv.org/abs/2006.14810}, year = {2020}, language = {en} } @article{KossenHirzelMadaietal.2022, author = {Kossen, Tabea and Hirzel, Manuel A. and Madai, Vince I. and Boenisch, Franziska and Hennemuth, Anja and Hildebrand, Kristian and Pokutta, Sebastian and Sharma, Kartikey and Hilbert, Adam and Sobesky, Jan and Galinovic, Ivana and Khalil, Ahmed A. and Fiebach, Jochen B. and Frey, Dietmar}, title = {Towards Sharing Brain Images: Differentially Private TOF-MRA Images with Segmentation Labels Using Generative Adversarial Networks}, journal = {Frontiers in Artificial Intelligence}, doi = {https://doi.org/10.3389/frai.2022.813842}, year = {2022}, abstract = {Sharing labeled data is crucial to acquire large datasets for various Deep Learning applications. In medical imaging, this is often not feasible due to privacy regulations. Whereas anonymization would be a solution, standard techniques have been shown to be partially reversible. Here, synthetic data using a Generative Adversarial Network (GAN) with differential privacy guarantees could be a solution to ensure the patient's privacy while maintaining the predictive properties of the data. In this study, we implemented a Wasserstein GAN (WGAN) with and without differential privacy guarantees to generate privacy-preserving labeled Time-of-Flight Magnetic Resonance Angiography (TOF-MRA) image patches for brain vessel segmentation. The synthesized image-label pairs were used to train a U-net which was evaluated in terms of the segmentation performance on real patient images from two different datasets. Additionally, the Fr{\´e}chet Inception Distance (FID) was calculated between the generated images and the real images to assess their similarity. During the evaluation using the U-Net and the FID, we explored the effect of different levels of privacy which was represented by the parameter ϵ. With stricter privacy guarantees, the segmentation performance and the similarity to the real patient images in terms of FID decreased. Our best segmentation model, trained on synthetic and private data, achieved a Dice Similarity Coefficient (DSC) of 0.75 for ϵ = 7.4 compared to 0.84 for ϵ = ∞ in a brain vessel segmentation paradigm (DSC of 0.69 and 0.88 on the second test set, respectively). We identified a threshold of ϵ <5 for which the performance (DSC <0.61) became unstable and not usable. Our synthesized labeled TOF-MRA images with strict privacy guarantees retained predictive properties necessary for segmenting the brain vessels. Although further research is warranted regarding generalizability to other imaging modalities and performance improvement, our results mark an encouraging first step for privacy-preserving data sharing in medical imaging.}, language = {en} } @inproceedings{WirthPokutta2022, author = {Wirth, Elias and Pokutta, Sebastian}, title = {Conditional Gradients for the Approximately Vanishing Ideal}, volume = {151}, booktitle = {Proceedings of The 25th International Conference on Artificial Intelligence and Statistics}, pages = {2191 -- 2209}, year = {2022}, abstract = {The vanishing ideal of a set of points X is the set of polynomials that evaluate to 0 over all points x in X and admits an efficient representation by a finite set of polynomials called generators. To accommodate the noise in the data set, we introduce the Conditional Gradients Approximately Vanishing Ideal algorithm (CGAVI) for the construction of the set of generators of the approximately vanishing ideal. The constructed set of generators captures polynomial structures in data and gives rise to a feature map that can, for example, be used in combination with a linear classifier for supervised learning. In CGAVI, we construct the set of generators by solving specific instances of (constrained) convex optimization problems with the Pairwise Frank-Wolfe algorithm (PFW). Among other things, the constructed generators inherit the LASSO generalization bound and not only vanish on the training but also on out-sample data. Moreover, CGAVI admits a compact representation of the approximately vanishing ideal by constructing few generators with sparse coefficient vectors.}, language = {en} } @misc{Franz2019, type = {Master Thesis}, author = {Franz, Henriette}, title = {Connected Subgraphs with Budget Constraints: Formulations and Algorithms}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-87792}, year = {2019}, language = {en} } @inproceedings{MartinezRubioPokutta2023, author = {Mart{\´i}nez-Rubio, David and Pokutta, Sebastian}, title = {Accelerated Riemannian Optimization: Handling Constraints with a Prox to Bound Geometric Penalties}, volume = {195}, booktitle = {Proceedings of Thirty Sixth Conference on Learning Theory}, pages = {359 -- 393}, year = {2023}, abstract = {We propose a globally-accelerated, first-order method for the optimization of smooth and (strongly or not) geodesically-convex functions in a wide class of Hadamard manifolds. We achieve the same convergence rates as Nesterov's accelerated gradient descent, up to a multiplicative geometric penalty and log factors. Crucially, we can enforce our method to stay within a compact set we define. Prior fully accelerated works \emph{resort to assuming} that the iterates of their algorithms stay in some pre-specified compact set, except for two previous methods of limited applicability. For our manifolds, this solves the open question in (Kim and Yang, 2022) about obtaining global general acceleration without iterates assumptively staying in the feasible set.In our solution, we design an accelerated Riemannian inexact proximal point algorithm, which is a result that was unknown even with exact access to the proximal operator, and is of independent interest. For smooth functions, we show we can implement the prox step inexactly with first-order methods in Riemannian balls of certain diameter that is enough for global accelerated optimization.}, language = {en} } @article{ŠofranacGleixnerPokutta2022, author = {Šofranac, Boro and Gleixner, Ambros and Pokutta, Sebastian}, title = {An Algorithm-independent Measure of Progress for Linear Constraint Propagation}, volume = {27}, journal = {Constraints}, doi = {10.1007/s10601-022-09338-9}, pages = {432 -- 455}, year = {2022}, language = {en} } @inproceedings{ParczykPokuttaSpiegeletal.2022, author = {Parczyk, Olaf and Pokutta, Sebastian and Spiegel, Christoph and Szab{\´o}, Tibor}, title = {New Ramsey Multiplicity Bounds and Search Heuristics}, booktitle = {Discrete Mathematics Days}, year = {2022}, abstract = {We study two related problems concerning the number of monochromatic cliques in two-colorings of the complete graph that go back to questions of Erdős. Most notably, we improve the 25-year-old upper bounds of Thomason on the Ramsey multiplicity of K4 and K5 and we settle the minimum number of independent sets of size 4 in graphs with clique number at most 4. Motivated by the elusiveness of the symmetric Ramsey multiplicity problem, we also introduce an off-diagonal variant and obtain tight results when counting monochromatic K4 or K5 in only one of the colors and triangles in the other. The extremal constructions for each problem turn out to be blow-ups of a finite graph and were found through search heuristics. They are complemented by lower bounds and stability results established using Flag Algebras, resulting in a fully computer-assisted approach. More broadly, these problems lead us to the study of the region of possible pairs of clique and independent set densities that can be realized as the limit of some sequence of graphs.}, language = {en} } @inproceedings{ParczykPokuttaSpiegeletal.2023, author = {Parczyk, Olaf and Pokutta, Sebastian and Spiegel, Christoph and Szab{\´o}, Tibor}, title = {Fully Computer-assisted Proofs in Extremal Combinatorics}, volume = {37}, booktitle = {Proceedings of the AAAI Conference on Artificial Intelligence}, number = {10}, doi = {10.1609/aaai.v37i10.26470}, pages = {12482 -- 12490}, year = {2023}, abstract = {We present a fully computer-assisted proof system for solving a particular family of problems in Extremal Combinatorics. Existing techniques using Flag Algebras have proven powerful in the past, but have so far lacked a computational counterpart to derive matching constructive bounds. We demonstrate that common search heuristics are capable of finding constructions far beyond the reach of human intuition. Additionally, the most obvious downside of such heuristics, namely a missing guarantee of global optimality, can often be fully eliminated in this case through lower bounds and stability results coming from the Flag Algebra approach. To illustrate the potential of this approach, we study two related and well-known problems in Extremal Graph Theory that go back to questions of Erdős from the 60s. Most notably, we present the first major improvement in the upper bound of the Ramsey multiplicity of the complete graph on 4 vertices in 25 years, precisely determine the first off-diagonal Ramsey multiplicity number, and settle the minimum number of independent sets of size four in graphs with clique number strictly less than five.}, language = {en} } @article{KamčevSpiegel2022, author = {Kamčev, Nina and Spiegel, Christoph}, title = {Another note on intervals in the Hales-Jewett theorem}, volume = {29}, journal = {Electronic Journal of Combinatorics}, number = {1}, doi = {10.37236/6730}, pages = {P1.62}, year = {2022}, abstract = {The Hales-Jewett Theorem states that any r-colouring of [m]ⁿ contains a monochromatic combinatorial line if n is large enough. Shelah's proof of the theorem implies that for m = 3 there always exists a monochromatic combinatorial line whose set of active coordinates is the union of at most r intervals. For odd r, Conlon and Kamčev constructed r-colourings for which it cannot be fewer than r intervals. However, we show that for even r and large n, any r-colouring of [3]ⁿ contains a monochromatic combinatorial line whose set of active coordinates is the union of at most r-1 intervals. This is optimal and extends a result of Leader and R{\"a}ty for r=2.}, language = {en} } @article{HunkenschroederPokuttaWeismantel2022, author = {Hunkenschr{\"o}der, Christoph and Pokutta, Sebastian and Weismantel, Robert}, title = {Optimizing a low-dimensional convex function over a high-dimensional cub}, journal = {SIAM Journal on Optimization}, year = {2022}, language = {en} } @inproceedings{MacDonaldBesanconPokutta2022, author = {MacDonald, Jan and Besan{\c{c}}on, Mathieu and Pokutta, Sebastian}, title = {Interpretable Neural Networks with Frank-Wolfe: Sparse Relevance Maps and Relevance Orderings}, booktitle = {Proceedings of the International Conference on Machine Learning}, year = {2022}, language = {en} } @inproceedings{TsujiTanakaPokutta2022, author = {Tsuji, Kazuma and Tanaka, Ken'ichiro and Pokutta, Sebastian}, title = {Pairwise Conditional Gradients without Swap Steps and Sparser Kernel Herding}, booktitle = {Proceedings of the International Conference on Machine Learning}, year = {2022}, language = {en} } @inproceedings{WaeldchenHuberPokutta2022, author = {W{\"a}ldchen, Stephan and Huber, Felix and Pokutta, Sebastian}, title = {Training Characteristic Functions with Reinforcement Learning: XAI-methods Play Connect Four}, booktitle = {Proceedings of the International Conference on Machine Learning}, year = {2022}, language = {en} } @article{RayFackeldeySteinetal.2023, author = {Ray, Sourav and Fackeldey, Konstantin and Stein, Christoph and Weber, Marcus}, title = {Coarse Grained MD Simulations of Opioid interactions with the µ-opioid receptor and the surrounding lipid membrane}, volume = {3}, journal = {Biophysica}, number = {2}, doi = {10.3390/biophysica3020017}, pages = {263 -- 275}, year = {2023}, abstract = {In our previous studies, a new opioid (NFEPP) was developed to only selectively bind to the 𝜇-opoid receptor (MOR) in inflamed tissue and thus avoid the severe side effects of fentanyl. We know that NFEPP has a reduced binding affinity to MOR in healthy tissue. Inspired by the modelling and simulations performed by Sutcliffe et al., we present our own results of coarse-grained molecular dynamics simulations of fentanyl and NFEPP with regards to their interaction with the 𝜇-opioid receptor embedded within the lipid cell membrane. For technical reasons, we have slightly modified Sutcliffe's parametrisation of opioids. The pH-dependent opioid simulations are of interest because while fentanyl is protonated at the physiological pH, NFEPP is deprotonated due to its lower pKa value than that of fentanyl. Here, we analyse for the first time whether pH changes have an effect on the dynamical behaviour of NFEPP when it is inside the cell membrane. Besides these changes, our analysis shows a possible alternative interaction of NFEPP at pH 7.4 outside the binding region of the MOR. The interaction potential of NFEPP with MOR is also depicted by analysing the provided statistical molecular dynamics simulations with the aid of an eigenvector analysis of a transition rate matrix. In our modelling, we see differences in the XY-diffusion profiles of NFEPP compared with fentanyl in the cell membrane.}, language = {en} } @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} }