TY - JOUR A1 - Sikorski, Alexander T1 - Voronoi Graph - Improved raycasting and integration schemes for high dimensional Voronoi diagrams N2 - The computation of Voronoi Diagrams, or their dual Delauney triangulations is difficult in high dimensions. In a recent publication Polianskii and Pokorny propose an iterative randomized algorithm facilitating the approximation of Voronoi tesselations in high dimensions. In this paper, we provide an improved vertex search method that is not only exact but even faster than the bisection method that was previously recommended. Building on this we also provide a depth-first graph-traversal algorithm which allows us to compute the entire Voronoi diagram. This enables us to compare the outcomes with those of classical algorithms like qHull, which we either match or marginally beat in terms of computation time. We furthermore show how the raycasting algorithm naturally lends to a Monte Carlo approximation for the volume and boundary integrals of the Voronoi cells, both of which are of importance for finite Volume methods. We compare the Monte-Carlo methods to the exact polygonal integration, as well as a hybrid approximation scheme. Y1 - 2024 ER - TY - JOUR A1 - Schaible, Jonas A1 - Nouri, Bijan A1 - Höpken, Lars A1 - Kotzab, Tim A1 - Loevenich, Matthias A1 - Blum, Niklas A1 - Hammer, Annette A1 - Stührenberg, Jonas A1 - Jäger, Klaus A1 - Becker, Christiane A1 - Wilbert, Stefan T1 - Application of nowcasting to reduce the impact of irradiance ramps on PV power plants JF - EPJ Photovolt. Y1 - 2024 U6 - https://doi.org/10.1051/epjpv/2024009 VL - 15 SP - 15 ER - TY - JOUR A1 - Krüger, Jan A1 - Manley, Phillip A1 - Bergmann, Detlef A1 - Köning, Rainer A1 - Bodermann, Bernd A1 - Eder, Christian A1 - Heinrich, Andreas A1 - Schneider, Philipp-Immanuel A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Manske, Eberhard T1 - Introduction and application of a new approach for model-based optical bidirectional measurements JF - Meas. Sci. Technol. Y1 - 2024 U6 - https://doi.org/10.1088/1361-6501/ad4b53 ER - TY - JOUR A1 - Klus, Stefan A1 - Djurdjevac Conrad, Natasa T1 - Dynamical systems and complex networks: A Koopman operator perspective N2 - The Koopman operator has entered and transformed many research areas over the last years. Although the underlying concept–representing highly nonlinear dynamical systems by infinite-dimensional linear operators–has been known for a long time, the availability of large data sets and efficient machine learning algorithms for estimating the Koopman operator from data make this framework extremely powerful and popular. Koopman operator theory allows us to gain insights into the characteristic global properties of a system without requiring detailed mathematical models. We will show how these methods can also be used to analyze complex networks and highlight relationships between Koopman operators and graph Laplacians. Y1 - 2024 ER - TY - GEN A1 - Secker, Christopher T1 - Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists (Dataset) N2 - Virtual Screening Dataset for the paper "Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists" by Secker et al. (https://doi.org/10.1186/s13321-023-00746-4) Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-96220 ER - TY - GEN A1 - Bopp, Julian M. A1 - Plock, Matthias A1 - Turan, Tim A1 - Pieplow, Gregor A1 - Burger, Sven A1 - Schröder, Tim T1 - ‘Sawfish’ Photonic Crystal Cavity for Near-Unity Emitter-to-Fiber Interfacing in Quantum Network Applications (Advanced Optical Materials 13/2024) T2 - Adv. Optical Mater. Y1 - 2024 U6 - https://doi.org/10.1002/adom.202470046 VL - 12 SP - 2470046 ER - TY - JOUR A1 - Zhang, Wei A1 - Schütte, Christof T1 - On finding optimal collective variables for complex systems by minimizing the deviation between effective and full dynamics N2 - This paper is concerned with collective variables, or reaction coordinates, that map a discrete-in-time Markov process X_n in R^d to a (much) smaller dimension k≪d. We define the effective dynamics under a given collective variable map ξ as the best Markovian representation of X_n under ξ. The novelty of the paper is that it gives strict criteria for selecting optimal collective variables via the properties of the effective dynamics. In particular, we show that the transition density of the effective dynamics of the optimal collective variable solves a relative entropy minimization problem from certain family of densities to the transition density of X_n. We also show that many transfer operator-based data-driven numerical approaches essentially learn quantities of the effective dynamics. Furthermore, we obtain various error estimates for the effective dynamics in approximating dominant timescales / eigenvalues and transition rates of the original process X_n and how optimal collective variables minimize these errors. Our results contribute to the development of theoretical tools for the understanding of complex dynamical systems, e.g. molecular kinetics, on large timescales. These results shed light on the relations among existing data-driven numerical approaches for identifying good collective variables, and they also motivate the development of new methods. Y1 - 2024 ER - TY - JOUR A1 - Erban, Radek A1 - Winkelmann, Stefanie T1 - Multi-grid reaction-diffusion master equation: applications to morphogen gradient modelling N2 - The multi-grid reaction-diffusion master equation (mgRDME) provides a generalization of stochastic compartment-based reaction-diffusion modelling described by the standard reaction-diffusion master equation (RDME). By enabling different resolutions on lattices for biochemical species with different diffusion constants, the mgRDME approach improves both accuracy and efficiency of compartment-based reaction-diffusion simulations. The mgRDME framework is examined through its application to morphogen gradient formation in stochastic reaction-diffusion scenarios, using both an analytically tractable first-order reaction network and a model with a second-order reaction. The results obtained by the mgRDME modelling are compared with the standard RDME model and with the (more detailed) particle-based Brownian dynamics simulations. The dependence of error and numerical cost on the compartment sizes is defined and investigated through a multi-objective optimization problem. Y1 - 2024 ER - TY - JOUR A1 - Müller, Gabriel A1 - Martínez-Lahuerta, V. J. A1 - Sekuliĉ, Ivan A1 - Burger, Sven A1 - Schneider, Philipp-Immanuel A1 - Gaaloul, Naceur T1 - Bayesian optimization for state engineering of quantum gases JF - arXiv Y1 - 2024 SP - arXiv:2404.18234 ER - TY - JOUR A1 - Pedersen, Jaap A1 - Weinand, Jann Michael A1 - Syranidou, Chloi A1 - Rehfeldt, Daniel T1 - An efficient solver for large-scale onshore wind farm siting including cable routing JF - European Journal of Operational Research N2 - Existing planning approaches for onshore wind farm siting and grid integration often do not meet minimum cost solutions or social and environmental considerations. In this paper, we develop an exact approach for the integrated layout and cable routing problem of onshore wind farm planning using the 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. In selected regions of Germany, the trade-offs between minimizing costs and landscape impact of onshore wind farm siting are investigated. Although our case studies 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, grid integration must be simultaneously optimized 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. Y1 - 2024 U6 - https://doi.org/10.1016/j.ejor.2024.04.026 VL - 317 IS - 2 SP - 616 EP - 630 ER - TY - GEN A1 - Kuen, Lilli A1 - Löffler, Lorenz A1 - Tsarapkin, Aleksei A1 - Zschiedrich, Lin A1 - Feichtner, Thorsten A1 - Burger, Sven A1 - Höflich, Katja T1 - Source Code and Simulation Results: Chiral and directional optical emission from a dipole source coupled to a helical plasmonic antenna T2 - Zenodo Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.10598255 SP - doi: 10.5281/zenodo.10598255 ER - TY - CHAP A1 - Pedersen, Jaap A1 - Ljubić, Ivana ED - Pardalos, Panos M. ED - Prokopyev, Oleg A. T1 - Prize Collecting Steiner Tree Problem and its Variants T2 - Encyclopedia of Optimization Y1 - 2024 PB - Springer International Publishing CY - Cham ER - TY - JOUR A1 - Rodrigues Pela, Ronaldo A1 - Draxl, Claudia T1 - Speeding up all-electron real-time TDDFT demonstrated by the exciting package Y1 - 2024 U6 - https://doi.org/10.48550/arXiv.2403.04351 ER - TY - JOUR A1 - Trepte, Philipp A1 - Secker, Christopher A1 - Olivet, Julien A1 - Blavier, Jeremy A1 - Kostova, Simona A1 - Maseko, Sibusiso B A1 - Minia, Igor A1 - Silva Ramos, Eduardo A1 - Cassonnet, Patricia A1 - Golusik, Sabrina A1 - Zenkner, Martina A1 - Beetz, Stephanie A1 - Liebich, Mara J A1 - Scharek, Nadine A1 - Schütz, Anja A1 - Sperling, Marcel A1 - Lisurek, Michael A1 - Wang, Yang A1 - Spirohn, Kerstin A1 - Hao, Tong A1 - Calderwood, Michael A A1 - Hill, David E A1 - Landthaler, Markus A1 - Choi, Soon Gang A1 - Twizere, Jean-Claude A1 - Vidal, Marc A1 - Wanker, Erich E T1 - AI-guided pipeline for protein–protein interaction drug discovery identifies a SARS-CoV-2 inhibitor JF - Molecular Systems Biology N2 - 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. KW - Applied Mathematics KW - Computational Theory and Mathematics KW - General Agricultural and Biological Sciences KW - General Immunology and Microbiology KW - General Biochemistry, Genetics and Molecular Biology KW - Information Systems Y1 - 2024 U6 - https://doi.org/https://doi.org/10.1038/s44320-024-00019-8 SN - 1744-4292 VL - 20 IS - 4 SP - 428 EP - 457 PB - Springer Science and Business Media LLC ER - TY - CHAP A1 - Prause, Felix T1 - A Multi-Swap Heuristic for Rolling Stock Rotation Planning with Predictive Maintenance T2 - Proceedings of the 11th International Network Optimization Conference (INOC), Dublin, Ireland, March 11-23, 2024 N2 - We present a heuristic solution approach for the rolling stock rotation problem with predictive maintenance (RSRP-PdM). The task of this problem is to assign a sequence of trips to each of the vehicles and to schedule their maintenance such that all trips can be operated. Here, the health states of the vehicles are considered to be random variables distributed by a family of probability distribution functions, and the maintenance services should be scheduled based on the failure probability of the vehicles. The proposed algorithm first generates a solution by solving an integer linear program and then heuristically improves this solution by applying a local search procedure. For this purpose, the trips assigned to the vehicles are split up and recombined, whereby additional deadhead trips can be inserted between the partial assignments. Subsequently, the maintenance is scheduled by solving a shortest path problem in a state-expanded version of a space-time graph restricted to the trips of the individual vehicles. The solution approach is tested and evaluated on a set of test instances based on real-world timetables. Y1 - 2024 U6 - https://doi.org/10.48786/inoc.2024.11 SP - 58 EP - 63 ER - TY - JOUR A1 - Prause, Felix A1 - Borndörfer, Ralf T1 - An Iterative Refinement Approach for the Rolling Stock Rotation Problem with Predictive Maintenance N2 - The rolling stock rotation problem with predictive maintenance (RSRP-PdM) involves the assignment of trips to a fleet of vehicles with integrated maintenance scheduling based on the predicted failure probability of the vehicles. These probabilities are determined by the health states of the vehicles, which are considered to be random variables distributed by a parameterized family of probability distribution functions. During the operation of the trips, the corresponding parameters get updated. In this article, we present a dual solution approach for RSRP-PdM and generalize a linear programming based lower bound for this problem to families of probability distribution functions with more than one parameter. For this purpose, we define a rounding function that allows for a consistent underestimation of the parameters and model the problem by a state-expanded event-graph in which the possible states are restricted to a discrete set. This induces a flow problem that is solved by an integer linear program. We show that the iterative refinement of the underlying discretization leads to solutions that converge from below to an optimal solution of the original instance. Thus, the linear relaxation of the considered integer linear program results in a lower bound for RSRP-PdM. Finally, we report on the results of computational experiments conducted on a library of test instances. Y1 - 2024 ER - TY - GEN A1 - Betz, Fridtjof A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Binkowski, Felix T1 - Source code and simulation results: Efficient rational approximation of optical response functions with the AAA algorithm T2 - Zenodo Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.10853692 SP - doi: 10.5281/zenodo.10853692 ER - TY - JOUR A1 - Winkler, Alexander T1 - Berliner Kulturerbe digital: Ein quantitativer Blick auf die Metadatenqualität JF - EVA BERLIN 2023. Elektronische Medien & Kunst, Kultur und Historie. 27. Berliner Veranstaltung der internationalen EVA-Serie (29. November 2023 – 01. Dezember 2023) N2 - Die Metadatenqualität bestimmt wesentlich den Nutzen und Wert von Kulturerbedaten. ‚Gute‘ Metadaten erhöhen die Auffindbarkeit, Interoperabilität und Nutzbarkeit von Daten signifikant. Mit Blick auf Retrieval bzw. Discovery, Vernetzung im Kontext von Linked Open Data und wissenschaftliches Data Mining hängt die Qualität dabei wesentlich von der Verwendung von maschinenlesbaren kontrollierten Vokabularen ab. Diese wird in der vorliegenden Arbeit quantitativ untersucht. Als Datengrundlage dienen die in der Deutschen Digitalen Bibliothek aggregierten Metadaten aus Berliner Museen (ca. 1,2 Millionen Metadatenobjekte im LIDO-Format) Y1 - 2023 SP - 101 EP - 108 ER - TY - JOUR A1 - Sherratt, Katharine A1 - Srivastava, Ajitesh A1 - Ainslie, Kylie A1 - Singh, David E. A1 - Cublier, Aymar A1 - Marinescu, Maria Cristina A1 - Carretero, Jesus A1 - Garcia, Alberto Cascajo A1 - Franco, Nicolas A1 - Willem, Lander A1 - Abrams, Steven A1 - Faes, Christel A1 - Beutels, Philippe A1 - Hens, Niel A1 - Müller, Sebastian A1 - Charlton, Billy A1 - Ewert, Ricardo A1 - Paltra, Sydney A1 - Rakow, Christian A1 - Rehmann, Jakob A1 - Conrad, Tim O.F. A1 - Schütte, Christof A1 - Nagel, Kai A1 - Abbott, Sam A1 - Grah, Rok A1 - Niehus, Rene A1 - Prasse, Bastian A1 - Sandmann, Frank A1 - Funk, Sebastian T1 - Characterising information gains and losses when collecting multiple epidemic model outputs JF - Epidemics N2 - Collaborative comparisons and combinations of epidemic models are used as policy-relevant evidence during epidemic outbreaks. In the process of collecting multiple model projections, such collaborations may gain or lose relevant information. Typically, modellers contribute a probabilistic summary at each time-step. We compared this to directly collecting simulated trajectories. We aimed to explore information on key epidemic quantities; ensemble uncertainty; and performance against data, investigating potential to continuously gain information from a single cross-sectional collection of model results. Methods We compared July 2022 projections from the European COVID-19 Scenario Modelling Hub. Five modelling teams projected incidence in Belgium, the Netherlands, and Spain. We compared projections by incidence, peaks, and cumulative totals. We created a probabilistic ensemble drawn from all trajectories, and compared to ensembles from a median across each model’s quantiles, or a linear opinion pool. We measured the predictive accuracy of individual trajectories against observations, using this in a weighted ensemble. We repeated this sequentially against increasing weeks of observed data. We evaluated these ensembles to reflect performance with varying observed data. Results. By collecting modelled trajectories, we showed policy-relevant epidemic characteristics. Trajectories contained a right-skewed distribution well represented by an ensemble of trajectories or a linear opinion pool, but not models’ quantile intervals. Ensembles weighted by performance typically retained the range of plausible incidence over time, and in some cases narrowed this by excluding some epidemic shapes. Conclusions. We observed several information gains from collecting modelled trajectories rather than quantile distributions, including potential for continuously updated information from a single model collection. The value of information gains and losses may vary with each collaborative effort’s aims, depending on the needs of projection users. Understanding the differing information potential of methods to collect model projections can support the accuracy, sustainability, and communication of collaborative infectious disease modelling efforts. Data availability All code and data available on Github: https://github.com/covid19-forecast-hub-europe/aggregation-info-loss KW - Virology KW - Infectious Diseases KW - Public Health, Environmental and Occupational Health KW - Microbiology KW - Parasitology KW - Epidemiology Y1 - 2024 U6 - https://doi.org/10.1016/j.epidem.2024.100765 SN - 1755-4365 PB - Elsevier BV ER - TY - JOUR A1 - Betz, Fridtjof A1 - Hammerschmidt, Martin A1 - Zschiedrich, Lin A1 - Burger, Sven A1 - Binkowski, Felix T1 - Efficient rational approximation of optical response functions with the AAA algorithm JF - arXiv Y1 - 2024 SP - arXiv:2403.19404 ER - TY - CHAP A1 - Kiessling, David A1 - Vanaret, Charlie A1 - Astudillo, Alejandro A1 - Decré, Wilm A1 - Swevers, Jan T1 - An Almost Feasible Sequential Linear Programming Algorithm T2 - European Control Conference 2024 N2 - This paper proposes an almost feasible Sequential Linear Programming (afSLP) algorithm. In the first part, the practical limitations of previously proposed Feasible Sequential Linear Programming (FSLP) methods are discussed along with illustrative examples. Then, we present a generalization of FSLP based on a tolerance-tube method that addresses the shortcomings of FSLP. The proposed algorithm afSLP consists of two phases. Phase I starts from random infeasible points and iterates towards a relaxation of the feasible set. Once the tolerance-tube around the feasible set is reached, phase II is started and all future iterates are kept within the tolerance-tube. The novel method includes enhancements to the originally proposed tolerance-tube method that are necessary for global convergence. afSLP is shown to outperform FSLP and the state-of-the-art solver IPOPT on a SCARA robot optimization problem. Y1 - 2024 ER - TY - JOUR A1 - Schintke, Florian A1 - Belhajjame, Khalid A1 - De Mecquenem, Ninon A1 - Frantz, David A1 - Guarino, Vanessa Emanuela A1 - Hilbrich, Marcus A1 - Lehmann, Fabian A1 - Missier, Paolo A1 - Sattler, Rebecca A1 - Sparka, Jan Arne A1 - Speckhard, Daniel T. A1 - Stolte, Hermann A1 - Vu, Anh Duc A1 - Leser, Ulf T1 - Validity constraints for data analysis workflows JF - Future Generation Computer Systems Y1 - 2024 U6 - https://doi.org/10.1016/j.future.2024.03.037 VL - 157 SP - 82 EP - 97 ER - TY - GEN A1 - Yueksel-Erguen, Inci A1 - Koch, Thorsten A1 - Zittel, Janina T1 - Mathematical optimization based flow scenario generation for operational analysis of European gas transport networks based on open data N2 - The decarbonization of the European energy system demands a rapid and comprehensive transformation while securing energy supplies at all times. Still, natural gas plays a crucial role in this process. Recent unexpected events forced drastic changes in gas routes throughout Europe. Therefore, operational-level analysis of the gas transport networks and technical capacities to cope with these transitions using unconventional scenarios has become essential. Unfortunately, data limitations often hinder such analyses. To overcome this challenge, we propose a mathematical model-based scenario generator that enables operational analysis of the European gas network using open data. Our approach focuses on the consistent analysis of specific partitions of the gas transport network, whose network topology data is readily available. We generate reproducible and consistent node-based gas in/out-flow scenarios for these defined network partitions to enable feasibility analysis and data quality assessment. Our proposed method is demonstrated through several applications that address the feasibility analysis and data quality assessment of the German gas transport network. By using open data and a mathematical modeling approach, our method allows for a more comprehensive understanding of the gas transport network's behavior and assists in decision-making during the transition to decarbonization. T3 - ZIB-Report - 24-03 Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-95789 SN - 1438-0064 ER - TY - GEN A1 - Cao, Karl-Kien A1 - Anderson, Lovis A1 - Böhme, Aileen A1 - Breuer, Thomas A1 - Buschmann, Jan A1 - Fiand, Frederick A1 - Frey, Ulrich A1 - Fuchs, Benjamin A1 - Kempe, Nils-Christian A1 - von Krbek, Kai A1 - Medjroubi, Wided A1 - Riehm, Judith A1 - Sasanpour, Shima A1 - Simon, Sonja A1 - Vanaret, Charlie A1 - Wetzel, Manuel A1 - Xiao, Mengzhu A1 - Zittel, Janina T1 - Evaluation of Uncertainties in Linear-Optimizing Energy System Models - Compendium T2 - DLR-Forschungsbericht N2 - Für die Energiesystemforschung sind Software-Modelle ein Kernelement zur Analyse von Szenarien. Das Forschungsprojekt UNSEEN hatte das Ziel eine bisher unerreichte Anzahl an modellbasierten Energieszenarien zu berechnen, um Unsicherheiten – vor allem unter Nutzung linear optimierender Energiesystem-Modelle - besser bewerten zu können. Hierfür wurden umfangreiche Parametervariationen auf Energieszenarien angewendet und das wesentliche methodische Hindernis in diesem Zusammenhang adressiert: die rechnerische Beherrschbarkeit der zu lösenden mathematischen Optimierungsprobleme. Im Vorläuferprojekt BEAM-ME wurde mit der Entwicklung und Anwendung des Open-Source-Lösers PIPS-IPM++ die Grundlage für den Einsatz von High-Performance-Computing (HPC) zur Lösung dieser Modelle gelegt. In UNSEEN war dieser Löser die zentrale Komponente eines Workflows, welcher zur Generierung, Lösung und multi-kriteriellen Bewertung von Energieszenarien auf dem Hochleistungscomputer JUWELS am Forschungszentrum Jülich implementiert wurde. Zur effizienten Generierung und Kommunikation von Modellinstanzen für Methoden der mathematischen Optimierung auf HPC wurde eine weitere Workflow-Komponente von der GAMS Software GmbH entwickelt: der Szenariogenerator. Bei der Weiterentwicklung von Lösungsalgorithmen für linear optimierende Energie-Systemmodelle standen gemischt-ganzzahlige Optimierungsprobleme im Fokus, welche für die Modellierung konkreter Infrastrukturen und Maßnahmen zur Umsetzung der Energiewende gelöst werden müssen. Die in diesem Zusammenhang stehenden Arbeiten zur Entwicklung von Algorithmen wurden von der Technischen Universität Berlin verantwortet. Bei Design und Implementierung dieser Methoden wurde sie vom Zuse Instituts Berlin unterstützt. Y1 - 2023 U6 - https://doi.org/10.57676/w2rq-bj85 IS - DLR-FB-2023-15 ER - TY - JOUR A1 - Betz, Fridtjof A1 - Binkowski, Felix A1 - Kuen, Lilli A1 - Burger, Sven T1 - Version 2 — RPExpand: Software for Riesz projection expansion of resonance phenomena JF - SoftwareX Y1 - 2024 U6 - https://doi.org/10.1016/j.softx.2024.101694 VL - 26 SP - 101694 ER - TY - JOUR A1 - Mukherjee, Deshabrato A1 - Kertész, Krisztián A1 - Zolnai, Zsolt A1 - Kovács, Zoltán A1 - Deák, András A1 - Pálinkás, András A1 - Osváth, Zoltán A1 - Olasz, Dániel A1 - Romanenko, Alekszej A1 - Fried, Miklós A1 - Burger, Sven A1 - Sáfrán, György A1 - Petrik, Peter T1 - Optimized Sensing on Gold Nanoparticles Created by Graded-Layer Magnetron Sputtering and Annealing Y1 - 2024 U6 - https://doi.org/10.2139/ssrn.4752470 ER - TY - JOUR A1 - Kofler, Andreas A1 - Wald, Christian A1 - Kolbitsch, Christoph A1 - von Tycowicz, Christoph A1 - Ambellan, Felix T1 - Joint Reconstruction and Segmentation in Undersampled 3D Knee MRI combining Shape Knowledge and Deep Learning JF - Physics in Medicine and Biology N2 - Task-adapted image reconstruction methods using end-to-end trainable neural networks (NNs) have been proposed to optimize reconstruction for subsequent processing tasks, such as segmentation. However, their training typically requires considerable hardware resources and thus, only relatively simple building blocks, e.g. U-Nets, are typically used, which, albeit powerful, do not integrate model-specific knowledge. In this work, we extend an end-to-end trainable task-adapted image reconstruction method for a clinically realistic reconstruction and segmentation problem of bone and cartilage in 3D knee MRI by incorporating statistical shape models (SSMs). The SSMs model the prior information and help to regularize the segmentation maps as a final post-processing step. We compare the proposed method to a state-of-the-art (SOTA) simultaneous multitask learning approach for image reconstruction and segmentation (MTL) and to a complex SSMs-informed segmentation pipeline (SIS). Our experiments show that the combination of joint end-to-end training and SSMs to further regularize the segmentation maps obtained by MTL highly improves the results, especially in terms of mean and maximal surface errors. In particular, we achieve the segmentation quality of SIS and, at the same time, a substantial model reduction that yields a five-fold decimation in model parameters and a computational speedup of an order of magnitude. Remarkably, even for undersampling factors of up to R=8, the obtained segmentation maps are of comparable quality to those obtained by SIS from ground-truth images. Y1 - 2024 U6 - https://doi.org/10.1088/1361-6560/ad3797 ER - TY - GEN A1 - Bolusani, Suresh A1 - Besançon, Mathieu A1 - Bestuzheva, Ksenia A1 - Chmiela, Antonia A1 - Dionísio, João A1 - Donkiewicz, Tim A1 - van Doornmalen, Jasper A1 - Eifler, Leon A1 - Ghannam, Mohammed A1 - Gleixner, Ambros A1 - Graczyk, Christoph A1 - Halbig, Katrin A1 - Hedtke, Ivo A1 - Hoen, Alexander A1 - Hojny, Christopher A1 - van der Hulst, Rolf A1 - Kamp, Dominik A1 - Koch, Thorsten A1 - Kofler, Kevin A1 - Lentz, Jurgen A1 - Manns, Julian A1 - Mexi, Gioni A1 - Mühmer, Erik A1 - E. Pfetsch, Marc A1 - Schlösser, Franziska A1 - Serrano, Felipe A1 - Shinano, Yuji A1 - Turner, Mark A1 - Vigerske, Stefan A1 - Weninger, Dieter A1 - Xu, Liding T1 - The SCIP Optimization Suite 9.0 N2 - The SCIP Optimization Suite provides a collection of software packages for mathematical optimization, centered around the constraint integer programming framework SCIP. This report discusses the enhancements and extensions included in the SCIP Optimization Suite 9.0. The updates in SCIP 9.0 include improved symmetry handling, additions and improvements of nonlinear handlers and primal heuristics, a new cut generator and two new cut selection schemes, a new branching rule, a new LP interface, and several bug fixes. The SCIP Optimization Suite 9.0 also features new Rust and C++ interfaces for SCIP, new Python interface for SoPlex, along with enhancements to existing interfaces. The SCIP Optimization Suite 9.0 also includes new and improved features in the LP solver SoPlex, the presolving library PaPILO, the parallel framework UG, the decomposition framework GCG, and the SCIP extension SCIP-SDP. These additions and enhancements have resulted in an overall performance improvement of SCIP in terms of solving time, number of nodes in the branch-and-bound tree, as well as the reliability of the solver. T3 - ZIB-Report - 24-02-29 KW - Constraint integer programming KW - Linear programming KW - Mixed-integer linear programming KW - Mixed-integer nonlinear programming KW - Optimization solver KW - Branch-and-cut KW - Branch-and-price KW - Column generation KW - Parallelization KW - Mixed-integer semidefinite programming Y1 - 2024 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-95528 SN - 1438-0064 ER - TY - JOUR A1 - Prause, Felix A1 - Borndörfer, Ralf A1 - Grimm, Boris A1 - Tesch, Alexander T1 - Approximating rolling stock rotations with integrated predictive maintenance JF - Journal of Rail Transport Planning & Management N2 - We study the solution of the rolling stock rotation problem with predictive maintenance (RSRP-PdM) by an iterative refinement approach that is based on a state-expanded event-graph. In this graph, the states are parameters of a failure distribution, and paths correspond to vehicle rotations with associated health state approximations. An optimal set of paths including maintenance can be computed by solving an integer linear program. Afterwards, the graph is refined and the procedure repeated. An associated linear program gives rise to a lower bound that can be used to determine the solution quality. Computational results for six instances derived from real-world timetables of a German railway company are presented. The results show the effectiveness of the approach and the quality of the solutions. Y1 - 2024 U6 - https://doi.org/https://doi.org/10.1016/j.jrtpm.2024.100434 VL - 30 SP - 100434 ER - TY - JOUR A1 - Sikorski, Alexander A1 - Rabben, Robert Julian A1 - Chewle, Surahit A1 - Weber, Marcus T1 - Capturing the Macroscopic Behaviour of Molecular Dynamics with Membership Functions N2 - Markov processes serve as foundational models in many scientific disciplines, such as molecular dynamics, and their simulation forms a common basis for analysis. While simulations produce useful trajectories, obtaining macroscopic information directly from microstate data presents significant challenges. This paper addresses this gap by introducing the concept of membership functions being the macrostates themselves. We derive equations for the holding times of these macrostates and demonstrate their consistency with the classical definition. Furthermore, we discuss the application of the ISOKANN method for learning these quantities from simulation data. In addition, we present a novel method for extracting transition paths based on the ISOKANN results and demonstrate its efficacy by applying it to simulations of the 𝜇-opioid receptor. With this approach we provide a new perspective on analyzing the macroscopic behaviour of Markov systems. Y1 - 2024 ER - TY - JOUR A1 - Sikorski, Alexander A1 - Niknejad, Amir A1 - Weber, Marcus A1 - Donati, Luca T1 - Tensor-SqRA: Modeling the transition rates of interacting molecular systems in terms of potential energies JF - Journal of Chemical Physics N2 - Estimating the rate of rare conformational changes in molecular systems is one of the goals of molecular dynamics simulations. In the past few decades, a lot of progress has been done in data-based approaches toward this problem. In contrast, model-based methods, such as the Square Root Approximation (SqRA), directly derive these quantities from the potential energy functions. In this article, we demonstrate how the SqRA formalism naturally blends with the tensor structure obtained by coupling multiple systems, resulting in the tensor-based Square Root Approximation (tSqRA). It enables efficient treatment of high-dimensional systems using the SqRA and provides an algebraic expression of the impact of coupling energies between molecular subsystems. Based on the tSqRA, we also develop the projected rate estimation, a hybrid data-model-based algorithm that efficiently estimates the slowest rates for coupled systems. In addition, we investigate the possibility of integrating low-rank approximations within this framework to maximize the potential of the tSqRA. Y1 - 2024 U6 - https://doi.org/10.1063/5.0187792 VL - 160 SP - 104112 ER - TY - CHAP A1 - Mexi, Gioni A1 - Shamsi, Somayeh A1 - Besançon, Mathieu A1 - Bodic, Pierre T1 - Probabilistic Lookahead Strong Branching via a Stochastic Abstract Branching Model T2 - Proceedings of International Conference on the Integration of Constraint Programming, Artificial Intelligence, and Operations Research Y1 - 2024 ER - TY - JOUR A1 - Tjusila, Gennesaret A1 - Besançon, Mathieu A1 - Turner, Mark A1 - Koch, Thorsten T1 - How Many Clues To Give? A Bilevel Formulation For The Minimum Sudoku Clue Problem JF - Operations Research Letters N2 - It has been shown that any 9 by 9 Sudoku puzzle must contain at least 17 clues to have a unique solution. This paper investigates the more specific question: given a particular completed Sudoku grid, what is the minimum number of clues in any puzzle whose unique solution is the given grid? We call this problem the Minimum Sudoku Clue Problem (MSCP). We formulate MSCP as a binary bilevel linear program, present a class of globally valid inequalities, and provide a computational study on 50 MSCP instances of 9 by 9 Sudoku grids. Using a general bilevel solver, we solve 95% of instances to optimality, and show that the solution process benefits from the addition of a moderate amount of inequalities. Finally, we extend the proposed model to other combinatorial problems in which uniqueness of the solution is of interest. Y1 - 2024 U6 - https://doi.org/10.1016/j.orl.2024.107105 VL - 54 SP - 107105 ER - TY - CHAP A1 - Sharma, Kartikey A1 - Hendrych, Deborah A1 - Besançon, Mathieu A1 - Pokutta, Sebastian T1 - Network Design for the Traffic Assignment Problem with Mixed-Integer Frank-Wolfe T2 - Proceedings of INFORMS Optimization Society Conference Y1 - 2024 ER - TY - JOUR A1 - Breugem, Thomas A1 - Schlechte, Thomas A1 - Schulz, Christof A1 - Borndörfer, Ralf T1 - A three-phase heuristic for the Fairness-Oriented Crew Rostering Problem JF - Computers & Operations Research N2 - The Fairness-Oriented Crew Rostering Problem (FCRP) considers the joint optimization of attractiveness and fairness in cyclic crew rostering. Like many problems in scheduling and logistics, the combinatorial complexity of cyclic rostering causes exact methods to fail for large-scale practical instances. In case of the FCRP, this is accentuated by the additionally imposed fairness requirements. Hence, heuristic methods are necessary. We present a three-phase heuristic for the FCRP combining column generation techniques with variable-depth neighborhood search. The heuristic exploits different mathematical formulations to find feasible solutions and to search for improvements. We apply our methodology to practical instances from Netherlands Railways (NS), the main passenger railway operator in the Netherlands Our results show the three-phase heuristic finds good solutions for most instances and outperforms a state-of-the-art commercial solver. Y1 - 2023 U6 - https://doi.org/https://doi.org/10.1016/j.cor.2023.106186 VL - 154 ER - TY - GEN A1 - Binkowski, Felix A1 - Kullig, Julius A1 - Betz, Fridtjof A1 - Zschiedrich, Lin A1 - Walther, Andrea A1 - Wiersig, Jan A1 - Burger, Sven T1 - Source code and simulation results: Computing eigenfrequency sensitivities near exceptional points T2 - Zenodo Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.10715639 SP - doi: 10.5281/zenodo.10715639 ER - TY - JOUR A1 - Binkowski, Felix A1 - Kullig, Julius A1 - Betz, Fridtjof A1 - Zschiedrich, Lin A1 - Walther, Andrea A1 - Wiersig, Jan A1 - Burger, Sven T1 - Computing eigenfrequency sensitivities near exceptional points JF - Phys. Rev. Research Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevResearch.6.023148 VL - 6 SP - 023148 ER - TY - GEN A1 - Iommazzo, Gabriele A1 - D'Ambrosio, Claudia A1 - Frangioni, Antonio A1 - Liberti, Leo T1 - Algorithm configuration problem T2 - Encyclopedia of Optimization Y1 - 2022 ER - TY - GEN A1 - Gahururu, Deborah A1 - Hintermüller, Michael A1 - Stengl, Steven-Marian A1 - Surowiec, Thomas M. T1 - Generalized Nash equilibrium problems with partial differential operators: theory, algorithms, and risk aversion T2 - Non-smooth and Complementarity-based Distributed Parameter Systems: Simulation and Hierarchical Optimization Y1 - 2022 ER - TY - JOUR A1 - Kreimeier, Timo A1 - Pokutta, Sebastian A1 - Walther, Andrea A1 - Woodstock, Zev T1 - On a Frank-Wolfe approach for abs-smooth functions JF - Optimization Methods and Software Y1 - U6 - https://doi.org/10.1080/10556788.2023.2296985 ER - TY - JOUR A1 - Hunkenschröder, Christoph A1 - Pokutta, Sebastian A1 - Weismantel, Robert T1 - Optimizing a low-dimensional convex function over a high-dimensional cube JF - SIAM Journal on Optimization Y1 - 2022 ER - TY - CHAP A1 - Thuerck, Daniel A1 - Sofranac, Boro A1 - Pfetsch, Marc A1 - Pokutta, Sebastian T1 - Learning cuts via enumeration oracles T2 - Proceedings of Conference on Neural Information Processing Systems Y1 - 2023 ER - TY - CHAP A1 - Martínez-Rubio, David A1 - Pokutta, Sebastian T1 - Accelerated Riemannian optimization: Handling constraints with a prox to bound geometric penalties T2 - Proceedings of Optimization for Machine Learning (NeurIPS Workshop OPT 2022) Y1 - 2022 ER - TY - CHAP A1 - Martínez-Rubio, David A1 - Roux, Christophe A1 - Criscitiello, Christopher A1 - Pokutta, Sebastian T1 - Accelerated Riemannian Min-Max Optimization Ensuring Bounded Geometric Penalties T2 - Proceedings of Optimization for Machine Learning (NeurIPS Workshop OPT 2023) Y1 - 2023 ER - TY - JOUR A1 - Designolle, Sébastien A1 - Vértesi, Tamás A1 - Pokutta, Sebastian T1 - Symmetric multipartite Bell inequalities via Frank-Wolfe algorithms JF - Physics Review A N2 - In multipartite Bell scenarios, we study the nonlocality robustness of the Greenberger-Horne-Zeilinger (GHZ) state. When each party performs planar measurements forming a regular polygon, we exploit the symmetry of the resulting correlation tensor to drastically accelerate the computation of (i) a Bell inequality via Frank-Wolfe algorithms and (ii) the corresponding local bound. The Bell inequalities obtained are facets of the symmetrized local polytope and they give the best-known upper bounds on the nonlocality robustness of the GHZ state for three to ten parties. Moreover, for four measurements per party, we generalize our facets and hence show, for any number of parties, an improvement on Mermin's inequality in terms of noise robustness. We also compute the detection efficiency of our inequalities and show that some give rise to the activation of nonlocality in star networks, a property that was only shown with an infinite number of measurements. Y1 - 2024 U6 - https://doi.org/10.1103/PhysRevA.109.022205 VL - 109 IS - 2 ER - TY - CHAP A1 - Ghannam, Mohammed A1 - Gleixner, Ambros T1 - Hybrid genetic search for dynamic vehicle routing with time windows T2 - Proceedings of Conference of the Society for Operations Research in Germany Y1 - 2023 ER - TY - CHAP A1 - Hoen, Alexander A1 - Oertel, Andy A1 - Gleixner, Ambros A1 - Nordström, Jakob T1 - Certifying MIP-based presolve reductions for 0-1 integer linear programs T2 - Proceedings of International Conference on the Integration of Constraint Programming, Artificial Intelligence, and Operations Research Y1 - 2024 ER - TY - JOUR A1 - Eifler, Leon A1 - Gleixner, Ambros T1 - Safe and verified Gomory mixed integer cuts in a rational MIP framework JF - SIAM Journal on Optimization Y1 - 2024 ER - TY - GEN A1 - Musial, Anna A1 - Sek, Grzegorz A1 - Schneider, Philipp-Immanuel A1 - Reitzenstein, Stephan T1 - Fiber-coupled solid-state-based single-photon sources T2 - Specialty Optical Fibers Y1 - 2024 U6 - https://doi.org/10.1016/B978-0-443-18495-6.00004-4 SP - 345 EP - 384 PB - Woodhead Publishing ER - TY - GEN A1 - Plock, Matthias A1 - Binkowski, Felix A1 - Zschiedrich, Lin A1 - Schneider, Phillip-Immanuel A1 - Burger, Sven T1 - Research data for "Fabrication uncertainty guided design optimization of a photonic crystal cavity by using Gaussian processes" T2 - Zenodo Y1 - 2024 U6 - https://doi.org/10.5281/zenodo.8131611 SP - doi: 10.5281/zenodo.8131611 ER -