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The landscape of applications and subroutines relying on shortest path computations continues to grow steadily. This growth is driven by the undeniable success of shortest path algorithms in theory and practice. It also introduces new challenges as the models and assessing the optimality of paths become more complicated. Hence, multiple recent publications in the field adapt existing labeling methods in an ad hoc fashion to their specific problem variant without considering the underlying general structure: they always deal with multi-criteria scenarios, and those criteria define different partial orders on the paths. In this paper, we introduce the partial order shortest path problem (POSP), a generalization of the multi-objective shortest path problem (MOSP) and in turn also of the classical shortest path problem. POSP captures the particular structure of many shortest path applications as special cases. In this generality, we study optimality conditions or the lack of them, depending on the objective functions’ properties. Our final contribution is a big lookup table summarizing our findings and providing the reader with an easy way to choose among the most recent multi-criteria shortest path algorithms depending on their problems’ weight structure. Examples range from time-dependent shortest path and bottleneck path problems to the electric vehicle shortest path problem with recharging and complex financial weight functions studied in the public transportation community. Our results hold for general digraphs and, therefore, surpass previous generalizations that were limited to acyclic graphs.
Muschner, Christoph ; Yüksel-Ergün, Inci ; Gehring, Marie-Claire ; Bartoszuk, Karolina ; Haas, Sabine ; Zittel, Janina
The investigation of energy transition paths toward a sustainable and decarbonized future under uncertainty is a critical aspect of contemporary energy planning and policy development. There are numerous methods for analysing uncertainties and sensitivities and many studies on sustainable transformation paths, but there is a lack of combined application to relevant use-cases.
In this study, we investigate the sensitivity of energy transition paths to uncertainties in operational and investment costs of power plants in the metropolitan area of Berlin and its rural surroundings.
By employing the linear programming energy system model oemof-B3, we extensively focus on the system's energy technologies, such as wind turbines, photovoltaics, hydro and combustion plants, and energy storages. Greenhouse gas reduction and electrification rates per commodity are realized by selected constraints.
Our research aims to discern how investments in energy production capacities are influenced by uncertainties of other energy technologies' investment and operational costs in the system. We apply a quantitative approach to investigate such interdependencies of cost variations and their impact on long-term energy planning. Thus, the analysis sheds light on the robustness of energy transition paths in the face of these uncertainties.
The region Berlin-Brandenburg serves as a case study and thus reflects on the present space conflicts to meet energy demands in urban and suburban areas and their rural surroundings. An electricity-intensive scenario is selected that assumes a 100 % reduction in greenhouse gas emissions by 2050. With the results of the case study, we show how our approach enables rural and metropolitan decision-makers to collaborate in achieving sustainable energy.
Decision-making in long-term energy planning can be made more robust and flexible by acknowledging the identified sensitivities and enable such regions better to navigate challenges and uncertainties associated with sustainable energy planning.
Compressible flows are prevalent in natural and technological processes, particularly in the energy transition to renewable energy systems. Consequently, extensive research has focused on understanding the stability of tangential--velocity discontinuity in compressible media. Despite recent advancements that address industrial challenges more realistically, many studies have ignored viscous stress tensors' impact, leading to inaccuracies in predicting interface stability. This omission becomes critical, especially in high Reynolds or low Mach number flows, where viscous forces dissipate kinetic energy across interfaces, affect total energy dissipation, and dampen flow instabilities. Our work is thus motivated to analyze the viscosity force effect by including the viscous stress tensor terms in the motion equations. Our results show that by considering the effect of viscous forces, the tangential-velocity discontinuity interface is constantly destabilized for the entire range of the Mach number.
We study a complex planning and scheduling problem arising from the build-up process of air cargo pallets and containers, collectively referred to as unit load devices (ULD), in which ULDs must be assigned to workstations for loading. Since air freight usually becomes available gradually along the planning horizon, ULD build-ups must be scheduled neither too early to avoid underutilizing ULD capacity, nor too late to avoid resource conflicts with other flights. Whenever possible, ULDs should be built up in batches, thereby giving ground handlers more freedom to rearrange cargo and utilize the ULD's capacity efficiently. The resulting scheduling problem has an intricate cost function and produces large time-expanded models, especially for longer planning horizons. We propose a logic-based Benders decomposition approach that assigns batches to time intervals and workstations in the master problem, while the actual schedule is decided in a subproblem. By choosing appropriate intervals, the subproblem becomes a feasibility problem that decomposes over the workstations. Additionally, the similarity of many batches is exploited by a strengthening procedure for no-good cuts. We benchmark our approach against a time-expanded MIP formulation from the literature on a publicly available data set. It solves 15% more instances to optimality and decreases run times by more than 50% in the geometric mean. This improvement is especially pronounced for longer planning horizons of up to one week, where the Benders approach solves over 50% instances more than the baseline
Zittel, Janina ; Clarner, Jan-Patrick ; Tawfik, Christine ; Dykes, Maxwell ; Rivetta, Fabian ; Riedmüller, Stephanie
The imperative to decarbonize energy systems has intensified the need for efficient transformations within the heating sector, with a particular focus on district heating networks. This study addresses this challenge by proposing a comprehensive optimization approach evaluated on the district heating
network of the Märkisches Viertel of Berlin. Our objective is to simultaneously optimize heat production with three targets: minimizing costs, minimizing CO2-emissions, and maximizing heat generation from Combined Heat and Power (CHP) plants for enhanced efficiency.
To tackle this optimization problem, we employed a Mixed-Integer Linear Program (MILP) that encompasses the conversion of various fuels into heat and power, integration with relevant markets, and considerations for technical constraints on power plant operation. These constraints include startup
and minimum downtime, activation costs, and storage limits. The ultimate goal is to delineate the Pareto front, representing the optimal trade-offs between the three targets. We evaluate variants of the 𝜖-constraint algorithm for their effectiveness in coordinating these objectives, with a simultaneous focus on the quality of the estimated Pareto front and computational efficiency. One algorithm explores solutions on an evenly spaced grid in the objective space, while another dynamically adjusts the grid based on identified solutions. Initial findings highlight the strengths and limitations of each algorithm, providing guidance on algorithm selection depending on desired outcomes and computational constraints.
Our study emphasizes that the optimal choice of algorithm hinges on the density and distribution of solutions in the feasible space. Whether solutions are clustered or evenly distributed significantly influences algorithm performance. These insights contribute to a nuanced understanding of algorithm selection for multi-objective multi-energy system optimization, offering valuable guidance for future research and practical applications for planning sustainable district heating networks.
Modeling-Simulation-Optimization workflows play a fundamental role in applied mathematics. The Mathematical Research Data Initiative, MaRDI, responded to this by developing a FAIR and machine-interpretable template for a comprehensive documentation of such workflows. MaRDMO, a Plugin for the Research Data Management Organiser, enables scientists from diverse fields to document and publish their workflows on the MaRDI Portal seamlessly using the MaRDI template. Central to these workflows are mathematical models. MaRDI addresses them with the MathModDB ontology, offering a structured formal model description. Here, we showcase the interaction between MaRDMO and the MathModDB Knowledge Graph through an algebraic modeling workflow from the Digital Humanities. This demonstration underscores the versatility of both services beyond their original numerical domain.
At present, data management plans (DMPs) are still often perceived as mere documents for funding agencies providing clarity on how research data will be handled during a funded project, but are not usually actively involved in the processes. However, they contain a great deal of information that can be shared automatically to facilitate active research data management (RDM) by providing metadata to research infrastructures and supporting communication between all involved stakeholders. This position paper brings together a number of ideas developed and collected during interdisciplinary workshops of the Data Management Planning Working Group (infra-dmp), which is part of the section Common Infrastructures of the National Research Data Infrastructure (NFDI) in Germany. We present our vision of a possible future role of DMPs, templates, and tools in the upcoming NFDI service architecture.
Schembera, Björn ; Wübbeling, Frank ; Kleikamp, Hendrik ; Biedinger, Christine ; Fiedler, Jochen ; Reidelbach, Marco ; Shehu, Aurela ; Schmidt, Burkhard ; Koprucki, Thomas ; Iglezakis, Dotothea ; Göddeke, Dominik
In applied mathematics and related disciplines, the modeling-simulation-optimization workflow is a prominent scheme, with mathematical models and numerical algorithms playing a crucial role. For these types of mathematical research data, the Mathematical Research Data Initiative has developed, merged and implemented ontologies and knowledge graphs. This contributes to making mathematical research data FAIR by introducing semantic technology and documenting the mathematical foundations accordingly. Using the concrete example of microfracture analysis of porous media, it is shown how the knowledge of the underlying mathematical model and the corresponding numerical algorithms for its solution can be represented by the ontologies.
Schembera, Björn ; Wübbeling, Frank ; Koprucki, Thomas ; Biedinger, Christine ; Reidelbach, Marco ; Schmidt, Burkhard ; Göddeke, Dominik ; Fiedler, Jochen
Ontologies and knowledge graphs for mathematical algorithms and models are presented, that have been developed by the Mathematical Research Data Initiative. This enables FAIR data handling in mathematics and the applied disciplines. Moreover, challenges of harmonization during the ontology development are discussed.
MaRDMO Plugin
(2023)
MaRDMO, a plugin for the Research Data Management Organiser, was developed in the Mathematical Research Data Initiative to document interdisciplinary workflows using a standardised scheme. Interdisciplinary workflows recorded this way are published directly on the MaRDI portal. In addition, central information is integrated into the MaRDI knowledge graph. Next to the documentation, MaRDMO offers the possibility to retrieve existing interdisciplinary workflows from the MaRDI Knowledge Graph to allow the reproduction of the initial work and to provide scientists with new researchimpulses. Thus, MaRDMO creates a community-driven knowledge loop that could help to overcome the replication crisis.
Benner, Peter ; Danabalan, Renita ; Gödekke, Dominik ; Kastner, Lars ; Krause, Tabea ; Mietchen, Daniel ; Reidelbach, Marco ; Schembera, Björn ; Schubotz, Moritz ; Sinn, Rainer ; Tabelow, Karsten
Research data are crucial in mathematics and all scientific disciplines, as they form the
foundation for empirical evidence, by enabling the validation and reproducibility of scientific findings. Mathematical research data (MathRD) have become vast and complex, and their interdisciplinary potential and abstract nature make them ubiquitous in various scientific fields. The volume of data and the velocity of its creation are rapidly increasing due to advancements in data science and computing power. This complexity extends to other disciplines, resulting in diverse research data and computational models. Thus, proper handling of research data is crucial both within mathematics and for its manifold connections and exchange with other disciplines. The National Research Data Infrastructure (NFDI), funded by the federal and state governments of Germany, consists of discipline-oriented consortia, including the Mathematical Research Data Initiative (MaRDI). MaRDI has been established to develop services, guidelines and outreach measures for all aspects of MathRD, and thus support the mathematical research community. Research data management (RDM) should be an integral component of every scientific project, and is becoming a mandatory component of grants with funding bodies such as the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation). At the core of RDM are the FAIR (Findable, Accessible, Interoperable, and Reusable) principles. This document aims to guide mathematicians and researchers from related disciplines who create RDM plans. It highlights the benefits and opportunities of RDM in mathematics and interdisciplinary studies, showcases examples of diverse MathRD, and suggests technical solutions that meet the requirements of funding agencies with specific examples. The document is regularly updated to reflect the latest developments within the mathematical community represented by MaRDI.
Voronoi Graph - Improved raycasting and integration schemes for high dimensional Voronoi diagrams
(2024)
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.
Schaible, Jonas ; Nouri, Bijan ; Höpken, Lars ; Kotzab, Tim ; Loevenich, Matthias ; Blum, Niklas ; Hammer, Annette ; Stührenberg, Jonas ; Jäger, Klaus ; Becker, Christiane ; Wilbert, Stefan
Introduction and application of a new approach for model-based optical bidirectional measurements
(2024)
Krüger, Jan ; Manley, Phillip ; Bergmann, Detlef ; Köning, Rainer ; Bodermann, Bernd ; Eder, Christian ; Heinrich, Andreas ; Schneider, Philipp-Immanuel ; Hammerschmidt, Martin ; Zschiedrich, Lin ; Manske, Eberhard
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.
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.
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.
Müller, Gabriel ; Martínez-Lahuerta, V. J. ; Sekuliĉ, Ivan ; Burger, Sven ; Schneider, Philipp-Immanuel ; Gaaloul, Naceur
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.
Kuen, Lilli ; Löffler, Lorenz ; Tsarapkin, Aleksei ; Zschiedrich, Lin ; Feichtner, Thorsten ; Burger, Sven ; Höflich, Katja
AI-guided pipeline for protein–protein interaction drug discovery identifies a SARS-CoV-2 inhibitor
(2024)
Trepte, Philipp ; Secker, Christopher ; Olivet, Julien ; Blavier, Jeremy ; Kostova, Simona ; Maseko, Sibusiso B ; Minia, Igor ; Silva Ramos, Eduardo ; Cassonnet, Patricia ; Golusik, Sabrina ; Zenkner, Martina ; Beetz, Stephanie ; Liebich, Mara J ; Scharek, Nadine ; Schütz, Anja ; Sperling, Marcel ; Lisurek, Michael ; Wang, Yang ; Spirohn, Kerstin ; Hao, Tong ; Calderwood, Michael A ; Hill, David E ; Landthaler, Markus ; Choi, Soon Gang ; Twizere, Jean-Claude ; Vidal, Marc ; Wanker, Erich E
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.
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.
An Iterative Refinement Approach for the Rolling Stock Rotation Problem with Predictive Maintenance
(2024)
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.
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)
Sherratt, Katharine ; Srivastava, Ajitesh ; Ainslie, Kylie ; Singh, David E. ; Cublier, Aymar ; Marinescu, Maria Cristina ; Carretero, Jesus ; Garcia, Alberto Cascajo ; Franco, Nicolas ; Willem, Lander ; Abrams, Steven ; Faes, Christel ; Beutels, Philippe ; Hens, Niel ; Müller, Sebastian ; Charlton, Billy ; Ewert, Ricardo ; Paltra, Sydney ; Rakow, Christian ; Rehmann, Jakob ; Conrad, Tim O.F. ; Schütte, Christof ; Nagel, Kai ; Abbott, Sam ; Grah, Rok ; Niehus, Rene ; Prasse, Bastian ; Sandmann, Frank ; Funk, Sebastian
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
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.
Schintke, Florian ; Belhajjame, Khalid ; De Mecquenem, Ninon ; Frantz, David ; Guarino, Vanessa Emanuela ; Hilbrich, Marcus ; Lehmann, Fabian ; Missier, Paolo ; Sattler, Rebecca ; Sparka, Jan Arne ; Speckhard, Daniel T. ; Stolte, Hermann ; Vu, Anh Duc ; Leser, Ulf
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.
Cao, Karl-Kien ; Anderson, Lovis ; Böhme, Aileen ; Breuer, Thomas ; Buschmann, Jan ; Fiand, Frederick ; Frey, Ulrich ; Fuchs, Benjamin ; Kempe, Nils-Christian ; von Krbek, Kai ; Medjroubi, Wided ; Riehm, Judith ; Sasanpour, Shima ; Simon, Sonja ; Vanaret, Charlie ; Wetzel, Manuel ; Xiao, Mengzhu ; Zittel, Janina
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.
Optimized Sensing on Gold Nanoparticles Created by Graded-Layer Magnetron Sputtering and Annealing
(2024)
Mukherjee, Deshabrato ; Kertész, Krisztián ; Zolnai, Zsolt ; Kovács, Zoltán ; Deák, András ; Pálinkás, András ; Osváth, Zoltán ; Olasz, Dániel ; Romanenko, Alekszej ; Fried, Miklós ; Burger, Sven ; Sáfrán, György ; Petrik, Peter
Kofler, Andreas ; Wald, Christian ; Kolbitsch, Christoph ; von Tycowicz, Christoph ; Ambellan, Felix
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.
Bolusani, Suresh ; Besançon, Mathieu ; Bestuzheva, Ksenia ; Chmiela, Antonia ; Dionísio, João ; Donkiewicz, Tim ; van Doornmalen, Jasper ; Eifler, Leon ; Ghannam, Mohammed ; Gleixner, Ambros ; Graczyk, Christoph ; Halbig, Katrin ; Hedtke, Ivo ; Hoen, Alexander ; Hojny, Christopher ; van der Hulst, Rolf ; Kamp, Dominik ; Koch, Thorsten ; Kofler, Kevin ; Lentz, Jurgen ; Manns, Julian ; Mexi, Gioni ; Mühmer, Erik ; E. Pfetsch, Marc ; Schlösser, Franziska ; Serrano, Felipe ; Shinano, Yuji ; Turner, Mark ; Vigerske, Stefan ; Weninger, Dieter ; Xu, Liding
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.
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.
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.
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.
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.
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.
Source code and simulation results: Computing eigenfrequency sensitivities near exceptional points
(2024)
Binkowski, Felix ; Kullig, Julius ; Betz, Fridtjof ; Zschiedrich, Lin ; Walther, Andrea ; Wiersig, Jan ; Burger, Sven
Binkowski, Felix ; Kullig, Julius ; Betz, Fridtjof ; Zschiedrich, Lin ; Walther, Andrea ; Wiersig, Jan ; Burger, Sven
Accelerated Riemannian optimization: Handling constraints with a prox to bound geometric penalties
(2022)
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.
We present EPR-Net, a novel and effective deep learning approach that tackles a crucial challenge in biophysics: constructing potential landscapes for high-dimensional non-equilibrium steady-state (NESS) systems. EPR-Net leverages a nice mathematical fact that the desired negative potential gradient is simply the orthogonal projection of the driving force of the underlying dynamics in a weighted inner-product space. Remarkably, our loss function has an intimate connection with the steady entropy production rate (EPR), enabling simultaneous landscape construction and EPR estimation. We introduce an enhanced learning strategy for systems with small noise, and extend our framework to include dimensionality reduction and state-dependent diffusion coefficient case in a unified fashion. Comparative evaluations on benchmark problems demonstrate the superior accuracy, effectiveness, and robustness of EPR-Net compared to existing methods. We apply our approach to challenging biophysical problems, such as an 8D limit cycle and a 52D multi-stability problem, which provide accurate solutions and interesting insights on constructed landscapes. With its versatility and power, EPR-Net offers a promising solution for diverse landscape construction problems in biophysics.
Conduction velocity in cardiac tissue is a crucial electrophysiological parameter for arrhythmia vulnerability. Pathologically reduced conduction velocity facilitates arrhythmogenesis because such conduction velocities decrease the wavelength with which re-entry may occur. Computational studies on CV and how it changes regionally in models at spatial scales multiple times larger than actual cardiac cells exist. However, microscopic conduction within cells and between them have been studied less in simulations. In this work, we study the relation of microscopic conduction patterns and clinically observable macroscopic conduction using an extracellular-membrane-intracellular model which represents cardiac tissue with these subdomains at subcellular resolution. By considering cell arrangement and non-uniform gap junction distribution, it yields anisotropic excitation propagation. This novel kind of model can for example be used to understand how discontinuous conduction on the microscopic level affects fractionation of electrograms in healthy and fibrotic tissue. Along the membrane of a cell, we observed a continuously propagating activation wavefront. When transitioning from one cell to the neighbouring one, jumps in local activation times occurred, which led to lower global conduction velocities than locally within each cell.
For decades, de Casteljau's algorithm has been used as a fundamental building block in curve and surface design and has found a wide range of applications in fields such as scientific computing, and discrete geometry to name but a few. With increasing interest in nonlinear data science, its constructive approach has been shown to provide a principled way to generalize parametric smooth curves to manifolds. These curves have found remarkable new applications in the analysis of parameter-dependent, geometric data. This article provides a survey of the recent theoretical developments in this exciting area as well as its applications in fields such as geometric morphometrics and longitudinal data analysis in medicine, archaeology, and meteorology.
In this work, we study the geodesics of the space of certain geometrically and physically motivated subspaces of the space of immersed curves endowed with a first order Sobolev metric. This includes elastic curves and also an extension of some results on planar concentric circles to surfaces. The work focuses on intrinsic and constructive approaches.
Statistical shape models are an essential tool for various tasks in medical image analysis, including shape generation, reconstruction and classification. Shape models are learned from a population of example shapes, which are typically obtained through segmentation of volumetric medical images. In clinical practice, highly anisotropic volumetric scans with large slice distances are prevalent, e.g., to reduce radiation exposure in CT or image acquisition time in MR imaging. For existing shape modeling approaches, the resolution of the emerging model is limited to the resolution of the training shapes. Therefore, any missing information between slices prohibits existing methods from learning a high-resolution shape prior. We propose a novel shape modeling approach that can be trained on sparse, binary segmentation masks with large slice distances. This is achieved through employing continuous shape representations based on neural implicit functions. After training, our model can reconstruct shapes from various sparse inputs at high target resolutions beyond the resolution of individual training examples. We successfully reconstruct high-resolution shapes from as few as three orthogonal slices. Furthermore, our shape model allows us to embed various sparse segmentation masks into a common, low-dimensional latent space — independent of the acquisition direction, resolution, spacing, and field of view. We show that the emerging latent representation discriminates between healthy and pathological shapes, even when provided with sparse segmentation masks. Lastly, we qualitatively demonstrate that the emerging latent space is smooth and captures characteristic modes of shape variation. We evaluate our shape model on two anatomical structures: the lumbar vertebra and the distal femur, both from publicly available datasets.
Periodic timetabling is a challenging planning task in public transport.
As safety requirements are crucial, track allocation is indispensable for validating the practical feasibility of a railway timetable. For busy stations with limited capacities, this requires a detailed planning of turnarounds. It is therefore desirable to integrate timetabling not only with track allocation, but also with vehicle scheduling and line planning. This is captured by the Integrated Line Planning and Turn-Sensitive Periodic Timetabling Problem with Track Choice, whose MIP formulation has been demonstrated to be effective for construction site railway rescheduling, as long as a good quality initial solution is available. In this paper, we discuss how to generate such a solution by extending the SAT formulation of the Periodic Event Scheduling Problem with track choice, track occupation, and minimum service frequency components. The SAT approach is superior to pure MIP on real-world instances of the S-Bahn Berlin network.
The recent COVID-19 pandemic has thrown the importance of accurately forecasting contagion dynamics and learning infection parameters into sharp focus. At the same time, effective policy-making requires knowledge of the uncertainty on such predictions, in order, for instance, to be able to ready hospitals and intensive care units for a worst-case scenario without needlessly wasting resources. In this work, we apply a novel and powerful computational method to the problem of learning probability densities on contagion parameters and providing uncertainty quantification for pandemic projections. Using a neural network, we calibrate an ODE model to data of the spread of COVID-19 in Berlin in 2020, achieving both a significantly more accurate calibration and prediction than Markov-Chain Monte Carlo (MCMC)-based sampling schemes. The uncertainties on our predictions provide meaningful confidence intervals e.g. on infection figures and hospitalisation rates, while training and running the neural scheme takes minutes where MCMC takes hours. We show convergence of our method to the true posterior on a simplified SIR model of epidemics, and also demonstrate our method's learning capabilities on a reduced dataset, where a complex model is learned from a small number of compartments for which data is available.
We have investigated how Langevin dynamics is affected by the friction
coefficient using the novel algorithm ISOKANN, which combines the transfer
operator approach with modern machine learning techniques. ISOKANN describes
the dynamics in terms of an invariant subspace projection of the Koopman
operator defined in the entire state space, avoiding approximations due to
dimensionality reduction and discretization. Our results are consistent with
the Kramers turnover and show that in the low and moderate friction regimes,
metastable macro-states and transition rates are defined in phase space, not
only in position space.
Chiral and directional optical emission from a dipole source coupled to a helical plasmonic antenna
(2024)
Kuen, Lilli ; Löffler, Lorenz ; Tsarapkin, Aleksei ; Zschiedrich, Lin ; Feichtner, Thorsten ; Burger, Sven ; Höflich, Katja
A major step in the planning process of passenger railway operators is the assignment of rolling stock, i.e., train units, to the trips of the timetable. A wide variety of mathematical optimization models have been proposed to support this task, which we discuss and argue to be justified in order to deal with operational differences between railway operators, and hence different planning requirements, in the best possible way. Our investigation focuses on two commonly used models, the Composition model and the Hypergraph model, that were developed for Netherlands Railways (NS) and DB Fernverkehr AG (DB), respectively. We compare these models in a rolling stock scheduling setting similar to that of NS, which we show to be strongly NP-hard, and propose different variants of the Hypergraph model to tune the model to the NS setting. We prove that, in this setting, the linear programming bounds of both models are equally strong as long as a Hypergraph model variant is chosen that is sufficiently expressive. However, through a numerical evaluation on NS instances, we show that the Composition model is generally more compact in practice and can find optimal solutions in the shortest running time.
a variational inequality model for the construction of signals from inconsistent nonlinear equations
(2022)
Wilken, St. Elmo ; Besançon, Mathieu ; Kratochvíl, Miroslav ; Kuate, Chilperic Armel Foko ; Trefois, Christophe ; Gu, Wei ; Ebenhöh, Oliver
The Machine Learning for Combinatorial Optimization Competition (ML4CO): results and insights
(2022)
Gasse, Maxime ; Bowly, Simon ; Cappart, Quentin ; Charfreitag, Jonas ; Charlin, Laurent ; Chételat, Didier ; Chmiela, Antonia ; Dumouchelle, Justin ; Gleixner, Ambros ; Kazachkov, Aleksandr M. ; Khalil, Elias ; Lichocki, Pawel ; Lodi, Andrea ; Lubin, Miles ; Maddison, Chris J. ; Christopher, Morris ; Papageorgiou, Dimitri J. ; Parjadis, Augustin ; Pokutta, Sebastian ; Prouvost, Antoine ; Scavuzzo, Lara ; Zarpellon, Giulia ; Yang, Linxin ; Lai, Sha ; Wang, Akang ; Luo, Xiaodong ; Zhou, Xiang ; Huang, Haohan ; Shao, Shengcheng ; Zhu, Yuanming ; Zhang, Dong ; Quan, Tao ; Cao, Zixuan ; Xu, Yang ; Huang, Zhewei ; Zhou, Shuchang ; Binbin, Chen ; Minggui, He ; Hao, Hao ; Zhiyu, Zhang ; Zhiwu, An ; Kun, Mao
a framework for generalized Benders' decomposition and its applications to multilevel optimization
(2022)
Schlechte, Thomas ; Blome, Christian ; Gerber, Stefan ; Hauser, Stefan ; Kasten, Jens ; Müller, Gilbert ; Schulz, Christof ; Thüring, Michel ; Weider, Steffen
Rolling stock is one of the major assets for a railway transportation company. Hence, their utilization should be as efficiently and effectively as possible. Railway undertakings are facing rolling stock scheduling challenges in different forms - from rather idealized weekly strategic problems to very concrete operational ones. Thus, a vast of optimization models with different features and objectives exist. Thorlacius et al. (2015) provides a comprehensive and valuable collection on technical requirements, models, and methods considered in
the scientific literature. We contribute with an update including recent works. The main focus of the paper is to present a classification and elaboration of the major features which our solver R-OPT is able to handle. Moreover, the basic optimization model and algorithmic ingredients of R-OPT are discussed. Finally, we present computational results for a cargo application at SBB CARGO AG and other railway undertakings for passenger traffic in Europe to show the capabilities of R-OPT.
Merlin-Arthur classifiers
(2024)
We introduce DiffOpt.jl, a Julia library to differentiate through the solution of optimization problems with respect to arbitrary parameters present in the objective and/or constraints. The library builds upon MathOptInterface, thus leveraging the rich ecosystem of solvers and composing well with modeling languages like JuMP. DiffOpt offers both forward and reverse differentiation modes, enabling multiple use cases from hyperparameter optimization to backpropagation and sensitivity analysis, bridging constrained optimization with end-to-end differentiable programming. DiffOpt is built on two known rules for differentiating quadratic programming and conic programming standard forms. However, thanks to its ability to differentiate through model transformations, the user is not limited to these forms and can differentiate with respect to the parameters of any model that can be reformulated into these standard forms. This notably includes programs mixing affine conic constraints and convex quadratic constraints or objective function.
Designolle, Sébastien ; Iommazzo, Gabriele ; Besançon, Mathieu ; Knebel, Sebastian ; Gelß, Patrick ; Pokutta, Sebastian
In Bell scenarios with two outcomes per party, we algorithmically consider the two sides of the membership problem for the local polytope: Constructing local models and deriving separating hyperplanes, that is, Bell inequalities. We take advantage of the recent developments in so-called Frank-Wolfe algorithms to significantly increase the convergence rate of existing methods. First, we study the threshold value for the nonlocality of two-qubit Werner states under projective measurements. Here, we improve on both the upper and lower bounds present in the literature. Importantly, our bounds are entirely analytical; moreover, they yield refined bounds on the value of the Grothendieck constant of order three: 1.4367⩽KG(3)⩽1.4546. Second, we demonstrate the efficiency of our approach in multipartite Bell scenarios, and present local models for all projective measurements with visibilities noticeably higher than the entanglement threshold. We make our entire code accessible as a julia library called BellPolytopes.jl.
The last milestone achievement for the roundoff-error-free solution of general mixed integer programs over the rational numbers was a hybrid-precision branch-and-bound algorithm published by Cook, Koch, Steffy, and Wolter in 2013. We describe a substantial revision and extension of this framework that integrates symbolic presolving, features an exact repair step for solutions from primal heuristics, employs a faster rational LP solver based on LP iterative refinement, and is able to produce independently verifiable certificates of optimality. We study the significantly improved performance and give insights into the computational behavior of the new algorithmic components. On the MIPLIB 2017 benchmark set, we observe an average speedup of 10.7x over the original framework and 2.9 times as many instances solved within a time limit of two hours.
The distance geometry problem asks to find a realization of a given simple edge-weighted graph in a Euclidean space of given dimension , where the edges are realized as straight segments of lengths equal (or as close as possible) to the edge weights. The problem is often modelled as a mathematical programming formulation involving decision variables that determine the position of the vertices in the given Euclidean space. Solution algorithms are generally constructed using local or global nonlinear optimization techniques. We present a new modelling technique for this problem where, instead of deciding vertex positions, the formulations decide the length of the segments representing the edges in each cycle in the graph, projected in every dimension. We propose an exact formulation and a relaxation based on a Eulerian cycle. We then compare computational results from protein conformation instances obtained with stochastic global optimization techniques on the new cycle-based formulation and on the existing edge-based formulation. While edge-based formulations take less time to reach termination, cycle-based formulations are generally better on solution quality measures.
Bestuzheva, Ksenia ; Besançon, Mathieu ; Chen, Wei-Kun ; Chmiela, Antonia ; Donkiewicz, Tim ; Doornmalen, Jasper ; Eifler, Leon ; Gaul, Oliver ; Gamrath, Gerald ; Gleixner, Ambros ; Gottwald, Leona ; Graczyk, Christoph ; Halbig, Katrin ; Hoen, Alexander ; Hojny, Christopher ; Hulst, Rolf ; Koch, Thorsten ; Lübbecke, Marco ; Maher, Stephen J. ; Matter, Frederic ; Mühmer, Erik ; Müller, Benjamin ; Pfetsch, Marc ; Rehfeldt, Daniel ; Schlein, Steffan ; Schlösser, Franziska ; Serrano, Felipe ; Shinano, Yuji ; Sofranac, Boro ; Turner, Mark ; Vigerske, Stefan ; Wegscheider, Fabian ; Wellner, Philipp ; Weninger, Dieter ; Witzig, Jakob
The SCIP Optimization Suite provides a collection of software packages for mathematical optimization centered around the constraint integer programming framework SCIP. The focus of this article is on the role of the SCIP Optimization Suite in supporting research. SCIP’s main design principles are discussed, followed by a presentation of the latest performance improvements and developments in version 8.0, which serve both as examples of SCIP’s application as a research tool and as a platform for further developments. Furthermore, this article gives an overview of interfaces to other programming and modeling languages, new features that expand the possibilities for user interaction with the framework, and the latest developments in several extensions built upon SCIP.
We propose two graph neural network layers for graphs with features in a Riemannian manifold. First, based on a manifold-valued graph diffusion equation, we construct a diffusion layer that can be applied to an arbitrary number of nodes and graph connectivity patterns. Second, we model a tangent multilayer perceptron by transferring ideas from the vector neuron framework to our general setting. Both layers are equivariant with respect to node permutations and isometries of the feature manifold. These properties have been shown to lead to a beneficial inductive bias in many deep learning tasks. Numerical examples on synthetic data as well as on triangle meshes of the right hippocampus to classify Alzheimer's disease demonstrate the very good performance of our layers.
AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor
(2023)
Trepte, Philipp ; Secker, Christopher ; Kostova, Simona ; Maseko, Sibusiso B. ; Gang Choi, Soon ; Blavier, Jeremy ; Minia, Igor ; Silva Ramos, Eduardo ; Cassonnet, Patricia ; Golusik, Sabrina ; Zenkner, Martina ; Beetz, Stephanie ; Liebich, Mara J. ; Scharek, Nadine ; Schütz, Anja ; Sperling, Marcel ; Lisurek, Michael ; Wang, Yang ; Spirohn, Kerstin ; Hao, Tong ; Calderwood, Michael A. ; Hill, David E. ; Landthaler, Markus ; Olivet, Julien ; Twizere, Jean-Claude ; Vidal, Marc ; Wanker, Erich E.
Bürger, Johanna ; Hayne, Paul ; Gundlach, Bastian ; Läuter, Matthias ; Kramer, Tobias ; Blum, Jürgen
The microphysical structure of the lunar regolith provides information on the geologic history of the Moon. We used remote sensing measurements of thermal emission and a thermophysical model to determine the microphysical properties of the lunar regolith. We expand upon previous investigations by developing a microphysical thermal model, which more directly simulates regolith properties, such as grain size and volume filling factor. The modeled temperatures are matched with surface temperatures measured by the Diviner Lunar Radiometer Experiment on board the Lunar Reconnaissance Orbiter. The maria and highlands are investigated separately and characterized in the model by a difference in albedo and grain density. We find similar regolith temperatures for both terrains, which can be well described by similar volume filling factor profiles and mean grain sizes obtained from returned Apollo samples. We also investigate a significantly lower thermal conductivity for highlands, which formally also gives a very good solution, but in a parameter range that is well outside the Apollo data. We then study the latitudinal dependence of regolith properties up to ±80° latitude. When assuming constant regolith properties, we find that a variation of the solar incidence-dependent albedo can reduce the initially observed latitudinal gradient between model and Diviner measurements significantly. A better match between measurements and model can be achieved by a variation in intrinsic regolith properties with a decrease in bulk density with increasing latitude. We find that a variation in grain size alone cannot explain the Diviner measurements at higher latitudes.
From August 2014 to September 2016, the ESA operated the Rosetta spacecraft mission alongside with comet 67P/Churyumov-Gerasimenko (67P). The mission provided valuable long-term data on the comet’s nucleus, including its volume, mass, tensor of inertia, spatial position of the orbital trajectory, and rotational state.
Majewski, Maciej ; Pérez, Adrià ; Thölke, Philipp ; Doerr, Stefan ; Charron, Nicholas ; Giorgino, Toni ; Husic, Brooke ; Clementi, Cecilia ; Noé, Frank ; De Fabritiis, Gianni
A generalized understanding of protein dynamics is an unsolved scientific problem, the solution of which is critical to the interpretation of the structure-function relationships that govern essential biological processes. Here, we approach this problem by constructing coarse-grained molecular potentials based on artificial neural networks and grounded in statistical mechanics. For training, we build a unique dataset of unbiased all-atom molecular dynamics simulations of approximately 9 ms for twelve different proteins with multiple secondary structure arrangements. The coarse-grained models are capable of accelerating the dynamics by more than three orders of magnitude while preserving the thermodynamics of the systems. Coarse-grained simulations identify relevant structural states in the ensemble with comparable energetics to the all-atom systems. Furthermore, we show that a single coarse-grained potential can integrate all twelve proteins and can capture experimental structural features of mutated proteins. These results indicate that machine learning coarse-grained potentials could provide a feasible approach to simulate and understand protein dynamics.
Bürger, Johanna ; Hayne, Paul ; Gundlach, Bastian ; Läuter, Matthias ; Kramer, Tobias ; Blum, Jürgen
Regolith is formed through weathering of the local rock by meteorite bombardment, space weathering (Pieters & Noble, 2016) and thermal erosion (Delbo et al., 2014). In the case of the Moon, the space weathering effects and diurnal temperature variations are reduced towards the poles. The aim of this study is to investigate whether the lunar regolith properties derived from the comparison of regolith temperatures measured by the Diviner radiometer (Paige et al., 2010) on board the Lunar Reconnaissance Orbiter (LRO) with simulated temperatures derived from a microphysical thermal model show a latitudinal dependence. The developed microphysical thermal model expands upon previous models by more directly simulating regolith properties, such as grain radius and volume filling factor.
Durumeric, Aleksander ; Charron, Nicholas ; Templeton, Clark ; Musil, Félix ; Bonneau, Klara ; Pasos-Trejo, Aldo ; Chen, Yaoyi ; Kelkar, Atharva ; Noé, Frank ; Clementi, Cecilia
The successful recent application of machine learning methods to scientific problems includes the learning of flexible and accurate atomic-level force-fields for materials and biomolecules from quantum chemical data. In parallel, the machine learning of force-fields at coarser resolutions is rapidly gaining relevance as an efficient way to represent the higher-body interactions needed in coarse-grained force-fields to compensate for the omitted degrees of freedom. Coarse-grained models are important for the study of systems at time and length scales exceeding those of atomistic simulations. However, the development of transferable coarse-grained models via machine learning still presents significant challenges. Here, we discuss recent developments in this field and current efforts to address the remaining challenges.