TY - CHAP A1 - Zimmer, Max A1 - Spiegel, Christoph A1 - Pokutta, Sebastian ED - Fackeldey, K. T1 - Compression-aware training of neural networks using Frank-Wolfe T2 - Mathematical Optimization for Machine Learning: Proceedings of the MATH+ Thematic Einstein Semester 2023 Y1 - 2025 U6 - https://doi.org/10.1515/9783111376776-010 SP - 137 EP - 168 PB - De Gruyter ER - TY - JOUR A1 - Ramos, Alejandro A1 - Kühn, Oliver T1 - Manipulating the dynamics of a Fermi resonance with light. A direct optimal control theory approach JF - Chemical Physics Y1 - 2022 ER - TY - JOUR A1 - Widler, Valeria A1 - Kaminska, Barbara A1 - Martins, Andre C. R. A1 - Puga-Gonzalez, Ivan T1 - An Investigation into the Causal Mechanism of Political Opinion Dynamics: A Model of Hierarchical Coarse-Graining with Community-Bounded Social Influence JF - Computational Social Science of Social Cohesion and Polarization N2 - The increasing polarization in democratic societies is an emergent outcome of political opinion dynamics. Yet, the fundamental mechanisms behind the formation of political opinions, from individual beliefs to collective consensus, remain unknown. Understanding that a causal mechanism must account for both bottom-up and top-down influences, we conceptualize political opinion dynamics as hierarchical coarse-graining, where microscale opinions integrate into a macro-scale state variable. Using the CODA (Continuous Opinions Discrete Actions) model, we simulate Bayesian opinion updating, social identity-based information integration, and migration between social identity groups to represent higher-level connectivity. This results in coarse-graining across micro, meso, and macro levels. Our findings show that higher-level connectivity shapes information integration, yielding three regimes: independent (disconnected, local convergence), parallel (fast, global convergence), and iterative (slow, stepwise convergence). In the iterative regime, low connectivity fosters transient diversity, indicating an informed consensus. In all regimes, time-scale separation leads to downward causation, where agents converge on the aggregate majority choice, driving consensus. Critically, any degree of coherent higher-level information integration can overcome misalignment via global downward causation. The results highlight how emergent properties of the causal mechanism, such as downward causation, are essential for consensus and may inform more precise investigations into polarized political discourse. Y1 - 2026 U6 - https://doi.org/10.1007/978-3-032-01373-6_10 SP - 225 EP - 256 PB - Springer, Cham. ET - Computational Social Science of Social Cohesion and Polarization ER - TY - JOUR A1 - Sterzik, Anna A1 - Krone, Michael A1 - Baum, Daniel A1 - Cunningham, Douglas W. A1 - Lawonn, Kai T1 - Uncertainty Visualization for Biomolecular Structures: An Empirical Evaluation JF - IEEE Transactions on Visualization and Computer Graphics N2 - Uncertainty is an intrinsic property of almost all data, regardless of the data being measured, simulated, or generated. It can significantly influence the results and reliability of subsequent analysis steps. Clearly communicating uncertainties is crucial for informed decision-making and understanding, especially in biomolecular data, where uncertainty is often difficult to infer. Uncertainty visualization (UV) is a powerful tool for this purpose. However, previously proposed UV methods lack sufficient empirical evaluation. We collected and categorized visualization methods for portraying positional uncertainty in biomolecular structures. We then organized the methods into metaphorical groups and extracted nine representatives: color, clouds, ensemble, hulls, sausages, contours, texture, waves, and noise. We assessed their strengths and weaknesses in a twofold approach: expert assessments with six domain experts and three perceptual evaluations involving 1,756 participants. Through the expert assessments, we aimed to highlight the advantages and limitations of the individual methods for the application domain and discussed areas for necessary improvements. Through the perceptual evaluation, we investigated whether the visualizations are intuitively associated with uncertainty and whether the directionality of the mapping is perceived as intended. We also assessed the accuracy of inferring uncertainty values from the visualizations. Based on our results, we judged the appropriateness of the metaphors for encoding uncertainty and suggest further areas for improvement. Y1 - 2025 U6 - https://doi.org/10.1109/TVCG.2025.3596385 VL - 31 IS - 12 SP - 10296 EP - 10310 ER - TY - JOUR A1 - van Lieshout, Rolf A1 - Lindner, Niels T1 - A Compact Cycle Formulation for the Multiperiodic Event Scheduling Problem N2 - The Periodic Event Scheduling Problem (PESP) is a fundamental model in periodic timetabling for public transport systems, assuming a common period across all events. However, real-world networks often feature heterogeneous service frequencies. This paper studies the Multiperiodic Event Scheduling Problem (MPESP), a generalization of PESP that allows each event to recur at its own individual period. While more expressive, MPESP presents new modeling challenges due to the loss of a global period. We present a cycle-based formulation for MPESP that extends the strongest known formulation for PESP and, in contrast to existing approaches, is valid for any MPESP instance. Crucially, the formulation requires a cycle basis derived from a spanning tree satisfying specific structural properties, which we formalize and algorithmically construct, extending the concept of sharp spanning trees to rooted instances. We further prove a multiperiodic analogue of the cycle periodicity property. Our new formulation solves nearly all tested instances, including several large-scale real-world public transport networks, to optimality or with small optimality gaps, dramatically outperforming existing arc-based models. The results demonstrate the practical potential of MPESP in capturing heterogeneous frequencies without resorting to artificial event duplication. Y1 - 2025 ER - TY - CHAP A1 - Löbel, Fabian A1 - Borndörfer, Ralf A1 - Weider, Steffen ED - Voigt, Guido ED - Fliedner, Malte ED - Haase, Knut ED - Brüggermann, Wolfgang ED - Hoberg, Kai ED - Meissner, Joern T1 - Non-linear Battery Behavior in Electric Vehicle Scheduling Problems T2 - Operations Research Proceedings 2023. OR 2023. N2 - The currently most popular approach to handle non-linear battery behavior for electric vehicle scheduling is to use a linear spline interpolation of the charge curve. We show that this can lead to approximate models that underestimate the charge duration and overestimate the state of charge, which is not desirable. While the error is of second order with respect to the interpolation step size, the associated mixed-integer linear programs do not scale well with the number of spline segments. It is therefore recommendable to use coarse interpolation grids adapted to the curvature of the charge curve, and to include sufficient safety margins to ensure solutions of approximate models remain feasible subjected to the exact charge curve. KW - Electric Vehicle Scheduling KW - Non-Linear Charging Y1 - 2025 SN - 9783031584046 U6 - https://doi.org/10.1007/978-3-031-58405-3_53 SN - 2731-040X SP - 415 EP - 421 PB - Springer Nature Switzerland CY - Cham ER - TY - JOUR A1 - Coomber, Celvic A1 - Chewle, Surahit A1 - Secker, Christopher A1 - Fackeldey, Konstantin A1 - Weber, Marcus A1 - Winkelmann, Stefanie A1 - Schütte, Christof A1 - Sunkara, Vikram T1 - Investigating Endogenous Opioids Unravels the Mechanisms Behind Opioid-Induced Constipation, a Mathematical Modeling Approach JF - International Journal of Molecular Sciences N2 - Endogenous opioids, such as Endomorphin-2, are not typically associated with severe constipation, unlike pharmaceutical opioids, which induce opioid-induced constipation (OIC) by activating μ-opioid receptors in the gastrointestinal tract. In this study, we present a mathematical model, which integrates the serotonergic and opioid pathways, simulating the interaction between serotonin and opioid signaling within the enteric nervous system (ENS). The model explores the mechanisms underlying OIC, with a focus on the change in adenylyl cyclase (AC) activity, cAMP accumulation, and the distinct functionalities of Endomorphin-2 compared to commonly used pharmaceutical opioids. We study the effects of Morphine, Fentanyl, and Methadone and contrast them with Endomorphin-2. Our findings reveal that opioids do not perturb the signaling of serotonin, but only the activity of AC, suggesting that serotonin levels have no influence on improving opioid-induced constipation. Furthermore, this study reveals that the primary difference between endogenous and pharmaceutical opioids is their degradation rates. This finding shows that modulating opioid degradation rates significantly improves cAMP recovery. In conclusion, our insights steer towards exploring opioid degrading enzymes, localized to the gut, as a strategy for mitigating OIC. Y1 - 2025 U6 - https://doi.org/10.3390/ijms26136207 VL - 26 IS - 13 ER - TY - CHAP A1 - Gotzes, Uwe A1 - Buchholz, Annika A1 - Kallrath, Josef A1 - Lindner, Niels A1 - Koch, Thorsten T1 - Flexible Pooling Pattern Design with Integer Programming T2 - Theory, Algorithms and Experiments in Applied Optimization. In Honor of the 70th Birthday of Panos Pardalos N2 - Sample pooling has the potential to significantly enhance large-scale screening procedures, especially in scenarios like the COVID-19 pandemic, where rapid and widespread PCR testing has been crucial. Efficient strategies are essential to increase the testing capacity, i.e., the number of tests that can be processed within a given timeframe. Non-adaptive pooling strategies can further streamline the testing process by reducing the required testing rounds. In contrast to adaptive strategies, where subsequent tests depend on prior results, non-adaptive pooling processes all samples in a single round, eliminating the need for sequential retesting and reducing delays. This paper presents a highly flexible method based on integer programming to design optimized pooling patterns suitable for various applications, including medical diagnostics and quality control in industrial production. Using coronavirus testing as a case study, we formulate and solve optimization and satisfiability models that compute efficient pool designs. Our optimized pooling does not only increase testing capacity, but also accelerates the testing process and reduces overall costs. The proposed method is adaptable and can be seamlessly integrated into automated testing systems. Y1 - 2025 VL - 226 PB - Springer ER - TY - CHAP A1 - Maignant, Elodie A1 - Conrad, Tim A1 - von Tycowicz, Christoph T1 - Tree inference with varifold distances T2 - Geometric Science of Information. GSI 2025 N2 - In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a process, we are interested in the problem of ordering the cells according to their progression in the process. This is known as trajectory inference. If the process is differentiation, this amounts to reconstructing the corresponding differentiation tree. One way of doing this in practice is to estimate the shortest-path distance between nodes based on cell similarities observed in sequencing data. Recent sequencing techniques make it possible to measure two types of data: gene expression levels, and RNA velocity, a vector that predicts changes in gene expression. The data then consist of a discrete vector field on a (subset of a) Euclidean space of dimension equal to the number of genes under consideration. By integrating this velocity field, we trace the evolution of gene expression levels in each single cell from some initial stage to its current stage. Eventually, we assume that we have a faithful embedding of the differentiation tree in a Euclidean space, but which we only observe through the curves representing the paths from the root to the nodes. Using varifold distances between such curves, we define a similarity measure between nodes which we prove approximates the shortest-path distance in a tree that is isomorphic to the target tree. Y1 - 2025 U6 - https://doi.org/10.1007/978-3-032-03921-7_30 VL - 16034 ER - TY - CHAP A1 - Kunt, Tim A1 - Buchholz, Annika A1 - Khebouri, Imene A1 - Koch, Thorsten A1 - Litzel, Ida A1 - Vu, Thi Huong T1 - Mapping the Web of Science, a large-scale graph and text-based dataset with LLM embeddings T2 - Operations Research Proceedings 2025. OR 2025 N2 - Large text data sets, such as publications, websites, and other text-based media, inherit two distinct types of features: (1) the text itself, its information conveyed through semantics, and (2) its relationship to other texts through links, references, or shared attributes. While the latter can be described as a graph structure and can be handled by a range of established algorithms for classification and prediction, the former has recently gained new potential through the use of LLM embedding models. Demonstrating these possibilities and their practicability, we investigate the Web of Science dataset, containing ~56 million scientific publications through the lens of our proposed embedding method, revealing a self-structured landscape of texts. T3 - ZIB-Report - 25-11 Y1 - 2025 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-100646 SN - 1438-0064 ER -