@misc{Lukanek2024, type = {Master Thesis}, author = {Lukanek, Sandra}, title = {3D Reconstruction of the Mandible from Panoramic Dental X-Ray Projections}, pages = {49}, year = {2024}, abstract = {Panoramic radiography is a popular imaging technique in dental medicine. It omprehensively represents the entire jaw, including the mandible, maxilla, and teeth in a compact two-dimensional (2D) image. It offers several advantages over three-dimensional (3D) imaging, such as Cone Beam Computed Tomography (CBCT), including cost-effectiveness and reduced radiation exposure. However, its major drawback lies in its ambiguities in spatial distribution, leading to inaccuracies in linear measurements due to the dependency on the parameters used for generating the image. In this thesis, we propose a methodology for reconstructing a 3D anatomy of the mandible from a given 2D panoramic X-ray image. Our approach involves extracting information from the 2D scan, considering the projection geometry, and aiming to achieve a realistic spatial distribution. The methodology builds upon an existing intensity-based 2D-3D registration algorithm, which is modified to accommodate the unique geometric parameters of panoramic radiography. By employing a virtual X-ray setup, we generate a panoramic X-ray from a Statistical Shape and Intensity Model (SSIM) derived from 25 tetrahedral meshes. The intensity information for each mesh is extracted from CBCT scans representing jaw anatomies. To reconstruct the true mandible, the model is iteratively optimized by comparing the simulated X-ray with the original panoramic X-ray. We evaluate and establish the setup using synthetically generated panoramic X-rays from multiple mandibles obtained from CBCT scans. After analyzing the feasibility of this method, we conclude that 2D-3D registration for panoramic X-rays presents a challenging task, as the ambiguity of the 2D projection involved in panoramic X-ray imaging can result in varied 3D shape representations.}, language = {en} } @article{SatoKochLe2026, author = {Sato, Mako and Koch, Thorsten and Le, Thi Thai}, title = {Influence of frictional drag on Kelvin-Helmholtz instability in viscous fluids}, volume = {38}, journal = {Physics of Fluids}, number = {1}, publisher = {AIP Publishing}, address = {Physics of Fluids}, doi = {10.1063/5.0306177}, year = {2026}, abstract = {The Kelvin-Helmholtz instability arises at the interface between two fluid layers with a tangential velocity discontinuity, significantly impacting the safety of systems in industrial applications. Despite extensive studies, many theoretical analyses neglect viscosity and frictional drag due to the complexity of solving the dispersion equation. However, including these effects is crucial, as viscosity alters the growth rate of the instability, while frictional drag influences energy dissipation and momentum transfer. In this study, these effects are incorporated into both finite and infinite flows. The assumption of a potential flow combined with a dissipation method is employed to derive the dispersion equation, providing a more tractable approach than direct calculation methods. The results indicate that, in the case of infinite flows, the frictional drag suppresses the growth of the instability for long waves (small wavenumber k) but enhances it for short waves (large k). In contrast, the surface tension dominates, while the frictional drag only slightly affects the growth rate in the case of finite flows bounded by solid walls.}, language = {en} } @article{HuTutikaDengetal.2025, author = {Hu, Chenhao and Tutika, Ravi and Deng, Zhifei and Jia, Zian and Chen, Liuni and Chen, Hongshun and Geng, Yang and Xiao, Xianghui and Shevchenko, Pavel D. and Pierre, Christoph and Weaver, James C. and Baum, Daniel and Bartlett, Michael D. and Li, Ling}, title = {Mineralized sclerites in the gorgonian coral Leptogorgia chilensis as a natural jamming system}, volume = {122}, journal = {PNAS}, number = {44}, doi = {10.1073/pnas.2504541122}, year = {2025}, language = {en} } @inproceedings{JaegerMandalRandetal.2025, author = {J{\"a}ger, Klaus and Mandal, Jyotirmoy and Rand, Barry P. and Meggers, Forrest and Becker, Christiane}, title = {Thermal Management of Solar Modules with Infrared-Antireflective Coatings}, volume = {SOLITH}, booktitle = {Advanced Photonics Congress}, doi = {10.1364/SOLITH.2025.SM4E.2}, pages = {SM4E.2}, year = {2025}, language = {en} } @article{ZittelPetkovicEinck2025, author = {Zittel, Janina and Petkovic, Milena and Einck, Mathias}, title = {Forecasting Hourly Gas Flows}, volume = {79}, journal = {Foresight - The International Journal of Applied Forecasting}, pages = {40 -- 44}, year = {2025}, language = {en} } @article{KiesslingLeyfferVanaret2025, author = {Kießling, David and Leyffer, Sven and Vanaret, Charlie}, title = {A Unified Funnel Restoration SQP Algorithm}, journal = {Mathematical Programming B}, doi = {10.1007/s10107-025-02284-3}, year = {2025}, abstract = {We consider nonlinearly constrained optimization problems and discuss a generic double-loop framework consisting of basic algorithmic ingredients that unifies a broad range of nonlinear optimization solvers. This framework has been implemented in the open-source solver Uno, a Swiss Army knife-like C++ optimization framework that unifies many nonlinearly constrained nonconvex optimization solvers. We illustrate the framework with a sequential quadratic programming (SQP) algorithm that maintains an acceptable upper bound on the constraint violation, called a funnel, that is monotonically decreased to control the feasibility of the iterates. Infeasible quadratic subproblems are handled by a feasibility restoration strategy. Globalization is controlled by a line search or a trust-region method. We prove global convergence of the trust-region funnel SQP method, building on known results from filter methods. We implement the algorithm in Uno, and we provide extensive test results for the trust-region line-search funnel SQP on small CUTEst instances.}, language = {en} } @article{BartoliSengupta2025, author = {Bartoli, Adrien and Sengupta, Agniva}, title = {Camera Pose in SfT and NRSfM under Isometric and Weaker Deformation Models}, volume = {261}, journal = {Computer Vision and Image Understanding}, doi = {10.1016/j.cviu.2025.104488}, year = {2025}, abstract = {Camera pose is a very natural concept in 3D vision in the rigid setting. It is however much more difficult to work with in deformable settings. Consequently, numerous deformable reconstruction methods simply ignore camera pose. We analyse the concept of pose in deformable settings and prove that it is unconstrained with the existing formulations, properly justifying the existing pose-less methods reconstructing structure only. We explain this result intuitively by the impossibility to define an intrinsic coordinate frame to a general deforming object. The proposed analysis uses the isometric deformation model and extends to the weaker models including conformality and equiareality. We propose a novel prior to rescue camera pose estimation in deformable settings, which attributes the deforming object's dominant rigid-body motion to the camera. We show that adding this prior to any existing formulation fully constrains camera pose and leads to elegant two-step solution methods, involving deformable structure reconstruction using a base method in the first step, and absolute orientation or Procrustes analysis in the second step. We derive the proposed approach for the template-based and template-less settings, respectively implemented using Shape-from-Template (SfT) and Non-Rigid Structure-from-Motion (NRSfM) as base methods, and validate them experimentally, showing that the computed pose is qualitatively and quantitatively plausible.}, language = {en} } @misc{DoerffelMikulaSchielickeetal.2025, author = {D{\"o}rffel, Tom and Mikula, Natalia and Schielicke, Lisa and Kiszler, Theresa and Faranda, Davide and Debrulle, B{\´e}reng{\`e}re and Vercauteren, Nikki}, title = {Characterizing inertial and diabatic energy transfers in tropical cyclones: Data}, doi = {10.12752/10135}, year = {2025}, abstract = {The multiscale organization of tropical cyclones (TCs) is investigated by means of three-dimensional data produced by the atmospheric model CM1. We provide a sample dataset in NetCDF format covering the TC evolution from incipient to mature under the influence of externally imposed wind shear. This dataset serves as a testbed for applying energy-tranfer analyses based on the Duchon-Robert index as well as diabatic transfer based on an asymptotic theory on TCs.}, language = {en} } @inproceedings{SchneiderSekulicPlocketal.2025, author = {Schneider, Philipp-Immanuel and Sekulic, Ivan and Plock, Matthias and Hammerschmidt, Martin and Rodt, Sven and Reitzenstein, Stephan and Burger, Sven}, title = {Physics-informed Bayesian optimization of nanophotonic devices}, volume = {IPRSN}, booktitle = {Advanced Photonics Congress}, doi = {10.1364/IPRSN.2025.ITu1A.2}, pages = {ITu1A.2}, year = {2025}, language = {en} } @article{ReussMacdonaldBeckeretal.2025, author = {Reuss, Joana and Macdonald, Jan and Becker, Simon and Schultka, Konrad and Richter, Lorenz and K{\"o}rner, Marco}, title = {Meta-learning For Few-Shot Time Series Crop Type Classification: A Benchmark On The EuroCropsML Dataset}, arxiv = {http://arxiv.org/abs/2504.11022}, year = {2025}, abstract = {Spatial imbalances in crop type data pose significant challenges for accurate classification in remote sensing applications. Algorithms aiming at transferring knowledge from data-rich to data-scarce tasks have thus surged in popularity. However, despite their effectiveness in previous evaluations, their performance in challenging real-world applications is unclear and needs to be evaluated. This study benchmarks transfer learning and several meta-learning algorithms, including (First-Order) Model-Agnostic Meta-Learning ((FO)-MAML), Almost No Inner Loop (ANIL), and Task-Informed Meta-Learning (TIML), on the real-world EuroCropsML time series dataset, which combines farmer-reported crop data with Sentinel-2 satellite observations from Estonia, Latvia, and Portugal. Our findings indicate that MAML-based meta-learning algorithms achieve slightly higher accuracy compared to simpler transfer learning methods when applied to crop type classification tasks in Estonia after pre-training on data from Latvia. However, this improvement comes at the cost of increased computational demands and training time. Moreover, we find that the transfer of knowledge between geographically disparate regions, such as Estonia and Portugal, poses significant challenges to all investigated algorithms. These insights underscore the trade-offs between accuracy and computational resource requirements in selecting machine learning methods for real-world crop type classification tasks and highlight the difficulties of transferring knowledge between different regions of the Earth. To facilitate future research in this domain, we present the first comprehensive benchmark for evaluating transfer and meta-learning methods for crop type classification under real-world conditions. The corresponding code is publicly available at this https URL.}, language = {en} } @inproceedings{ChenRichterBerneretal.2025, author = {Chen, Junhua and Richter, Lorenz and Berner, Julius and Blessing, Denis and Neumann, Gerhard and Anandkumar, Anima}, title = {Sequential Controlled Langevin Diffusions}, booktitle = {13th International Conference on Learning Representations (ICLR 2025)}, arxiv = {http://arxiv.org/abs/2412.07081}, year = {2025}, abstract = {An effective approach for sampling from unnormalized densities is based on the idea of gradually transporting samples from an easy prior to the complicated target distribution. Two popular methods are (1) Sequential Monte Carlo (SMC), where the transport is performed through successive annealed densities via prescribed Markov chains and resampling steps, and (2) recently developed diffusion-based sampling methods, where a learned dynamical transport is used. Despite the common goal, both approaches have different, often complementary, advantages and drawbacks. The resampling steps in SMC allow focusing on promising regions of the space, often leading to robust performance. While the algorithm enjoys asymptotic guarantees, the lack of flexible, learnable transitions can lead to slow convergence. On the other hand, diffusion-based samplers are learned and can potentially better adapt themselves to the target at hand, yet often suffer from training instabilities. In this work, we present a principled framework for combining SMC with diffusion-based samplers by viewing both methods in continuous time and considering measures on path space. This culminates in the new Sequential Controlled Langevin Diffusion (SCLD) sampling method, which is able to utilize the benefits of both methods and reaches improved performance on multiple benchmark problems, in many cases using only 10\% of the training budget of previous diffusion-based samplers.}, language = {en} } @article{BernerRichterSenderaetal.2025, author = {Berner, Julius and Richter, Lorenz and Sendera, Marcin and Rector-Brooks, Jarrid and Malkin, Nikolay}, title = {From discrete-time policies to continuous-time diffusion samplers: Asymptotic equivalences and faster training}, arxiv = {http://arxiv.org/abs/2501.06148}, year = {2025}, abstract = {We study the problem of training neural stochastic differential equations, or diffusion models, to sample from a Boltzmann distribution without access to target samples. Existing methods for training such models enforce time-reversal of the generative and noising processes, using either differentiable simulation or off-policy reinforcement learning (RL). We prove equivalences between families of objectives in the limit of infinitesimal discretization steps, linking entropic RL methods (GFlowNets) with continuous-time objects (partial differential equations and path space measures). We further show that an appropriate choice of coarse time discretization during training allows greatly improved sample efficiency and the use of time-local objectives, achieving competitive performance on standard sampling benchmarks with reduced computational cost.}, language = {en} } @inproceedings{BlessingBernerRichteretal.2025, author = {Blessing, Denis and Berner, Julius and Richter, Lorenz and Neumann, Gerhard}, title = {Underdamped Diffusion Bridges with Applications to Sampling}, booktitle = {13th International Conference on Learning Representations (ICLR 2025)}, arxiv = {http://arxiv.org/abs/2503.01006}, year = {2025}, abstract = {We provide a general framework for learning diffusion bridges that transport prior to target distributions. It includes existing diffusion models for generative modeling, but also underdamped versions with degenerate diffusion matrices, where the noise only acts in certain dimensions. Extending previous findings, our framework allows to rigorously show that score matching in the underdamped case is indeed equivalent to maximizing a lower bound on the likelihood. Motivated by superior convergence properties and compatibility with sophisticated numerical integration schemes of underdamped stochastic processes, we propose \emph{underdamped diffusion bridges}, where a general density evolution is learned rather than prescribed by a fixed noising process. We apply our method to the challenging task of sampling from unnormalized densities without access to samples from the target distribution. Across a diverse range of sampling problems, our approach demonstrates state-of-the-art performance, notably outperforming alternative methods, while requiring significantly fewer discretization steps and no hyperparameter tuning.}, language = {en} } @article{BlessingBernerRichteretal.2025, author = {Blessing, Denis and Berner, Julius and Richter, Lorenz and Domingo-Enrich, Carles and Du, Yuanqi and Vahdat, Arash and Neumann, Gerhard}, title = {Trust Region Constrained Measure Transport in Path Space for Stochastic Optimal Control and Inference}, arxiv = {http://arxiv.org/abs/2508.12511}, year = {2025}, abstract = {Solving stochastic optimal control problems with quadratic control costs can be viewed as approximating a target path space measure, e.g. via gradient-based optimization. In practice, however, this optimization is challenging in particular if the target measure differs substantially from the prior. In this work, we therefore approach the problem by iteratively solving constrained problems incorporating trust regions that aim for approaching the target measure gradually in a systematic way. It turns out that this trust region based strategy can be understood as a geometric annealing from the prior to the target measure, where, however, the incorporated trust regions lead to a principled and educated way of choosing the time steps in the annealing path. We demonstrate in multiple optimal control applications that our novel method can improve performance significantly, including tasks in diffusion-based sampling, transition path sampling, and fine-tuning of diffusion models.}, language = {en} } @article{ReussMacdonaldBeckeretal.2025, author = {Reuss, Joana and Macdonald, Jan and Becker, Simon and Richter, Lorenz and K{\"o}rner, Marco}, title = {The EuroCropsML time series benchmark dataset for few-shot crop type classification in Europe}, volume = {12}, journal = {Scientific Data}, doi = {10.1038/s41597-025-04952-7}, year = {2025}, abstract = {We introduce EuroCropsML, an analysis-ready remote sensing dataset based on the open-source EuroCrops collection, for machine learning (ML) benchmarking of time series crop type classification in Europe. It is the first time-resolved remote sensing dataset designed to benchmark transnational few-shot crop type classification algorithms that supports advancements in algorithmic development and research comparability. It comprises 706683 multi-class labeled data points across 176 crop classes. Each data point features a time series of per-parcel median pixel values extracted from Sentinel-2 L1C data and precise geospatial coordinates. EuroCropsML is publicly available on Zenodo.}, language = {en} } @article{EigenLadenburgerBrenceetal.2025, author = {Eigen, Lennart and Ladenburger, Pius and Brence, Blaž and Shubitidze, Ani and Baum, Daniel and Hildebrandt, Thomas and Brecht, Michael}, title = {Elephant trunk tip musculature reflects species differences in grasping behavior}, volume = {8}, journal = {Communications Biology}, doi = {10.1038/s42003-025-08998-6}, year = {2025}, abstract = {Elephants use their trunks, muscular hydrostats, to perform a plethora of tasks. Trunk tip morphology as well as grasping behavior differ between elephant species. While African savanna elephants (Loxodonta africana) use their dorsal and ventral finger for pinching movements, Asian elephants (Elephas maximus) prefer to wrap around objects with their one dorsal finger and ventral bulb trunk tip lip. Moreover, E. maximus can flip their ventral bulb backwards to clamp objects behind the trunk tip. Whether trunk tip musculature differs between elephant species and muscle architecture is reflected by preferred grasping behavior is, however, not clear. In this study, we performed dense muscle fascicle reconstruction of three L. africana and three E. maximus hemi-trunk tips using a combination of manual and automated segmentation of high-resolution microfocus tomography (microCT) scans. We distinguish three types of muscle fascicles: longitudinal (bending and shortening), radial (elongating) and transversal muscle fascicles (elongating). We found that trunk tips of L. africana consist to one third of longitudinal and two thirds radial/transversal muscle fascicles, likely aiding in their grasping behavior, while E. maximus trunk tips consist to two thirds of longitudinal and one third radial/transversal muscle fascicles, which is advantageous for their wrapping and backward clamping behavior.}, language = {en} } @article{BrenceWandeltWalteretal.2025, author = {Brence, Blaž and Wandelt, Laura R. and Walter, Sophie and Sigrist, Stephan J. and Petzoldt, Astrid G. and Baum, Daniel}, title = {Semi-automatic 3D-quantification of in-vivo synapse formation}, journal = {ResearchSquare}, doi = {10.21203/rs.3.rs-6073150/v1}, year = {2025}, abstract = {Background: Synapses, as specialised cell-cell contacts, allow for a faithful and controlled signal transmission between a neuron and a target cell. Presynapses, the sites of neurotransmitter release, form de novo throughout the development of an organism. Although this process is fundamental to the development and function of synaptic circuits, how developing neurons control number and distribution of individual synapses remains poorly understood. In-vivo imaging analysis of synapse formation at the neuromuscular junction of anaesthetised Drosophila third instar larvae allows for spatial and temporal resolution of the underlying molecular processes. However, high-throughput, comprehensive analysis are hampered by the manual and time-consuming imaging analysis methods applied hitherto. Here, we focus on the early presynaptic formation steps, that is, the presynaptic seeding, initiated by the formation of transient Liprin-a/SYD1 seeding sites, either stabilised or disintegrated over a time span of 30-90 min. Results: To investigate the dynamics of the Liprin-a/SYD1 seeding sites, we developed an automated analysis pipeline for 3D confocal images from in-vivo imaging at distinct time points to analyse fluorescently labelled presynaptic protein dynamics during early synapse formation. The workflow is realised in the data analysis software Amira, utilising the hierarchical watershed algorithm, and was designed for automatic processing with an option for manual proofreading. Compared to the previous 2D manual quantification, this automated approach provides a higher sensitivity in single Liprin-a seeding site detection in low-intensity areas and in regions of dense seeding sites.In addition, it substantially reduces the work time. To account for possible errors occurring in the automated processing, we implemented an additional proofreading step allowing for a manual correction of Liprin-a seeding site segmentation and assignment, thus greatly improving the analysis while only marginally increasing work time by 10\% to a total work time reduction of 80\% compared to the 2D manual analysis paradigm. Conclusion: The process of synaptogenesis underlies the general principles of locomotion, learning and memory formation. The developed fast and accurate semi-automated 3D workflow provides a substantial progress in the analysis of this molecular process and its application can be easily extended to other dynamic in-vivo research approaches across species.}, language = {en} } @article{BrenceBrummerDercksenetal.2025, author = {Brence, Blaž and Brummer, Josephine and Dercksen, Vincent J. and {\"O}zel, Mehmet Neset and Kulkarni, Abhishkek and Wolterhoff, Neele and Prohaska, Steffen and Hiesinger, Peter Robin and Baum, Daniel}, title = {Semi-automatic Geometrical Reconstruction and Analysis of Filopodia Dynamics in 4D Two-Photon Microscopy Images}, journal = {bioRxiv}, doi = {10.1101/2025.05.20.654789}, year = {2025}, abstract = {Background: Filopodia are thin and dynamic membrane protrusions that play a crucial role in cell migration, axon guidance, and other processes where cells explore and interact with their surroundings. Historically, filopodial dynamics have been studied in great detail in 2D in cultured cells, and more recently in 3D culture as well as living brains. However, there is a lack of efficient tools to trace and track filopodia in 4D images of complex brain cells. Results: To address this issue, we have developed a semi-automatic workflow for tracing filopodia in 3D images and tracking the traced filopodia over time. The workflow was developed based on high-resolution data of photoreceptor axon terminals in the in vivo context of normal Drosophila brain development, but devised to be applicable to filopodia in any system, including at different temporal and spatial scales. In contrast to the pre-existing methods, our workflow relies solely on the original intensity images without the requirement for segmentation or complex preprocessing. The workflow was realized in C++ within the Amira software system and consists of two main parts, dataset pre-processing, and geometrical filopodia reconstruction, where each of the two parts comprises multiple steps. In this paper, we provide an extensive workflow description and demonstrate its versatility for two different axo-dendritic morphologies, R7 and Dm8 cells. Finally, we provide an analysis of the time requirements for user input and data processing. Conclusion: To facilitate simple application within Amira or other frameworks, we share the source code, which is available athttps://github.com/zibamira/filopodia-tool.}, language = {en} } @inproceedings{BrenceFuchsHiesingeretal.2025, author = {Brence, Blaž and Fuchs, Joachim and Hiesinger, Peter Robin and Baum, Daniel}, title = {Fully automated quantification of synaptic locations in multi-channel Drosophila photoreceptor microscopy data}, booktitle = {Eurographics Workshop on Visual Computing for Biology and Medicine}, editor = {Garrison, Laura and Krueger, Robert}, doi = {10.2312/vcbm.20251254}, year = {2025}, abstract = {The workload posed by image analysis remains a major bottleneck for advances across the life sciences. To address this challenge, we have developed a fully automated workflow for processing complex 3D multi-channel microscopy images. Specifically, our workflow addresses the analysis of photoreceptor synapses in confocal images of the Drosophila melanogaster optic lobe. The workflow consists of multiple stages, combining traditional and machine learning-based approaches for image analysis and visual computing. It performs segmentation of brain regions, photoreceptor instance identification, and precise localization of synapses. The key novelty of the workflow is an automatic alignment of synapses into a cylindrical reference coordinate system, enabling comparative synaptic analysis across photoreceptors. To demonstrate the workflow's applicability, preliminary biological results and their interpretation based on 50 images are presented. While the workflow is still being improved further, here, we showcase its capacity for efficient and objective data processing for high-throughput neurobiological analyses.}, language = {en} } @article{TrepczynskiKneifelHeylandetal.2025, author = {Trepczynski, Adam and Kneifel, Paul and Heyland, Mark and Leskovar, Marko and Moewis, Philippe and Damm, Philipp and Taylor, William R. and Zachow, Stefan and Duda, Georg N.}, title = {Impact of the external knee flexion moment on patello-femoral loading derived from in vivo loads and kinematics}, volume = {12/2024}, journal = {Frontiers in Bioengineering and Biotechnology}, publisher = {Frontiers Media SA}, organization = {Charit{\´e} - Universit{\"a}tsmedizin Berlin}, issn = {2296-4185}, doi = {10.3389/fbioe.2024.1473951}, year = {2025}, abstract = {Introduction: Anterior knee pain and other patello-femoral (PF) complications frequently limit the success of total knee arthroplasty as the final treatment of end stage osteoarthritis. However, knowledge about the in-vivo loading conditions at the PF joint remains limited, as no direct measurements are available. We hypothesised that the external knee flexion moment (EFM) is highly predictive of the PF contact forces during activities with substantial flexion of the loaded knee. Materials and methods: Six patients (65-80 years, 67-101 kg) with total knee arthroplasty (TKA) performed two activities of daily living: sit-stand-sit and squat. Tibio-femoral (TF) contact forces were measured in vivo using instrumented tibial components, while synchronously internal TF and PF kinematics were captured with mobile fluoroscopy. The measurements were used to compute PF contact forces using patient specific musculoskeletal models. The relationship between the EFM and the PF contact force was quantified using linear regression. Results: Mean peak TF contact forces of 1.97-3.24 times body weight (BW) were found while peak PF forces reached 1.75 to 3.29 times body weight (BW). The peak EFM ranged from 3.2 to 5.9 \%BW times body height, and was a good predictor of the PF contact force (R2 = 0.95 and 0.88 for sit-stand-sit and squat, respectively). Discussion: The novel combination of in vivo TF contact forces and internal patellar kinematics enabled a reliable assessment of PF contact forces. The results of the regression analysis suggest that PF forces can be estimated based solely on the EFM from quantitative gait analysis. Our study also demonstrates the relevance of PF contact forces, which reach magnitudes similar to TF forces during activities of daily living.}, language = {en} } @misc{PedersenLindnerRehfeldtetal.2025, author = {Pedersen, Jaap and Lindner, Niels and Rehfeldt, Daniel and Koch, Thorsten}, title = {Comparing Branching Rules for the Quota Steiner Tree Problem with Interference}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-101250}, year = {2025}, abstract = {Branching decisions play a crucial role in branch-and-bound algorithms for solving combinatorial optimization problems. In this paper, we investigate several branching rules applied to the Quota Steiner Tree Problem with Interference (QSTPI). The Quota Steiner Tree Problem (QSTP) generalizes the classical Steiner Tree Problem (STP) in graphs by seeking a minimum-cost tree that connects a subset of profit-associated vertices to meet a given quota. The extended version, QSTPI, introduces interference among vertices: Selecting certain vertices simultaneously reduces their individual contributions to the overall profit. This problem arises, for example, in positioning and connecting wind turbines, where turbines possibly shadow other turbines, reducing their energy yield. While exact solvers for standard STP-related problems often rely heavily on reduction techniques and cutting-plane methods - rarely generating large branch-and-bound trees - experiments reveal that large instances of QSTPI require significantly more branching to compute provably optimal solutions. In contrast to branching on variables, we utilize the combinatorial structure of the QSTPI by branching on the graph's vertices. We adapt classical and problem-specific branching rules and present a comprehensive computational study comparing the effectiveness of these branching strategies.}, language = {en} } @misc{MehlLindnerBartoszuketal.2025, author = {Mehl, Lukas and Lindner, Niels and Bartoszuk, Karolina and Zittel, Janina}, title = {Prototypical warm-starts for demand-robust LP-based energy system optimization}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-101242}, year = {2025}, abstract = {The expressiveness of energy system optimization models (ESOMs) depends on a multitude of exogenous parameters. For example, sound estimates of the future energy demand are essential to enable qualified decisions on long-term investments. However, the enormous demand fluctuations even on a fine-grained scale diminish the computational performance of large-scale ESOMs. We therefore propose a clustering-and-decomposition method for linear programming based ESOMs that first identifies and solves prototypical demand scenarios with the dual simplex algorithm, and then composes dual optimal prototype bases to a warm-start basis for the full model. We evaluate the feasibility and computational efficiency our approach on a real-world case study, using a sector-coupled ESOM with hourly resolution for the Berlin-Brandenburg area in Germany, based on the oemof framework.}, language = {en} } @misc{LindnerLiebchen2025, author = {Lindner, Niels and Liebchen, Christian}, title = {A two-stage model for periodic timetabling with fixed line activities}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-101234}, year = {2025}, abstract = {The timetable is a central pillar of any public transportation system. Constructing and optimizing periodic timetables in terms of passenger comfort and operational efficiency leads to NP-hard optimization problems that are also computationally challenging in applications. The Periodic Event Scheduling Problem (PESP) as standard mathematical tool benefits from its succinct formulation and rich combinatorial structure, but suffers from poor linear programming relaxations and weak dual bounds. These difficulties persist in a reduced version, where driving and dwelling activities of the lines are assumed to be fixed. In this case, fixing the initial departure time of each line fully determines the timetable, and for each pair of lines, the resulting (weighted) transfer durations can be expressed in terms of a piecewise linear non-convex function in terms of the difference of the initial times. When the number of activities between two lines is bounded, this function can be computed in polynomial time. By inserting precomputed piecewise linear functions into a mixed-integer program with the initial departure times as variables, we introduce an equivalent formulation for reduced PESP instances. The model bears analogies with quadratic semi-assignment approaches and offers alternative ways to compute primal and dual bounds. We evaluate the computational behavior of our approach on realistic benchmarking instances.}, language = {en} } @article{RongChenMaetal.2025, author = {Rong, Guoyang and Chen, Ying and Ma, Feicheng and Koch, Thorsten}, title = {Exploring Interdisciplinary Research Trends through Critical Years for Interdisciplinary Citation}, volume = {19}, journal = {Journal of Informetrics}, number = {4}, doi = {10.1016/j.joi.2025.101726}, year = {2025}, language = {en} } @article{ShinanoFujii2025, author = {Shinano, Yuji and Fujii, Koichi}, title = {Introduction to Quadratic Programming Solvers}, volume = {64}, journal = {Journal of The Society of Instrument and Control Engineers}, number = {8}, doi = {10.11499/sicejl.64.532}, pages = {532 -- 540}, year = {2025}, language = {en} } @inproceedings{HammerschmidtPlockBurgeretal.2025, author = {Hammerschmidt, Martin and Plock, Matthias and Burger, Sven and Truong, Vinh and Soltwisch, Victor and Schneider, Philipp-Immanuel}, title = {Machine learning approach for full Bayesian parameter reconstruction}, volume = {13568}, booktitle = {Proc. SPIE}, doi = {10.1117/12.3062268}, pages = {1356806}, year = {2025}, language = {en} } @inproceedings{SekulicSchneiderHammerschmidtetal.2025, author = {Sekulic, Ivan and Schneider, Philipp-Immanuel and Hammerschmidt, Martin and Schaible, Jonas and Burger, Sven}, title = {Physics informed Bayesian optimization for inverse design of diffractive optical elements}, volume = {PC13573}, booktitle = {Proc. SPIE}, doi = {10.1117/12.3064372}, pages = {PC135730R}, year = {2025}, language = {en} } @article{BauerGaltungGesericketal.2025, author = {Bauer, Wolfgang and Galtung, Noa and Geserick, Peter and Friedrich, Katharina and Weber, Marcus and Somasundaram, Rajan and Diehl-Wiesenecker, Eva and Kappert, Kai}, title = {Pentraxin-3, MyD88, GLP-1, and PD-L1: Performance assessment and composite algorithmic analysis for sepsis identification}, volume = {91}, journal = {Journal of Infection}, number = {3}, doi = {10.1016/j.jinf.2025.106599}, pages = {106599}, year = {2025}, abstract = {This study examines nine emerging biomarkers as possible indicators for diagnosing sepsis in emergency department patient.}, language = {en} } @article{KourovSamoilovaStraube2025, author = {Kourov, Mikhail N. and Samoilova, Anna E. and Straube, Arthur}, title = {Dynamics of a chain of interacting magnetic particles in a one-dimensional periodic energy landscape}, volume = {89}, journal = {Bull. Russ. Acad. Sci. Phys.}, number = {7}, issn = {1062-8738}, doi = {10.1134/S1062873825711742}, pages = {1086 -- 1092}, year = {2025}, abstract = {We explore the dynamics of a one-dimensional chain of paramagnetic colloidal particles in a periodic potential. The model accounts for a constant external force, along with magnetic dipolar attraction and hard-core repulsive interactions between particles. Numerical simulations reveal the emergence of a traveling kink - a chain defect propagating along the chain. We show that the kink emerges beyond a critical force threshold and identify parameter regimes corresponding to distinct dynamic modes such as a pinned kink, a running kink, a cluster kink, and chain drift.}, language = {en} } @article{StraubeOliconMendezWinkelmannetal.2025, author = {Straube, Arthur and Olic{\´o}n M{\´e}ndez, Guillermo and Winkelmann, Stefanie and H{\"o}fling, Felix and Engel, Maximilian}, title = {Unfolding the geometric structure and multiple timescales of the urea-urease pH oscillator}, arxiv = {http://arxiv.org/abs/2508.07275}, year = {2025}, abstract = {We study a two-variable dynamical system modeling pH oscillations in the urea-urease reaction within giant lipid vesicles - a problem that intrinsically contains multiple, well-separated timescales. Building on an existing, deterministic formulation via ordinary differential equations, we resolve different orders of magnitude within a small parameter and analyze the system's limit cycle behavior using geometric singular perturbation theory (GSPT). By introducing two different coordinate scalings - each valid in a distinct region of the phase space - we resolve the local dynamics near critical fold points, using the extension of GSPT through such singular points due to Krupa and Szmolyan. This framework enables a geometric decomposition of the periodic orbits into slow and fast segments and yields closed-form estimates for the period of oscillation. In particular, we link the existence of such oscillations to an underlying biochemical asymmetry, namely, the differential transport across the vesicle membrane.}, language = {en} } @inproceedings{RiedmuellerZittelKoch2026, author = {Riedm{\"u}ller, Stephanie and Zittel, Janina and Koch, Thorsten}, title = {Warm-starting Strategies in Scalarization Methods for Multi-Objective Optimization}, booktitle = {Operations Research Proceedings 2025}, arxiv = {http://arxiv.org/abs/2507.21933}, year = {2026}, abstract = {We explore how warm-starting strategies can be integrated into scalarization-based approaches for multi-objective optimization in (mixed) integer linear programming. Scalarization methods remain widely used classical techniques to compute Pareto-optimal solutions in applied settings. They are favored due to their algorithmic simplicity and broad applicability across continuous and integer programs with an arbitrary number of objectives. While warm-starting has been applied in this context before, a systematic methodology and analysis remain lacking. We address this gap by providing a theoretical characterization of warm-starting within scalarization methods, focusing on the sequencing of subproblems. However, optimizing the order of subproblems to maximize warm-start efficiency may conflict with alternative criteria, such as early identification of infeasible regions. We quantify these trade-offs through an extensive computational study.}, language = {en} } @misc{RiedmuellerZittelKoch2025, author = {Riedm{\"u}ller, Stephanie and Zittel, Janina and Koch, Thorsten}, title = {Warm-starting Strategies in Scalarization Methods for Multi-Objective Optimization}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-101073}, year = {2025}, abstract = {We explore how warm-starting strategies can be integrated into scalarization-based approaches for multi-objective optimization in (mixed) integer linear programming. Scalarization methods remain widely used classical techniques to compute Pareto-optimal solutions in applied settings. They are favored due to their algorithmic simplicity and broad applicability across continuous and integer programs with an arbitrary number of objectives. While warm-starting has been applied in this context before, a systematic methodology and analysis remain lacking. We address this gap by providing a theoretical characterization of warm-starting within scalarization methods, focusing on the sequencing of subproblems. However, optimizing the order of subproblems to maximize warm-start efficiency may conflict with alternative criteria, such as early identification of infeasible regions. We quantify these trade-offs through an extensive computational study.}, language = {en} } @misc{BinkowskiKoulasSimosBetzetal.2025, author = {Binkowski, Felix and Koulas-Simos, Aris and Betz, Fridtjof and Plock, Matthias and Sekulic, Ivan and Manley, Phillip and Hammerschmidt, Martin and Schneider, Philipp-Immanuel and Zschiedrich, Lin and Munkhbat, Battulga and Reitzenstein, Stephan and Burger, Sven}, title = {Source code and simulation results: High Purcell enhancement in all-TMDC nanobeam resonator designs with active monolayers for nanolasers}, journal = {Zenodo}, doi = {10.5281/zenodo.16533803}, year = {2025}, language = {en} } @article{BinkowskiKoulasSimosBetzetal.2025, author = {Binkowski, Felix and Koulas-Simos, Aris and Betz, Fridtjof and Plock, Matthias and Sekulic, Ivan and Manley, Phillip and Hammerschmidt, Martin and Schneider, Philipp-Immanuel and Zschiedrich, Lin and Munkhbat, Battulga and Reitzenstein, Stephan and Burger, Sven}, title = {High Purcell enhancement in all-TMDC nanobeam resonator designs with active monolayers for nanolasers}, volume = {112}, journal = {Phys. Rev. B}, arxiv = {http://arxiv.org/abs/2508.05333}, doi = {10.1103/nxh9-dhvx}, pages = {235410}, year = {2025}, language = {en} } @article{WeimannConrad2025, author = {Weimann, Kuba and Conrad, Tim}, title = {Self-supervised pre-training with joint-embedding predictive architecture boosts ECG classification performance}, volume = {196}, journal = {Computers in Biology and Medicine}, publisher = {Elsevier BV}, issn = {0010-4825}, doi = {10.1016/j.compbiomed.2025.110809}, year = {2025}, abstract = {Accurate diagnosis of heart arrhythmias requires the interpretation of electrocardiograms (ECG), which capture the electrical activity of the heart. Automating this process through machine learning is challenging due to the need for large annotated datasets, which are difficult and costly to collect. To address this issue, transfer learning is often employed, where models are pre-trained on large datasets and fine-tuned for specific ECG classification tasks with limited labeled data. Self-supervised learning has become a widely adopted pre-training method, enabling models to learn meaningful representations from unlabeled datasets. In this work, we explore the joint-embedding predictive architecture (JEPA) for self-supervised learning from ECG data. Unlike invariance-based methods, JEPA does not rely on hand-crafted data augmentations, and unlike generative methods, it predicts latent features rather than reconstructing input data. We create a large unsupervised pre-training dataset by combining ten public ECG databases, amounting to over one million records. We pre-train Vision Transformers using JEPA on this dataset and fine-tune them on various PTB-XL benchmarks. Our results show that JEPA outperforms existing invariance-based and generative approaches, achieving an AUC of 0.945 on the PTB-XL all statements task. JEPA consistently learns the highest quality representations, as demonstrated in frozen evaluations, and proves advantageous for pre-training even in the absence of additional data.}, language = {en} } @inproceedings{FayadZimmerSchwartzetal.2025, author = {Fayad, Ibrahim and Zimmer, Max and Schwartz, Martin and Ciais, Philippe and Gieseke, Fabian and Belouze, Gabriel and Brood, Sarah and De Truchis, Aurelien and d'Aspremont, Alexandre}, title = {DUNIA: Pixel-Sized Embeddings via Cross-Modal Alignment for Earth Observation Applications}, volume = {267}, booktitle = {Proceedings of the 42nd International Conference on Machine Learning}, arxiv = {http://arxiv.org/abs/2502.17066}, pages = {16375 -- 16406}, year = {2025}, language = {en} } @inproceedings{PaulsZimmerTuranetal.2025, author = {Pauls, Jan and Zimmer, Max and Turan, Berkant and Saatchi, Sassan and Ciais, Philippe and Pokutta, Sebastian and Gieseke, Fabian}, title = {Capturing Temporal Dynamics in Large-Scale Canopy Tree Height Estimation}, volume = {267}, booktitle = {Proceedings of the 42nd International Conference on Machine Learning}, arxiv = {http://arxiv.org/abs/2501.19328}, pages = {48422 -- 48438}, year = {2025}, language = {en} } @article{KlusGelss2025, author = {Klus, Stefan and Gelß, Patrick}, title = {Continuous optimization methods for the graph isomorphism problem}, volume = {14}, journal = {Information and Inference: A Journal of the IMA}, number = {2}, doi = {10.1093/imaiai/iaaf011}, year = {2025}, language = {en} } @inproceedings{MundingerZimmerKiemetal.2025, author = {Mundinger, Konrad and Zimmer, Max and Kiem, Aldo and Spiegel, Christoph and Pokutta, Sebastian}, title = {Neural Discovery in Mathematics: Do Machines Dream of Colored Planes?}, volume = {267}, booktitle = {Proceedings of the 42nd International Conference on Machine Learning}, arxiv = {http://arxiv.org/abs/2501.18527}, pages = {45236 -- 45255}, year = {2025}, language = {en} } @inproceedings{PelleritiZimmerWirthetal.2025, author = {Pelleriti, Nico and Zimmer, Max and Wirth, Elias and Pokutta, Sebastian}, title = {Approximating Latent Manifolds in Neural Networks via Vanishing Ideals}, volume = {267}, booktitle = {Proceedings of the 42nd International Conference on Machine Learning}, arxiv = {http://arxiv.org/abs/2502.15051}, pages = {48734 -- 48761}, year = {2025}, language = {en} } @inproceedings{RouxMartinezRubioPokutta2025, author = {Roux, Christophe and Mart{\´i}nez-Rubio, David and Pokutta, Sebastian}, title = {Implicit Riemannian optimism with applications to min-max problems}, volume = {267}, booktitle = {Proceedings of the 42nd International Conference on Machine Learning}, arxiv = {http://arxiv.org/abs/2501.18381}, pages = {52139 -- 52172}, year = {2025}, language = {en} } @inproceedings{TuranAsadullaSteinmannetal.2025, author = {Turan, Berkant and Asadulla, Suhrab and Steinmann, David and Stammer, Wolfgang and Pokutta, Sebastian}, title = {Neural Concept Verifier: Scaling Prover-Verifier Games via Concept Encodings}, booktitle = {Proceedings of the ICML Workshop on Actionable Interpretability}, year = {2025}, language = {en} } @inproceedings{XuMexiBestuzheva2025, author = {Xu, Liding and Mexi, Gioni and Bestuzheva, Ksenia}, title = {Sparsity-driven Aggregation of Mixed Integer Programs}, volume = {338}, booktitle = {23rd International Symposium on Experimental Algorithms (SEA 2025)}, address = {Schloss Dagstuhl - Leibniz-Zentrum f{\"u}r Informatik}, doi = {10.4230/LIPIcs.SEA.2025.27}, pages = {27:1 -- 27:15}, year = {2025}, language = {en} } @inproceedings{HendrychBesanconMartinezRubioetal.2025, author = {Hendrych, Deborah and Besan{\c{c}}on, Mathieu and Mart{\´i}nez-Rubio, David and Pokutta, Sebastian}, title = {Secant line search for Frank-Wolfe algorithms}, volume = {267}, booktitle = {Proceedings of the 42nd International Conference on Machine Learning}, arxiv = {http://arxiv.org/abs/2501.18775}, pages = {23005 -- 23029}, year = {2025}, language = {en} } @inproceedings{HaaseHanelPokutta2025, author = {Haase, Jennifer and Hanel, Paul H. P. and Pokutta, Sebastian}, title = {S-DAT: a multilingual, GenAI-driven framework for automated divergent thinking assessment}, volume = {8}, booktitle = {Proceedings of the AAAI/ACM Conference on AI, Ethics, and Society (AIES)}, pages = {1194 -- 1205}, year = {2025}, language = {en} } @article{GelssKleinMateraetal.2025, author = {Gelß, Patrick and Klein, Rupert and Matera, Sebastian and Schmidt, Burkhard}, title = {Quantum dynamics of coupled excitons and phonons in chain-like systems: tensor train approaches and higher-order propagators}, volume = {162}, journal = {The Journal of Chemical Physics}, doi = {10.1063/5.0258904}, year = {2025}, language = {en} } @article{WirthPenaPokutta2025, author = {Wirth, Elias and Pe{\~n}a, Javier and Pokutta, Sebastian}, title = {Fast convergence of Frank-Wolfe algorithms on polytopes}, journal = {INFORMS Journal on Mathematics of Operations Research}, doi = {10.1287/moor.2024.0580}, year = {2025}, language = {en} } @article{RamosFischerSaalfranketal.2024, author = {Ramos, Alejandro and Fischer, Eric W. and Saalfrank, Peter and K{\"u}hn, Oliver}, title = {Shaping the laser control landscape of a hydrogen transfer reaction by vibrational strong coupling. A direct optimal control approach}, journal = {The Journal of Chemical Physics}, year = {2024}, language = {en} } @article{HalbigHoenGleixneretal.2025, author = {Halbig, Katrin and Hoen, Alexander and Gleixner, Ambros and Witzig, Jakob and Weninger, Dieter}, title = {A diving heuristic for mixed-integer problems with unbounded semi-continuous variables}, volume = {13}, journal = {EURO Journal on Computational Optimization}, doi = {10.1016/j.ejco.2025.100107}, year = {2025}, language = {en} } @inproceedings{UrbanoRomero2024, author = {Urbano, Alonso and Romero, David W.}, title = {Self-Supervised Detection of Perfect and Partial Input-Dependent Symmetries}, booktitle = {Proceedings of the Geometry-grounded Representation Learning and Generative Modeling Workshop (GRaM) at ICML 2024}, year = {2024}, language = {en} }