@inproceedings{MortagyGuptaPokutta2020, author = {Mortagy, Hassan and Gupta, Swati and Pokutta, Sebastian}, title = {Walking in the Shadow: A New Perspective on Descent Directions for Constrained Minimization}, booktitle = {Proceedings of NeurIPS}, arxiv = {http://arxiv.org/abs/2006.08426}, year = {2020}, language = {en} } @inproceedings{Pokutta2020, author = {Pokutta, Sebastian}, title = {Restarting Algorithms: Sometimes there is Free Lunch}, booktitle = {Proceedings of CPAIOR}, arxiv = {http://arxiv.org/abs/2006.14810}, year = {2020}, language = {en} } @article{KossenHirzelMadaietal.2022, author = {Kossen, Tabea and Hirzel, Manuel A. and Madai, Vince I. and Boenisch, Franziska and Hennemuth, Anja and Hildebrand, Kristian and Pokutta, Sebastian and Sharma, Kartikey and Hilbert, Adam and Sobesky, Jan and Galinovic, Ivana and Khalil, Ahmed A. and Fiebach, Jochen B. and Frey, Dietmar}, title = {Towards Sharing Brain Images: Differentially Private TOF-MRA Images with Segmentation Labels Using Generative Adversarial Networks}, journal = {Frontiers in Artificial Intelligence}, doi = {https://doi.org/10.3389/frai.2022.813842}, year = {2022}, abstract = {Sharing labeled data is crucial to acquire large datasets for various Deep Learning applications. In medical imaging, this is often not feasible due to privacy regulations. Whereas anonymization would be a solution, standard techniques have been shown to be partially reversible. Here, synthetic data using a Generative Adversarial Network (GAN) with differential privacy guarantees could be a solution to ensure the patient's privacy while maintaining the predictive properties of the data. In this study, we implemented a Wasserstein GAN (WGAN) with and without differential privacy guarantees to generate privacy-preserving labeled Time-of-Flight Magnetic Resonance Angiography (TOF-MRA) image patches for brain vessel segmentation. The synthesized image-label pairs were used to train a U-net which was evaluated in terms of the segmentation performance on real patient images from two different datasets. Additionally, the Fr{\´e}chet Inception Distance (FID) was calculated between the generated images and the real images to assess their similarity. During the evaluation using the U-Net and the FID, we explored the effect of different levels of privacy which was represented by the parameter ϵ. With stricter privacy guarantees, the segmentation performance and the similarity to the real patient images in terms of FID decreased. Our best segmentation model, trained on synthetic and private data, achieved a Dice Similarity Coefficient (DSC) of 0.75 for ϵ = 7.4 compared to 0.84 for ϵ = ∞ in a brain vessel segmentation paradigm (DSC of 0.69 and 0.88 on the second test set, respectively). We identified a threshold of ϵ <5 for which the performance (DSC <0.61) became unstable and not usable. Our synthesized labeled TOF-MRA images with strict privacy guarantees retained predictive properties necessary for segmenting the brain vessels. Although further research is warranted regarding generalizability to other imaging modalities and performance improvement, our results mark an encouraging first step for privacy-preserving data sharing in medical imaging.}, language = {en} } @inproceedings{WirthPokutta2022, author = {Wirth, Elias and Pokutta, Sebastian}, title = {Conditional Gradients for the Approximately Vanishing Ideal}, volume = {151}, booktitle = {Proceedings of The 25th International Conference on Artificial Intelligence and Statistics}, pages = {2191 -- 2209}, year = {2022}, abstract = {The vanishing ideal of a set of points X is the set of polynomials that evaluate to 0 over all points x in X and admits an efficient representation by a finite set of polynomials called generators. To accommodate the noise in the data set, we introduce the Conditional Gradients Approximately Vanishing Ideal algorithm (CGAVI) for the construction of the set of generators of the approximately vanishing ideal. The constructed set of generators captures polynomial structures in data and gives rise to a feature map that can, for example, be used in combination with a linear classifier for supervised learning. In CGAVI, we construct the set of generators by solving specific instances of (constrained) convex optimization problems with the Pairwise Frank-Wolfe algorithm (PFW). Among other things, the constructed generators inherit the LASSO generalization bound and not only vanish on the training but also on out-sample data. Moreover, CGAVI admits a compact representation of the approximately vanishing ideal by constructing few generators with sparse coefficient vectors.}, language = {en} } @misc{Franz2019, type = {Master Thesis}, author = {Franz, Henriette}, title = {Connected Subgraphs with Budget Constraints: Formulations and Algorithms}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-87792}, year = {2019}, language = {en} } @inproceedings{MartinezRubioPokutta2023, author = {Mart{\´i}nez-Rubio, David and Pokutta, Sebastian}, title = {Accelerated Riemannian Optimization: Handling Constraints with a Prox to Bound Geometric Penalties}, volume = {195}, booktitle = {Proceedings of Thirty Sixth Conference on Learning Theory}, pages = {359 -- 393}, year = {2023}, abstract = {We propose a globally-accelerated, first-order method for the optimization of smooth and (strongly or not) geodesically-convex functions in a wide class of Hadamard manifolds. We achieve the same convergence rates as Nesterov's accelerated gradient descent, up to a multiplicative geometric penalty and log factors. Crucially, we can enforce our method to stay within a compact set we define. Prior fully accelerated works \emph{resort to assuming} that the iterates of their algorithms stay in some pre-specified compact set, except for two previous methods of limited applicability. For our manifolds, this solves the open question in (Kim and Yang, 2022) about obtaining global general acceleration without iterates assumptively staying in the feasible set.In our solution, we design an accelerated Riemannian inexact proximal point algorithm, which is a result that was unknown even with exact access to the proximal operator, and is of independent interest. For smooth functions, we show we can implement the prox step inexactly with first-order methods in Riemannian balls of certain diameter that is enough for global accelerated optimization.}, language = {en} } @article{ŠofranacGleixnerPokutta2022, author = {Šofranac, Boro and Gleixner, Ambros and Pokutta, Sebastian}, title = {An Algorithm-independent Measure of Progress for Linear Constraint Propagation}, volume = {27}, journal = {Constraints}, doi = {10.1007/s10601-022-09338-9}, pages = {432 -- 455}, year = {2022}, language = {en} } @inproceedings{ParczykPokuttaSpiegeletal.2022, author = {Parczyk, Olaf and Pokutta, Sebastian and Spiegel, Christoph and Szab{\´o}, Tibor}, title = {New Ramsey Multiplicity Bounds and Search Heuristics}, booktitle = {Discrete Mathematics Days}, year = {2022}, abstract = {We study two related problems concerning the number of monochromatic cliques in two-colorings of the complete graph that go back to questions of Erdős. Most notably, we improve the 25-year-old upper bounds of Thomason on the Ramsey multiplicity of K4 and K5 and we settle the minimum number of independent sets of size 4 in graphs with clique number at most 4. Motivated by the elusiveness of the symmetric Ramsey multiplicity problem, we also introduce an off-diagonal variant and obtain tight results when counting monochromatic K4 or K5 in only one of the colors and triangles in the other. The extremal constructions for each problem turn out to be blow-ups of a finite graph and were found through search heuristics. They are complemented by lower bounds and stability results established using Flag Algebras, resulting in a fully computer-assisted approach. More broadly, these problems lead us to the study of the region of possible pairs of clique and independent set densities that can be realized as the limit of some sequence of graphs.}, language = {en} } @inproceedings{ParczykPokuttaSpiegeletal.2023, author = {Parczyk, Olaf and Pokutta, Sebastian and Spiegel, Christoph and Szab{\´o}, Tibor}, title = {Fully Computer-assisted Proofs in Extremal Combinatorics}, volume = {37}, booktitle = {Proceedings of the AAAI Conference on Artificial Intelligence}, number = {10}, doi = {10.1609/aaai.v37i10.26470}, pages = {12482 -- 12490}, year = {2023}, abstract = {We present a fully computer-assisted proof system for solving a particular family of problems in Extremal Combinatorics. Existing techniques using Flag Algebras have proven powerful in the past, but have so far lacked a computational counterpart to derive matching constructive bounds. We demonstrate that common search heuristics are capable of finding constructions far beyond the reach of human intuition. Additionally, the most obvious downside of such heuristics, namely a missing guarantee of global optimality, can often be fully eliminated in this case through lower bounds and stability results coming from the Flag Algebra approach. To illustrate the potential of this approach, we study two related and well-known problems in Extremal Graph Theory that go back to questions of Erdős from the 60s. Most notably, we present the first major improvement in the upper bound of the Ramsey multiplicity of the complete graph on 4 vertices in 25 years, precisely determine the first off-diagonal Ramsey multiplicity number, and settle the minimum number of independent sets of size four in graphs with clique number strictly less than five.}, language = {en} } @article{KamčevSpiegel2022, author = {Kamčev, Nina and Spiegel, Christoph}, title = {Another note on intervals in the Hales-Jewett theorem}, volume = {29}, journal = {Electronic Journal of Combinatorics}, number = {1}, doi = {10.37236/6730}, pages = {P1.62}, year = {2022}, abstract = {The Hales-Jewett Theorem states that any r-colouring of [m]ⁿ contains a monochromatic combinatorial line if n is large enough. Shelah's proof of the theorem implies that for m = 3 there always exists a monochromatic combinatorial line whose set of active coordinates is the union of at most r intervals. For odd r, Conlon and Kamčev constructed r-colourings for which it cannot be fewer than r intervals. However, we show that for even r and large n, any r-colouring of [3]ⁿ contains a monochromatic combinatorial line whose set of active coordinates is the union of at most r-1 intervals. This is optimal and extends a result of Leader and R{\"a}ty for r=2.}, language = {en} } @article{HunkenschroederPokuttaWeismantel2022, author = {Hunkenschr{\"o}der, Christoph and Pokutta, Sebastian and Weismantel, Robert}, title = {Optimizing a low-dimensional convex function over a high-dimensional cub}, journal = {SIAM Journal on Optimization}, year = {2022}, language = {en} } @inproceedings{MacDonaldBesanconPokutta2022, author = {MacDonald, Jan and Besan{\c{c}}on, Mathieu and Pokutta, Sebastian}, title = {Interpretable Neural Networks with Frank-Wolfe: Sparse Relevance Maps and Relevance Orderings}, booktitle = {Proceedings of the International Conference on Machine Learning}, year = {2022}, language = {en} } @inproceedings{TsujiTanakaPokutta2022, author = {Tsuji, Kazuma and Tanaka, Ken'ichiro and Pokutta, Sebastian}, title = {Pairwise Conditional Gradients without Swap Steps and Sparser Kernel Herding}, booktitle = {Proceedings of the International Conference on Machine Learning}, year = {2022}, language = {en} } @inproceedings{WaeldchenHuberPokutta2022, author = {W{\"a}ldchen, Stephan and Huber, Felix and Pokutta, Sebastian}, title = {Training Characteristic Functions with Reinforcement Learning: XAI-methods Play Connect Four}, booktitle = {Proceedings of the International Conference on Machine Learning}, year = {2022}, language = {en} } @article{RayFackeldeySteinetal.2023, author = {Ray, Sourav and Fackeldey, Konstantin and Stein, Christoph and Weber, Marcus}, title = {Coarse Grained MD Simulations of Opioid interactions with the µ-opioid receptor and the surrounding lipid membrane}, volume = {3}, journal = {Biophysica}, number = {2}, doi = {10.3390/biophysica3020017}, pages = {263 -- 275}, year = {2023}, abstract = {In our previous studies, a new opioid (NFEPP) was developed to only selectively bind to the 𝜇-opoid receptor (MOR) in inflamed tissue and thus avoid the severe side effects of fentanyl. We know that NFEPP has a reduced binding affinity to MOR in healthy tissue. Inspired by the modelling and simulations performed by Sutcliffe et al., we present our own results of coarse-grained molecular dynamics simulations of fentanyl and NFEPP with regards to their interaction with the 𝜇-opioid receptor embedded within the lipid cell membrane. For technical reasons, we have slightly modified Sutcliffe's parametrisation of opioids. The pH-dependent opioid simulations are of interest because while fentanyl is protonated at the physiological pH, NFEPP is deprotonated due to its lower pKa value than that of fentanyl. Here, we analyse for the first time whether pH changes have an effect on the dynamical behaviour of NFEPP when it is inside the cell membrane. Besides these changes, our analysis shows a possible alternative interaction of NFEPP at pH 7.4 outside the binding region of the MOR. The interaction potential of NFEPP with MOR is also depicted by analysing the provided statistical molecular dynamics simulations with the aid of an eigenvector analysis of a transition rate matrix. In our modelling, we see differences in the XY-diffusion profiles of NFEPP compared with fentanyl in the cell membrane.}, language = {en} } @article{TrepteSeckerKostovaetal.2023, author = {Trepte, Philipp and Secker, Christopher and Kostova, Simona and Maseko, Sibusiso B. and Gang Choi, Soon and Blavier, Jeremy and Minia, Igor and Silva Ramos, Eduardo and Cassonnet, Patricia and Golusik, Sabrina and Zenkner, Martina and Beetz, Stephanie and Liebich, Mara J. and Scharek, Nadine and Sch{\"u}tz, Anja and Sperling, Marcel and Lisurek, Michael and Wang, Yang and Spirohn, Kerstin and Hao, Tong and Calderwood, Michael A. and Hill, David E. and Landthaler, Markus and Olivet, Julien and Twizere, Jean-Claude and Vidal, Marc and Wanker, Erich E.}, title = {AI-guided pipeline for protein-protein interaction drug discovery identifies a SARS-CoV-2 inhibitor}, journal = {bioRxiv}, doi = {10.1101/2023.06.14.544560}, year = {2023}, language = {en} } @misc{LindnerLiebchen2020, author = {Lindner, Niels and Liebchen, Christian}, title = {Determining all integer vertices of the PESP polytope by flipping arcs}, issn = {1438-0064}, doi = {10.4230/OASIcs.ATMOS.2020.5}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-78793}, year = {2020}, abstract = {We investigate polyhedral aspects of the Periodic Event Scheduling Problem (PESP), the mathematical basis for periodic timetabling problems in public transport. Flipping the orientation of arcs, we obtain a new class of valid inequalities, the flip inequalities, comprising both the known cycle and change-cycle inequalities. For a point of the LP relaxation, a violated flip inequality can be found in pseudo-polynomial time, and even in linear time for a spanning tree solution. Our main result is that the integer vertices of the polytope described by the flip inequalities are exactly the vertices of the PESP polytope, i.e., the convex hull of all feasible periodic slacks with corresponding modulo parameters. Moreover, we show that this flip polytope equals the PESP polytope in some special cases. On the computational side, we devise several heuristic approaches concerning the separation of cutting planes from flip inequalities. These produce better dual bounds for the smallest and largest instance of the benchmarking library PESPlib.}, language = {en} } @article{BorndoerferDaneckerWeiser2021, author = {Bornd{\"o}rfer, Ralf and Danecker, Fabian and Weiser, Martin}, title = {A Discrete-Continuous Algorithm for Free Flight Planning}, volume = {14}, journal = {Algorithms}, number = {1}, publisher = {MDPI}, issn = {1438-0064}, doi = {10.3390/a14010004}, pages = {4}, year = {2021}, abstract = {We propose a hybrid discrete-continuous algorithm for flight planning in free flight airspaces. In a first step, our DisCOptER method discrete-continuous optimization for enhanced resolution) computes a globally optimal approximate flight path on a discretization of the problem using the A* method. This route initializes a Newton method that converges rapidly to the smooth optimum in a second step. The correctness, accuracy, and complexity of the method are goverened by the choice of the crossover point that determines the coarseness of the discretization. We analyze the optimal choice of the crossover point and demonstrate the asymtotic superority of DisCOptER over a purely discrete approach.}, language = {en} } @misc{BorndoerferDaneckerWeiser2020, author = {Bornd{\"o}rfer, Ralf and Danecker, Fabian and Weiser, Martin}, title = {A Discrete-Continuous Algorithm for Free Flight Planning}, issn = {1438-0064}, doi = {10.3390/a14010004}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-81343}, year = {2020}, abstract = {We propose a hybrid discrete-continuous algorithm for flight planning in free flight airspaces. In a first step, our DisCOptER method discrete-continuous optimization for enhanced resolution) computes a globally optimal approximate flight path on a discretization of the problem using the A* method. This route initializes a Newton method that converges rapidly to the smooth optimum in a second step. The correctness, accuracy, and complexity of the method are goverened by the choice of the crossover point that determines the coarseness of the discretization. We analyze the optimal choice of the crossover point and demonstrate the asymtotic superority of DisCOptER over a purely discrete approach.}, language = {en} } @misc{KempkeMaherRehfeldtetal.2026, author = {Kempke, Nils-Christian and Maher, Stephen John and Rehfeldt, Daniel and Gleixner, Ambros and Koch, Thorsten and Uslu, Svenja}, title = {Distributed Parallel Structure-Aware Presolving for Arrowhead Linear Programs}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-103034}, year = {2026}, abstract = {We present a structure-aware parallel presolve framework specialized to arrowhead linear programs (AHLPs) and designed for high-performance computing (HPC) environments, integrated into the parallel interior point solver PIPS-IPM++. Large-scale LPs arising from automated model generation frequently contain redundancies and numerical pathologies that necessitate effective presolve, yet existing presolve techniques are primarily serial or structure-agnostic and can become time-consuming in parallel solution workflows. Within PIPS-IPM++, AHLPs are stored in distributed memory, and our presolve builds on this to apply a highly parallel, distributed presolve across compute nodes while keeping communication overhead low and preserving the underlying arrowhead structure. We demonstrate the scalability and effectiveness of our approach on a diverse set of AHLPs and compare it against state-of-the-art presolve implementations, including PaPILO and the presolve implemented within Gurobi. Even on a single machine, our presolve significantly outperforms PaPILO by a factor of 18 and Gurobi's presolve by a factor of 6 in terms of shifted geometric mean runtime, while reducing the problems by a similar amount to PaPILO. Using a distributed compute environment, we outperform Gurobi's presolve by a factor of 13.}, language = {en} }