@inproceedings{BraunPokuttaZink2015, author = {Braun, G{\´a}bor and Pokutta, Sebastian and Zink, Daniel}, title = {Inapproximability of combinatorial problems via small LPs and SDPs}, booktitle = {Proceeedings of STOC}, arxiv = {http://arxiv.org/abs/1410.8816}, year = {2015}, language = {en} } @inproceedings{Pokutta2015, author = {Pokutta, Sebastian}, title = {Information Theory and Polyhedral Combinatorics}, booktitle = {Proceedings of 53rd Annual Allerton Conference on Communication, Control, and Computing}, year = {2015}, language = {en} } @inproceedings{SongXiePokutta2015, author = {Song, R. and Xie, Y. and Pokutta, Sebastian}, title = {Sequential Sensing with Model Mismatch}, booktitle = {Proceedings of ISIT}, year = {2015}, language = {en} } @inproceedings{XieLiPokutta2015, author = {Xie, Y. and Li, Q. and Pokutta, Sebastian}, title = {Supervised Online Subspace Tracking}, booktitle = {Proceedings of Asilomar Conference on Signals, Systems, and Computers}, year = {2015}, language = {en} } @inproceedings{RoyPokutta2016, author = {Roy, Aurko and Pokutta, Sebastian}, title = {Hierarchical Clustering via Spreading Metrics}, booktitle = {Proceedings of NIPS}, arxiv = {http://arxiv.org/abs/1610.09269}, year = {2016}, language = {en} } @inproceedings{BraunRoyPokutta2016, author = {Braun, G{\´a}bor and Roy, Aurko and Pokutta, Sebastian}, title = {Stronger Reductions for Extended Formulations}, booktitle = {Proceedings of IPCO}, arxiv = {http://arxiv.org/abs/1512.04932}, year = {2016}, language = {en} } @inproceedings{BraunBrownCohenHuqetal.2016, author = {Braun, G{\´a}bor and Brown-Cohen, Jonah and Huq, Arefin and Pokutta, Sebastian and Raghavendra, Prasad and Weitz, Benjamin and Zink, Daniel}, title = {The matching problem has no small symmetric SDP}, booktitle = {Proceddings of SODA 2016}, arxiv = {http://arxiv.org/abs/1504.00703}, year = {2016}, language = {en} } @inproceedings{RoyXuPokutta2017, author = {Roy, Aurko and Xu, Huan and Pokutta, Sebastian}, title = {Reinforcement Learning under Model Mismatch}, booktitle = {Proceedings of NIPS}, arxiv = {http://arxiv.org/abs/1706.04711}, year = {2017}, language = {en} } @inproceedings{BaermannPokuttaSchneider2017, author = {B{\"a}rmann, Andreas and Pokutta, Sebastian and Schneider, Oskar}, title = {Emulating the Expert: Inverse Optimization through Online Learning}, booktitle = {Proceedings of the International Conference on Machine Learning (ICML)}, arxiv = {http://arxiv.org/abs/1810.12997}, year = {2017}, language = {en} } @phdthesis{Omari2019, author = {Omari, Mohamed}, title = {A Mathematical Model of Bovine Metabolism and Reproduction: Application to Feeding Strategies, Drug Administration and Experimental Design}, year = {2019}, language = {en} } @phdthesis{Reidelbach2019, author = {Reidelbach, Marco}, title = {Optimal Network Generation for the Simulation of Proton Transfer Processes}, year = {2019}, language = {en} } @phdthesis{Donati2019, author = {Donati, Luca}, title = {Reweighting methods for Molecular Dynamics}, publisher = {Freie Universit{\"a}t Berlin}, doi = {10.17169/refubium-2305}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:188-refubium-24541-6}, year = {2019}, abstract = {The dynamical response of molecular systems, when the potential energy function is perturbed at a microscopic level, is difficult to predict without a numerical or laboratory experiment. This is due to the non-linearity and high-dimensionality of molecular systems. An efficient investigation of such a behaviour is necessary to better understand the nature of molecules and to improve the predictability of Molecular Dynamics simulations. In this thesis we propose a reweighting scheme for Markov State Models (MSMs), based on the Girsanov theorem, that permits to reduce the computational cost of the analysis when the potential energy function of a molecule is perturbed. The method has been successfully extended and implemented with metadynamics, in order to build the MSM of a molecular system in a significantly shorter computational time compared to a standard unbiased MD simulation. We also propose a new method to discretize the infinitesimal generator into a rate matrix, that could be used to efficiently study Hamiltonian perturbations as well.}, language = {en} } @misc{Zumbansen2019, type = {Master Thesis}, author = {Zumbansen, Max}, title = {Parameter estimation of multivalent processes on ITC datasets}, year = {2019}, language = {en} } @misc{Hoffmann2019, type = {Master Thesis}, author = {Hoffmann, Lara}, title = {Automating PCCA+ applied to Eye-Tracking Data}, year = {2019}, language = {en} } @misc{OPUS4-7738, title = {Uncertainty Quantification, 11-15 March 2019}, volume = {16}, journal = {Oberwolfach Reports}, number = {1}, editor = {Ernst, Oliver and Nobile, Fabio and Schillings, Claudia and Sullivan, T. J.}, doi = {10.4171/OWR/2019/12}, pages = {695 -- 772}, year = {2019}, language = {en} } @article{KostreSchuetteNoeetal.2021, author = {Kostre, Margarita and Sch{\"u}tte, Christof and No{\´e}, Frank and del Razo Sarmina, Mauricio}, title = {Coupling Particle-Based Reaction-Diffusion Simulations with Reservoirs Mediated by Reaction-Diffusion PDEs}, volume = {19}, journal = {Multiscale Modeling \& Simulation}, number = {4}, publisher = {Society for Industrial and Applied Mathematics}, arxiv = {http://arxiv.org/abs/2006.00003}, doi = {10.1137/20M1352739}, pages = {1659 -- 1683}, year = {2021}, abstract = {Open biochemical systems of interacting molecules are ubiquitous in life-related processes. However, established computational methodologies, like molecular dynamics, are still mostly constrained to closed systems and timescales too small to be relevant for life processes. Alternatively, particle-based reaction-diffusion models are currently the most accurate and computationally feasible approach at these scales. Their efficiency lies in modeling entire molecules as particles that can diffuse and interact with each other. In this work, we develop modeling and numerical schemes for particle-based reaction-diffusion in an open setting, where the reservoirs are mediated by reaction-diffusion PDEs. We derive two important theoretical results. The first one is the mean-field for open systems of diffusing particles; the second one is the mean-field for a particle-based reaction-diffusion system with second-order reactions. We employ these two results to develop a numerical scheme that consistently couples particle-based reaction-diffusion processes with reaction-diffusion PDEs. This allows modeling open biochemical systems in contact with reservoirs that are time-dependent and spatially inhomogeneous, as in many relevant real-world applications.}, language = {en} } @inproceedings{AllenDramlitschGoodaleetal.2001, author = {Allen, Gabrielle and Dramlitsch, Thomas and Goodale, Tom and Lanfermann, Gerd and Radke, Thomas and Seidel, Edward and Kielmann, Thilo and Verstoep, Kees and Balaton, Zolt{\´a}n and Kacsuk, P{\´e}ter and Szalai, Ferenc and Gehring, J{\"o}rn and Keller, Axel and Streit, Achim and Matyska, Ludek and Ruda, Miroslav and Krenek, Ales and Knipp, Harald and Merzky, Andr{\´e} and Reinefeld, Alexander and Schintke, Florian and Ludwiczak, Bogdan and Nabrzyski, Jarek and Pukacki, Juliusz and Kersken, Hans-Peter and Aloisio, Giovanni and Cafaro, Massimo and Ziegler, Wolfgang and Russell, Michael}, title = {Early experiences with the EGrid testbed}, booktitle = {Proceedings First IEEE/ACM International Symposium on Cluster Computing and the Grid}, doi = {10.1109/CCGRID.2001.923185}, pages = {130 -- 137}, year = {2001}, language = {en} } @inproceedings{MillerLabartaSchintkeetal.2002, author = {Miller, Barton P. and Labarta, Jes{\´u}s and Schintke, Florian and Simon, Jens}, title = {Performance Evaluation, Analysis and Optimization}, volume = {2400}, booktitle = {Euro-Par 2002 Parallel Processing}, doi = {10.1007/3-540-45706-2_15}, pages = {131 -- 131}, year = {2002}, language = {en} } @inproceedings{IamnitchiTrunfioLedlieetal.2010, author = {Iamnitchi, Adriana and Trunfio, Paolo and Ledlie, Jonathan and Schintke, Florian}, title = {Peer-to-Peer Computing}, volume = {6271}, booktitle = {Euro-Par 2010 - Parallel Processing}, doi = {10.1007/978-3-642-15277-1_42}, pages = {444 -- 445}, year = {2010}, language = {en} } @inproceedings{SchintkeSimonReinefeld2001, author = {Schintke, Florian and Simon, Jens and Reinefeld, Alexander}, title = {A Cache Simulator for Shared Memory Systems}, volume = {2074}, booktitle = {Computational Science - ICCS 2001}, doi = {10.1007/3-540-45718-6_62}, pages = {569 -- 578}, year = {2001}, language = {en} } @misc{Clausecker2020, author = {Clausecker, Robert}, title = {The Quality of Heuristic Functions for IDA*}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-78489}, year = {2020}, abstract = {The aim of this thesis is to deepen our understand of how IDA* heuristics influence the number of nodes expanded during search. To this end, we develop Korf's formula for the number of expanded nodes into a heuristic quality η which expresses the quality of a heuristic function as a constant factor on the number of expanded nodes, independent of a particular problem instance. We proceed to show how to compute η for some common kinds of heuristics and how to estimate η by means of a random sample for arbitrary heuristics. Using the value of η for some concrete examples, we then inspect for which parts of the search space the values of h(v) are particularly critical to the performance of the heuristic, allowing us to build better heuristics for future problems. This report originally appeared as a master thesis at Humboldt University of Berlin.}, language = {en} } @article{GorgullaDasLeighetal.2021, author = {Gorgulla, Christoph and Das, Krishna M. Padmanabha and Leigh, Kendra E and Cespugli, Marco and Fischer, Patrick D. and Wang, Zi-Fu and Tesseyre, Guilhem and Pandita, Shreya and Shnapir, Alex and Calderaio, Anthony and Hutcheson, Colin and Gechev, Minko and Rose, Alexander and Lewis, Noam and Yaffe, Erez and Luxenburg, Roni and Herce, Henry D. and Durmaz, Vedat and Halazonetis, Thanos D. and Fackeldey, Konstantin and Patten, Justin J. and Chuprina, Alexander and Dziuba, Igor and Plekhova, Alla and Moroz, Yurii and Radchenko, Dmytro and Tarkhanova, Olga and Yavnyuk, Irina and Gruber, Christian C. and Yust, Ryan and Payne, Dave and N{\"a}{\"a}r, Anders M. and Namchuk, Mark N. and Davey, Robert A. and Wagner, Gerhard and Kinney, Jamie and Arthanari, Haribabu}, title = {A Multi-Pronged Approach Targeting SARS-CoV-2 Proteins Using Ultra-Large Virtual Screening}, volume = {24}, journal = {iScience}, number = {2}, publisher = {CellPress}, doi = {10.26434/chemrxiv.12682316}, pages = {102021}, year = {2021}, abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), previously known as 2019 novel coronavirus (2019-nCoV), has spread rapidly across the globe, creating an unparalleled global health burden and spurring a deepening economic crisis. As of July 7th, 2020, almost seven months into the outbreak, there are no approved vaccines and few treatments available. Developing drugs that target multiple points in the viral life cycle could serve as a strategy to tackle the current as well as future coronavirus pandemics. Here we leverage the power of our recently developed in silico screening platform, VirtualFlow, to identify inhibitors that target SARS-CoV-2. VirtualFlow is able to efficiently harness the power of computing clusters and cloud-based computing platforms to carry out ultra-large scale virtual screens. In this unprecedented structure-based multi-target virtual screening campaign, we have used VirtualFlow to screen an average of approximately 1 billion molecules against each of 40 different target sites on 17 different potential viral and host targets in the cloud. In addition to targeting the active sites of viral enzymes, we also target critical auxiliary sites such as functionally important protein-protein interaction interfaces. This multi-target approach not only increases the likelihood of finding a potent inhibitor, but could also help identify a collection of anti-coronavirus drugs that would retain efficacy in the face of viral mutation. Drugs belonging to different regimen classes could be combined to develop possible combination therapies, and top hits that bind at highly conserved sites would be potential candidates for further development as coronavirus drugs. Here, we present the top 200 in silico hits for each target site. While in-house experimental validation of some of these compounds is currently underway, we want to make this array of potential inhibitor candidates available to researchers worldwide in consideration of the pressing need for fast-tracked drug development.}, language = {en} } @article{BonnetAkianSavinetal.2020, author = {Bonnet, Luc and Akian, Jean-Luc and Savin, {\´E}ric and Sullivan, T. J.}, title = {Adaptive reconstruction of imperfectly-observed monotone functions, with applications to uncertainty quantification}, volume = {13}, journal = {Algorithms}, number = {8}, arxiv = {http://arxiv.org/abs/2007.05236}, doi = {10.3390/a13080196}, pages = {196}, year = {2020}, abstract = {Motivated by the desire to numerically calculate rigorous upper and lower bounds on deviation probabilities over large classes of probability distributions, we present an adaptive algorithm for the reconstruction of increasing real-valued functions. While this problem is similar to the classical statistical problem of isotonic regression, the optimisation setting alters several characteristics of the problem and opens natural algorithmic possibilities. We present our algorithm, establish sufficient conditions for convergence of the reconstruction to the ground truth, and apply the method to synthetic test cases and a real-world example of uncertainty quantification for aerodynamic design.}, language = {en} } @inproceedings{Hartung2020, author = {Hartung, Marc}, title = {CTSat: C++ Template Abstractions for Dynamic Interchangeable SAT Solver Features}, booktitle = {Proceedings of SAT Competition 2020: Solver and Benchmark Descriptions}, pages = {32 -- 33}, year = {2020}, language = {en} } @inproceedings{KaiserHartung2020, author = {Kaiser, Benjamin and Hartung, Marc}, title = {PauSat}, booktitle = {Proceedings of SAT Competition 2020: Solver and Benchmark Descriptions}, pages = {34 -- 35}, year = {2020}, language = {en} } @inproceedings{HartungKaiser2020, author = {Hartung, Marc and Kaiser, Benjamin}, title = {Crafted Benchmarks with Artificial Community Structure and Known Complexity}, booktitle = {Proceedings of SAT Competition 2020: Solver and Benchmark Descriptions}, pages = {89 -- 90}, year = {2020}, language = {en} } @inproceedings{BaerringLopezCancioetal.2003, author = {B{\"a}rring, Olof and Lopez, Maite Barroso and Cancio, German and R{\"o}blitz, Thomas and Schintke, Florian and et al.,}, title = {Towards automation of computing fabrics using tools from the fabric management workpackage of the EU DataGrid project}, booktitle = {Computing in High Energy and Nuclear Physics (CHEP03)}, arxiv = {http://arxiv.org/abs/cs/0305050}, pages = {1 -- 8}, year = {2003}, language = {en} } @article{StraubeKowalikNetzetal.2020, author = {Straube, Arthur and Kowalik, Bartosz G. and Netz, Roland R. and H{\"o}fling, Felix}, title = {Rapid onset of molecular friction in liquids bridging between the atomistic and hydrodynamic pictures}, volume = {3}, journal = {Commun. Phys.}, publisher = {Nature}, doi = {10.1038/s42005-020-0389-0}, pages = {126}, year = {2020}, abstract = {Friction in liquids arises from conservative forces between molecules and atoms. Although the hydrodynamics at the nanoscale is subject of intense research and despite the enormous interest in the non-Markovian dynamics of single molecules and solutes, the onset of friction from the atomistic scale so far could not be demonstrated. Here, we fill this gap based on frequency-resolved friction data from high-precision simulations of three prototypical liquids, including water. Combining with theory, we show that friction in liquids emerges abruptly at a characteristic frequency, beyond which viscous liquids appear as non-dissipative, elastic solids. Concomitantly, the molecules experience Brownian forces that display persistent correlations. A critical test of the generalised Stokes-Einstein relation, mapping the friction of single molecules to the visco-elastic response of the macroscopic sample, disproves the relation for Newtonian fluids, but substantiates it exemplarily for water and a moderately supercooled liquid. The employed approach is suitable to yield insights into vitrification mechanisms and the intriguing mechanical properties of soft materials.}, language = {en} } @article{FackeldeyOsterSallandtetal.2022, author = {Fackeldey, Konstantin and Oster, Mathias and Sallandt, Leon and Schneider, Reinhold}, title = {Approximative Policy Iteration for Exit Time Feedback Control Problems driven by Stochastic Differential Equations using Tensor Train format}, volume = {20}, journal = {SIAM Journal on Multiscale Modeling and Simulation}, number = {1}, arxiv = {http://arxiv.org/abs/2010.04465}, doi = {10.1137/20M1372500}, pages = {379 -- 403}, year = {2022}, abstract = {We consider a stochastic optimal exit time feedback control problem. The Bellman equation is solved approximatively via the Policy Iteration algorithm on a polynomial ansatz space by a sequence of linear equations. As high degree multi-polynomials are needed, the corresponding equations suffer from the curse of dimensionality even in moderate dimensions. We employ tensor-train methods to account for this problem. The approximation process within the Policy Iteration is done via a Least-Squares ansatz and the integration is done via Monte-Carlo methods. Numerical evidences are given for the (multi dimensional) double well potential and a three-hole potential.}, language = {en} } @article{SoaresBaumHesseetal.2020, author = {Soares, Ana Prates and Baum, Daniel and Hesse, Bernhard and Kupsch, Andreas and M{\"u}ller, Bernd and Zaslansky, Paul}, title = {Scattering and phase-contrast X-ray methods reveal damage to glass fibers in endodontic posts following dental bur trimming}, volume = {37}, journal = {Dental Materials}, number = {2}, doi = {10.1016/j.dental.2020.10.018}, pages = {201 -- 211}, year = {2020}, language = {en} } @article{RathConradMylesetal.2017, author = {Rath, Barbara and Conrad, Tim and Myles, Puja and Alchikh, Maren and Ma, Xiaolin and Hoppe, Christian and Tief, Franziska and Chen, Xi and Obermeier, Patrick and Kisler, Bron and Schweiger, Brunhilde}, title = {Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials}, volume = {15}, journal = {Expert Review of Anti-infective Therapy}, number = {6}, doi = {10.1080/14787210.2017.1295847}, pages = {545 -- 568}, year = {2017}, abstract = {Introduction: Influenza-Like Illness is a leading cause of hospitalization in children. Disease burden due to influenza and other respiratory viral infections is reported on a population level, but clinical scores measuring individual changes in disease severity are urgently needed. Areas covered: We present a composite clinical score allowing individual patient data analyses of disease severity based on systematic literature review and WHO-criteria for uncomplicated and complicated disease. The 22-item ViVI Disease Severity Score showed a normal distribution in a pediatric cohort of 6073 children aged 0-18 years (mean age 3.13; S.D. 3.89; range: 0 to 18.79). Expert commentary: The ViVI Score was correlated with risk of antibiotic use as well as need for hospitalization and intensive care. The ViVI Score was used to track children with influenza, respiratory syncytial virus, human metapneumovirus, human rhinovirus, and adenovirus infections and is fully compliant with regulatory data standards. The ViVI Disease Severity Score mobile application allows physicians to measure disease severity at the point-of care thereby taking clinical trials to the next level.}, language = {en} } @article{ShaoCannistraciConrad2017, author = {Shao, Borong and Cannistraci, Carlo Vittorio and Conrad, Tim}, title = {Epithelial Mesenchymal Transition Network-Based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data}, volume = {3}, journal = {Genomics and Computational Biology}, number = {3}, doi = {10.18547/gcb.2017.vol3.iss3.e57}, pages = {e57}, year = {2017}, abstract = {Epithelial mesenchymal transition (EMT) process has been shown as highly relevant to cancer prognosis. However, although different biological network-based biomarker identification methods have been proposed to predict cancer prognosis, EMT network has not been directly used for this purpose. In this study, we constructed an EMT regulatory network consisting of 87 molecules and tried to select features that are useful for prognosis prediction in Lung Adenocarcinoma (LUAD). To incorporate multiple molecular profiles, we obtained four types of molecular data including mRNA-Seq, copy number alteration (CNA), DNA methylation, and miRNA-Seq data from The Cancer Genome Atlas. The data were mapped to the EMT network in three alternative ways: mRNA-Seq and miRNA-Seq, DNA methylation, and CNA and miRNA-Seq. Each mapping was employed to extract five different sets of features using discretization and network-based biomarker identification methods. Each feature set was then used to predict prognosis with SVM and logistic regression classifiers. We measured the prediction accuracy with AUC and AUPR values using 10 times 10-fold cross validation. For a more comprehensive evaluation, we also measured the prediction accuracies of clinical features, EMT plus clinical features, randomly picked 87 molecules from each data mapping, and using all molecules from each data type. Counter-intuitively, EMT features do not always outperform randomly selected features and the prediction accuracies of the five feature sets are mostly not significantly different. Clinical features are shown to give the highest prediction accuracies. In addition, the prediction accuracies of both EMT features and random features are comparable as using all features (more than 17,000) from each data type.}, language = {en} } @article{JayrannejadConrad2017, author = {Jayrannejad, Fahrnaz and Conrad, Tim}, title = {Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining}, journal = {Springer Lecture Notes in Artificial Intelligence}, year = {2017}, abstract = {Recent advances in -omics technology has yielded in large data-sets in many areas of biology, such as mass spectrometry based proteomics. However, analyzing this data is still a challenging task mainly due to the very high dimensionality and high noise content of the data. One of the main objectives of the analysis is the identification of relevant patterns (or features) which can be used for classification of new samples to healthy or diseased. So, a method is required to find easily interpretable models from this data. To gain the above mentioned goal, we have adapted the disjunctive association rule mining algorithm, TitanicOR, to identify emerging patterns from our mass spectrometry proteomics data-sets. Comparison to five state-of-the-art methods shows that our method is advantageous them in terms of identifying the inter-dependency between the features and the TP-rate and precision of the features selected. We further demonstrate the applicability of our algorithm to one previously published clinical data-set.}, language = {en} } @article{MarzbanConradMarbanetal.2018, author = {Marzban, Forough and Conrad, Tim and Marban, Pouria and Sodoudi, Sahar}, title = {Estimation of the Near-Surface Air Temperature during the Day and Nighttime from MODIS in Berlin, Germany}, volume = {7}, journal = {International Journal of Advanced Remote Sensing and GIS}, number = {1}, doi = {10.23953/cloud.ijarsg.337}, pages = {2478 -- 2517}, year = {2018}, abstract = {Air temperature (Tair or T2m) is an important climatological variable for forest biosphere processes and climate change research. Due to the low density and the uneven distribution of weather stations, traditional ground-based observations cannot accurately capture the spatial distribution of Tair. In this study, Tair in Berlin is estimated during the day and night time over six land cover/land use (LC/LU) types by satellite remote sensing data over a large domain and a relatively long period (7 years). Aqua and Terra MODIS (Moderate Resolution Imaging Spectroradiometer) data and meteorological data for the period from 2007 to 2013 were collected to estimate Tair. Twelve environmental variables (land surface temperature (LST), normalized difference vegetation index (NDVI), Julian day, latitude, longitude, Emissivity31, Emissivity32, altitude, albedo, wind speed, wind direction and air pressure) were selected as predictors. Moreover, a comparison between LST from MODIS Terra and Aqua with daytime and night time air temperatures (Tday, Tnight) was done respectively and in addition, the spatial variability of LST and Tair relationship by applying a varying window size on the MODIS LST grid was examined. An analysis of the relationship between the observed Tair and the spatially averaged remotely sensed LST, indicated that 3 × 3 and 1 × 1 pixel size was the optimal window size for the statistical model estimating Tair from MODIS data during the day and night time, respectively. Three supervised learning methods (Adaptive Neuro Fuzzy Inference system (ANFIS), Artificial Neural Network (ANN) and Support vector machine (SVR)) were used to estimate Tair during the day and night time, and their performances were validated by cross-validation for each LC/LU. Moreover, tuning the hyper parameters of some models like SVR and ANN were investigated. For tuning the hyper parameters of SVR, Simulated Annealing (SA) was applied (SA-SVR model) and a multiple-layer feed-forward (MLF) neural networks with three layers and different nodes in hidden layers are used with Levenber-Marquardt back-propagation (LM-BP), in order to achieve higher accuracy in the estimation of Tair. Results indicated that the ANN model achieved better accuracy (RMSE= 2.16°C, MAE = 1.69°C, R2 = 0.95) than SA_SVR model (RMSE= 2.50°C, MAE = 1.92°C, R2 = 0.91) and ANFIS model (RMSE= 2.88°C, MAE= 2.2°C, R2 = 0.89) over six LC/LU during the day and night time. The Q-Q diagram of SA-SVR, ANFIS and NN show that all three models slightly tended to underestimate and overestimate the extreme and low temperatures for all LC/LU classes during the day and night time. The weak performance in the extreme and low temperatures are a consequence of the small number of data in these temperatures. These satisfactory results indicate that this approach is proper for estimating air temperature and spatial window size is an important factor that should be considered in the estimation of air temperature.}, language = {en} } @article{KorkConradWeissetal.2018, author = {Kork, F. and Conrad, Tim and Weiss, B. and Roenneberg, T. and Wernecke, K.-D. and Balzer, Felix}, title = {Associations of postoperative mortality with the time of day, week and year}, volume = {73}, journal = {Anaesthesia}, number = {6}, issn = {0959-2962}, pages = {711 -- 718}, year = {2018}, language = {en} } @inproceedings{Sullivan2017, author = {Sullivan, T. J.}, title = {Well-posedness of Bayesian inverse problems in quasi-Banach spaces with stable priors}, volume = {17}, booktitle = {88th Annual Meeting of the International Association of Applied Mathematics and Mechanics (GAMM), Weimar 2017}, number = {1}, arxiv = {http://arxiv.org/abs/1710.05610}, doi = {10.1002/pamm.201710402}, pages = {871 -- 874}, year = {2017}, language = {en} } @article{Sullivan2017, author = {Sullivan, T. J.}, title = {Well-posed Bayesian inverse problems and heavy-tailed stable quasi-Banach space priors}, volume = {11}, journal = {Inverse Problems and Imaging}, number = {5}, arxiv = {http://arxiv.org/abs/1605.05898}, doi = {10.3934/ipi.2017040}, pages = {857 -- 874}, year = {2017}, language = {en} } @article{SchmidtkeErleben2018, author = {Schmidtke, Robert and Erleben, Kenny}, title = {Chunked Bounding Volume Hierarchies for Fast Digital Prototyping using Volumetric Meshes}, volume = {24}, journal = {IEEE Transactions on Visualization and Computer Graphics}, number = {12}, issn = {1941-0506}, doi = {10.1109/TVCG.2017.2784441}, pages = {3044 -- 3057}, year = {2018}, abstract = {We present a novel approach to using Bounding Volume Hierarchies (BVHs) for collision detection of volumetric meshes for digital prototyping based on accurate simulation. In general, volumetric meshes contain more primitives than surface meshes, which in turn means larger BVHs. To manage these larger BVHs, we propose an algorithm for splitting meshes into smaller chunks with a limited-size BVH each. Limited-height BVHs make guided, all-pairs testing of two chunked meshes well-suited for GPU implementation. This is because the dynamically generated work during BVH traversal becomes bounded. Chunking is simple to implement compared to dynamic load balancing methods and can result in an overall two orders of magnitude speedup on GPUs. This indicates that dynamic load balancing may not be a well suited scheme for the GPU. The overall application timings showed that data transfers were not the bottleneck. Instead, the conversion to and from OpenCL friendly data structures was causing serious performance impediments. Still, a simple OpenMP acceleration of the conversion allowed the GPU solution to beat the CPU solution by 20\%. We demonstrate our results using rigid and deformable body scenes of varying complexities on a variety of GPUs.}, language = {en} } @article{LieSullivanStuart2019, author = {Lie, Han Cheng and Sullivan, T. J. and Stuart, Andrew}, title = {Strong convergence rates of probabilistic integrators for ordinary differential equations}, volume = {29}, journal = {Statistics and Computing}, number = {6}, arxiv = {http://arxiv.org/abs/1703.03680}, doi = {10.1007/s11222-019-09898-6}, pages = {1265 -- 1283}, year = {2019}, abstract = {Probabilistic integration of a continuous dynamical system is a way of systematically introducing model error, at scales no larger than errors inroduced by standard numerical discretisation, in order to enable thorough exploration of possible responses of the system to inputs. It is thus a potentially useful approach in a number of applications such as forward uncertainty quantification, inverse problems, and data assimilation. We extend the convergence analysis of probabilistic integrators for deterministic ordinary differential equations, as proposed by Conrad et al.\ (\textit{Stat.\ Comput.}, 2016), to establish mean-square convergence in the uniform norm on discrete- or continuous-time solutions under relaxed regularity assumptions on the driving vector fields and their induced flows. Specifically, we show that randomised high-order integrators for globally Lipschitz flows and randomised Euler integrators for dissipative vector fields with polynomially-bounded local Lipschitz constants all have the same mean-square convergence rate as their deterministic counterparts, provided that the variance of the integration noise is not of higher order than the corresponding deterministic integrator.}, language = {en} } @inproceedings{CockayneOatesSullivanetal.2017, author = {Cockayne, Jon and Oates, Chris and Sullivan, T. J. and Girolami, Mark}, title = {Probabilistic Numerical Methods for PDE-constrained Bayesian Inverse Problems}, volume = {1853}, booktitle = {Proceedings of the 36th International Workshop on Bayesian Inference and Maximum Entropy Methods in Science and Engineering}, arxiv = {http://arxiv.org/abs/1701.04006}, doi = {10.1063/1.4985359}, pages = {060001-1 -- 060001-8}, year = {2017}, abstract = {This paper develops meshless methods for probabilistically describing discretisation error in the numerical solution of partial differential equations. This construction enables the solution of Bayesian inverse problems while accounting for the impact of the discretisation of the forward problem. In particular, this drives statistical inferences to be more conservative in the presence of significant solver error. Theoretical results are presented describing rates of convergence for the posteriors in both the forward and inverse problems. This method is tested on a challenging inverse problem with a nonlinear forward model}, language = {en} } @article{SchaeferSullivanOwhadi2021, author = {Sch{\"a}fer, Florian and Sullivan, T. J. and Owhadi, Houman}, title = {Compression, inversion, and approximate PCA of dense kernel matrices at near-linear computational complexity}, volume = {19}, journal = {Multiscale Modeling and Simulation}, number = {2}, arxiv = {http://arxiv.org/abs/1706.02205}, doi = {10.1137/19M129526X}, pages = {688 -- 730}, year = {2021}, language = {en} } @article{LieSullivan2018, author = {Lie, Han Cheng and Sullivan, T. J.}, title = {Equivalence of weak and strong modes of measures on topological vector spaces}, volume = {34}, journal = {Inverse Problems}, number = {11}, arxiv = {http://arxiv.org/abs/1708.02516}, doi = {10.1088/1361-6420/aadef2}, pages = {115013}, year = {2018}, abstract = {Modes of a probability measure on an infinite-dimensional Banach space X are often defined by maximising the small-radius limit of the ratio of measures of norm balls. Helin and Burger weakened the definition of such modes by considering only balls with centres in proper subspaces of X, and posed the question of when this restricted notion coincides with the unrestricted one. We generalise these definitions to modes of arbitrary measures on topological vector spaces, defined by arbitrary bounded, convex, neighbourhoods of the origin. We show that a coincident limiting ratios condition is a necessary and sufficient condition for the equivalence of these two types of modes, and show that the coincident limiting ratios condition is satisfied in a wide range of topological vector spaces.}, language = {en} } @inproceedings{SchusterStrathmannPaigeetal.2017, author = {Schuster, Ingmar and Strathmann, Heiko and Paige, Brooks and Sejdinovic, Dino}, title = {Kernel Sequential Monte Carlo}, booktitle = {Joint European Conference on Machine Learning and Knowledge Discovery in Databases}, doi = {10.1007/978-3-319-71249-9_24}, pages = {390 -- 409}, year = {2017}, abstract = {We propose kernel sequential Monte Carlo (KSMC), a framework for sampling from static target densities. KSMC is a family of sequential Monte Carlo algorithms that are based on building emulator models of the current particle system in a reproducing kernel Hilbert space. We here focus on modelling nonlinear covariance structure and gradients of the target. The emulator's geometry is adaptively updated and subsequently used to inform local proposals. Unlike in adaptive Markov chain Monte Carlo, continuous adaptation does not compromise convergence of the sampler. KSMC combines the strengths of sequental Monte Carlo and kernel methods: superior performance for multimodal targets and the ability to estimate model evidence as compared to Markov chain Monte Carlo, and the emulator's ability to represent targets that exhibit high degrees of nonlinearity. As KSMC does not require access to target gradients, it is particularly applicable on targets whose gradients are unknown or prohibitively expensive. We describe necessary tuning details and demonstrate the benefits of the the proposed methodology on a series of challenging synthetic and real-world examples.}, language = {en} } @article{KlusSchusterMuandet2017, author = {Klus, Stefan and Schuster, Ingmar and Muandet, Krikamol}, title = {Eigendecompositions of Transfer Operators in Reproducing Kernel Hilbert Spaces}, journal = {Journal of Machine Learning Research}, arxiv = {http://arxiv.org/abs/1712.01572}, year = {2017}, abstract = {Transfer operators such as the Perron-Frobenius or Koopman operator play an important role in the global analysis of complex dynamical systems. The eigenfunctions of these operators can be used to detect metastable sets, to project the dynamics onto the dominant slow processes, or to separate superimposed signals. We extend transfer operator theory to reproducing kernel Hilbert spaces and show that these operators are related to Hilbert space representations of conditional distributions, known as conditional mean embeddings in the machine learning community. Moreover, numerical methods to compute empirical estimates of these embeddings are akin to data-driven methods for the approximation of transfer operators such as extended dynamic mode decomposition and its variants. In fact, most of the existing methods can be derived from our framework, providing a unifying view on the approximation of transfer operators. One main benefit of the presented kernel-based approaches is that these methods can be applied to any domain where a similarity measure given by a kernel is available. We illustrate the results with the aid of guiding examples and highlight potential applications in molecular dynamics as well as video and text data analysis.}, language = {en} } @masterthesis{Clausecker2017, type = {Bachelor Thesis}, author = {Clausecker, Robert}, title = {Notes on the Construction of Tablebases}, year = {2017}, language = {en} } @article{Sullivan2019, author = {Sullivan, T. J.}, title = {Contributed discussion on the article "A Bayesian conjugate gradient method"}, volume = {14}, journal = {Bayesian Analysis}, number = {3}, arxiv = {http://arxiv.org/abs/1906.10240}, doi = {10.1214/19-BA1145}, pages = {985 -- 989}, year = {2019}, abstract = {The recent article "A Bayesian conjugate gradient method" by Cockayne, Oates, Ipsen, and Girolami proposes an approximately Bayesian iterative procedure for the solution of a system of linear equations, based on the conjugate gradient method, that gives a sequence of Gaussian/normal estimates for the exact solution. The purpose of the probabilistic enrichment is that the covariance structure is intended to provide a posterior measure of uncertainty or confidence in the solution mean. This note gives some comments on the article, poses some questions, and suggests directions for further research.}, language = {en} } @inproceedings{FroehlerdaCunhaMeloWeissenboecketal.2019, author = {Fr{\"o}hler, Bernhard and da Cunha Melo, Lucas and Weissenb{\"o}ck, Johannes and Kastner, Johann and M{\"o}ller, Torsten and Hege, Hans-Christian and Gr{\"o}ller, Eduard M. and Sanctorum, Jonathan and De Beenhouwer, Jan and Sijbers, Jan and Heinzl, Christoph}, title = {Tools for the analysis of datasets from X-ray computed tomography based on Talbot-Lau grating interferometry}, booktitle = {Proceedings of iCT 2019, (9th Conference on Industrial Computed Tomography, Padova, Italy - iCT 2019, February 13-15, 2019)}, number = {paper 52}, pages = {8}, year = {2019}, abstract = {This work introduces methods for analyzing the three imaging modalities delivered by Talbot-Lau grating interferometry X-ray computed tomography (TLGI-XCT). The first problem we address is providing a quick way to show a fusion of all three modal- ities. For this purpose the tri-modal transfer function widget is introduced. The widget controls a mixing function that uses the output of the transfer functions of all three modalities, allowing the user to create one customized fused image. A second problem prevalent in processing TLGI-XCT data is a lack of tools for analyzing the segmentation process of such multimodal data. We address this by providing methods for computing three types of uncertainty: From probabilistic segmentation algorithms, from the voxel neighborhoods as well as from a collection of results. We furthermore introduce a linked views interface to explore this data. The techniques are evaluated on a TLGI-XCT scan of a carbon-fiber reinforced dataset with impact damage. We show that the transfer function widget accelerates and facilitates the exploration of this dataset, while the uncertainty analysis methods give insights into how to tweak and improve segmentation algorithms for more suitable results.}, language = {en} } @article{GoubergritsHellmeierBrueningetal.2019, author = {Goubergrits, Leonid and Hellmeier, Florian and Bruening, Jan Joris and Spuler, Andreas and Hege, Hans-Christian and Voss, Samuel and Janiga, G{\´a}bor and Saalfeld, Sylvia and Beuing, Oliver and Berg, Philipp}, title = {Multiple Aneurysms AnaTomy CHallenge 2018 (MATCH): Uncertainty Quantification of Geometric Rupture Risk Parameters}, volume = {18}, journal = {BioMedical Engineering OnLine}, number = {35}, doi = {10.1186/s12938-019-0657-y}, year = {2019}, abstract = {Background Geometric parameters have been proposed for prediction of cerebral aneurysm rupture risk. Predicting the rupture risk for incidentally detected unruptured aneurysms could help clinicians in their treatment decision. However, assessment of geometric parameters depends on several factors, including the spatial resolution of the imaging modality used and the chosen reconstruction procedure. The aim of this study was to investigate the uncertainty of a variety of previously proposed geometric parameters for rupture risk assessment, caused by variability of reconstruction procedures. Materials 26 research groups provided segmentations and surface reconstructions of five cerebral aneurysms as part of the Multiple Aneurysms AnaTomy CHallenge (MATCH) 2018. 40 dimensional and non-dimensional geometric parameters, describing aneurysm size, neck size, and irregularity of aneurysm shape, were computed. The medians as well as the absolute and relative uncertainties of the parameters were calculated. Additionally, linear regression analysis was performed on the absolute uncertainties and the median parameter values. Results A large variability of relative uncertainties in the range between 3.9 and 179.8\% was found. Linear regression analysis indicates that some parameters capture similar geometric aspects. The lowest uncertainties < 6\% were found for the non-dimensional parameters isoperimetric ratio, convexity ratio, and ellipticity index. Uncertainty of 2D and 3D size parameters was significantly higher than uncertainty of 1D parameters. The most extreme uncertainties > 80\% were found for some curvature parameters. Conclusions Uncertainty analysis is essential on the road to clinical translation and use of rupture risk prediction models. Uncertainty quantification of geometric rupture risk parameters provided by this study may help support development of future rupture risk prediction models.}, language = {en} } @article{FroehlerElberfeldMoelleretal.2019, author = {Fr{\"o}hler, Bernhard and Elberfeld, Tim and M{\"o}ller, Torsten and Hege, Hans-Christian and Weissenb{\"o}ck, Johannes and De Beenhouwer, Jan and Sijbers, Jan and Kastner, Johann and Heinzl, Christoph}, title = {A Visual Tool for the Analysis of Algorithms for Tomographic Fiber Reconstruction in Materials Science}, volume = {38}, journal = {Computer Graphics Forum}, number = {3}, doi = {10.1111/cgf.13688}, pages = {273 -- 283}, year = {2019}, abstract = {We present visual analysis methods for the evaluation of tomographic fiber reconstruction algorithms by means of analysis, visual debugging and comparison of reconstructed fibers in materials science. The methods are integrated in a tool (FIAKER) that supports the entire workflow. It enables the analysis of various fiber reconstruction algorithms, of differently parameterized fiber reconstruction algorithms and of individual steps in iterative fiber reconstruction algorithms. Insight into the performance of fiber reconstruction algorithms is obtained by a list-based ranking interface. A 3D view offers interactive visualization techniques to gain deeper insight, e.g., into the aggregated quality of the examined fiber reconstruction algorithms and parameterizations. The tool was designed in close collaboration with researchers who work with fiber-reinforced polymers on a daily basis and develop algorithms for tomographic reconstruction and characterization of such materials. We evaluate the tool using synthetic datasets as well as tomograms of real materials. Five case studies certify the usefulness of the tool, showing that it significantly accelerates the analysis and provides valuable insights that make it possible to improve the fiber reconstruction algorithms. The main contribution of the paper is the well-considered combination of methods and their seamless integration into a visual tool that supports the entire workflow. Further findings result from the analysis of (dis-)similarity measures for fibers as well as from the discussion of design decisions. It is also shown that the generality of the analytical methods allows a wider range of applications, such as the application in pore space analysis.}, language = {en} } @misc{BaumGiliardHasleretal.2019, author = {Baum, Daniel and Giliard, Nicole and Hasler, Tim and Peters-Kottig, Wolfgang}, title = {Leitlinien zum Umgang mit Forschungsdaten am Zuse-Institut Berlin}, address = {Berlin}, doi = {10.12752/7378}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-73781}, year = {2019}, abstract = {Die nachhaltige Sicherung und Bereitstellung von Forschungsdaten dienen nicht nur der Reproduzierbarkeit fr{\"u}herer Ergebnisse, sondern in hohem Maße auch der Erzielung k{\"u}nftiger Ergebnisse mit dem Ziel, die Qualit{\"a}t, Produktivit{\"a}t und Wettbewerbsf{\"a}higkeit der Wissenschaft zu f{\"o}rdern. Die folgenden Grunds{\"a}tze gelten als Leitlinien zur Handhabung von Forschungsdaten im ZIB.}, language = {de} } @article{ThielDjurdjevacConradNtinietal.2019, author = {Thiel, Denise and Djurdjevac Conrad, Natasa and Ntini, Evgenia and Peschutter, Ria and Siebert, Heike and Marsico, Annalisa}, title = {Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis}, volume = {20}, journal = {BMC Bioinformatics}, number = {1471-2105}, doi = {10.1186/s12859-019-2900-8}, year = {2019}, abstract = {Background: Although several studies have provided insights into the role of long non-coding RNAs (lncRNAs), the majority of them have unknown function. Recent evidence has shown the importance of both lncRNAs and chromatin interactions in transcriptional regulation. Although network-based methods, mainly exploiting gene-lncRNA co-expression, have been applied to characterize lncRNA of unknown function by means of 'guilt-by-association', no strategy exists so far which identifies mRNA-lncRNA functional modules based on the 3D chromatin interaction graph. Results: To better understand the function of chromatin interactions in the context of lncRNA-mediated gene regulation, we have developed a multi-step graph analysis approach to examine the RNA polymerase II ChIA-PET chromatin interaction network in the K562 human cell line. We have annotated the network with gene and lncRNA coordinates, and chromatin states from the ENCODE project. We used centrality measures, as well as an adaptation of our previously developed Markov State Models (MSM) clustering method, to gain a better understanding of lncRNAs in transcriptional regulation. The novelty of our approach resides in the detection of fuzzy regulatory modules based on network properties and their optimization based on co-expression analysis between genes and gene-lncRNA pairs. This results in our method returning more bona fide regulatory modules than other state-of-the art approaches for clustering on graphs. Conclusions: Interestingly, we find that lncRNA network hubs tend to be significantly enriched in evolutionary conserved lncRNAs and enhancer-like functions. We validated regulatory functions for well known lncRNAs, such as MALAT1 and the enhancer-like lncRNA FALEC. In addition, by investigating the modular structure of bigger components we mine putative regulatory functions for uncharacterized lncRNAs.}, language = {en} } @misc{OPUS4-6998, title = {Two Approximate Dynamic Programming Algorithms for Managing Complete SIS Networks}, editor = {COMPASS '18,}, publisher = {ACM New York, NY, USA}, isbn = {978-1-4503-5816-3}, doi = {10.1145/3209811.3209814}, year = {2018}, abstract = {Inspired by the problem of best managing the invasive mosquito Aedes albopictus across the 17 Torres Straits islands of Australia, we aim at solving a Markov decision process on large Susceptible-Infected-Susceptible (SIS) networks that are highly connected. While dynamic programming approaches can solve sequential decision-making problems on sparsely connected networks, these approaches are intractable for highly connected networks. Inspired by our case study, we focus on problems where the probability of nodes changing state is low and propose two approximate dynamic programming approaches. The first approach is a modified version of value iteration where only those future states that are similar to the current state are accounted for. The second approach models the state space as continuous instead of binary, with an on-line algorithm that takes advantage of Bellman's adapted equation. We evaluate the resulting policies through simulations and provide a priority order to manage the 17 infested Torres Strait islands. Both algorithms show promise, with the continuous state approach being able to scale up to high dimensionality (50 nodes). This work provides a successful example of how AI algorithms can be designed to tackle challenging computational sustainability problems.}, language = {en} } @misc{Mexi2021, type = {Master Thesis}, author = {Mexi, Gioni}, title = {New Ideas for the Feasibility Pump: Using Multiple Reference Vectors}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-83724}, year = {2021}, language = {en} } @misc{Kunt2023, type = {Master Thesis}, author = {Kunt, Tim}, title = {The n-Queens Problem in Higher Dimensions}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-96468}, pages = {84}, year = {2023}, abstract = {How many mutually non-attacking queens can be placed on a d-dimensional chessboard of size n? The n-queens problem in higher dimensions is a generalization of the well-known n-queens problem. We provide a comprehensive overview of theoretical results, bounds, solution methods, and the interconnectivity of the problem within topics of discrete optimization and combinatorics. We present an integer programming formulation of the n-queens problem in higher dimensions and several strengthenings through additional valid inequalities. Compared to recent benchmarks, we achieve a speedup in computational time between 15-70x over all instances of the integer programs. Our computational results prove optimality of certificates for several large instances. Breaking additional, previously unsolved instances with the proposed methods is likely possible. On the primal side, we further discuss heuristic approaches to constructing solutions that turn out to be optimal when compared to the IP. We conclude with preliminary results on the number and density of the solutions.}, language = {en} } @article{TawfikGendronLimbourg2021, author = {Tawfik, Christine and Gendron, Bernard and Limbourg, Sabine}, title = {An iterative two-stage heuristic algorithm for a bilevel service network design and pricing model}, journal = {European Journal of Operational Research}, publisher = {Elsevier}, address = {European Journal of Operational Research}, doi = {https://doi.org/10.1016/j.ejor.2021.07.052}, year = {2021}, abstract = {Building upon earlier research, we revisit a bilevel formulation of service design and pricing for freight networks, with the aim of investigating its algorithmic aspects. The model adds substantial computational challenges to the existing literature, as it deals with general integer network design variables. An iterative heuristic algorithm is introduced, based on the concepts of inverse optimization and neighbourhood search. The procedure alternates between two versions of restricted formulations of the model while inducing promising changes into the service assignments. The approach has proven a high performance for all of the considered real-world instances. Its efficiency rests on its ability to deliver results within a close proximity to those obtained by the exact solver in terms of quality, yet within a significantly smaller amount of time, and to land feasible solutions for the large-sized instances that could not be previously solved. In line with the sustainable transport goals, a deeper observation of the transport management side highlights the strategy of the algorithm favouring freight consolidation and achieving high load factors.}, language = {en} } @misc{Roessig2019, type = {Master Thesis}, author = {R{\"o}ssig, Ansgar}, title = {Verification of Neural Networks}, pages = {143}, year = {2019}, language = {en} } @inproceedings{PeronBartlettBeckeretal.2018, author = {P{\´e}ron, Martin and Bartlett, Peter L. and Becker, Kai-Helge and Helmstedt, Kate and Chad{\`e}s, Iadine}, title = {Two Approximate Dynamic Programming Algorithms for Managing Complete SIS Networks}, booktitle = {COMPASS '18 Proceedings of the 1st ACM SIGCAS Conference on Computing and Sustainable Societies}, publisher = {ACM}, doi = {10.1145/3209811.3209814}, year = {2018}, abstract = {Inspired by the problem of best managing the invasive mosquito Aedes albopictus across the 17 Torres Straits islands of Australia, we aim at solving a Markov decision process on large Susceptible-Infected-Susceptible (SIS) networks that are highly connected. While dynamic programming approaches can solve sequential decision-making problems on sparsely connected networks, these approaches are intractable for highly connected networks. Inspired by our case study, we focus on problems where the probability of nodes changing state is low and propose two approximate dynamic programming approaches. The first approach is a modified version of value iteration where only those future states that are similar to the current state are accounted for. The second approach models the state space as continuous instead of binary, with an on-line algorithm that takes advantage of Bellman's adapted equation. We evaluate the resulting policies through simulations and provide a priority order to manage the 17 infested Torres Strait islands. Both algorithms show promise, with the continuous state approach being able to scale up to high dimensionality (50 nodes). This work provides a successful example of how AI algorithms can be designed to tackle challenging computational sustainability problems.}, language = {en} } @inproceedings{DiakonikolasCardereraPokutta2019, author = {Diakonikolas, Jelena and Carderera, Alejandro and Pokutta, Sebastian}, title = {Breaking the Curse of Dimensionality (Locally) to Accelerate Conditional Gradients}, booktitle = {OPTML Workshop Paper}, arxiv = {http://arxiv.org/abs/1906.07867}, year = {2019}, language = {en} } @inproceedings{CombettesPokutta2019, author = {Combettes, Cyrille W. and Pokutta, Sebastian}, title = {Blended Matching Pursuit}, booktitle = {Proceedings of NeurIPS}, arxiv = {http://arxiv.org/abs/1904.12335}, year = {2019}, language = {en} } @inproceedings{PokuttaSinghTorrico2019, author = {Pokutta, Sebastian and Singh, M. and Torrico, A.}, title = {On the Unreasonable Effectiveness of the Greedy Algorithm: Greedy Adapts to Sharpness}, booktitle = {OPTML Workshop Paper}, year = {2019}, language = {en} } @incollection{KochRehfeldtShinano2020, author = {Koch, Thorsten and Rehfeldt, Daniel and Shinano, Yuji}, title = {An exact high performance solver for Steiner tree problems in graphs and related problems}, booktitle = {Modeling, Simulation and Optimization of Complex Processes HPSC 2018}, publisher = {Springer}, year = {2020}, language = {en} } @misc{OPUS4-5505, title = {Annual Report 2014}, volume = {2014}, organization = {Konrad-Zuse-Zentrum f{\"u}r Informationstechnik Berlin}, issn = {0934-5892}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-55050}, pages = {62}, year = {2015}, language = {en} } @incollection{BaumannLaubenderLaeuteretal.2015, author = {Baumann, Wolfgang and Laubender, Guido and L{\"a}uter, Matthias and Reinefeld, Alexander and Schimmel, Christian and Steinke, Thomas and Tuma, Christian and Wollny, Stefan}, title = {HLRN-III at Zuse Institute Berlin}, booktitle = {Contemporary High Performance Computing: From Petascale toward Exascale, Volume Two}, editor = {Vetter, Jeffrey S.}, publisher = {Chapman and Hall/CRC}, isbn = {9781498700627}, pages = {81 -- 114}, year = {2015}, language = {en} } @misc{TaentzerGolas2015, author = {Taentzer, Gabriele and Golas, Ulrike}, title = {Local Confluence Analysis for Amalgamated Graph Transformation: Long Version}, issn = {1438-0064}, doi = {10.1007/978-3-319-21145-9_5}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54943}, year = {2015}, abstract = {Amalgamated graph transformation allows to define schemes of rules coinciding in common core activities and differing over additional parallel independent activities. Consequently, a rule scheme is specified by a kernel rule and a set of extending multi-rules forming an interaction scheme. Amalgamated transformations have been increasingly used in various modeling contexts. Critical Pair Analysis (CPA) can be used to show local confluence of graph transformation systems. It is an open challenge to lift the CPA to amalgamated graph transformation systems, especially since infinite many pairs of amalgamated rules occur in general. As a first step towards an efficient local confluence analysis of amalgamated graph transformation systems, we show that the analysis of a finite set of critical pairs suffices to prove local confluence.}, language = {en} } @misc{Schaefer2015, author = {Sch{\"a}fer, Patrick}, title = {Bag-Of-SFA-Symbols in Vector Space (BOSS VS)}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54984}, year = {2015}, abstract = {Time series classification mimics the human understanding of similarity. When it comes to larger datasets, state of the art classifiers reach their limits in terms of unreasonable training or testing times. One representative example is the 1-nearest-neighbor DTW classifier (1-NN DTW) that is commonly used as the benchmark to compare to and has several shortcomings: it has a quadratic time and it degenerates in the presence of noise. To reduce the computational complexity lower bounding techniques or recently a nearest centroid classifier have been introduced. Still, execution times to classify moderately sized datasets on a single core are in the order of hours. We present our Bag-Of-SFA-Symbols in Vector Space (BOSS VS) classifier that is robust and accurate due to invariance to noise, phase shifts, offsets, amplitudes and occlusions. We show that it is as accurate while being multiple orders of magnitude faster than state of the art classifiers. Using the BOSS VS allows for mining massive time series datasets and real-time analytics.}, language = {en} } @inproceedings{TaentzerGolas2015, author = {Taentzer, Gabriele and Golas, Ulrike}, title = {Towards Local Confluence Analysis for Amalgamated Graph Transformation}, volume = {9151}, booktitle = {Graph Transformations. Proceedings of ICGT 2015}, editor = {Parisi-Presicce, F. and Westfechtel, B.}, publisher = {Springer}, doi = {10.1007/978-3-319-21145-9_5}, pages = {69 -- 86}, year = {2015}, abstract = {Amalgamated graph transformation allows to define schemes of rules coinciding in common core activities and differing over additional parallel independent activities. Consequently, a rule scheme is specified by a kernel rule and a set of extending multi-rules forming an interaction scheme. Amalgamated transformations have been increasingly used in various modeling contexts. Critical Pair Analysis (CPA) can be used to show local confluence of graph transformation systems. It is an open challenge to lift the CPA to amalgamated graph transformation systems, especially since infinite many pairs of amalgamated rules occur in general. As a first step towards an efficient local confluence analysis of amalgamated graph transformation systems, we show that the analysis of a finite set of critical pairs suffices to prove local confluence.}, language = {en} } @misc{Kulagina2014, type = {Master Thesis}, author = {Kulagina, Svetlana}, title = {Distributed Multi-Stage Time Series Similarity Search}, year = {2014}, language = {en} } @misc{CostaOstrovskyMantonetal.2015, author = {Costa, Marta and Ostrovsky, Aaron D. and Manton, James D. and Prohaska, Steffen and Jefferis, Gregory S.X.E.}, title = {NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases}, journal = {bioRxiv preprint}, doi = {10.1101/006346}, year = {2015}, language = {en} } @inproceedings{WendeSteinke2013, author = {Wende, Florian and Steinke, Thomas}, title = {Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU}, booktitle = {Proceeding SC '13 Proceedings of SC13: International Conference for High Performance Computing, Networking, Storage and Analysis Article No. 83 ACM New York, NY, USA, 2013}, doi = {http://dx.doi.org/10.1145/2503210.2503254}, year = {2013}, language = {en} } @article{Schaefer2014, author = {Sch{\"a}fer, Patrick}, title = {The BOSS is concerned with time series classification in the presence of noise}, volume = {29}, journal = {Data Mining and Knowledge Discovery}, number = {6}, publisher = {Springer}, doi = {10.1007/s10618-014-0377-7}, pages = {1505 -- 1530}, year = {2014}, language = {en} } @misc{OPUS4-5149, title = {Special issue of the Journal of Parallel and Distributed Computing (JDPC) on novel architectures for high-performance computing}, volume = {73}, journal = {Journal of Parallel and Distributed Computing}, number = {11}, editor = {McIntosh-Smith, Simon and Gillan, Charles and Sanna, Nico and Scott, Stan and Steinke, Thomas}, issn = {0743-7315}, doi = {10.1016/j.jpdc.2013.08.013}, pages = {1415 -- 1416}, year = {2013}, language = {en} } @misc{BenkridElArabyHuangetal.2012, author = {Benkrid, Khaled and El-Araby, Esam and Huang, Miaoqing and Sano, Kentaro and Steinke, Thomas}, title = {High-Performance Reconfigurable Computing - editorial for Special Issue of the International Journal of Reconfigurable Computing}, volume = {2012}, journal = {International Journal of Reconfigurable Computing}, doi = {10.1155/2012/104963}, pages = {1 -- 2}, year = {2012}, language = {en} } @article{TumaLainoMartinetal.2013, author = {Tuma, Christian and Laino, Teodoro and Martin, Elyette and Stolz, Steffen and Curioni, Alessandro}, title = {Modeling the Impact of Solid Surfaces in Thermal Degradation Processes}, volume = {14}, journal = {ChemPhysChem}, doi = {10.1002/cphc.201200921}, pages = {88 -- 91}, year = {2013}, language = {en} } @article{AboulhassanBaumWodoetal.2015, author = {Aboulhassan, Amal and Baum, Daniel and Wodo, Olga and Ganapathysubramanian, Baskar and Amassian, Aram and Hadwiger, Markus}, title = {A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials}, volume = {34}, journal = {Computer Graphics Forum}, number = {3}, publisher = {Wiley}, doi = {10.1111/cgf.12652}, pages = {401 -- 410}, year = {2015}, abstract = {The current characterization methods of the Bulk Heterojunction (BHJ) - the main material of the new Organic Photovoltaic solar cells - are limited to the analysis of global fabrication parameters. This reduces the efficiency of the BHJ design process, since it misses critical information about the local performance bottlenecks in the morphology of the material. In this paper, we propose a novel framework that fills this gap through visual charac- terization and exploration of local structure-performance correlations. We propose a new formula that correlates the structural features to the performance bottlenecks. Since research into BHJ materials is highly multidisci- plinary, we enable a visual feedback strategy that allows the scientists to build intuition about the best choices of fabrication parameters. We evaluate the usefulness of our proposed system by obtaining new BHJ characteri- zations. We furthermore show that our approach could reduce the previous work-flow time from days to minutes.}, language = {en} } @article{Schaefer2014, author = {Sch{\"a}fer, Patrick}, title = {Experiencing the Shotgun Distance for Time Series Analysis}, volume = {7}, journal = {Transactions on Machine Learning and Data Mining}, number = {1}, issn = {1864-9734}, pages = {3 -- 25}, year = {2014}, language = {en} } @misc{AboulhassanBaumWodoetal.2015, author = {Aboulhassan, Amal and Baum, Daniel and Wodo, Olga and Ganapathysubramanian, Baskar and Amassian, Aram and Hadwiger, Markus}, title = {A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-54353}, year = {2015}, abstract = {Current characterization methods of the so-called Bulk Heterojunction (BHJ), which is the main material of Organic Photovoltaic (OPV) solar cells, are limited to the analysis of global fabrication parameters. This reduces the efficiency of the BHJ design process, since it misses critical information about the local performance bottlenecks in the morphology of the material. In this paper, we propose a novel framework that fills this gap through visual characterization and exploration of local structure-performance correlations. We also propose a formula that correlates the structural features with the performance bottlenecks. Since research into BHJ materials is highly multidisciplinary, our framework enables a visual feedback strategy that allows scientists to build intuition about the best choices of fabrication parameters. We evaluate the usefulness of our proposed system by obtaining new BHJ characterizations. Furthermore, we show that our approach could substantially reduce the turnaround time.}, language = {en} } @misc{OPUS4-5284, title = {Annual Report 2013}, volume = {2013}, organization = {Konrad-Zuse-Zentrum f{\"u}r Informationstechnik Berlin}, issn = {0934-5892}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-52848}, pages = {124}, year = {2014}, language = {en} } @article{DierkesOrtmann2015, author = {Dierkes, Thomas and Ortmann, Karl Michael}, title = {On the efficient utilisation of duration}, volume = {60}, journal = {Insurance: Mathematics and Economics}, doi = {10.1016/j.insmatheco.2014.11.002}, pages = {29 -- 37}, year = {2015}, abstract = {In this article we present a new approach to estimate the change of the present value of a given cashflow pattern caused by an interest rate shift. Our approximation is based on analysing the evolution of the present value function through a linear differential equation. The outcome is far more accurate than the standard approach achieved by a Taylor expansion. Furthermore, we derive an approximation formula of second order that produces nearly accurate results. In particular, we prove that our method is superior to any known alternative approximation formula based on duration. In order to demonstrate the power of this improved approximation we apply it to coupon bonds, level annuities, and level perpetuities. We finally generalise the approach to a non-flat term structure. As for applications in insurance, we estimate the change of the discounted value of future liabilities due to a proportional shift in the set of capital accumulation factors. These findings are of particular importance to capital adequacy calculations with respect to interest rate stress scenarios that are part of regulatory solvency requirements.}, language = {en} } @inproceedings{Lange2017, author = {Lange, Alexander}, title = {A mathematical framework for predicting lifestyles of viral pathogens}, booktitle = {Modelling Biological Evolution 2017: Developing Novel Approaches}, year = {2017}, language = {en} } @article{KramerLaeuterRubinetal.2017, author = {Kramer, Tobias and L{\"a}uter, Matthias and Rubin, Martin and Altwegg, Kathrin}, title = {Seasonal changes of the volatile density in the coma and on the surface of comet 67P/Churyumov-Gerasimenko}, volume = {469}, journal = {Monthly Notices of the Royal Astronomical Society}, arxiv = {http://arxiv.org/abs/1704.03874}, doi = {10.1093/mnras/stx866}, pages = {S20 -- S28}, year = {2017}, abstract = {Starting from several monthly data sets of Rosetta's COmetary Pressure Sensor we reconstruct the gas density in the coma around comet 67P/Churyumov-Gerasimenko. The underlying inverse gas model is constructed by fitting ten thousands of measurements to thousands of potential gas sources distributed across the entire nucleus surface. The ensuing self-consistent solution for the entire coma density and surface activity reproduces the temporal and spatial variations seen in the data for monthly periods with Pearson correlation coefficients of 0.93 and higher. For different seasonal illumination conditions before and after perihelion we observe a systematic shift of gas sources on the nucleus.}, language = {en} } @misc{AboulhassanSicatBaumetal.2017, author = {Aboulhassan, Amal and Sicat, Ronell and Baum, Daniel and Wodo, Olga and Hadwiger, Markus}, title = {Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-63239}, year = {2017}, abstract = {The structure of Bulk-Heterojunction (BHJ) materials, the main component of organic photovoltaic solar cells, is very complex, and the relationship between structure and performance is still largely an open question. Overall, there is a wide spectrum of fabrication configurations resulting in different BHJ morphologies and correspondingly different performances. Current state- of-the-art methods for assessing the performance of BHJ morphologies are either based on global quantification of morphological features or simply on visual inspection of the morphology based on experimental imaging. This makes finding optimal BHJ structures very challenging. Moreover, finding the optimal fabrication parameters to get an optimal structure is still an open question. In this paper, we propose a visual analysis framework to help answer these questions through comparative visualization and parameter space exploration for local morphology features. With our approach, we enable scientists to explore multivariate correlations between local features and performance indicators of BHJ morphologies. Our framework is built on shape-based clustering of local cubical regions of the morphology that we call patches. This enables correlating the features of clusters with intuition-based performance indicators computed from geometrical and topological features of charge paths.}, language = {en} } @article{ZanderDreischarfTimmetal.2016, author = {Zander, Thomas and Dreischarf, Marcel and Timm, Anne-Katrin and Baumann, Wolfgang and Schmidt, Hendrik}, title = {Impact of material and morphological parameters on the mechanical response of the lumbar spine - A finite element sensitivity study}, volume = {53}, journal = {Journal of Biomechanics}, doi = {10.1016/j.jbiomech.2016.12.014}, pages = {185 -- 190}, year = {2016}, language = {en} } @article{RitterBelavyBaumannetal.2017, author = {Ritter, Zully and Belavy, Daniel and Baumann, Wolfgang and Felsenberg, Dieter}, title = {In vivo bone remodeling rates determination and compressive stiffness variations before, during 60 days bed rest and two years follow up: a micro-FE-analysis from HR-pQCT measurements of the Berlin bed rest study-2}, volume = {132}, journal = {Acta Astronautica}, doi = {10.1016/j.actaastro.2016.12.002}, pages = {67 -- 77}, year = {2017}, language = {en} } @article{LieSullivan2018, author = {Lie, Han Cheng and Sullivan, T. J.}, title = {Quasi-invariance of countable products of Cauchy measures under non-unitary dilations}, volume = {23}, journal = {Electronic Communications in Probability}, number = {8}, arxiv = {http://arxiv.org/abs/1611.10289}, doi = {10.1214/18-ECP113}, pages = {1 -- 6}, year = {2018}, language = {en} } @inproceedings{CoconuHege2017, author = {Coconu, Liviu and Hege, Hans-Christian}, title = {devEyes: Tangible Devices on Augmented Passive Surfaces}, booktitle = {TEI '17 Proceedings of the Eleventh International Conference on Tangible, Embedded, and Embodied Interaction, Yokohama, Japan, March 20 - 23, 2017}, doi = {10.1145/3024969.3025065}, pages = {409 -- 411}, year = {2017}, abstract = {We present a novel approach to turn smartphones/ tablets into tangible near-surface devices with augmented reality (AR) capability on virtually any passive surface, like desks, tables and wallboards. A low-cost optoelectronic add-on for the device back camera enables position tracking on an almost invisible printable fiducial marker grid. This approach is promising in terms of adoption potential because it can be used anywhere with existing devices, requires no dedicated hardware installations and is applicable to a broad range of real-world applications.}, language = {en} } @phdthesis{Conrad2004, author = {Conrad, Tim}, title = {Metabolic Pathways}, year = {2004}, language = {en} } @article{AboulhassanSicatBaumetal.2017, author = {Aboulhassan, Amal and Sicat, Ronell and Baum, Daniel and Wodo, Olga and Hadwiger, Markus}, title = {Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies}, volume = {36}, journal = {Computer Graphics Forum}, number = {3}, publisher = {Wiley}, doi = {10.1111/cgf.13191}, pages = {329 -- 339}, year = {2017}, abstract = {The structure of Bulk-Heterojunction (BHJ) materials, the main component of organic photovoltaic solar cells, is very complex, and the relationship between structure and performance is still largely an open question. Overall, there is a wide spectrum of fabrication configurations resulting in different BHJ morphologies and correspondingly different performances. Current state- of-the-art methods for assessing the performance of BHJ morphologies are either based on global quantification of morphological features or simply on visual inspection of the morphology based on experimental imaging. This makes finding optimal BHJ structures very challenging. Moreover, finding the optimal fabrication parameters to get an optimal structure is still an open question. In this paper, we propose a visual analysis framework to help answer these questions through comparative visualization and parameter space exploration for local morphology features. With our approach, we enable scientists to explore multivariate correlations between local features and performance indicators of BHJ morphologies. Our framework is built on shape-based clustering of local cubical regions of the morphology that we call patches. This enables correlating the features of clusters with intuition-based performance indicators computed from geometrical and topological features of charge paths.}, language = {en} } @article{GelssMateraSchuette2016, author = {Gelß, Patrick and Matera, Sebastian and Sch{\"u}tte, Christof}, title = {Solving the master equation without kinetic Monte Carlo: Tensor train approximations for a CO oxidation model}, volume = {314}, journal = {Journal of Computational Physics}, doi = {10.1016/j.jcp.2016.03.025}, pages = {489 -- 502}, year = {2016}, abstract = {In multiscale modeling of heterogeneous catalytic processes, one crucial point is the solution of a Markovian master equation describing the stochastic reaction kinetics. Usually, this is too high-dimensional to be solved with standard numerical techniques and one has to rely on sampling approaches based on the kinetic Monte Carlo method. In this study we break the curse of dimensionality for the direct solution of the Markovian master equation by exploiting the Tensor Train Format for this purpose. The performance of the approach is demonstrated on a first principles based, reduced model for the CO oxidation on the RuO2(110) surface. We investigate the complexity for increasing system size and for various reaction conditions. The advantage over the stochastic simulation approach is illustrated by a problem with increased}, language = {en} } @article{OrgisLaeuterHandorfetal.2017, author = {Orgis, Thomas and L{\"a}uter, Matthias and Handorf, D{\"o}rthe and Dethloff, Klaus}, title = {Baroclinic waves on the β plane using low-order Discontinuous Galerkin discretisation}, volume = {339}, journal = {Journal of Computational Physics}, doi = {10.1016/j.jcp.2017.03.029}, pages = {461 -- 481}, year = {2017}, abstract = {A classic Discontinuous Galerkin Method with low-order polynomials and explicit as well as semi-implicit time-stepping is applied to an atmospheric model employing the Euler equations on the β plane. The method, which was initially proposed without regard for the source terms and their balance with the pressure gradient that dominates atmospheric dynamics, needs to be adapted to be able to keep the combined geostrophic and hydrostatic balance in three spatial dimensions. This is achieved inside the discretisation through a polynomial mapping of both source and flux terms without imposing filters between time steps. After introduction and verification of this balancing, the realistic development of barotropic and baroclinic waves in the model is demonstrated, including the formation of a retrograde Rossby wave pattern. A prerequesite is the numerical solution of the thermal wind equation to construct geostrophically balanced initial states in z coordinates with arbitrary prescribed zonal wind profile, offering a new set of test cases for atmospheric models employing z coordinates. The resulting simulations demonstrate that the balanced low-order Discontinous Galerkin discretisation with polynomial degrees down to k=1 can be a viable option for atmospheric modelling.}, language = {en} } @misc{OPUS4-6433, title = {Annual Report 2016}, volume = {2016}, organization = {Konrad-Zuse-Zentrum f{\"u}r Informationstechnik Berlin}, issn = {0934-5892}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-64339}, pages = {122}, year = {2017}, language = {en} } @misc{RohrHerrmannIlmetal.2017, author = {Rohr, Ulrich-Peter and Herrmann, Pia and Ilm, Katharina and Zhang, Hai and Lohmann, Sabine and Reiser, Astrid and Muranyi, Andrea and Smith, Janice and Burock, Susen and Osterland, Marc and Leith, Katherine and Singh, Shalini and Brunhoeber, Patrick and Bowermaster, Rebecca and Tie, Jeanne and Christie, Michael and Wong, Hui-Li and Waring, Paul and Shanmugam, Kandavel and Gibbs, Peter and Stein, Ulrike}, title = {Prognostic value of MACC1 and proficient mismatch repair status for recurrence risk prediction in stage II colon cancer patients: the BIOGRID studies}, issn = {1438-0064}, doi = {10.1093/annonc/mdx207}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-64184}, year = {2017}, abstract = {Background We assessed the novel MACC1 gene to further stratify stage II colon cancer patients with proficient mismatch repair (pMMR). Patients and methods Four cohorts with 596 patients were analyzed: Charit{\´e} 1 discovery cohort was assayed for MACC1 mRNA expression and MMR in cryo-preserved tumors. Charit{\´e} 2 comparison cohort was used to translate MACC1 qRT- PCR analyses to FFPE samples. In the BIOGRID 1 training cohort MACC1 mRNA levels were related to MACC1 protein levels from immunohistochemistry in FFPE sections; also analyzed for MMR. Chemotherapy-na{\"i}ve pMMR patients were stratified by MACC1 mRNA and protein expression to establish risk groups based on recurrence-free survival (RFS). Risk stratification from BIOGRID 1 was confirmed in the BIOGRID 2 validation cohort. Pooled BIOGRID datasets produced a best effect-size estimate. Results In BIOGRID 1, using qRT-PCR and immunohistochemistry for MACC1 detection, pMMR/MACC1-low patients had a lower recurrence probability versus pMMR/MACC1-high patients (5-year RFS of 92\% and 67\% versus 100\% and 68\%, respectively). In BIOGRID 2, longer RFS was confirmed for pMMR/MACC1-low versus pMMR/MACC1-high patients (5-year RFS of 100\% versus 90\%, respectively). In the pooled dataset, 6.5\% of patients were pMMR/MACC1-low with no disease recurrence, resulting in a 17\% higher 5-year RFS (95\% CI (12.6-21.3\%)) versus pMMR/MACC1-high patients (P=0.037). Outcomes were similar for pMMR/MACC1-low and deficient MMR (dMMR) patients (5-year RFS of 100\% and 96\%, respectively). Conclusions MACC1 expression stratifies colon cancer patients with unfavorable pMMR status. Stage II colon cancer patients with pMMR/MACC1-low tumors have a similar favorable prognosis to those with dMMR with potential implications for the role of adjuvant therapy.}, language = {en} } @article{RohrHerrmannIlmetal.2017, author = {Rohr, Ulrich-Peter and Herrmann, Pia and Ilm, Katharina and Zhang, Hai and Lohmann, Sabine and Reiser, Astrid and Muranyi, Andrea and Smith, Janice and Burock, Susen and Osterland, Marc and Leith, Katherine and Singh, Shalini and Brunhoeber, Patrick and Bowermaster, Rebecca and Tie, Jeanne and Christie, Michael and Wong, Hui-Li and Waring, Paul and Shanmugam, Kandavel and Gibbs, Peter and Stein, Ulrike}, title = {Prognostic value of MACC1 and proficient mismatch repair status for recurrence risk prediction in stage II colon cancer patients: the BIOGRID studies}, volume = {28}, journal = {Annals of Oncology}, number = {8}, doi = {10.1093/annonc/mdx207}, pages = {1869 -- 1875}, year = {2017}, abstract = {Background We assessed the novel MACC1 gene to further stratify stage II colon cancer patients with proficient mismatch repair (pMMR). Patients and methods Four cohorts with 596 patients were analyzed: Charit{\´e} 1 discovery cohort was assayed for MACC1 mRNA expression and MMR in cryo-preserved tumors. Charit{\´e} 2 comparison cohort was used to translate MACC1 qRT-PCR analyses to FFPE samples. In the BIOGRID 1 training cohort MACC1 mRNA levels were related to MACC1 protein levels from immunohistochemistry in FFPE sections; also analyzed for MMR. Chemotherapy-na{\"i}ve pMMR patients were stratified by MACC1 mRNA and protein expression to establish risk groups based on recurrence-free survival (RFS). Risk stratification from BIOGRID 1 was confirmed in the BIOGRID 2 validation cohort. Pooled BIOGRID datasets produced a best effect-size estimate. Results In BIOGRID 1, using qRT-PCR and immunohistochemistry for MACC1 detection, pMMR/MACC1-low patients had a lower recurrence probability versus pMMR/MACC1-high patients (5-year RFS of 92\% and 67\% versus 100\% and 68\%, respectively). In BIOGRID 2, longer RFS was confirmed for pMMR/MACC1-low versus pMMR/MACC1-high patients (5-year RFS of 100\% versus 90\%, respectively). In the pooled dataset, 6.5\% of patients were pMMR/MACC1-low with no disease recurrence, resulting in a 17\% higher 5-year RFS (95\% CI (12.6-21.3\%)) versus pMMR/MACC1-high patients (P=0.037). Outcomes were similar for pMMR/MACC1-low and deficient MMR (dMMR) patients (5-year RFS of 100\% and 96\%, respectively). Conclusions MACC1 expression stratifies colon cancer patients with unfavorable pMMR status. Stage II colon cancer patients with pMMR/MACC1-low tumors have a similar favorable prognosis to those with dMMR with potential implications for the role of adjuvant therapy.}, language = {en} } @phdthesis{Agarwal2016, author = {Agarwal, Animesh}, title = {Path Integral Techniques in Molecular Dynamics Simulations of Open Boundary Systems}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:188-fudissthesis000000103020-4}, year = {2016}, language = {en} } @phdthesis{Badowski2016, author = {Badowski, Tomasz}, title = {Adaptive importance sampling via minimization of estimators of cross-entropy, mean square and inefficiency constants}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:188-fudissthesis000000102823-3}, year = {2016}, language = {en} } @phdthesis{Daragmeh2016, author = {Daragmeh, Adman}, title = {Model Order Reduction of Linear Control Systems: Comparison of Balance Truncation and Singular Perturbation Approximation with Application to Optimal Control}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:188-fudissthesis000000102586-2}, year = {2016}, language = {en} } @phdthesis{Gul2016, author = {Gul, Raheem}, title = {Mathematical Modeling and Sensitivity Analysis of Lumped­ Parameter Model of the Human Cardiovascular System}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:188-fudissthesis000000101271-2}, year = {2016}, language = {en} } @phdthesis{Lie2016, author = {Lie, Han Cheng}, title = {On a strongly convex approximation of a stochastic optimal control problem for importance sampling of metastable diffusions}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:188-fudissthesis000000101680-4}, year = {2016}, language = {en} } @phdthesis{Sriwattanaworachai2016, author = {Sriwattanaworachai, Nisara}, title = {Spectral approach to metastability of non-reversible complex processes}, year = {2016}, language = {en} } @phdthesis{Vega2016, author = {Vega, Iliusi}, title = {Reconstruction and analysis of the state space for the identification of dynamical states in real-world time-series}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:188-fudissthesis000000104520-1}, year = {2016}, language = {en} } @misc{KoltaiSchuette2017, author = {Koltai, P{\´e}ter and Sch{\"u}tte, Christof}, title = {A multi scale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-64868}, year = {2017}, abstract = {We investigate metastable dynamical systems subject to non-stationary forcing as they appear in molecular dynamics for systems driven by external fields. We show, that if the strength of the forcing is inversely proportional to the length of the slow metastable time scales of the unforced system, then the effective behavior of the forced system on slow time scales can be described by a low-dimensional reduced master equation. Our construction is explicit and uses the multiscale perturbation expansion method called two-timing, or method of multiple scales. The reduced master equation—a Markov state model—can be assembled by constructing two equilibrium Markov state models; one for the unforced system, and one for a slightly perturbed one.}, language = {en} } @misc{WolfAmadi2017, author = {Wolf, Thomas and Amadi, Chimaobi}, title = {Rational Solutions of Underdetermined Polynomial Equations}, issn = {1438-0064}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-64488}, year = {2017}, abstract = {In this paper we report on an application of computer algebra in which mathematical puzzles are generated of a type that had been widely used in mathematics contests by a large number of participants worldwide. The algorithmic aspect of our work provides a method to compute rational solutions of single polynomial equations that are typically large with 10^2 ... 10^5 terms and that are heavily underdetermined. It was possible to obtain this functionality by adding a number of new modules for a new type of splitting of equations to the existing package CRACK that is normally used to solve polynomial algebraic and differential systems of equations.}, language = {en} }