TY - CHAP A1 - Schintke, Florian A1 - Simon, Jens A1 - Reinefeld, Alexander T1 - A Cache Simulator for Shared Memory Systems T2 - Computational Science - ICCS 2001 Y1 - 2001 U6 - https://doi.org/10.1007/3-540-45718-6_62 VL - 2074 SP - 569 EP - 578 ER - TY - GEN A1 - Clausecker, Robert T1 - The Quality of Heuristic Functions for IDA* N2 - 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. T3 - ZIB-Report - 20-17 KW - IDA* heuristic search sampling random walks Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-78489 SN - 1438-0064 ER - TY - JOUR A1 - Gorgulla, Christoph A1 - Das, Krishna M. Padmanabha A1 - Leigh, Kendra E A1 - Cespugli, Marco A1 - Fischer, Patrick D. A1 - Wang, Zi-Fu A1 - Tesseyre, Guilhem A1 - Pandita, Shreya A1 - Shnapir, Alex A1 - Calderaio, Anthony A1 - Hutcheson, Colin A1 - Gechev, Minko A1 - Rose, Alexander A1 - Lewis, Noam A1 - Yaffe, Erez A1 - Luxenburg, Roni A1 - Herce, Henry D. A1 - Durmaz, Vedat A1 - Halazonetis, Thanos D. A1 - Fackeldey, Konstantin A1 - Patten, Justin J. A1 - Chuprina, Alexander A1 - Dziuba, Igor A1 - Plekhova, Alla A1 - Moroz, Yurii A1 - Radchenko, Dmytro A1 - Tarkhanova, Olga A1 - Yavnyuk, Irina A1 - Gruber, Christian C. A1 - Yust, Ryan A1 - Payne, Dave A1 - Näär, Anders M. A1 - Namchuk, Mark N. A1 - Davey, Robert A. A1 - Wagner, Gerhard A1 - Kinney, Jamie A1 - Arthanari, Haribabu T1 - A Multi-Pronged Approach Targeting SARS-CoV-2 Proteins Using Ultra-Large Virtual Screening JF - iScience N2 - 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. Y1 - 2021 U6 - https://doi.org/10.26434/chemrxiv.12682316 VL - 24 IS - 2 SP - 102021 PB - CellPress ER - TY - JOUR A1 - Bonnet, Luc A1 - Akian, Jean-Luc A1 - Savin, Éric A1 - Sullivan, T. J. T1 - Adaptive reconstruction of imperfectly-observed monotone functions, with applications to uncertainty quantification JF - Algorithms N2 - 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. Y1 - 2020 U6 - https://doi.org/10.3390/a13080196 VL - 13 IS - 8 SP - 196 ER - TY - CHAP A1 - Hartung, Marc T1 - CTSat: C++ Template Abstractions for Dynamic Interchangeable SAT Solver Features T2 - Proceedings of SAT Competition 2020: Solver and Benchmark Descriptions Y1 - 2020 UR - http://hdl.handle.net/10138/318450 SP - 32 EP - 33 ER - TY - CHAP A1 - Kaiser, Benjamin A1 - Hartung, Marc T1 - PauSat T2 - Proceedings of SAT Competition 2020: Solver and Benchmark Descriptions Y1 - 2020 UR - http://hdl.handle.net/10138/318450 SP - 34 EP - 35 ER - TY - CHAP A1 - Hartung, Marc A1 - Kaiser, Benjamin T1 - Crafted Benchmarks with Artificial Community Structure and Known Complexity T2 - Proceedings of SAT Competition 2020: Solver and Benchmark Descriptions Y1 - 2020 UR - http://hdl.handle.net/10138/318450 SP - 89 EP - 90 ER - TY - CHAP A1 - Bärring, Olof A1 - Lopez, Maite Barroso A1 - Cancio, German A1 - Röblitz, Thomas A1 - Schintke, Florian A1 - et al., T1 - Towards automation of computing fabrics using tools from the fabric management workpackage of the EU DataGrid project T2 - Computing in High Energy and Nuclear Physics (CHEP03) Y1 - 2003 SP - 1 EP - 8 ER - TY - JOUR A1 - Straube, Arthur A1 - Kowalik, Bartosz G. A1 - Netz, Roland R. A1 - Höfling, Felix T1 - Rapid onset of molecular friction in liquids bridging between the atomistic and hydrodynamic pictures JF - Commun. Phys. N2 - 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. Y1 - 2020 U6 - https://doi.org/10.1038/s42005-020-0389-0 VL - 3 SP - 126 PB - Nature ER - TY - JOUR A1 - Fackeldey, Konstantin A1 - Oster, Mathias A1 - Sallandt, Leon A1 - Schneider, Reinhold T1 - Approximative Policy Iteration for Exit Time Feedback Control Problems driven by Stochastic Differential Equations using Tensor Train format JF - SIAM Journal on Multiscale Modeling and Simulation N2 - 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. Y1 - 2022 U6 - https://doi.org/10.1137/20M1372500 VL - 20 IS - 1 SP - 379 EP - 403 ER - TY - JOUR A1 - Soares, Ana Prates A1 - Baum, Daniel A1 - Hesse, Bernhard A1 - Kupsch, Andreas A1 - Müller, Bernd A1 - Zaslansky, Paul T1 - Scattering and phase-contrast X-ray methods reveal damage to glass fibers in endodontic posts following dental bur trimming JF - Dental Materials Y1 - 2020 U6 - https://doi.org/10.1016/j.dental.2020.10.018 VL - 37 IS - 2 SP - 201 EP - 211 ER - TY - JOUR A1 - Rath, Barbara A1 - Conrad, Tim A1 - Myles, Puja A1 - Alchikh, Maren A1 - Ma, Xiaolin A1 - Hoppe, Christian A1 - Tief, Franziska A1 - Chen, Xi A1 - Obermeier, Patrick A1 - Kisler, Bron A1 - Schweiger, Brunhilde T1 - Influenza and other respiratory viruses: standardizing disease severity in surveillance and clinical trials JF - Expert Review of Anti-infective Therapy N2 - 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. KW - Disease severity KW - influenza-like illness KW - influenza KW - respiratory syncytial virus KW - human metapneumovirus KW - human rhinovirus KW - adenovirus KW - seasonality KW - antivirals KW - clinical trials Y1 - 2017 U6 - https://doi.org/10.1080/14787210.2017.1295847 VL - 15 IS - 6 SP - 545 EP - 568 ER - TY - JOUR A1 - Shao, Borong A1 - Cannistraci, Carlo Vittorio A1 - Conrad, Tim T1 - Epithelial Mesenchymal Transition Network-Based Feature Engineering in Lung Adenocarcinoma Prognosis Prediction Using Multiple Omic Data JF - Genomics and Computational Biology N2 - 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. Y1 - 2017 U6 - https://doi.org/10.18547/gcb.2017.vol3.iss3.e57 VL - 3 IS - 3 SP - e57 ER - TY - JOUR A1 - Jayrannejad, Fahrnaz A1 - Conrad, Tim T1 - Better Interpretable Models for Proteomics Data Analysis Using rule-based Mining JF - Springer Lecture Notes in Artificial Intelligence N2 - 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. Y1 - 2017 ER - TY - JOUR A1 - Marzban, Forough A1 - Conrad, Tim A1 - Marban, Pouria A1 - Sodoudi, Sahar T1 - Estimation of the Near-Surface Air Temperature during the Day and Nighttime from MODIS in Berlin, Germany JF - International Journal of Advanced Remote Sensing and GIS N2 - 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. KW - ANFIS KW - ANN KW - Cross-validation KW - MODIS KW - Simulated annealing KW - SVR Y1 - 2018 U6 - https://doi.org/10.23953/cloud.ijarsg.337 VL - 7 IS - 1 SP - 2478 EP - 2517 ER - TY - JOUR A1 - Kork, F. A1 - Conrad, Tim A1 - Weiss, B. A1 - Roenneberg, T. A1 - Wernecke, K.-D. A1 - Balzer, Felix T1 - Associations of postoperative mortality with the time of day, week and year JF - Anaesthesia Y1 - 2018 SN - 0959-2962 VL - 73 IS - 6 SP - 711 EP - 718 ER - TY - CHAP A1 - Sullivan, T. J. T1 - Well-posedness of Bayesian inverse problems in quasi-Banach spaces with stable priors T2 - 88th Annual Meeting of the International Association of Applied Mathematics and Mechanics (GAMM), Weimar 2017 Y1 - 2017 U6 - https://doi.org/10.1002/pamm.201710402 VL - 17 IS - 1 SP - 871 EP - 874 ER - TY - JOUR A1 - Sullivan, T. J. T1 - Well-posed Bayesian inverse problems and heavy-tailed stable quasi-Banach space priors JF - Inverse Problems and Imaging Y1 - 2017 U6 - https://doi.org/10.3934/ipi.2017040 VL - 11 IS - 5 SP - 857 EP - 874 ER - TY - JOUR A1 - Schmidtke, Robert A1 - Erleben, Kenny T1 - Chunked Bounding Volume Hierarchies for Fast Digital Prototyping using Volumetric Meshes JF - IEEE Transactions on Visualization and Computer Graphics N2 - 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. Y1 - 2018 U6 - https://doi.org/10.1109/TVCG.2017.2784441 SN - 1941-0506 VL - 24 IS - 12 SP - 3044 EP - 3057 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. A1 - Stuart, Andrew T1 - Strong convergence rates of probabilistic integrators for ordinary differential equations JF - Statistics and Computing N2 - 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. Y1 - 2019 U6 - https://doi.org/10.1007/s11222-019-09898-6 VL - 29 IS - 6 SP - 1265 EP - 1283 ER - TY - CHAP A1 - Cockayne, Jon A1 - Oates, Chris A1 - Sullivan, T. J. A1 - Girolami, Mark T1 - Probabilistic Numerical Methods for PDE-constrained Bayesian Inverse Problems T2 - Proceedings of the 36th International Workshop on Bayesian Inference and Maximum Entropy Methods in Science and Engineering N2 - 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 Y1 - 2017 U6 - https://doi.org/10.1063/1.4985359 VL - 1853 SP - 060001-1 EP - 060001-8 ER - TY - JOUR A1 - Schäfer, Florian A1 - Sullivan, T. J. A1 - Owhadi, Houman T1 - Compression, inversion, and approximate PCA of dense kernel matrices at near-linear computational complexity JF - Multiscale Modeling and Simulation Y1 - 2021 U6 - https://doi.org/10.1137/19M129526X VL - 19 IS - 2 SP - 688 EP - 730 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Equivalence of weak and strong modes of measures on topological vector spaces JF - Inverse Problems N2 - 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. Y1 - 2018 U6 - https://doi.org/10.1088/1361-6420/aadef2 VL - 34 IS - 11 SP - 115013 ER - TY - CHAP A1 - Schuster, Ingmar A1 - Strathmann, Heiko A1 - Paige, Brooks A1 - Sejdinovic, Dino T1 - Kernel Sequential Monte Carlo T2 - Joint European Conference on Machine Learning and Knowledge Discovery in Databases N2 - 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. Y1 - 2017 U6 - https://doi.org/10.1007/978-3-319-71249-9_24 SP - 390 EP - 409 ER - TY - JOUR A1 - Klus, Stefan A1 - Schuster, Ingmar A1 - Muandet, Krikamol T1 - Eigendecompositions of Transfer Operators in Reproducing Kernel Hilbert Spaces JF - Journal of Machine Learning Research N2 - 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. Y1 - 2017 ER - TY - THES A1 - Clausecker, Robert T1 - Notes on the Construction of Tablebases Y1 - 2017 ER - TY - JOUR A1 - Sullivan, T. J. T1 - Contributed discussion on the article "A Bayesian conjugate gradient method" JF - Bayesian Analysis N2 - 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. Y1 - 2019 U6 - https://doi.org/10.1214/19-BA1145 VL - 14 IS - 3 SP - 985 EP - 989 ER - TY - CHAP A1 - Fröhler, Bernhard A1 - da Cunha Melo, Lucas A1 - Weissenböck, Johannes A1 - Kastner, Johann A1 - Möller, Torsten A1 - Hege, Hans-Christian A1 - Gröller, Eduard M. A1 - Sanctorum, Jonathan A1 - De Beenhouwer, Jan A1 - Sijbers, Jan A1 - Heinzl, Christoph T1 - Tools for the analysis of datasets from X-ray computed tomography based on Talbot-Lau grating interferometry T2 - Proceedings of iCT 2019, (9th Conference on Industrial Computed Tomography, Padova, Italy – iCT 2019, February 13-15, 2019) N2 - 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. Y1 - 2019 N1 - PDF | open access: https://www.ndt.net/article/ctc2019/papers/iCT2019_Full_paper_52.pdf IS - paper 52 ER - TY - JOUR A1 - Goubergrits, Leonid A1 - Hellmeier, Florian A1 - Bruening, Jan Joris A1 - Spuler, Andreas A1 - Hege, Hans-Christian A1 - Voss, Samuel A1 - Janiga, Gábor A1 - Saalfeld, Sylvia A1 - Beuing, Oliver A1 - Berg, Philipp T1 - Multiple Aneurysms AnaTomy CHallenge 2018 (MATCH): Uncertainty Quantification of Geometric Rupture Risk Parameters JF - BioMedical Engineering OnLine N2 - 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. Y1 - 2019 U6 - https://doi.org/10.1186/s12938-019-0657-y VL - 18 IS - 35 ER - TY - JOUR A1 - Fröhler, Bernhard A1 - Elberfeld, Tim A1 - Möller, Torsten A1 - Hege, Hans-Christian A1 - Weissenböck, Johannes A1 - De Beenhouwer, Jan A1 - Sijbers, Jan A1 - Kastner, Johann A1 - Heinzl, Christoph T1 - A Visual Tool for the Analysis of Algorithms for Tomographic Fiber Reconstruction in Materials Science JF - Computer Graphics Forum N2 - 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. Y1 - 2019 U6 - https://doi.org/10.1111/cgf.13688 VL - 38 IS - 3 SP - 273 EP - 283 ER - TY - GEN A1 - Baum, Daniel A1 - Giliard, Nicole A1 - Hasler, Tim A1 - Peters-Kottig, Wolfgang T1 - Leitlinien zum Umgang mit Forschungsdaten am Zuse-Institut Berlin N2 - Die nachhaltige Sicherung und Bereitstellung von Forschungsdaten dienen nicht nur der Reproduzierbarkeit früherer Ergebnisse, sondern in hohem Maße auch der Erzielung künftiger Ergebnisse mit dem Ziel, die Qualität, Produktivität und Wettbewerbsfähigkeit der Wissenschaft zu fördern. Die folgenden Grundsätze gelten als Leitlinien zur Handhabung von Forschungsdaten im ZIB. Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-73781 CY - Berlin ER - TY - JOUR A1 - Thiel, Denise A1 - Djurdjevac Conrad, Natasa A1 - Ntini, Evgenia A1 - Peschutter, Ria A1 - Siebert, Heike A1 - Marsico, Annalisa T1 - Identifying lncRNA-mediated regulatory modules via ChIA-PET network analysis JF - BMC Bioinformatics N2 - 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. Y1 - 2019 U6 - https://doi.org/10.1186/s12859-019-2900-8 VL - 20 IS - 1471-2105 ER - TY - GEN ED - COMPASS '18, T1 - Two Approximate Dynamic Programming Algorithms for Managing Complete SIS Networks N2 - 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. Y1 - 2018 SN - 978-1-4503-5816-3 U6 - https://doi.org/10.1145/3209811.3209814 PB - ACM New York, NY, USA ER - TY - THES A1 - Mexi, Gioni T1 - New Ideas for the Feasibility Pump: Using Multiple Reference Vectors Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-83724 ER - TY - THES A1 - Kunt, Tim T1 - The n-Queens Problem in Higher Dimensions N2 - 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. T3 - ZIB-Report - 24-05 KW - Integer Programming KW - Maximum Independent Set KW - n-Queens Y1 - 2023 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-96468 ER - TY - JOUR A1 - Tawfik, Christine A1 - Gendron, Bernard A1 - Limbourg, Sabine T1 - An iterative two-stage heuristic algorithm for a bilevel service network design and pricing model JF - European Journal of Operational Research N2 - 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. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1016/j.ejor.2021.07.052 PB - Elsevier CY - European Journal of Operational Research ER - TY - THES A1 - Rössig, Ansgar T1 - Verification of Neural Networks KW - Neural Network Verification Y1 - 2019 ER - TY - CHAP A1 - Péron, Martin A1 - Bartlett, Peter L. A1 - Becker, Kai-Helge A1 - Helmstedt, Kate A1 - Chadès, Iadine T1 - Two Approximate Dynamic Programming Algorithms for Managing Complete SIS Networks T2 - COMPASS '18 Proceedings of the 1st ACM SIGCAS Conference on Computing and Sustainable Societies N2 - 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. Y1 - 2018 U6 - https://doi.org/10.1145/3209811.3209814 PB - ACM ER - TY - CHAP A1 - Diakonikolas, Jelena A1 - Carderera, Alejandro A1 - Pokutta, Sebastian T1 - Breaking the Curse of Dimensionality (Locally) to Accelerate Conditional Gradients T2 - OPTML Workshop Paper Y1 - 2019 N1 - URL of the Code: https://colab.research.google.com/drive/1ejjfCan7xnEhWWJXCIzb03CwQRG9iW_O N1 - URL of the PDF: https://opt-ml.org/papers/2019/paper_26.pdf N1 - URL of the Poster: https://app.box.com/s/d7p038u7df422q4jsccbmj15mngqv2ws N1 - URL of the Slides: https://app.box.com/s/gphkhapso7d1vrfnzqykkb3vx0agxh8w N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2019/07/04/LaCG-abstract.html ER - TY - CHAP A1 - Combettes, Cyrille W. A1 - Pokutta, Sebastian T1 - Blended Matching Pursuit T2 - Proceedings of NeurIPS Y1 - 2019 N1 - URL of the Code: https://colab.research.google.com/drive/17XYIxnCcJjKswba9mAaXFWnNGVZdsaXQ N1 - URL of the PDF: https://papers.nips.cc/paper/8478-blended-matching-pursuit N1 - URL of the Poster: https://app.box.com/s/j6lbh49udjd45krhxcypufxwdofw6br8 N1 - URL of the Slides: https://app.box.com/s/8lfktq6h3dqp9t2gqydu2tp8h2uxgz7m N1 - URL of the Abstract: http://www.pokutta.com/blog/research/2019/05/27/bmp-abstract.html ER - TY - CHAP A1 - Pokutta, Sebastian A1 - Singh, M. A1 - Torrico, A. T1 - On the Unreasonable Effectiveness of the Greedy Algorithm: Greedy Adapts to Sharpness T2 - OPTML Workshop Paper Y1 - 2019 N1 - URL of the PDF: https://opt-ml.org/papers/2019/paper_16.pdf N1 - URL of the Poster: https://app.box.com/s/24vbh1s2vib11upqyepzen3lzdl13skr ER - TY - CHAP A1 - Koch, Thorsten A1 - Rehfeldt, Daniel A1 - Shinano, Yuji T1 - An exact high performance solver for Steiner tree problems in graphs and related problems T2 - Modeling, Simulation and Optimization of Complex Processes HPSC 2018 Y1 - 2020 PB - Springer ER - TY - GEN T1 - Annual Report 2014 T3 - Jahresbericht - 2014 KW - Jahresbericht Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-55050 SN - 0934-5892 VL - 2014 ER - TY - CHAP A1 - Baumann, Wolfgang A1 - Laubender, Guido A1 - Läuter, Matthias A1 - Reinefeld, Alexander A1 - Schimmel, Christian A1 - Steinke, Thomas A1 - Tuma, Christian A1 - Wollny, Stefan ED - Vetter, Jeffrey S. T1 - HLRN-III at Zuse Institute Berlin T2 - Contemporary High Performance Computing: From Petascale toward Exascale, Volume Two Y1 - 2015 UR - http://www.crcpress.com/product/isbn/9781498700627 SN - 9781498700627 SP - 81 EP - 114 PB - Chapman and Hall/CRC ER - TY - GEN A1 - Taentzer, Gabriele A1 - Golas, Ulrike T1 - Local Confluence Analysis for Amalgamated Graph Transformation: Long Version N2 - 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. T3 - ZIB-Report - 15-29 KW - amalgamated graph transformation KW - parallel independence KW - critical pair analysis Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54943 SN - 1438-0064 ER - TY - GEN A1 - Schäfer, Patrick T1 - Bag-Of-SFA-Symbols in Vector Space (BOSS VS) N2 - 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. T3 - ZIB-Report - 15-30 KW - Time Series KW - Classification KW - Data Mining Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54984 SN - 1438-0064 ER - TY - CHAP A1 - Taentzer, Gabriele A1 - Golas, Ulrike ED - Parisi-Presicce, F. ED - Westfechtel, B. T1 - Towards Local Confluence Analysis for Amalgamated Graph Transformation T2 - Graph Transformations. Proceedings of ICGT 2015 N2 - 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. Y1 - 2015 U6 - https://doi.org/10.1007/978-3-319-21145-9_5 VL - 9151 SP - 69 EP - 86 PB - Springer ER - TY - THES A1 - Kulagina, Svetlana T1 - Distributed Multi-Stage Time Series Similarity Search Y1 - 2014 ER - TY - GEN A1 - Costa, Marta A1 - Ostrovsky, Aaron D. A1 - Manton, James D. A1 - Prohaska, Steffen A1 - Jefferis, Gregory S.X.E. T1 - NBLAST: Rapid, sensitive comparison of neuronal structure and construction of neuron family databases T2 - bioRxiv preprint Y1 - 2015 U6 - https://doi.org/10.1101/006346 ER - TY - CHAP A1 - Wende, Florian A1 - Steinke, Thomas T1 - Swendsen-Wang Multi-Cluster Algorithm for the 2D/3D Ising Model on Xeon Phi and GPU T2 - 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 Y1 - 2013 U6 - https://doi.org/http://dx.doi.org/10.1145/2503210.2503254 ER - TY - JOUR A1 - Schäfer, Patrick T1 - The BOSS is concerned with time series classification in the presence of noise JF - Data Mining and Knowledge Discovery Y1 - 2014 U6 - https://doi.org/10.1007/s10618-014-0377-7 VL - 29 IS - 6 SP - 1505 EP - 1530 PB - Springer ER - TY - GEN ED - McIntosh-Smith, Simon ED - Gillan, Charles ED - Sanna, Nico ED - Scott, Stan ED - Steinke, Thomas T1 - Special issue of the Journal of Parallel and Distributed Computing (JDPC) on novel architectures for high-performance computing T2 - Journal of Parallel and Distributed Computing Y1 - 2013 U6 - https://doi.org/10.1016/j.jpdc.2013.08.013 SN - 0743-7315 VL - 73 IS - 11 SP - 1415 EP - 1416 ER - TY - GEN A1 - Benkrid, Khaled A1 - El-Araby, Esam A1 - Huang, Miaoqing A1 - Sano, Kentaro A1 - Steinke, Thomas T1 - High-Performance Reconfigurable Computing - editorial for Special Issue of the International Journal of Reconfigurable Computing T2 - International Journal of Reconfigurable Computing Y1 - 2012 U6 - https://doi.org/10.1155/2012/104963 VL - 2012 SP - 1 EP - 2 ER - TY - JOUR A1 - Tuma, Christian A1 - Laino, Teodoro A1 - Martin, Elyette A1 - Stolz, Steffen A1 - Curioni, Alessandro T1 - Modeling the Impact of Solid Surfaces in Thermal Degradation Processes JF - ChemPhysChem Y1 - 2013 U6 - https://doi.org/10.1002/cphc.201200921 VL - 14 SP - 88 EP - 91 ER - TY - JOUR A1 - Aboulhassan, Amal A1 - Baum, Daniel A1 - Wodo, Olga A1 - Ganapathysubramanian, Baskar A1 - Amassian, Aram A1 - Hadwiger, Markus T1 - A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials JF - Computer Graphics Forum N2 - 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. Y1 - 2015 U6 - https://doi.org/10.1111/cgf.12652 VL - 34 IS - 3 SP - 401 EP - 410 PB - Wiley ER - TY - JOUR A1 - Schäfer, Patrick T1 - Experiencing the Shotgun Distance for Time Series Analysis JF - Transactions on Machine Learning and Data Mining Y1 - 2014 SN - 1864-9734 VL - 7 IS - 1 SP - 3 EP - 25 ER - TY - GEN A1 - Aboulhassan, Amal A1 - Baum, Daniel A1 - Wodo, Olga A1 - Ganapathysubramanian, Baskar A1 - Amassian, Aram A1 - Hadwiger, Markus T1 - A Novel Framework for Visual Detection and Exploration of Performance Bottlenecks in Organic Photovoltaic Solar Cell Materials N2 - 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. T3 - ZIB-Report - 15-20 Y1 - 2015 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-54353 SN - 1438-0064 ER - TY - GEN T1 - Annual Report 2013 T3 - Jahresbericht - 2013 KW - Jahresbericht Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-52848 SN - 0934-5892 VL - 2013 ER - TY - JOUR A1 - Dierkes, Thomas A1 - Ortmann, Karl Michael T1 - On the efficient utilisation of duration JF - Insurance: Mathematics and Economics N2 - 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. Y1 - 2015 U6 - https://doi.org/10.1016/j.insmatheco.2014.11.002 VL - 60 SP - 29 EP - 37 ER - TY - CHAP A1 - Lange, Alexander T1 - A mathematical framework for predicting lifestyles of viral pathogens T2 - Modelling Biological Evolution 2017: Developing Novel Approaches Y1 - 2017 ER - TY - JOUR A1 - Kramer, Tobias A1 - Läuter, Matthias A1 - Rubin, Martin A1 - Altwegg, Kathrin T1 - Seasonal changes of the volatile density in the coma and on the surface of comet 67P/Churyumov-Gerasimenko JF - Monthly Notices of the Royal Astronomical Society N2 - 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. Y1 - 2017 U6 - https://doi.org/10.1093/mnras/stx866 VL - 469 SP - S20 EP - S28 ER - TY - GEN A1 - Aboulhassan, Amal A1 - Sicat, Ronell A1 - Baum, Daniel A1 - Wodo, Olga A1 - Hadwiger, Markus T1 - Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies N2 - 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. T3 - ZIB-Report - 17-16 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-63239 SN - 1438-0064 ER - TY - JOUR A1 - Zander, Thomas A1 - Dreischarf, Marcel A1 - Timm, Anne-Katrin A1 - Baumann, Wolfgang A1 - Schmidt, Hendrik T1 - Impact of material and morphological parameters on the mechanical response of the lumbar spine - A finite element sensitivity study JF - Journal of Biomechanics KW - finite element modelling KW - lumbar spine KW - sensitivity analysis KW - model validation KW - coefficient of determination Y1 - 2016 U6 - https://doi.org/10.1016/j.jbiomech.2016.12.014 VL - 53 SP - 185 EP - 190 ER - TY - JOUR A1 - Ritter, Zully A1 - Belavy, Daniel A1 - Baumann, Wolfgang A1 - Felsenberg, Dieter T1 - 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 JF - Acta Astronautica KW - finite-element analysis KW - bone structure KW - compressive stiffness KW - bed rest KW - HR-pQCT measurement Y1 - 2017 U6 - https://doi.org/10.1016/j.actaastro.2016.12.002 VL - 132 SP - 67 EP - 77 ER - TY - JOUR A1 - Lie, Han Cheng A1 - Sullivan, T. J. T1 - Quasi-invariance of countable products of Cauchy measures under non-unitary dilations JF - Electronic Communications in Probability Y1 - 2018 U6 - https://doi.org/10.1214/18-ECP113 VL - 23 IS - 8 SP - 1 EP - 6 ER - TY - CHAP A1 - Coconu, Liviu A1 - Hege, Hans-Christian T1 - devEyes: Tangible Devices on Augmented Passive Surfaces T2 - TEI '17 Proceedings of the Eleventh International Conference on Tangible, Embedded, and Embodied Interaction, Yokohama, Japan, March 20 - 23, 2017 N2 - 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. Y1 - 2017 U6 - https://doi.org/10.1145/3024969.3025065 SP - 409 EP - 411 ER - TY - THES A1 - Conrad, Tim T1 - Metabolic Pathways Y1 - 2004 UR - http://publications.imp.fu-berlin.de/10/ ER - TY - JOUR A1 - Aboulhassan, Amal A1 - Sicat, Ronell A1 - Baum, Daniel A1 - Wodo, Olga A1 - Hadwiger, Markus T1 - Comparative Visual Analysis of Structure-Performance Relations in Complex Bulk-Heterojunction Morphologies JF - Computer Graphics Forum N2 - 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. Y1 - 2017 U6 - https://doi.org/10.1111/cgf.13191 VL - 36 IS - 3 SP - 329 EP - 339 PB - Wiley ER - TY - JOUR A1 - Gelß, Patrick A1 - Matera, Sebastian A1 - Schütte, Christof T1 - Solving the master equation without kinetic Monte Carlo: Tensor train approximations for a CO oxidation model JF - Journal of Computational Physics N2 - 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 Y1 - 2016 U6 - https://doi.org/10.1016/j.jcp.2016.03.025 VL - 314 SP - 489 EP - 502 ER - TY - JOUR A1 - Orgis, Thomas A1 - Läuter, Matthias A1 - Handorf, Dörthe A1 - Dethloff, Klaus T1 - Baroclinic waves on the β plane using low-order Discontinuous Galerkin discretisation JF - Journal of Computational Physics N2 - 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. Y1 - 2017 U6 - https://doi.org/10.1016/j.jcp.2017.03.029 VL - 339 SP - 461 EP - 481 ER - TY - GEN T1 - Annual Report 2016 T3 - Jahresbericht - 2016 KW - Jahresbericht Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64339 SN - 0934-5892 VL - 2016 ER - TY - GEN A1 - Rohr, Ulrich-Peter A1 - Herrmann, Pia A1 - Ilm, Katharina A1 - Zhang, Hai A1 - Lohmann, Sabine A1 - Reiser, Astrid A1 - Muranyi, Andrea A1 - Smith, Janice A1 - Burock, Susen A1 - Osterland, Marc A1 - Leith, Katherine A1 - Singh, Shalini A1 - Brunhoeber, Patrick A1 - Bowermaster, Rebecca A1 - Tie, Jeanne A1 - Christie, Michael A1 - Wong, Hui-Li A1 - Waring, Paul A1 - Shanmugam, Kandavel A1 - Gibbs, Peter A1 - Stein, Ulrike T1 - Prognostic value of MACC1 and proficient mismatch repair status for recurrence risk prediction in stage II colon cancer patients: the BIOGRID studies N2 - 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: Charité 1 discovery cohort was assayed for MACC1 mRNA expression and MMR in cryo-preserved tumors. Charité 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-naïve 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. T3 - ZIB-Report - 17-28 Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64184 SN - 1438-0064 ER - TY - JOUR A1 - Rohr, Ulrich-Peter A1 - Herrmann, Pia A1 - Ilm, Katharina A1 - Zhang, Hai A1 - Lohmann, Sabine A1 - Reiser, Astrid A1 - Muranyi, Andrea A1 - Smith, Janice A1 - Burock, Susen A1 - Osterland, Marc A1 - Leith, Katherine A1 - Singh, Shalini A1 - Brunhoeber, Patrick A1 - Bowermaster, Rebecca A1 - Tie, Jeanne A1 - Christie, Michael A1 - Wong, Hui-Li A1 - Waring, Paul A1 - Shanmugam, Kandavel A1 - Gibbs, Peter A1 - Stein, Ulrike T1 - Prognostic value of MACC1 and proficient mismatch repair status for recurrence risk prediction in stage II colon cancer patients: the BIOGRID studies JF - Annals of Oncology N2 - 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: Charité 1 discovery cohort was assayed for MACC1 mRNA expression and MMR in cryo-preserved tumors. Charité 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-naïve 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. Y1 - 2017 U6 - https://doi.org/10.1093/annonc/mdx207 VL - 28 IS - 8 SP - 1869 EP - 1875 ER - TY - THES A1 - Agarwal, Animesh T1 - Path Integral Techniques in Molecular Dynamics Simulations of Open Boundary Systems Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000103020-4 ER - TY - THES A1 - Badowski, Tomasz T1 - Adaptive importance sampling via minimization of estimators of cross-entropy, mean square and inefficiency constants Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000102823-3 ER - TY - THES A1 - Daragmeh, Adman T1 - Model Order Reduction of Linear Control Systems: Comparison of Balance Truncation and Singular Perturbation Approximation with Application to Optimal Control Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000102586-2 ER - TY - THES A1 - Gul, Raheem T1 - Mathematical Modeling and Sensitivity Analysis of Lumped­ Parameter Model of the Human Cardiovascular System Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000101271-2 ER - TY - THES A1 - Lie, Han Cheng T1 - On a strongly convex approximation of a stochastic optimal control problem for importance sampling of metastable diffusions Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000101680-4 ER - TY - THES A1 - Sriwattanaworachai, Nisara T1 - Spectral approach to metastability of non-reversible complex processes Y1 - 2016 ER - TY - THES A1 - Vega, Iliusi T1 - Reconstruction and analysis of the state space for the identification of dynamical states in real-world time-series Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:188-fudissthesis000000104520-1 ER - TY - GEN A1 - Koltai, Péter A1 - Schütte, Christof T1 - A multi scale perturbation expansion approach for Markov state modeling of non-stationary molecular dynamics N2 - 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. T3 - ZIB-Report - 17-49 KW - Markov state model KW - non-equilibrium molecular dynamics KW - two timescale master equation KW - non-stationary forcing KW - metastability Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64868 SN - 1438-0064 ER - TY - GEN A1 - Wolf, Thomas A1 - Amadi, Chimaobi T1 - Rational Solutions of Underdetermined Polynomial Equations N2 - 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. T3 - ZIB-Report - 17-33 KW - underdetermined polynomial systems, rational solutions, computer algebra, recreational mathematics Y1 - 2017 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-64488 SN - 1438-0064 ER - TY - JOUR A1 - Leeners, Brigitte A1 - Krüger, Tillmann H. C. A1 - Geraedts, Kirsten A1 - Tronci, Enrico A1 - Mancini, Toni A1 - Ille, Fabian A1 - Egli, Marcel A1 - Röblitz, Susanna A1 - Saleh, Lanja A1 - Spanhaus, K. A1 - Schippert, Cordula A1 - Zhang, Y. A1 - Hengartner, M. P. T1 - Lack of association between female hormone levels and visuospatial working memory, divided attention and cognitive bias across two consecutive menstrual cycles JF - Front. Behav. Neurosci. Y1 - 2017 U6 - https://doi.org/10.3389/fnbeh.2017.00120 ER - TY - JOUR A1 - Hermann, Frank A1 - Ehrig, Hartmut A1 - Golas, Ulrike A1 - Orejas, Fernando T1 - Formal Analysis of Model Transformations Based on Triple Graph Grammars JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000370 VL - 24 IS - 4 SP - 1 EP - 57 ER - TY - JOUR A1 - Ehrig, Hartmut A1 - Golas, Ulrike A1 - Habel, A. A1 - Lambers, L. A1 - Orejas, Fernando T1 - M-Adhesive Transformation Systems with Nested Application Conditions. Part 1: Parallelism, Concurreny and Amalgamation JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000357 VL - 24 IS - 4 SP - 1 EP - 48 ER - TY - JOUR A1 - Gabriel, Karsten A1 - Braatz, Benjamin A1 - Ehrig, Hartmut A1 - Golas, Ulrike T1 - Finitary M-Adhesive Categories JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000321 VL - 24 IS - 4 SP - 1 EP - 40 ER - TY - JOUR A1 - Golas, Ulrike A1 - Habel, A. A1 - Ehrig, Hartmut T1 - Multi-Amalgamation of Rules with Application Conditions in M-Adhesive Categories JF - Mathematical Structures in Computer Science Y1 - 2014 U6 - https://doi.org/10.1017/S0960129512000345 VL - 24 IS - 4 SP - 1 EP - 68 ER - TY - CHAP A1 - Schäfer, Patrick T1 - Towards Time Series Classification without Human Preprocessing T2 - MLDM 2014 Y1 - 2014 U6 - https://doi.org/10.1007/978-3-319-08979-9_18 VL - 8556 SP - 228 EP - 242 ER - TY - JOUR A1 - Potamitis, Ilyas A1 - Schäfer, Patrick T1 - On Classifying Insects from their Wing-Beat: New Results JF - Ecology and acoustics: emergent properties from community to landscape, Paris, France Y1 - 2014 ER - TY - GEN A1 - Deuflhard, Peter A1 - Schütte, Christof ED - Deuflhard, Peter ED - Grötschel, Martin ED - Hömberg, Dietmar ED - Horst, Ulrich ED - Kramer, Jürg ED - Mehrmann, Volker ED - Polthier, Konrad ED - Schmidt, Frank ED - Schütte, Christof ED - Skutella, Martin ED - Sprekels, Jürgen T1 - Life Sciences T2 - MATHEON-Mathematics for Key Technologies Y1 - 2014 VL - 1 SP - 1 EP - 5 PB - European Mathematical Society ER - TY - THES A1 - Merkulow, Igor T1 - Parameter selection and evaluation for programming of heterogeneous architectures Y1 - 2013 ER - TY - JOUR A1 - Fodor, Bálint A1 - Kozma, Peter A1 - Burger, Sven A1 - Fried, Miklos A1 - Petrik, Peter T1 - Effective medium approximation of ellipsometric response from random surface roughness simulated by finite-element method JF - Thin Solid Films Y1 - 2016 U6 - https://doi.org/10.1016/j.tsf.2016.01.054 VL - 617 SP - 20 ER - TY - JOUR A1 - Tuma, Christian A1 - Sauer, Joachim T1 - Quantum chemical ab initio prediction of proton exchange barriers between CH4 and different H-zeolites JF - The Journal of Chemical Physics Y1 - 2015 U6 - https://doi.org/10.1063/1.4923086 VL - 143 IS - 10 SP - 102810-1 EP - 102810-13 ER - TY - JOUR A1 - Schäfer, Patrick T1 - Scalable time series classification JF - Data Mining and Knowledge Discovery N2 - Time series classification tries to mimic the human understanding of similarity. When it comes to long or larger time series datasets, state-of-the-art classifiers reach their limits because of unreasonably high training or testing times. One representative example is the 1-nearest-neighbor dynamic time warping classifier (1-NN DTW) that is commonly used as the benchmark to compare to. It has several shortcomings: it has a quadratic time complexity in the time series length and its accuracy degenerates in the presence of noise. To reduce the computational complexity, early abandoning techniques, cascading lower bounds, or recently, a nearest centroid classifier have been introduced. Still, classification times on datasets of a few thousand time series are in the order of hours. We present our Bag-Of-SFA-Symbols in Vector Space classifier that is accurate, fast and robust to noise. We show that it is significantly more accurate than 1-NN DTW while being multiple orders of magnitude faster. Its low computational complexity combined with its good classification accuracy makes it relevant for use cases like long or large amounts of time series or real-time analytics. Y1 - 2015 U6 - https://doi.org/10.1007/s10618-015-0441-y SP - 1 EP - 26 ER - TY - GEN A1 - Deuflhard, Peter A1 - Hege, Hans-Christian ED - Lepper, Verena ED - Deuflhard, Peter ED - Markschies, Christoph T1 - Raumtiefe in Malerei und Computergrafik T2 - Räume - Bilder - Kulturen N2 - Einführung: Die Tiefenwirkung dreidimensionaler Räume in einem zweidimensionalen Bild einzufangen, ist ein Faszinosum nahezu aller Kulturen der Menschheitsgeschichte. Der vorliegende Aufsatz folgt den Spuren dieses Faszinosums, vergleichend in der Malerei und der mathematisierten Computergrafik. Die Entdeckung der Zentralperspektive in der italienischen Renaissance zeigt bereits den engen Zusammenhang von Malerei und Mathematik. Auf der Suche nach Maltechniken, mit denen Raumtiefe bildnerisch dargestellt werden kann, beginnen wir in Kap. 2 mit einem chronologischen Gang durch verschiedene Epochen der europäischen Malerei. Hieraus abgeleitete Prinzipien, soweit sie im Rechner realisierbar scheinen, stellen wir in Kap. 3 am Beispiel moderner Methoden der mathematischen Visualisierung vor. Y1 - 2015 SN - 978-3-11-035993-0 SP - 33 EP - 46 PB - Walter De Gruyter ER - TY - BOOK ED - Lepper, Verena ED - Deuflhard, Peter ED - Markschies, Christoph T1 - Räume - Bilder - Kulturen Y1 - 2015 SN - 978-3-11-035993-0 PB - De Gruyter ER - TY - BOOK A1 - Ehrig, Hartmut A1 - Ermel, Claudia A1 - Golas, Ulrike A1 - Hermann, Frank T1 - Graph and Model Transformation BT - General Framework and Applications N2 - This book is a comprehensive explanation of graph and model transformation. It contains a detailed introduction, including basic results and applications of the algebraic theory of graph transformations, and references to the historical context. Then in the main part the book contains detailed chapters on M-adhesive categories, M-adhesive transformation systems, and multi-amalgamated transformations, and model transformation based on triple graph grammars. In the final part of the book the authors examine application of the techniques in various domains, including chapters on case studies and tool support. The book will be of interest to researchers and practitioners in the areas of theoretical computer science, software engineering, concurrent and distributed systems, and visual modelling. Y1 - 2015 SN - 978-3-662-47979-7 U6 - https://doi.org/10.1007/978-3-662-47980-3 PB - Springer-Verlag Berlin Heidelberg ER - TY - GEN A1 - Willenbockel, Christian Tobias A1 - Schütte, Christof T1 - Variational Bayesian Inference and Model Selection for the Stochastic Block Model with Irrelevant Vertices N2 - Real World networks often exhibit a significant number of vertices which are sparsely and irregularly connected to other vertices in the network. For clustering theses networks with a model based algorithm, we propose the Stochastic Block Model with Irrelevant Vertices (SBMIV) for weighted net- works. We propose an original Variational Bayesian Expectation Maximiza- tion inference algorithm for the SBMIV which is an advanced version of our Blockloading algorithm for the Stochastic Block Model. We introduce a model selection criterion for the number of clusters of the SBMIV which is based on the lower variational bound of the model likelihood. We propose a fully Bayesian inference process, based on plausible informative priors, which is independent of other algorithms for preprocessing start values for the cluster assignment of vertices. Our inference methods allow for a multi level identification of irrelevant vertices which are hard to cluster reliably ac- cording to the SBM. We demonstrate that our methods improve on the normal Stochastic Block model by applying it to to Earthquake Networks which are an example of networks with a large number of sparsely and irregularly con- nected vertices. T3 - ZIB-Report - 16-01 KW - Clustering KW - Variational Bayes EM KW - Model Selection, KW - Stochastic Block Model KW - Networks KW - unsupervised classification KW - Noise Y1 - 2016 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:0297-zib-57003 SN - 1438-0064 ER - TY - THES A1 - Schäfer, Patrick T1 - Scalable Time Series Similarity Search for Data Analytics Y1 - 2015 UR - http://edoc.hu-berlin.de/docviews/abstract.php?id=42117 ER - TY - GEN A1 - Fackeldey, Konstantin T1 - Challenges in Atomistic-to-Continuum Coupling T2 - ZIB Report N2 - This paper is concerned with the design, analysis, and implementation of concurrent coupling approaches where different (atomic and continuous) models are used simultaneously within a single simulation process. Thereby, several problems or pitfalls can happen, for example, the reflection of molecular movements at the “boundary” between the atomic and continuum regions which leads to an unphysical increase in energy in the atomic model. We investigate the problems with the aim of giving an introduction into this field and preventing errors for scientists starting their research towards multiscale methods. Y1 - 2010 U6 - https://doi.org/10.1155/2015/834517 VL - 2010 ET - 10-12 ER - TY - JOUR A1 - Bienefeld, Kaspar A1 - Zautke, Fred A1 - Gupta, Pooja T1 - A novel method for undisturbed long-term observation of the honey bee (Apis mellifera) behaviour – illustrated by the hygienic behaviour towards Varroa infestation JF - Journal of Apicultural Research Y1 - 2016 VL - 54(5) SP - 541 EP - 547 ER -