@article{藤澤品野2014, author = {藤澤, 克樹 and 品野, 勇治}, title = {最適化と計算の今後 ―大規模問題をどこまで解決できるのか?―}, volume = {59}, journal = {機関誌「オペレーションズ・リサーチ」}, number = {1}, pages = {11 -- 19}, year = {2014}, abstract = {近年,大規模かつ複雑な最適化問題を高速に解く需要はさまざまな産業界や学術分野において急速に高まりつつある.これからの研究においては最先端理論 (Theory)+超大規模実データ (Practice)+最新計算技術(Computation) の三つを有機的に組み合わせることによって,実用に耐えうる解決策の提示と大規模最適化問題を扱う際の先例となることが求められている.本稿では最適化と計算に関する最新の傾向に触れるとともに,最適化の計算の今後についても考えていきたい.}, language = {ja} } @article{品野藤井2019, author = {品野, 勇治 and 藤井, 浩一}, title = {使ってみよう線形計画ソルバ}, volume = {64}, journal = {機関誌「オペレーションズ・リサーチ」}, number = {4}, pages = {238 -- 245}, year = {2019}, abstract = {本稿では,線形計画問題を解くソフトウェアである線形計画ソルバの標準的な利用方法と,原稿執筆時点で利用可能なソルバを可能な限り紹介する.筆者らはソルバ開発コミュニティの中で仕事をしているので,この機会に現在のソルバ開発現場の様子も紹介するとともに,各ソルバの特徴として何を紹介するべきかは,できる限り開発者,または,開発者に近い研究者に問い合わせて記述した.本稿は,多くの線形計画ソルバの選択肢がある中で,読者がもつ問題を解くのに最も適当なソルバを選択するための指針を与えることを主たる目的としている.}, language = {ja} } @article{品野2014, author = {品野, 勇治}, title = {最適化研究における数値実験を中心とした アプリケーション駆動研究サイクル}, volume = {59}, journal = {機関誌「オペレーションズ・リサーチ」}, number = {5}, pages = {247 -- 253}, year = {2014}, abstract = {最適化研究におけるアプリケーション駆動研究サイクルを紹介する.アプリケーション駆動研究サイクルは,学術機関での研究と企業における研究成果の利用とのつながりを良くする点では優れている.一方で,ソフトウェア開発・維持に多大な労力を要するため,日本の大学や研究機関における実施には困難さが伴う.ZIBにおいてアプリケーション駆動研究サイクルが,比較的うまく機能している背景を説明する.また,日本においてアプリケーション駆動研究サイクルを活性化するための第一歩として,論文投稿時に,論文中の数値実験に利用した全データ提出の義務化を提案したい.}, language = {ja} } @article{品野2020, author = {品野, 勇治}, title = {MIPLIB と Hans Mittelmann's benchmarks}, volume = {65}, journal = {機関誌「オペレーションズ・リサーチ」}, number = {1}, pages = {49 -- 56}, year = {2020}, abstract = {混合整数計画法 (Mixed Integer Programming: MIP) は,MIP を解くソフトウェアである MIP ソルバが大規模な現実問題を解けるようになったこともあり,現実問題を解く有用な OR の手法として広く知られるようになった.しかしながら,MIP ソルバの開発に欠かせないベンチマーク・データセットおよび性能測定方法についてはそれほど広く知られているとは言い難い.ベンチマーク・データセットは注意を払って作成しないと,多くのバイアスがかかってしまう.それらのバイアスを可能な限りのぞき,真に有用なベンチマーク・テストの結果を得るためには複数の人数で多大な労力を割く必要がある.本稿では,そのような MIP ソルバ開発の背景として重要な役割を果たしてきた MIPLIB と Hans Mittelmann's benchmarks について解説する.また,本稿において Hans Mittelmann's benchmarks は,BENCHMARKS FOR OPTIMIZATION SOFTWAREのページ (http://plato.asu.edu/bench.html) に示されているベンチマークである.}, language = {ja} } @article{ŻołnaczMusiałSrockaetal.2019, author = {Żołnacz, Kinga and Musiał, Anna and Srocka, Nicole and Große, Jan and Schl{\"o}singer, Maximilian and Schneider, Philipp-Immanuel and Kravets, Oleh and Mikulicz, Monika and Olszewski, Jacek and Poturaj, Krzysztof and W{\´o}jcik, Grzegorz and Mergo, Paweł and Dybka, Kamil and Dyrkacz, Mariusz and Dłubek, Michał and Rodt, Sven and Burger, Sven and Zschiedrich, Lin and Sęk, Grzegorz and Reitzenstein, Stephan and Urbańczyk, Wacław}, title = {Method for direct coupling of a semiconductor quantum dot to an optical fiber for single-photon source applications}, volume = {27}, journal = {Opt. Express}, doi = {10.1364/OE.27.026772}, pages = {26772}, year = {2019}, language = {en} } @article{ŠofranacGleixnerPokutta2022, author = {Šofranac, Boro and Gleixner, Ambros and Pokutta, Sebastian}, title = {Accelerating domain propagation: An efficient GPU-parallel algorithm over sparse matrices}, volume = {109}, journal = {Parallel Computing}, doi = {10.1016/j.parco.2021.102874}, pages = {102874}, year = {2022}, abstract = {• Currently, domain propagation in state-of-the-art MIP solvers is single thread only. • The paper presents a novel, efficient GPU algorithm to perform domain propagation. • Challenges are dynamic algorithmic behavior, dependency structures, sparsity patterns. • The algorithm is capable of running entirely on the GPU with no CPU involvement. • We achieve speed-ups of around 10x to 20x, up to 180x on favorably-large instances.}, language = {en} } @article{ŠofranacGleixnerPokutta2022, author = {Šofranac, Boro and Gleixner, Ambros and Pokutta, Sebastian}, title = {An Algorithm-independent Measure of Progress for Linear Constraint Propagation}, volume = {27}, journal = {Constraints}, doi = {10.1007/s10601-022-09338-9}, pages = {432 -- 455}, year = {2022}, language = {en} } @misc{Şirin2023, type = {Master Thesis}, author = {Şirin, Ege}, title = {Probabilistic Image Segmentation With Continuous Shape Representations}, year = {2023}, language = {en} } @incollection{ŞahinLindnerSchlechte2023, author = {Şahin, G{\"u}ven{\c{c}} and Lindner, Niels and Schlechte, Thomas}, title = {Line Planning Problem}, booktitle = {Encyclopedia of Optimization}, editor = {Pardalos, P. M. and Prokopyev, O. A.}, publisher = {Springer International Publishing}, address = {Cham}, isbn = {978-3-030-54621-2}, doi = {10.1007/978-3-030-54621-2_782-1}, pages = {1 -- 6}, year = {2023}, language = {en} } @misc{Oezmen2022, type = {Master Thesis}, author = {{\"O}zmen, Mahmut}, title = {Medical Image registration with B-Spline Transformation}, pages = {64}, year = {2022}, abstract = {Medical image registration is an important task in various applications such as temporal analysis of medical images from a single modality (where structural or anatomical changes over time are studied), multi-modal image fusion (in which data acquired from different imaging devices or protocols is fused to help with diagnosis and treatment planning), or atlas matching (where uses normal anatomical variability). Establishing functional and/or spatial anatomical correspondences between different image acquisitions is the goal of image registration. As rigid alignment might be insufficient to describe variations of images in certain applications where deformations play a role, we should rely on non-rigid image registration. Non-rigid registration methods are capable of aligning images where correspondence cannot be achieved without localized deformations and can therefore better accommodate anatomical, physiological, and pathological variability between patients. Elastix image registration software is employed in this thesis to conduct our experiments. In this thesis, we use interpolation-based B-spline transformation models that parameterize a Free-Form Deformation Field. B-splines interpolate the dense deformation field from a given set of control points. B-spline transformation model assumes the smoothness and continuity of the deformation field on the image. However, when aligning two images that contain sliding contact, B-spline transformation leads to an inaccurate registration result, and the deformation field is not always smooth or the deformation field is always discontinuous, but not necessarily everywhere. When the knee is bent, the sliding contact occurs at the knee cartilage and around the capsular tissues. Different types of discontinuities in the overall deformation field may occur when sliding contact occurs. Imposing smoothness and continuity in the registration will generate artifacts in the consequent deformations, as well as any quantities derived from it. To handle the artifacts in the resulting deformations, one can use a regularizer or implement the sliding motion in the transformation model. Hence, in this thesis, we compare the B-spline registration, B-spline with Transform Rigidity Penalty, B-spline with Distance Rigidity Penalty, and the sliding motion with B-splines. B-spline with Transform Rigidity Penalty (TRP) and B-spline with Distance Rigidity Penalty (DPRP) models use a regularizer to handle the sliding motion. However, the sliding Motion with B-splines model handles sliding motion in the transformation model itself. The chosen registration parameters and registration algorithm were assessed first using three synthetic datasets. In a second validation, Knee MRI images that belong to two different patient datasets are registered on a temporal sequence of each patient. Registration accuracy was assessed based on the corresponding segmented bones and neighboring soft tissue. Compared to B-spline approach, the B-spline with TRP, B-spline with DPRP, and the sliding motion with B-splines gave deformation fields that represented more plausible image correspondences, while giving rise to comparable registration accuracy. In one dataset, the B-spline with TRP and B-spline with DPRP models reflected the deformation better than other approaches. However, sliding motion with B-splines model outperformed all other approaches in the other dataset.}, language = {en} } @misc{OezelKulkarniHasanetal.2019, author = {{\"O}zel, M. Neset and Kulkarni, Abhishek and Hasan, Amr and Brummer, Josephine and Moldenhauer, Marian and Daumann, Ilsa-Maria and Wolfenberg, Heike and Dercksen, Vincent J. and Kiral, F. Ridvan and Weiser, Martin and Prohaska, Steffen and von Kleist, Max and Hiesinger, Peter Robin}, title = {Serial synapse formation through filopodial competition for synaptic seeding factors}, issn = {1438-0064}, doi = {10.1016/j.devcel.2019.06.014}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-74397}, year = {2019}, abstract = {Following axon pathfinding, growth cones transition from stochastic filopodial exploration to the formation of a limited number of synapses. How the interplay of filopodia and synapse assembly ensures robust connectivity in the brain has remained a challenging problem. Here, we developed a new 4D analysis method for filopodial dynamics and a data-driven computational model of synapse formation for R7 photoreceptor axons in developing Drosophila brains. Our live data support a 'serial synapse formation' model, where at any time point only a single 'synaptogenic' filopodium suppresses the synaptic competence of other filopodia through competition for synaptic seeding factors. Loss of the synaptic seeding factors Syd-1 and Liprin-α leads to a loss of this suppression, filopodial destabilization and reduced synapse formation, which is sufficient to cause the destabilization of entire axon terminals. Our model provides a filopodial 'winner-takes-all' mechanism that ensures the formation of an appropriate number of synapses.}, language = {en} } @article{OettingerMontefuscoPeletier2021, author = {{\"O}ttinger, Hans Christian and Montefusco, Alberto and Peletier, Mark A.}, title = {A Framework of Nonequilibrium Statistical Mechanics. I. Role and Types of Fluctuations}, volume = {46}, journal = {Journal of Non-Equilibrium Thermodynamics}, number = {1}, publisher = {De Gruyter}, doi = {10.1515/jnet-2020-0068}, pages = {1 -- 13}, year = {2021}, abstract = {Understanding the fluctuations by which phenomenological evolution equations with thermodynamic structure can be enhanced is the key to a general framework of nonequilibrium statistical mechanics. These fluctuations provide an idealized representation of microscopic details. We consider fluctuation-enhanced equations associated with Markov processes and elaborate the general recipes for evaluating dynamic material properties, which characterize force-flux constitutive laws, by statistical mechanics. Markov processes with continuous trajectories are conveniently characterized by stochastic differential equations and lead to Green-Kubo-type formulas for dynamic material properties. Markov processes with discontinuous jumps include transitions over energy barriers with the rates calculated by Kramers. We describe a unified approach to Markovian fluctuations and demonstrate how the appropriate type of fluctuations (continuous versus discontinuous) is reflected in the mathematical structure of the phenomenological equations.}, language = {en} } @article{ZoecklerStallingHege2000, author = {Z{\"o}ckler, Malte and Stalling, Detlev and Hege, Hans-Christian}, title = {Fast and Intuitive Generation of Geometric Shape Transitions}, volume = {16(5)}, journal = {The Visual Computer}, doi = {10.1007/PL00013396}, pages = {241 -- 253}, year = {2000}, language = {en} } @inproceedings{ZoecklerStallingHege1996, author = {Z{\"o}ckler, Malte and Stalling, Detlev and Hege, Hans-Christian}, title = {Parallel Line Integral Convolution}, booktitle = {Proc. First Eurographics Workshop on Parallel Graphics and Visualization}, address = {Bristol, U.K.}, doi = {10.1016/S0167-8191(97)00039-2}, pages = {111 -- 128}, year = {1996}, language = {en} } @inproceedings{ZoecklerStallingHege1996, author = {Z{\"o}ckler, Malte and Stalling, Detlev and Hege, Hans-Christian}, title = {Interactive Visualization of 3D-Vector Fields Using Illuminated Streamlines}, booktitle = {Proc. IEEE Visualization 1996}, address = {San Fransisco}, doi = {10.1109/VISUAL.1996.567777}, pages = {107 -- 113}, year = {1996}, language = {en} } @misc{ZoecklerStallingHege1999, author = {Z{\"o}ckler, Malte and Stalling, Detlev and Hege, Hans-Christian}, title = {Fast and Intuitive Generation of Geometric Shape Transitions}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-4219}, number = {SC-99-33}, year = {1999}, abstract = {We describe a novel method for continuously transforming two triangulated models of arbitrary topology into each other. Equal global topology for both objects is assumed, extensions for genus changes during metamorphosis are provided. The proposed method addresses the major challenge in 3D metamorphosis, namely specifying the morphing process intuitively, with minimal user interaction and sufficient detail. Corresponding regions and point features are interactively identified. These regions are parametrized automatically and consistently, providing a basis for smooth interpolation. Utilizing suitable 3D interaction techniques a simple and intuitive control over the whole morphing process is offered.}, language = {en} } @article{ZoecklerStalling2002, author = {Z{\"o}ckler, Malte and Stalling, Detlev}, title = {Using confocal microscopy and advanced 3-d visualization to investigate the Drosophila brain}, journal = {Scientific Computing \& Instrumentation}, year = {2002}, language = {en} } @misc{ZoecklerReinBrandtetal.2001, author = {Z{\"o}ckler, Malte and Rein, Karlheinz and Brandt, Robert and Stalling, Detlev and Hege, Hans-Christian}, title = {Creating Virtual Insect Brains with Amira}, url = {http://nbn-resolving.de/urn:nbn:de:0297-zib-6589}, number = {01-32}, year = {2001}, abstract = {By combining techniques of preparation, histology, confocal microscopy, data visualization and data processing, we have created and recently published a standard brain model for drosophila and honey bee brains. This report describes the algorithms and implementation of the corresponding software modules. At the same time it serves as a user's guide for scientist who want to reproduce the results for differerent species or mutants.}, language = {en} } @misc{Zoeckler1997, type = {Master Thesis}, author = {Z{\"o}ckler, Malte}, title = {Molekulardynamische Simulation des Wachstums zirkumstellarer Silikatstaubteilchen}, year = {1997}, language = {en} } @phdthesis{Zoeckler2006, author = {Z{\"o}ckler, Maja}, title = {Modellgebundene Cranioplastie - Operationstechnik zur Umformung fr{\"u}hkindlicher Sch{\"a}deldeformit{\"a}ten unter Verwendung dreidimensionaler Standardformmodelle aus MRT-basierten Rekonstruktionen nicht deformierter Kinder}, year = {2006}, language = {de} }