TY - CHAP A1 - Clausecker, Robert A1 - Kaiser, Benjamin T1 - Sliding Tile Puzzles T2 - Proceedings of SAT Competition 2021 : Solver and Benchmark Descriptions Y1 - 2021 UR - http://hdl.handle.net/10138/333647 SP - 57 ER - TY - GEN A1 - Sikorski, Alexander A1 - Sechi, Renata A1 - Helfmann, Luzie T1 - cmdtools N2 - Python implementation of severals tools (PCCA, AJC, SQRA, P/Q estimation) for the analysis of dynamical systems from the transfer operator perspective. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.5281/zenodo.4749331 ER - TY - JOUR A1 - Donati, Luca A1 - Weber, Marcus A1 - Keller, Bettina G. T1 - Markov models from the square root approximation of the Fokker–Planck equation: calculating the grid-dependent flux JF - Journal of Physics: Condensed Matter N2 - Molecular dynamics (MD) are extremely complex, yet understanding the slow components of their dynamics is essential to understanding their macroscopic properties. To achieve this, one models the MD as a stochastic process and analyses the dominant eigenfunctions of the associated Fokker–Planck operator, or of closely related transfer operators. So far, the calculation of the discretized operators requires extensive MD simulations. The square-root approximation of the Fokker–Planck equation is a method to calculate transition rates as a ratio of the Boltzmann densities of neighboring grid cells times a flux, and can in principle be calculated without a simulation. In a previous work we still used MD simulations to determine the flux. Here, we propose several methods to calculate the exact or approximate flux for various grid types, and thus estimate the rate matrix without a simulation. Using model potentials we test computational efficiency of the methods, and the accuracy with which they reproduce the dominant eigenfunctions and eigenvalues. For these model potentials, rate matrices with up to $\mathcal{O}\left(1{0}^{6}\right)$ states can be obtained within seconds on a single high-performance compute server if regular grids are used. Y1 - 2021 U6 - https://doi.org/10.1088/1361-648X/abd5f7 VL - 33 IS - 11 SP - 115902 ER - TY - JOUR A1 - Yokoyama, Ryohei A1 - Shinano, Yuji A1 - Wakui, Tetsuya T1 - エネルギー供給システムの設計および運用の 階層的関係を考慮した最適化 (蓄エネルギー機器を有するシステムへの適用) T1 - Optimization of Energy Supply Systems in Consideration of Hierarchical Relationship Between Design and Operation (Application to Systems With Energy Storage Units) JF - 第40回エネルギー・資源学会研究発表会講演論文集 N2 - Mixed-integer linear programming (MILP) methods have been applied widely to optimal design of energy supply systems. A hierarchical MILP method has been proposed to solve such optimal design problems efficiently. In addition, some strategies have been proposed to enhance the computation efficiency furthermore. As one of the strategies, a method of reducing model by time aggregation has been proposed to search design candidates efficiently in the relaxed optimal design problem at the upper level. In this paper, the hierarchical MILP method with the strategies has been extendedly applied to the optimal design of energy supply systems with storage units. Especially, the method of re- ducing model is extended by aggregating representative days and sampling times differently in consideration of the characteristics of storage units. A case study is conducted on the optimal design of a gas turbine cogeneration system with a thermal storage unit for district energy supply. Through the study, it turns out the hierarchical MILP method is effective to derive the optimal solution as compared with a conventional method. It also turns out that the model reduction with the special time aggregation is effective to shorten the computation time as compared with that without time aggregation in case that the number of candidates for equipment capacities is relatively small. Y1 - 2021 SP - 398 EP - 403 ER - TY - CHAP A1 - Binkowski, Felix A1 - Betz, Fridtjof A1 - Colom, Remi A1 - Hammerschmidt, Martin A1 - Schneider, Philipp-Immanuel A1 - Zschiedrich, Lin A1 - Burger, Sven ED - Zouhdi, S. ED - Pawlak, D. ED - Kudelski, A. T1 - Contour integral methods for resonance phenomena in nano-optics T2 - The 11th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2021) Y1 - 2021 SN - 2429-1390 SP - 523 ER - TY - CHAP A1 - Kramer, Tobias A1 - Läuter, Matthias T1 - Matching the activity of comet 67P/Churyumov-Gerasimenko with long-term ground-based astrometry T2 - Europlanet Science Congress N2 - 50 years of astrometric data for comet 67P/C-G (orbital period about 6.45 years) provides a unique opportunity to benchmark non-gravitational acceleration models to the in situ measurements of the volatile release performed from the Rosetta rendezvous mission (2014-2016). Taken together, the Earth-bound and in-situ data yields lower fit errors and serves as a test-case for our ability to deduce thermophysical quantities of cometary nuclei from the Earth-bound observations. Y1 - 2021 U6 - https://doi.org/10.5194/epsc2021-337 VL - 15 SP - EPSC2021-337 PB - Europlanet Science Congress ER - TY - CHAP A1 - Chmiela, Antonia A1 - Muñoz, Gonzalo A1 - Serrano, Felipe T1 - On the implementation and strengthening of intersection cuts for QCQPs T2 - Integer Programming and Combinatorial Optimization: 22nd International Conference, IPCO 2021 N2 - The generation of strong linear inequalities for QCQPs has been recently tackled by a number of authors using the intersection cut paradigm - a highly studied tool in integer programming whose flexibility has triggered these renewed efforts in non-linear settings. In this work, we consider intersection cuts using the recently proposed construction of maximal quadratic-free sets. Using these sets, we derive closed-form formulas to compute intersection cuts which allow for quick cut-computations by simply plugging-in parameters associated to an arbitrary quadratic inequality being violated by a vertex of an LP relaxation. Additionally, we implement a cut-strengthening procedure that dates back to Glover and evaluate these techniques with extensive computational experiments. Y1 - 2021 U6 - https://doi.org/10.1007/978-3-030-73879-2_10 VL - 22 SP - 134 EP - 147 ER - TY - THES A1 - Francobaldi, Matteo T1 - Learning to Use Local Cuts N2 - We propose a machine learning approach to address a specific algorithmic question that arises during the solving process of a mixed-integer linear programming problem, namely, whether to use cutting planes only at the root node or also at internal nodes of the branch-and-bound search tree, or equivalently, whether to run a cut-and-branch or rather a branch-and-cut algorithm. Within a supervised regression framework, we develop three machine learning models, Linear Model, Random Forest and Neural Network, for predicting the relative performance between the two methods, local-cut and no-local-cut. Hence, through an extensive computational study conducted with FICO Xpress over a large test bed of problems, we evaluate the produced strategies, and we show that they are able to provide, upon the existing policies, a significant improvement to the performance of the solver. In fact, a variant of the random forest suggested in the present work has already been implemented by the development team of Xpress, and released with version 8.13 of the software. KW - Mathematical Programming KW - Machine Learning KW - Artificial Intelligence Y1 - 2021 ER - TY - JOUR A1 - Dai, Chengxin A1 - Füllgrabe, Anja A1 - Pfeuffer, Julianus A1 - Solovyeva, Elizaveta M. A1 - Deng, Jingwen A1 - Moreno, Pablo A1 - Kamatchinathan, Selvakumar A1 - Kundu, Deepti Jaiswal A1 - George, Nancy A1 - Fexovy, Silvie A1 - Grüning, Björn A1 - Föll, Melanie Christine A1 - Griss, Johannes A1 - Vaudel, Marc A1 - Audain, Enrique A1 - Locard-Paulet, Marie A1 - Turewicz, Michael A1 - Eisenacher, Martin A1 - Uszkoreit, Julian A1 - Van Den Bossche, Tim A1 - Schwämmle, Veit A1 - Webel, Henry A1 - Schulze, Stefan A1 - Bouyssié, David A1 - Jayaram, Savita A1 - Duggineni, Vinay Kumar A1 - Samaras, Patroklos A1 - Wilhelm, Mathias A1 - Choi, Meena A1 - Wang, Mingxun A1 - Kohlbacher, Oliver A1 - Brazma, Alvis A1 - Papatheodorou, Irene A1 - Bandeira, Nuno A1 - Deutsch, Eric W. A1 - Vizcaíno, Juan Antonio A1 - Bai, Mingze A1 - Sachsenberg, Timo A1 - Levitsky, Lev I. A1 - Perez-Riverol, Yasset T1 - A proteomics sample metadata representation for multiomics integration and big data analysis JF - Nature Communications N2 - The amount of public proteomics data is rapidly increasing but there is no standardized format to describe the sample metadata and their relationship with the dataset files in a way that fully supports their understanding or reanalysis. Here we propose to develop the transcriptomics data format MAGE-TAB into a standard representation for proteomics sample metadata. We implement MAGE-TAB-Proteomics in a crowdsourcing project to manually curate over 200 public datasets. We also describe tools and libraries to validate and submit sample metadata-related information to the PRIDE repository. We expect that these developments will improve the reproducibility and facilitate the reanalysis and integration of public proteomics datasets. Y1 - 2021 U6 - https://doi.org/https://doi.org/10.1038/s41467-021-26111-3 VL - 12 IS - 5854 ER - TY - JOUR A1 - Umer, Husen M. A1 - Zhu, Yafeng A1 - Pfeuffer, Julianus A1 - Sachsenberg, Timo A1 - Lehtiö, Janne A1 - Branca, Rui A1 - Perez-Riverol, Yasset T1 - Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides JF - Bioinformatics N2 - We have implemented the pypgatk package and the pgdb workflow to create proteogenomics databases based on ENSEMBL resources. The tools allow the generation of protein sequences from novel protein-coding transcripts by performing a three-frame translation of pseudogenes, lncRNAs, and other non-canonical transcripts, such as those produced by alternative splicing events. It also includes exonic out-of-frame translation from otherwise canonical protein-coding mRNAs. Moreover, the tool enables the generation of variant protein sequences from multiple sources of genomic variants including COSMIC, cBioportal, gnomAD, and mutations detected from sequencing of patient samples. pypgatk and pgdb provide multiple functionalities for database handling, notably optimized target/decoy generation by the algorithm DecoyPyrat. Finally, we perform a reanalysis of four public datasets in PRIDE by generating cell-type specific databases for 65 cell lines using the pypgatk and pgdb workflow, revealing a wealth of non-canonical or cryptic peptides amounting to more than 10% of the total number of peptides identified (43,501 out of 402,512). Y1 - 2021 IS - 5 SP - 1470 EP - 1472 PB - Oxford Academic ET - 38 ER -