@inproceedings{ClauseckerKaiser2021, author = {Clausecker, Robert and Kaiser, Benjamin}, title = {Sliding Tile Puzzles}, booktitle = {Proceedings of SAT Competition 2021 : Solver and Benchmark Descriptions}, pages = {57}, year = {2021}, language = {en} } @misc{SikorskiSechiHelfmann2021, author = {Sikorski, Alexander and Sechi, Renata and Helfmann, Luzie}, title = {cmdtools}, doi = {https://doi.org/10.5281/zenodo.4749331}, year = {2021}, abstract = {Python implementation of severals tools (PCCA, AJC, SQRA, P/Q estimation) for the analysis of dynamical systems from the transfer operator perspective.}, language = {en} } @article{DonatiWeberKeller2021, author = {Donati, Luca and Weber, Marcus and Keller, Bettina G.}, title = {Markov models from the square root approximation of the Fokker-Planck equation: calculating the grid-dependent flux}, volume = {33}, journal = {Journal of Physics: Condensed Matter}, number = {11}, doi = {10.1088/1361-648X/abd5f7}, pages = {115902}, year = {2021}, abstract = {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.}, language = {en} } @article{YokoyamaShinanoWakui2021, author = {Yokoyama, Ryohei and Shinano, Yuji and Wakui, Tetsuya}, title = {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)}, journal = {第40回エネルギー・資源学会研究発表会講演論文集}, pages = {398 -- 403}, year = {2021}, abstract = {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.}, language = {ja} } @inproceedings{BinkowskiBetzColometal.2021, author = {Binkowski, Felix and Betz, Fridtjof and Colom, Remi and Hammerschmidt, Martin and Schneider, Philipp-Immanuel and Zschiedrich, Lin and Burger, Sven}, title = {Contour integral methods for resonance phenomena in nano-optics}, booktitle = {The 11th International Conference on Metamaterials, Photonic Crystals and Plasmonics (META 2021)}, editor = {Zouhdi, S. and Pawlak, D. and Kudelski, A.}, issn = {2429-1390}, pages = {523}, year = {2021}, language = {en} } @inproceedings{KramerLaeuter2021, author = {Kramer, Tobias and L{\"a}uter, Matthias}, title = {Matching the activity of comet 67P/Churyumov-Gerasimenko with long-term ground-based astrometry}, volume = {15}, booktitle = {Europlanet Science Congress}, publisher = {Europlanet Science Congress}, doi = {10.5194/epsc2021-337}, pages = {EPSC2021-337}, year = {2021}, abstract = {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.}, language = {en} } @inproceedings{ChmielaMunozSerrano2021, author = {Chmiela, Antonia and Mu{\~n}oz, Gonzalo and Serrano, Felipe}, title = {On the implementation and strengthening of intersection cuts for QCQPs}, volume = {22}, booktitle = {Integer Programming and Combinatorial Optimization: 22nd International Conference, IPCO 2021}, doi = {10.1007/978-3-030-73879-2_10}, pages = {134 -- 147}, year = {2021}, abstract = {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.}, language = {en} } @misc{Francobaldi2021, type = {Master Thesis}, author = {Francobaldi, Matteo}, title = {Learning to Use Local Cuts}, year = {2021}, abstract = {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.}, language = {en} } @article{DaiFuellgrabePfeufferetal.2021, author = {Dai, Chengxin and F{\"u}llgrabe, Anja and Pfeuffer, Julianus and Solovyeva, Elizaveta M. and Deng, Jingwen and Moreno, Pablo and Kamatchinathan, Selvakumar and Kundu, Deepti Jaiswal and George, Nancy and Fexovy, Silvie and Gr{\"u}ning, Bj{\"o}rn and F{\"o}ll, Melanie Christine and Griss, Johannes and Vaudel, Marc and Audain, Enrique and Locard-Paulet, Marie and Turewicz, Michael and Eisenacher, Martin and Uszkoreit, Julian and Van Den Bossche, Tim and Schw{\"a}mmle, Veit and Webel, Henry and Schulze, Stefan and Bouyssi{\´e}, David and Jayaram, Savita and Duggineni, Vinay Kumar and Samaras, Patroklos and Wilhelm, Mathias and Choi, Meena and Wang, Mingxun and Kohlbacher, Oliver and Brazma, Alvis and Papatheodorou, Irene and Bandeira, Nuno and Deutsch, Eric W. and Vizca{\´i}no, Juan Antonio and Bai, Mingze and Sachsenberg, Timo and Levitsky, Lev I. and Perez-Riverol, Yasset}, title = {A proteomics sample metadata representation for multiomics integration and big data analysis}, volume = {12}, journal = {Nature Communications}, number = {5854}, doi = {https://doi.org/10.1038/s41467-021-26111-3}, year = {2021}, abstract = {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.}, language = {en} } @article{UmerZhuPfeufferetal.2021, author = {Umer, Husen M. and Zhu, Yafeng and Pfeuffer, Julianus and Sachsenberg, Timo and Lehti{\"o}, Janne and Branca, Rui and Perez-Riverol, Yasset}, title = {Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides}, journal = {Bioinformatics}, number = {5}, edition = {38}, publisher = {Oxford Academic}, pages = {1470 -- 1472}, year = {2021}, abstract = {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).}, language = {en} }