We present a generator of virtual molecules that selects valid chem- istry on the basis of the octet rule. Also, we introduce a mesomer group key that allows a fast detection of duplicates in the generated *** to exis...
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scientific workflows have emerged as an important tool for combining computational power with data analysis for all scientific domains in e-science. They help scientists to design and execute complex in silico experim...
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scientific workflows have emerged as an important tool for combining computational power with data analysis for all scientific domains in e-science. They help scientists to design and execute complex in silico experiments. However, with increasing complexity it becomes more and more infeasible to optimize scientific workflows by trial and error. To address this issue, this paper describes the design of a new optimization phase integrated in the established scientific workflow life cycle. We have also developed a flexible optimization application programming interface (API) and have integrated it into a scientific workflow management system. A sample plugin for parameter optimization based on genetic algorithms illustrates, how the API enables rapid implementation of concrete workflow optimization methods. Finally, a use case taken from the area of structural bioinformatics validates how the optimization approach facilitates setup, execution and monitoring of workflow parameter optimization in high performance computing e-science environments.
The solution of coupled problems is one of the grand challenges in scientificcomputing. Many problems can only be solved partially. Not all dependencies can be taken into account, e.g. only subproblems can be solved ...
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The ever increasing number of experimentally resolved crystal structures supports the possibility of fully empirical crystal structure prediction for small organic molecules. Empirical methods promise to be significan...
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In this paper we suggest a novel systematization of Information Retrieval and Natural Language Processing problems. Using this rather general description of problems we are able to discuss and proof the equivalence of...
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ISBN:
(纸本)9781538623718
In this paper we suggest a novel systematization of Information Retrieval and Natural Language Processing problems. Using this rather general description of problems we are able to discuss and proof the equivalence of some problems. We provide reformulations of well-known problems like Named Entity Recognition using our novel description and discuss further research and the expected outcome. We will discuss the relation of two problems, cluster labeling and search query finding. With these results we are able to provide a novel optimization approach to both problems. This novel systematization approach provides a yet unknown view generating new classes of problems in NLP. It brings application and algorithmic approaches together and offers a better description with concepts of theoretical computer science.
We discuss and analyze a neural network architecture, that enables learning a model class for a set of different data samples rather than just learning a single model for a specific data sample. In this sense, it may ...
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In this paper we describe a multi-scale approach to ion migration processes, which involves a bridging from the atomic scale to the macroscopic scale. To this end, the diffusion coefficient of a material i.e. a macros...
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In this paper we describe a multi-scale approach to ion migration processes, which involves a bridging from the atomic scale to the macroscopic scale. To this end, the diffusion coefficient of a material i.e. a macroscopic physical quantity, will be appropriately determined from molecular dynamics simulations on the microscale. This way, performance predictions become possible prior to material synthesis. However, standard methods produce in general wrong results for ensemble setups which correspond to battery or capacitor *** introduce a novel method to derive correct values also for such problems. These values are then used in a macroscopic system of partial differential equation (Poisson-Nernst-Planck system) for the numerical simulation of ion migration in a battery.
The fast wavelet transform is an important workhorse in signal processing. Wavelets are local in the spatial- or temporal- and the frequency-domain. This property enables frequency domain analysis while preserving som...
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The fast wavelet transform is an important workhorse in signal processing. Wavelets are local in the spatial- or temporal- and the frequency-domain. This property enables frequency domain analysis while preserving some spatiotemporal information. Until recently, wavelets rarely appeared in the machine learning literature. We provide the PyTorch Wavelet Toolbox to make wavelet methods more accessible to the deep learning community. Our PyTorch Wavelet Toolbox is well documented. A pip package is installable with pip install ptwt.
We have developed a system for the automatic reconstruction of chemical molecules from images. The system takes as input an electronically produced image of a chemical molecule and produces an SDF file containing the ...
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