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Ice accumulation in the blades of wind turbines can cause them to describe anomalous rotations or no rotations at all, thus affecting the generation of electricity and power output. In this work, we investigate the problem of ice accumulation in wind turbines by framing it as anomaly detection of multi-variate time series. Our approach focuses on two main parts: first, learning low-dimensional representations of time series using a Variational Recurrent Autoencoder (VRAE), and second, using unsupervised clustering algorithms to classify the learned representations as normal (no ice accumulated) or abnormal (ice accumulated). We have evaluated our approach on a custom wind turbine time series dataset, for the two-classes problem (one normal versus one abnormal class), we obtained a classification accuracy of up to 96$\%$ on test data. For the multiple-class problem (one normal versus multiple abnormal classes), we present a qualitative analysis of the low-dimensional learned latent space, providing insights into the capacities of our approach to tackle such problem. The code to reproduce this work can be found here https://github.com/agrija9/Wind-Turbines-VRAE-Paper.
Machine learning and neural networks are now ubiquitous in sonar perception, but it lags behind the computer vision field due to the lack of data and pre-trained models specifically for sonar images. In this paper we present the Marine Debris Turntable dataset and produce pre-trained neural networks trained on this dataset, meant to fill the gap of missing pre-trained models for sonar images. We train Resnet 20, MobileNets, DenseNet121, SqueezeNet, MiniXception, and an Autoencoder, over several input image sizes, from 32 x 32 to 96 x 96, on the Marine Debris turntable dataset. We evaluate these models using transfer learning for low-shot classification in the Marine Debris Watertank and another dataset captured using a Gemini 720i sonar. Our results show that in both datasets the pre-trained models produce good features that allow good classification accuracy with low samples (10-30 samples per class). The Gemini dataset validates that the features transfer to other kinds of sonar sensors. We expect that the community benefits from the public release of our pre-trained models and the turntable dataset.
It has been well proved that deep networks are efficient at extracting features from a given (source) labeled dataset. However, it is not always the case that they can generalize well to other (target) datasets which very often have a different underlying distribution. In this report, we evaluate four different domain adaptation techniques for image classification tasks: DeepCORAL, DeepDomainConfusion, CDAN and CDAN+E. These techniques are unsupervised given that the target dataset dopes not carry any labels during training phase. We evaluate model performance on the office-31 dataset. A link to the github repository of this report can be found here: https://github.com/agrija9/Deep-Unsupervised-Domain-Adaptation.
Recent experimental evidence suggest that mebendazole, a popular antiparasitic drug, binds to heat shock protein 90 (Hsp90) and inhibit acute myeloid leukemia cell growth. In this study we use quantum mechanics (QM), molecular similarity and molecular dynamics (MD) calculations to predict possible binding poses of mebendazole to the adenosine triphosphate (ATP) binding site of Hsp90. Extensive conformational searches and minimization of the five tautomers of mebendazole using MP2/aug-cc-pVTZ theory level resulting in 152 minima being identified. Mebendazole-Hsp90 complex models were created using the QM optimized conformations and protein coordinates obtained from experimental crystal structures that were chosen through similarity calculations. Nine different poses were identified from a total of 600 ns of explicit solvent, all-atom MD simulations using two different force fields. All simulations support the hypothesis that mebendazole is able to bind to the ATP binding site of Hsp90.
Urban LoRa networks promise to provide a cost-efficient and scalable communication backbone for smart cities. One core challenge in rolling out and operating these networks is radio network planning, i.e., precise predictions about possible new locations and their impact on network coverage. Path loss models aid in this task, but evaluating and comparing different models requires a sufficiently large set of high-quality received packet power samples. In this paper, we report on a corresponding large-scale measurement study covering an urban area of 200km2 over a period of 230 days using sensors deployed on garbage trucks, resulting in more than 112 thousand high-quality samples for received packet power. Using this data, we compare eleven previously proposed path loss models and additionally provide new coefficients for the Log-distance model. Our results reveal that the Log-distance model and other well-known empirical models such as Okumura or Winner+ provide reasonable estimations in an urban environment, and terrain based models such as ITM or ITWOM have no advantages. In addition, we derive estimations for the needed sample size in similar measurement campaigns. To stimulate further research in this direction, we make all our data publicly available.
The majority of biomedical knowledge is stored in structured databases or as unstructured text in scientific publications. This vast amount of information has led to numerous machine learning-based biological applications using either text through natural language processing (NLP) or structured data through knowledge graph embedding models (KGEMs). However, representations based on a single modality are inherently limited. To generate better representations of biological knowledge, we propose STonKGs, a Sophisticated Transformer trained on biomedical text and Knowledge Graphs. This multimodal Transformer uses combined input sequences of structured information from KGs and unstructured text data from biomedical literature to learn joint representations. First, we pre-trained STonKGs on a knowledge base assembled by the Integrated Network and Dynamical Reasoning Assembler (INDRA) consisting of millions of text-triple pairs extracted from biomedical literature by multiple NLP systems. Then, we benchmarked STonKGs against two baseline models trained on either one of the modalities (i.e., text or KG) across eight different classification tasks, each corresponding to a different biological application. Our results demonstrate that STonKGs outperforms both baselines, especially on the more challenging tasks with respect to the number of classes, improving upon the F1-score of the best baseline by up to 0.083. Additionally, our pre-trained model as well as the model architecture can be adapted to various other transfer learning applications. Finally, the source code and pre-trained STonKGs models are available at https://github.com/stonkgs/stonkgs and https://huggingface.co/stonkgs/stonkgs-150k.
Application of underwater robots are on the rise, most of them are dependent on sonar for underwater vision, but the lack of strong perception capabilities limits them in this task. An important issue in sonar perception is matching image patches, which can enable other techniques like localization, change detection, and mapping. There is a rich literature for this problem in color images, but for acoustic images, it is lacking, due to the physics that produce these images. In this paper we improve on our previous results for this problem (Valdenegro-Toro et al, 2017), instead of modeling features manually, a Convolutional Neural Network (CNN) learns a similarity function and predicts if two input sonar images are similar or not. With the objective of improving the sonar image matching problem further, three state of the art CNN architectures are evaluated on the Marine Debris dataset, namely DenseNet, and VGG, with a siamese or two-channel architecture, and contrastive loss. To ensure a fair evaluation of each network, thorough hyper-parameter optimization is executed. We find that the best performing models are DenseNet Two-Channel network with 0.955 AUC, VGG-Siamese with contrastive loss at 0.949 AUC and DenseNet Siamese with 0.921 AUC. By ensembling the top performing DenseNet two-channel and DenseNet-Siamese models overall highest prediction accuracy obtained is 0.978 AUC, showing a large improvement over the 0.91 AUC in the state of the art.
The ability to discriminate between different ionic species, termed ion selectivity, is a key feature of ion channels and forms the basis for their physiological function. Members of the degenerin/epithelial sodium channel (DEG/ENaC) superfamily of trimeric ion channels are typically sodium selective, but to a surprisingly variable degree. While acid-sensing ion channels (ASICs) are weakly sodium selective (sodium:potassium around 10:1), ENaCs show a remarkably high preference for sodium over potassium (>500:1). The most obvious explanation for this discrepancy may be expected to originate from differences in the pore-lining second transmembrane segment (M2). However, these show a relatively high degree of sequence conservation between ASICs and ENaCs and previous functional and structural studies could not unequivocally establish that differences in M2 alone can account for the disparate degrees of ion selectivity. By contrast, surprisingly little is known about the contributions of the first transmembrane segment (M1) and the preceding pre-M1 region. In this study, we use conventional and non-canonical amino acid-based mutagenesis in combination with a variety of electrophysiological approaches to show that the pre-M1 and M1 regions of mASIC1a channels are major determinants of ion selectivity. Mutational investigations of the corresponding regions in hENaC show that they contribute less to ion selectivity, despite affecting ion conductance. In conclusion, our work supports the notion that the remarkably different degrees of sodium selectivity in ASICs and ENaCs are achieved through different mechanisms. The results further highlight how M1 and pre-M1 are likely to differentially affect pore structure in these related channels.
The clear-sky radiative effect of aerosol-radiation interactions is of relevance for our understanding of the climate system. The influence of aerosol on the surface energy budget is of high interest for the renewable energy sector. In this study, the radiative effect is investigated in particular with respect to seasonal and regional variations for the region of Germany and the year 2015 at the surface and top of atmosphere using two complementary approaches.
First, an ensemble of clear-sky models which explicitly consider aerosols is utilized to retrieve the aerosol optical depth and the surface direct radiative effect of aerosols by means of a clear sky fitting technique. For this, short-wave broadband irradiance measurements in the absence of clouds are used as a basis. A clear sky detection algorithm is used to identify cloud free observations. Considered are measurements of the shortwave broadband global and diffuse horizontal irradiance with shaded and unshaded pyranometers at 25 stations across Germany within the observational network of the German Weather Service (DWD). Clear sky models used are MMAC, MRMv6.1, METSTAT, ESRA, Heliosat-1, CEM and the simplified Solis model. The definition of aerosol and atmospheric characteristics of the models are examined in detail for their suitability for this approach.
Second, the radiative effect is estimated using explicit radiative transfer simulations with inputs on the meteorological state of the atmosphere, trace-gases and aerosol from CAMS reanalysis. The aerosol optical properties (aerosol optical depth, Ångström exponent, single scattering albedo and assymetrie parameter) are first evaluated with AERONET direct sun and inversion products. The largest inconsistency is found for the aerosol absorption, which is overestimated by about 0.03 or about 30 % by the CAMS reanalysis. Compared to the DWD observational network, the simulated global, direct and diffuse irradiances show reasonable agreement within the measurement uncertainty. The radiative kernel method is used to estimate the resulting uncertainty and bias of the simulated direct radiative effect. The uncertainty is estimated to −1.5 ± 7.7 and 0.6 ± 3.5 W m−2 at the surface and top of atmosphere, respectively, while the annual-mean biases at the surface, top of atmosphere and total atmosphere are −10.6, −6.5 and 4.1 W m−2, respectively.
The retrieval of the aerosol radiative effect with the clear sky models shows a high level of agreement with the radiative transfer simulations, with an RMSE of 5.8 W m−2 and a correlation of 0.75. The annual mean of the REari at the surface for the 25 DWD stations shows a value of −12.8 ± 5 W m−2 as average over the clear sky models, compared to −11 W m−2 from the radiative transfer simulations. Since all models assume a fixed aerosol characterisation, the annual cycle of the aerosol radiation effect cannot be reproduced. Out of this set of clear sky models, the largest level of agreement is shown by the ESRA and MRMv6.1 models.
The lattice Boltzmann method (LBM) is an efficient simulation technique for computational fluid mechanics and beyond. It is based on a simple stream-and-collide algorithm on Cartesian grids, which is easily compatible with modern machine learning architectures. While it is becoming increasingly clear that deep learning can provide a decisive stimulus for classical simulation techniques, recent studies have not addressed possible connections between machine learning and LBM. Here, we introduce Lettuce, a PyTorch-based LBM code with a threefold aim. Lettuce enables GPU accelerated calculations with minimal source code, facilitates rapid prototyping of LBM models, and enables integrating LBM simulations with PyTorch's deep learning and automatic differentiation facility. As a proof of concept for combining machine learning with the LBM, a neural collision model is developed, trained on a doubly periodic shear layer and then transferred to a different flow, a decaying turbulence. We also exemplify the added benefit of PyTorch's automatic differentiation framework in flow control and optimization. To this end, the spectrum of a forced isotropic turbulence is maintained without further constraining the velocity field.
The promotion of sustainable packaging is part of the European Green Deal and plays a key role in the EU’s social and political strategy. One option is the use of renewable resources and biomass waste as raw materials for polymer production. Lignocellulose biomass from annual and perennial industrial crops and agricultural residues are a major source of polysaccharides, proteins, and lignin, and can also be used to obtain plant-based extracts and essential oils. Therefore, these biomasses are considered as potential substitute for fossil-based resources. Here, the status quo of bio-based polymers is discussed and evaluated in terms of properties related to packaging applications such as gas and water vapor permeability as well as mechanical properties. So far, their practical use is still restricted due to lower performance in fundamental packaging functions that directly influence food quality and safety, the length of shelf life and thus the amount of food waste. Besides bio-based polymers, this review focuses on plant extracts as active packaging agents. Incorporating extracts of herbs, flowers, trees, and their fruits is inevitable to achieve desired material properties that are capable to prolong the food shelf life. Finally, the adoption potential of packaging based on polymers from renewable resources is discussed from a bioeconomy perspective.
The Covid-19 pandemic has challenged educators across the world to move their teaching and mentoring from in-person to remote. During nonpandemic semesters at their institutes (e.g. universities), educators can directly provide students the software environment needed to support their learning - either in specialized computer laboratories (e.g. computational chemistry labs) or shared computer spaces. These labs are often supported by staff that maintains the operating systems (OS) and software. But how does one provide a specialized software environment for remote teaching? One solution is to provide students a customized operating system (e.g., Linux) that includes open-source software for supporting your teaching goals. However, such a solution should not require students to install the OS alongside their existing one (i.e. dual/multi-booting) or be used as a complete replacement. Such approaches are risky because of a) the students' possible lack of software expertise, b) the possible disruption of an existing software workflow that is needed in other classes or by other family members, and c) the importance of maintaining a working computer when isolated (e.g. societal restrictions). To illustrate possible solutions, we discuss our approach that used a customized Linux OS and a Docker container in a course that teaches computational chemistry and Python3.
In this contribution, we perform computer simulations to expedite the development of hydrogen storages based on metal hydride. These simulations enable in-depth analysis of the processes within the systems which otherwise could not be achieved. That is, because the determination of crucial process properties require measurement instruments in the setup which are currently not available. Therefore, we investigate the reliability of reaction values that are determined by a design of experiments.
Specifically, we first explain our model setup in detail. We define the mathematical terms to obtain insights into the thermal processes and reaction kinetics. We then compare the simulated results to measurements of a 5-gram sample consisting of iron-titanium-manganese (FeTiMn) to obtain the values with the highest agreement with the experimental data. In addition, we improve the model by replacing the commonly used Van’t-Hoff equation by a mathematical expression of the pressure-composition-isotherms (PCI) to calculate the equilibrium pressure.
Finally, the parameters’ accuracy is checked in yet another with an existing metal hydride system. The simulated results demonstrate high concordance with experimental data, which advocate the usage of approximated kinetic reaction properties by a design of experiments for further design studies. Furthermore, we are able to determine process parameters like the entropy and enthalpy.
Risk-based authentication (RBA) aims to strengthen password-based authentication rather than replacing it. RBA does this by monitoring and recording additional features during the login process. If feature values at login time differ significantly from those observed before, RBA requests an additional proof of identification. Although RBA is recommended in the NIST digital identity guidelines, it has so far been used almost exclusively by major online services. This is partly due to a lack of open knowledge and implementations that would allow any service provider to roll out RBA protection to its users.
To close this gap, we provide a first in-depth analysis of RBA characteristics in a practical deployment. We observed N=780 users with 247 unique features on a real-world online service for over 1.8 years. Based on our collected data set, we provide (i) a behavior analysis of two RBA implementations that were apparently used by major online services in the wild, (ii) a benchmark of the features to extract a subset that is most suitable for RBA use, (iii) a new feature that has not been used in RBA before, and (iv) factors which have a significant effect on RBA performance. Our results show that RBA needs to be carefully tailored to each online service, as even small configuration adjustments can greatly impact RBA's security and usability properties. We provide insights on the selection of features, their weightings, and the risk classification in order to benefit from RBA after a minimum number of login attempts.
Off-lattice Boltzmann methods increase the flexibility and applicability of lattice Boltzmann methods by decoupling the discretizations of time, space, and particle velocities. However, the velocity sets that are mostly used in off-lattice Boltzmann simulations were originally tailored to on-lattice Boltzmann methods. In this contribution, we show how the accuracy and efficiency of weakly and fully compressible semi-Lagrangian off-lattice Boltzmann simulations is increased by velocity sets derived from cubature rules, i.e. multivariate quadratures, which have not been produced by the Gauss-product rule. In particular, simulations of 2D shock-vortex interactions indicate that the cubature-derived degree-nine D2Q19 velocity set is capable to replace the Gauss-product rule-derived D2Q25. Likewise, the degree-five velocity sets D3Q13 and D3Q21, as well as a degree-seven D3V27 velocity set were successfully tested for 3D Taylor-Green vortex flows to challenge and surpass the quality of the customary D3Q27 velocity set. In compressible 3D Taylor-Green vortex flows with Mach numbers Ma={0.5;1.0;1.5;2.0} on-lattice simulations with velocity sets D3Q103 and D3V107 showed only limited stability, while the off-lattice degree-nine D3Q45 velocity set accurately reproduced the kinetic energy provided by literature.