@article{WickHarteltPuppe2019, author = {Wick, Christoph and Hartelt, Alexander and Puppe, Frank}, title = {Staff, symbol and melody detection of Medieval manuscripts written in square notation using deep Fully Convolutional Networks}, series = {Applied Sciences}, volume = {9}, journal = {Applied Sciences}, number = {13}, issn = {2076-3417}, doi = {10.3390/app9132646}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-197248}, year = {2019}, abstract = {Even today, the automatic digitisation of scanned documents in general, but especially the automatic optical music recognition (OMR) of historical manuscripts, still remains an enormous challenge, since both handwritten musical symbols and text have to be identified. This paper focuses on the Medieval so-called square notation developed in the 11th-12th century, which is already composed of staff lines, staves, clefs, accidentals, and neumes that are roughly spoken connected single notes. The aim is to develop an algorithm that captures both the neumes, and in particular its melody, which can be used to reconstruct the original writing. Our pipeline is similar to the standard OMR approach and comprises a novel staff line and symbol detection algorithm based on deep Fully Convolutional Networks (FCN), which perform pixel-based predictions for either staff lines or symbols and their respective types. Then, the staff line detection combines the extracted lines to staves and yields an F\(_1\) -score of over 99\% for both detecting lines and complete staves. For the music symbol detection, we choose a novel approach that skips the step to identify neumes and instead directly predicts note components (NCs) and their respective affiliation to a neume. Furthermore, the algorithm detects clefs and accidentals. Our algorithm predicts the symbol sequence of a staff with a diplomatic symbol accuracy rate (dSAR) of about 87\%, which includes symbol type and location. If only the NCs without their respective connection to a neume, all clefs and accidentals are of interest, the algorithm reaches an harmonic symbol accuracy rate (hSAR) of approximately 90\%. In general, the algorithm recognises a symbol in the manuscript with an F\(_1\) -score of over 96\%.}, language = {en} } @article{WeissSchultz2015, author = {Weiß, Clemens Leonard and Schultz, J{\"o}rg}, title = {Identification of divergent WH2 motifs by HMM-HMM alignments}, series = {BMC Research Notes}, volume = {8}, journal = {BMC Research Notes}, number = {18}, doi = {10.1186/s13104-015-0981-7}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-126413}, year = {2015}, abstract = {Background The actin cytoskeleton is a hallmark of eukaryotic cells. Its regulation as well as its interaction with other proteins is carefully orchestrated by actin interaction domains. One of the key players is the WH2 motif, which enables binding to actin monomers and filaments and is involved in the regulation of actin nucleation. Contrasting conserved domains, the identification of this motif in protein sequences is challenging, as it is short and poorly conserved. Findings To identify divergent members, we combined Hidden-Markov-Model (HMM) to HMM alignments with orthology predictions. Thereby, we identified nearly 500 proteins containing so far not annotated WH2 motifs. This included shootin-1, an actin binding protein involved in neuron polarization. Among others, WH2 motifs of 'proximal to raf' (ptr)-orthologs, which are described in the literature, but not annotated in genome databases, were identified. Conclusion In summary, we increased the number of WH2 motif containing proteins substantially. This identification of candidate regions for actin interaction could steer their experimental characterization. Furthermore, the approach outlined here can easily be adapted to the identification of divergent members of further domain families.}, language = {en} } @article{WamserSeufertHalletal.2021, author = {Wamser, Florian and Seufert, Anika and Hall, Andrew and Wunderer, Stefan and Hoßfeld, Tobias}, title = {Valid statements by the crowd: statistical measures for precision in crowdsourced mobile measurements}, series = {Network}, volume = {1}, journal = {Network}, number = {2}, issn = {2673-8732}, doi = {10.3390/network1020013}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-284154}, pages = {215 -- 232}, year = {2021}, abstract = {Crowdsourced network measurements (CNMs) are becoming increasingly popular as they assess the performance of a mobile network from the end user's perspective on a large scale. Here, network measurements are performed directly on the end-users' devices, thus taking advantage of the real-world conditions end-users encounter. However, this type of uncontrolled measurement raises questions about its validity and reliability. The problem lies in the nature of this type of data collection. In CNMs, mobile network subscribers are involved to a large extent in the measurement process, and collect data themselves for the operator. The collection of data on user devices in arbitrary locations and at uncontrolled times requires means to ensure validity and reliability. To address this issue, our paper defines concepts and guidelines for analyzing the precision of CNMs; specifically, the number of measurements required to make valid statements. In addition to the formal definition of the aspect, we illustrate the problem and use an extensive sample data set to show possible assessment approaches. This data set consists of more than 20.4 million crowdsourced mobile measurements from across France, measured by a commercial data provider.}, language = {en} } @article{vonMammenWagnerKnoteetal.2017, author = {von Mammen, Sebastian Albrecht and Wagner, Daniel and Knote, Andreas and Taskin, Umut}, title = {Interactive simulations of biohybrid systems}, series = {Frontiers in Robotics and AI}, volume = {4}, journal = {Frontiers in Robotics and AI}, issn = {2296-9144}, doi = {10.3389/frobt.2017.00050}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-195755}, year = {2017}, abstract = {In this article, we present approaches to interactive simulations of biohybrid systems. These simulations are comprised of two major computational components: (1) agent-based developmental models that retrace organismal growth and unfolding of technical scaffoldings and (2) interfaces to explore these models interactively. Simulations of biohybrid systems allow us to fast forward and experience their evolution over time based on our design decisions involving the choice, configuration and initial states of the deployed biological and robotic actors as well as their interplay with the environment. We briefly introduce the concept of swarm grammars, an agent-based extension of L-systems for retracing growth processes and structural artifacts. Next, we review an early augmented reality prototype for designing and projecting biohybrid system simulations into real space. In addition to models that retrace plant behaviors, we specify swarm grammar agents to braid structures in a self-organizing manner. Based on this model, both robotic and plant-driven braiding processes can be experienced and explored in virtual worlds. We present an according user interface for use in virtual reality. As we present interactive models concerning rather diverse description levels, we only ensured their principal capacity for interaction but did not consider efficiency analyzes beyond prototypic operation. We conclude this article with an outlook on future works on melding reality and virtuality to drive the design and deployment of biohybrid systems.}, language = {en} } @article{VainshteinSanchezBrazmaetal.2010, author = {Vainshtein, Yevhen and Sanchez, Mayka and Brazma, Alvis and Hentze, Matthias W. and Dandekar, Thomas and Muckenthaler, Martina U.}, title = {The IronChip evaluation package: a package of perl modules for robust analysis of custom microarrays}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-67869}, year = {2010}, abstract = {Background: Gene expression studies greatly contribute to our understanding of complex relationships in gene regulatory networks. However, the complexity of array design, production and manipulations are limiting factors, affecting data quality. The use of customized DNA microarrays improves overall data quality in many situations, however, only if for these specifically designed microarrays analysis tools are available. Results: The IronChip Evaluation Package (ICEP) is a collection of Perl utilities and an easy to use data evaluation pipeline for the analysis of microarray data with a focus on data quality of custom-designed microarrays. The package has been developed for the statistical and bioinformatical analysis of the custom cDNA microarray IronChip but can be easily adapted for other cDNA or oligonucleotide-based designed microarray platforms. ICEP uses decision tree-based algorithms to assign quality flags and performs robust analysis based on chip design properties regarding multiple repetitions, ratio cut-off, background and negative controls. Conclusions: ICEP is a stand-alone Windows application to obtain optimal data quality from custom-designed microarrays and is freely available here (see "Additional Files" section) and at: http://www.alice-dsl.net/evgeniy. vainshtein/ICEP/}, subject = {Microarray}, language = {en} } @article{UnruhLandeckOberdoerferetal.2021, author = {Unruh, Fabian and Landeck, Maximilian and Oberd{\"o}rfer, Sebastian and Lugrin, Jean-Luc and Latoschik, Marc Erich}, title = {The Influence of Avatar Embodiment on Time Perception - Towards VR for Time-Based Therapy}, series = {Frontiers in Virtual Reality}, volume = {2}, journal = {Frontiers in Virtual Reality}, doi = {10.3389/frvir.2021.658509}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-259076}, pages = {658509}, year = {2021}, abstract = {Psycho-pathological conditions, such as depression or schizophrenia, are often accompanied by a distorted perception of time. People suffering from this conditions often report that the passage of time slows down considerably and that they are "stuck in time." Virtual Reality (VR) could potentially help to diagnose and maybe treat such mental conditions. However, the conditions in which a VR simulation could correctly diagnose a time perception deviation are still unknown. In this paper, we present an experiment investigating the difference in time experience with and without a virtual body in VR, also known as avatar. The process of substituting a person's body with a virtual body is called avatar embodiment. Numerous studies demonstrated interesting perceptual, emotional, behavioral, and psychological effects caused by avatar embodiment. However, the relations between time perception and avatar embodiment are still unclear. Whether or not the presence or absence of an avatar is already influencing time perception is still open to question. Therefore, we conducted a between-subjects design with and without avatar embodiment as well as a real condition (avatar vs. no-avatar vs. real). A group of 105 healthy subjects had to wait for seven and a half minutes in a room without any distractors (e.g., no window, magazine, people, decoration) or time indicators (e.g., clocks, sunlight). The virtual environment replicates the real physical environment. Participants were unaware that they will be asked to estimate their waiting time duration as well as describing their experience of the passage of time at a later stage. Our main finding shows that the presence of an avatar is leading to a significantly faster perceived passage of time. It seems to be promising to integrate avatar embodiment in future VR time-based therapy applications as they potentially could modulate a user's perception of the passage of time. We also found no significant difference in time perception between the real and the VR conditions (avatar, no-avatar), but further research is needed to better understand this outcome.}, language = {en} } @article{TsouliasJoerissenNuechter2022, author = {Tsoulias, Nikos and J{\"o}rissen, Sven and N{\"u}chter, Andreas}, title = {An approach for monitoring temperature on fruit surface by means of thermal point cloud}, series = {MethodsX}, volume = {9}, journal = {MethodsX}, issn = {2215-0161}, doi = {10.1016/j.mex.2022.101712}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-300270}, year = {2022}, abstract = {Heat and excessive solar radiation can produce abiotic stresses during apple maturation, resulting fruit quality. Therefore, the monitoring of temperature on fruit surface (FST) over the growing period can allow to identify thresholds, above of which several physiological disorders such as sunburn may occur in apple. The current approaches neglect spatial variation of FST and have reduced repeatability, resulting in unreliable predictions. In this study, LiDAR laser scanning and thermal imaging were employed to detect the temperature on fruit surface by means of 3D point cloud. A process for calibrating the two sensors based on an active board target and producing a 3D thermal point cloud was suggested. After calibration, the sensor system was utilised to scan the fruit trees, while temperature values assigned in the corresponding 3D point cloud were based on the extrinsic calibration. Whereas a fruit detection algorithm was performed to segment the FST from each apple. • The approach allows the calibration of LiDAR laser scanner with thermal camera in order to produce a 3D thermal point cloud. • The method can be applied in apple trees for segmenting FST in 3D. Whereas the approach can be utilised to predict several physiological disorders including sunburn on fruit surface.}, language = {en} } @article{ToepferCorovicFetteetal.2015, author = {Toepfer, Martin and Corovic, Hamo and Fette, Georg and Kl{\"u}gl, Peter and St{\"o}rk, Stefan and Puppe, Frank}, title = {Fine-grained information extraction from German transthoracic echocardiography reports}, series = {BMC Medical Informatics and Decision Making}, volume = {15}, journal = {BMC Medical Informatics and Decision Making}, number = {91}, doi = {doi:10.1186/s12911-015-0215-x}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-125509}, year = {2015}, abstract = {Background Information extraction techniques that get structured representations out of unstructured data make a large amount of clinically relevant information about patients accessible for semantic applications. These methods typically rely on standardized terminologies that guide this process. Many languages and clinical domains, however, lack appropriate resources and tools, as well as evaluations of their applications, especially if detailed conceptualizations of the domain are required. For instance, German transthoracic echocardiography reports have not been targeted sufficiently before, despite of their importance for clinical trials. This work therefore aimed at development and evaluation of an information extraction component with a fine-grained terminology that enables to recognize almost all relevant information stated in German transthoracic echocardiography reports at the University Hospital of W{\"u}rzburg. Methods A domain expert validated and iteratively refined an automatically inferred base terminology. The terminology was used by an ontology-driven information extraction system that outputs attribute value pairs. The final component has been mapped to the central elements of a standardized terminology, and it has been evaluated according to documents with different layouts. Results The final system achieved state-of-the-art precision (micro average.996) and recall (micro average.961) on 100 test documents that represent more than 90 \% of all reports. In particular, principal aspects as defined in a standardized external terminology were recognized with f 1=.989 (micro average) and f 1=.963 (macro average). As a result of keyword matching and restraint concept extraction, the system obtained high precision also on unstructured or exceptionally short documents, and documents with uncommon layout. Conclusions The developed terminology and the proposed information extraction system allow to extract fine-grained information from German semi-structured transthoracic echocardiography reports with very high precision and high recall on the majority of documents at the University Hospital of W{\"u}rzburg. Extracted results populate a clinical data warehouse which supports clinical research.}, language = {en} } @article{SirbuBeckerCaminitietal.2015, author = {S{\^i}rbu, Alina and Becker, Martin and Caminiti, Saverio and De Baets, Bernard and Elen, Bart and Francis, Louise and Gravino, Pietro and Hotho, Andreas and Ingarra, Stefano and Loreto, Vittorio and Molino, Andrea and Mueller, Juergen and Peters, Jan and Ricchiuti, Ferdinando and Saracino, Fabio and Servedio, Vito D.P. and Stumme, Gerd and Theunis, Jan and Tria, Francesca and Van den Bossche, Joris}, title = {Participatory Patterns in an International Air Quality Monitoring Initiative}, series = {PLoS ONE}, volume = {10}, journal = {PLoS ONE}, number = {8}, doi = {10.1371/journal. pone.0136763}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-151379}, pages = {e0136763}, year = {2015}, abstract = {The issue of sustainability is at the top of the political and societal agenda, being considered of extreme importance and urgency. Human individual action impacts the environment both locally (e.g., local air/water quality, noise disturbance) and globally (e.g., climate change, resource use). Urban environments represent a crucial example, with an increasing realization that the most effective way of producing a change is involving the citizens themselves in monitoring campaigns (a citizen science bottom-up approach). This is possible by developing novel technologies and IT infrastructures enabling large citizen participation. Here, in the wider framework of one of the first such projects, we show results from an international competition where citizens were involved in mobile air pollution monitoring using low cost sensing devices, combined with a web-based game to monitor perceived levels of pollution. Measures of shift in perceptions over the course of the campaign are provided, together with insights into participatory patterns emerging from this study. Interesting effects related to inertia and to direct involvement in measurement activities rather than indirect information exposure are also highlighted, indicating that direct involvement can enhance learning and environmental awareness. In the future, this could result in better adoption of policies towards decreasing pollution.}, language = {en} } @article{SteiningerKobsDavidsonetal.2021, author = {Steininger, Michael and Kobs, Konstantin and Davidson, Padraig and Krause, Anna and Hotho, Andreas}, title = {Density-based weighting for imbalanced regression}, series = {Machine Learning}, volume = {110}, journal = {Machine Learning}, number = {8}, issn = {1573-0565}, doi = {10.1007/s10994-021-06023-5}, url = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-269177}, pages = {2187-2211}, year = {2021}, abstract = {In many real world settings, imbalanced data impedes model performance of learning algorithms, like neural networks, mostly for rare cases. This is especially problematic for tasks focusing on these rare occurrences. For example, when estimating precipitation, extreme rainfall events are scarce but important considering their potential consequences. While there are numerous well studied solutions for classification settings, most of them cannot be applied to regression easily. Of the few solutions for regression tasks, barely any have explored cost-sensitive learning which is known to have advantages compared to sampling-based methods in classification tasks. In this work, we propose a sample weighting approach for imbalanced regression datasets called DenseWeight and a cost-sensitive learning approach for neural network regression with imbalanced data called DenseLoss based on our weighting scheme. DenseWeight weights data points according to their target value rarities through kernel density estimation (KDE). DenseLoss adjusts each data point's influence on the loss according to DenseWeight, giving rare data points more influence on model training compared to common data points. We show on multiple differently distributed datasets that DenseLoss significantly improves model performance for rare data points through its density-based weighting scheme. Additionally, we compare DenseLoss to the state-of-the-art method SMOGN, finding that our method mostly yields better performance. Our approach provides more control over model training as it enables us to actively decide on the trade-off between focusing on common or rare cases through a single hyperparameter, allowing the training of better models for rare data points.}, language = {en} }