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Background: The technical development of imaging techniques in life sciences has enabled the three-dimensional recording of living samples at increasing temporal resolutions. Dynamic 3D data sets of developing organisms allow for time-resolved quantitative analyses of morphogenetic changes in three dimensions, but require efficient and automatable analysis pipelines to tackle the resulting Terabytes of image data. Particle image velocimetry (PIV) is a robust and segmentation-free technique that is suitable for quantifying collective cellular migration on data sets with different labeling schemes. This paper presents the implementation of an efficient 3D PIV package using the Julia programming language—quickPIV. Our software is focused on optimizing CPU performance and ensuring the robustness of the PIV analyses on biological data.
Results: QuickPIV is three times faster than the Python implementation hosted in openPIV, both in 2D and 3D. Our software is also faster than the fastest 2D PIV package in openPIV, written in C++. The accuracy evaluation of our software on synthetic data agrees with the expected accuracies described in the literature. Additionally, by applying quickPIV to three data sets of the embryogenesis of Tribolium castaneum, we obtained vector fields that recapitulate the migration movements of gastrulation, both in nuclear and actin-labeled embryos. We show normalized squared error cross-correlation to be especially accurate in detecting translations in non-segmentable biological image data.
Conclusions: The presented software addresses the need for a fast and open-source 3D PIV package in biological research. Currently, quickPIV offers efficient 2D and 3D PIV analyses featuring zero-normalized and normalized squared error cross-correlations, sub-pixel/voxel approximation, and multi-pass. Post-processing options include filtering and averaging of the resulting vector fields, extraction of velocity, divergence and collectiveness maps, simulation of pseudo-trajectories, and unit conversion. In addition, our software includes functions to visualize the 3D vector fields in Paraview.
AttendAffectNet-emotion prediction of movie viewers using multimodal fusion with self-attention
(2021)
In this paper, we tackle the problem of predicting the affective responses of movie viewers, based on the content of the movies. Current studies on this topic focus on video representation learning and fusion techniques to combine the extracted features for predicting affect. Yet, these typically, while ignoring the correlation between multiple modality inputs, ignore the correlation between temporal inputs (i.e., sequential features). To explore these correlations, a neural network architecture—namely AttendAffectNet (AAN)—uses the self-attention mechanism for predicting the emotions of movie viewers from different input modalities. Particularly, visual, audio, and text features are considered for predicting emotions (and expressed in terms of valence and arousal). We analyze three variants of our proposed AAN: Feature AAN, Temporal AAN, and Mixed AAN. The Feature AAN applies the self-attention mechanism in an innovative way on the features extracted from the different modalities (including video, audio, and movie subtitles) of a whole movie to, thereby, capture the relationships between them. The Temporal AAN takes the time domain of the movies and the sequential dependency of affective responses into account. In the Temporal AAN, self-attention is applied on the concatenated (multimodal) feature vectors representing different subsequent movie segments. In the Mixed AAN, we combine the strong points of the Feature AAN and the Temporal AAN, by applying self-attention first on vectors of features obtained from different modalities in each movie segment and then on the feature representations of all subsequent (temporal) movie segments. We extensively trained and validated our proposed AAN on both the MediaEval 2016 dataset for the Emotional Impact of Movies Task and the extended COGNIMUSE dataset. Our experiments demonstrate that audio features play a more influential role than those extracted from video and movie subtitles when predicting the emotions of movie viewers on these datasets. The models that use all visual, audio, and text features simultaneously as their inputs performed better than those using features extracted from each modality separately. In addition, the Feature AAN outperformed other AAN variants on the above-mentioned datasets, highlighting the importance of taking different features as context to one another when fusing them. The Feature AAN also performed better than the baseline models when predicting the valence dimension.
Background: Clinical trial registries increase transparency in medical research by making information and results of planned, ongoing, and completed studies publicly available. However, the registration of clinical trials remains a time-consuming manual task complicated by the fact that the same studies often need to be registered in different registries with different data entry requirements and interfaces.
Objective: This study investigates how Health Level 7 (HL7) Fast Healthcare Interoperability Resources (FHIR) may be used as a standardized format for exchanging and storing clinical trial records.
Methods: We designed and prototypically implemented an open-source central trial registry containing records from university hospitals, which are automatically exported and updated by local study management systems.
Results: We provided an architecture and implementation of a multisite clinical trials registry based on HL7 FHIR as a data storage and exchange format.
Conclusions: The results show that FHIR resources establish a harmonized view of study information from heterogeneous sources by enabling automated data exchange between trial centers and central study registries.
A deep convolutional neural network (CNN) is developed to study symmetry energy (Esym(ρ)) effects by learning the mapping between the symmetry energy and the two-dimensional (transverse momentum and rapidity) distributions of protons and neutrons in heavy-ion collisions. Supervised training is performed with labeled data-set from the ultrarelativistic quantum molecular dynamics (UrQMD) model simulation. It is found that, by using proton spectra on event-by-event basis as input, the accuracy for classifying the soft and stiff Esym(ρ) is about 60% due to large event-by-event fluctuations, while by setting event-summed proton spectra as input, the classification accuracy increases to 98%. The accuracies for 5-label (5 different Esym(ρ)) classification task are about 58% and 72% by using proton and neutron spectra, respectively. For the regression task, the mean absolute errors (MAE) which measure the average magnitude of the absolute differences between the predicted and actual L (the slope parameter of Esym(ρ)) are about 20.4 and 14.8 MeV by using proton and neutron spectra, respectively. Fingerprints of the density-dependent nuclear symmetry energy on the transverse momentum and rapidity distributions of protons and neutrons can be identified by convolutional neural network algorithm.
Because it is associated with central nervous changes, and olfactory dysfunction has been reported with increased prevalence among persons with diabetes, this study addressed the question of whether the risk of developing diabetes in the next 10 years is reflected in olfactory symptoms. In a cross-sectional study, in 164 individuals seeking medical consulting for possible diabetes, olfactory function was evaluated using a standardized clinical test assessing olfactory threshold, odor discrimination, and odor identification. Metabolomics parameters were assessed via blood concentrations. The individual diabetes risk was quantified according to the validated German version of the “FINDRISK” diabetes risk score. Machine learning algorithms trained with metabolomics patterns predicted low or high diabetes risk with a balanced accuracy of 63–75%. Similarly, olfactory subtest results predicted the olfactory dysfunction category with a balanced accuracy of 85–94%, occasionally reaching 100%. However, olfactory subtest results failed to improve the prediction of diabetes risk based on metabolomics data, and metabolomics data did not improve the prediction of the olfactory dysfunction category based on olfactory subtest results. Results of the present study suggest that olfactory function is not a useful predictor of diabetes.
The use of artificial intelligence (AI) systems in biomedical and clinical settings can disrupt the traditional doctor–patient relationship, which is based on trust and transparency in medical advice and therapeutic decisions. When the diagnosis or selection of a therapy is no longer made solely by the physician, but to a significant extent by a machine using algorithms, decisions become nontransparent. Skill learning is the most common application of machine learning algorithms in clinical decision making. These are a class of very general algorithms (artificial neural networks, classifiers, etc.), which are tuned based on examples to optimize the classification of new, unseen cases. It is pointless to ask for an explanation for a decision. A detailed understanding of the mathematical details of an AI algorithm may be possible for experts in statistics or computer science. However, when it comes to the fate of human beings, this “developer’s explanation” is not sufficient. The concept of explainable AI (XAI) as a solution to this problem is attracting increasing scientific and regulatory interest. This review focuses on the requirement that XAIs must be able to explain in detail the decisions made by the AI to the experts in the field.
Consciousness transiently fades away during deep sleep, more stably under anesthesia, and sometimes permanently due to brain injury. The development of an index to quantify the level of consciousness across these different states is regarded as a key problem both in basic and clinical neuroscience. We argue that this problem is ill-defined since such an index would not exhaust all the relevant information about a given state of consciousness. While the level of consciousness can be taken to describe the actual brain state, a complete characterization should also include its potential behavior against external perturbations. We developed and analyzed whole-brain computational models to show that the stability of conscious states provides information complementary to their similarity to conscious wakefulness. Our work leads to a novel methodological framework to sort out different brain states by their stability and reversibility, and illustrates its usefulness to dissociate between physiological (sleep), pathological (brain-injured patients), and pharmacologically-induced (anesthesia) loss of consciousness.
Artificial neural networks, taking inspiration from biological neurons, have become an invaluable tool for machine learning applications. Recent studies have developed techniques to effectively tune the connectivity of sparsely-connected artificial neural networks, which have the potential to be more computationally efficient than their fully-connected counterparts and more closely resemble the architectures of biological systems. We here present a normalisation, based on the biophysical behaviour of neuronal dendrites receiving distributed synaptic inputs, that divides the weight of an artificial neuron’s afferent contacts by their number. We apply this dendritic normalisation to various sparsely-connected feedforward network architectures, as well as simple recurrent and self-organised networks with spatially extended units. The learning performance is significantly increased, providing an improvement over other widely-used normalisations in sparse networks. The results are two-fold, being both a practical advance in machine learning and an insight into how the structure of neuronal dendritic arbours may contribute to computation.
Diminished sense of smell impairs the quality of life but olfactorily disabled people are hardly considered in measures of disability inclusion. We aimed to stratify perceptual characteristics and odors according to the extent to which they are perceived differently with reduced sense of smell, as a possible basis for creating olfactory experiences that are enjoyed in a similar way by subjects with normal or impaired olfactory function. In 146 subjects with normal or reduced olfactory function, perceptual characteristics (edibility, intensity, irritation, temperature, familiarity, hedonics, painfulness) were tested for four sets of 10 different odors each. Data were analyzed with (i) a projection based on principal component analysis and (ii) the training of a machine-learning algorithm in a 1000-fold cross-validated setting to distinguish between olfactory diagnosis based on odor property ratings. Both analytical approaches identified perceived intensity and familiarity with the odor as discriminating characteristics between olfactory diagnoses, while evoked pain sensation and perceived temperature were not discriminating, followed by edibility. Two disjoint sets of odors were identified, i.e., d = 4 “discriminating odors” with respect to olfactory diagnosis, including cis-3-hexenol, methyl salicylate, 1-butanol and cineole, and d = 7 “non-discriminating odors”, including benzyl acetate, heptanal, 4-ethyl-octanoic acid, methional, isobutyric acid, 4-decanolide and p-cresol. Different weightings of the perceptual properties of odors with normal or reduced sense of smell indicate possibilities to create sensory experiences such as food, meals or scents that by emphasizing trigeminal perceptions can be enjoyed by both normosmic and hyposmic individuals.
Sample-based longitudinal discrete choice experiments: preferences for electric vehicles over time
(2021)
Discrete choice experiments have emerged as the state-of-the-art method for measuring preferences, but they are mostly used in cross-sectional studies. In seeking to make them applicable for longitudinal studies, our study addresses two common challenges: working with different respondents and handling altering attributes. We propose a sample-based longitudinal discrete choice experiment in combination with a covariate-extended hierarchical Bayes logit estimator that allows one to test the statistical significance of changes. We showcase this method’s use in studies about preferences for electric vehicles over six years and empirically observe that preferences develop in an unpredictable, non-monotonous way. We also find that inspecting only the absolute differences in preferences between samples may result in misleading inferences. Moreover, surveying a new sample produced similar results as asking the same sample of respondents over time. Finally, we experimentally test how adding or removing an attribute affects preferences for the other attributes.
Correction to: Computational Economics https://doi.org/10.1007/s10614-020-10061-x
The original publication has been updated. In the original publication of this article, under the Introduction heading section, the corrections to the second paragraph’s inline equation were not incorporated. The author’s additional corrections have also been incorporated. The publisher apologizes for the error made during production.
Modeling long-term neuronal dynamics may require running long-lasting simulations. Such simulations are computationally expensive, and therefore it is advantageous to use simplified models that sufficiently reproduce the real neuronal properties. Reducing the complexity of the neuronal dendritic tree is one option. Therefore, we have developed a new reduced-morphology model of the rat CA1 pyramidal cell which retains major dendritic branch classes. To validate our model with experimental data, we used HippoUnit, a recently established standardized test suite for CA1 pyramidal cell models. The HippoUnit allowed us to systematically evaluate the somatic and dendritic properties of the model and compare them to models publicly available in the ModelDB database. Our model reproduced (1) somatic spiking properties, (2) somatic depolarization block, (3) EPSP attenuation, (4) action potential backpropagation, and (5) synaptic integration at oblique dendrites of CA1 neurons. The overall performance of the model in these tests achieved higher biological accuracy compared to other tested models. We conclude that, due to its realistic biophysics and low morphological complexity, our model captures key physiological features of CA1 pyramidal neurons and shortens computational time, respectively. Thus, the validated reduced-morphology model can be used for computationally demanding simulations as a substitute for more complex models.
Korrektur zu: Höllbacher, S., Wittum, G. Correction to: A sharp interface method using enriched finite elements for elliptic interface problems. Numer. Math. 147, 783 (2021). DOI: 10.1007/s00211-021-01180-0.
We present an immersed boundary method for the solution of elliptic interface problems with discontinuous coefficients which provides a second-order approximation of the solution. The proposed method can be categorised as an extended or enriched finite element method. In contrast to other extended FEM approaches, the new shape functions get projected in order to satisfy the Kronecker-delta property with respect to the interface. The resulting combination of projection and restriction was already derived in Höllbacher and Wittum (TBA, 2019a) for application to particulate flows. The crucial benefits are the preservation of the symmetry and positive definiteness of the continuous bilinear operator. Besides, no additional stabilisation terms are necessary. Furthermore, since our enrichment can be interpreted as adaptive mesh refinement, the standard integration schemes can be applied on the cut elements. Finally, small cut elements do not impair the condition of the scheme and we propose a simple procedure to ensure good conditioning independent of the location of the interface. The stability and convergence of the solution will be proven and the numerical tests demonstrate optimal order of convergence.
Solving High-Dimensional Dynamic Portfolio Choice Models with Hierarchical B-Splines on Sparse Grids
(2021)
Discrete time dynamic programming to solve dynamic portfolio choice models has three immanent issues: firstly, the curse of dimensionality prohibits more than a handful of continuous states. Secondly, in higher dimensions, even regular sparse grid discretizations need too many grid points for sufficiently accurate approximations of the value function. Thirdly, the models usually require continuous control variables, and hence gradient-based optimization with smooth approximations of the value function is necessary to obtain accurate solutions to the optimization problem. For the first time, we enable accurate and fast numerical solutions with gradient-based optimization while still allowing for spatial adaptivity using hierarchical B-splines on sparse grids. When compared to the standard linear bases on sparse grids or finite difference approximations of the gradient, our approach saves an order of magnitude in total computational complexity for a representative dynamic portfolio choice model with varying state space dimensionality, stochastic sample space, and choice variables.
Gegenstände und Gesichter können Computer schon recht gut erkennen, auch dass sich etwas bewegt und in welche Richtung. Schwierigkeiten bereiten der Künstlichen Intelligenz aber noch zu erfassen, um welche Art von Bewegungen es sich handelt. Das lernen Computer jetzt im Labor von Prof. Hilde Kühne an der Goethe-Universität.
Biodiversity information is contained in countless digitized and unprocessed scholarly texts. Although automated extraction of these data has been gaining momentum for years, there are still innumerable text sources that are poorly accessible and require a more advanced range of methods to extract relevant information. To improve the access to semantic biodiversity information, we have launched the BIOfid project (www.biofid.de) and have developed a portal to access the semantics of German language biodiversity texts, mainly from the 19th and 20th century. However, to make such a portal work, a couple of methods had to be developed or adapted first. In particular, text-technological information extraction methods were needed, which extract the required information from the texts. Such methods draw on machine learning techniques, which in turn are trained by learning data. To this end, among others, we gathered the BIOfid text corpus, which is a cooperatively built resource, developed by biologists, text technologists, and linguists. A special feature of BIOfid is its multiple annotation approach, which takes into account both general and biology-specific classifications, and by this means goes beyond previous, typically taxon- or ontology-driven proper name detection. We describe the design decisions and the genuine Annotation Hub Framework underlying the BIOfid annotations and present agreement results. The tools used to create the annotations are introduced, and the use of the data in the semantic portal is described. Finally, some general lessons, in particular with multiple annotation projects, are drawn.
The mobile games business is an ever-increasing sub-sector of the entertainment industry. Due to its high profitability but also high risk and competitive atmosphere, game publishers need to develop strategies that allow them to release new products at a high rate, but without compromising the already short lifespan of the firms' existing games. Successful game publishers must enlarge their user base by continually releasing new and entertaining games, while simultaneously motivating the current user base of existing games to remain active for more extended periods. Since the core-component reuse strategy has proven successful in other software products, this study investigates the advantages and drawbacks of this strategy in mobile games. Drawing on the widely accepted Product Life Cycle concept, the study investigates whether the introduction of a new mobile game built with core-components of an existing mobile game curtails the incumbent's product life cycle. Based on real and granular data on the gaming activity of a popular mobile game, the authors find that by promoting multi-homing (i.e., by smartly interlinking the incumbent and new product with each other so that users start consuming both games in parallel), the core-component reuse strategy can prolong the lifespan of the incumbent game.
Digital distractions can interfere with goal attainment and lead to undesirable habits that are hard to get red rid of. Various digital self-control interventions promise support to alleviate the negative impact of digital distractions. These interventions use different approaches, such as the blocking of apps and websites, goal setting, or visualizations of device usage statistics. While many apps and browser extensions make use of these features, little is known about their effectiveness. This systematic review synthesizes the current research to provide insights into the effectiveness of the different kinds of interventions. From a search of the ‘ACM’, ‘Springer Link’, ‘Web of Science’, ’IEEE Xplore’ and ‘Pubmed’ databases, we identified 28 digital self-control interventions. We categorized these interventions according to their features and their outcomes. The interventions showed varying degrees of effectiveness, and especially interventions that relied purely on increasing the participants' awareness were barely effective. For those interventions that sanctioned the use of distractions, the current literature indicates that the sanctions have to be sufficiently difficult to overcome, as they will otherwise be quickly dismissed. The overall confidence in the results is low, with small sample sizes, short study duration, and unclear study contexts. From these insights, we highlight research gaps and close with suggestions for future research.