Respiratory Viruses Dynamics and Interactions: Ten Years of Surveillance in Central Europe

Background: Lower respiratory tract infections are among the main causes of death. Although there are many respiratory viruses, diagnostic efforts are focused mainly on influenza. The Respiratory Viruses Network (RespVir) collects infection data, primarily from German university hospitals, for a high diversity of infections by respiratory pathogens. In this study, we computationally analysed a subset of the RespVir database, covering 217,150 samples tested for 17 different viral pathogens in the time span from 2010 to 2019. Methods: We calculated the prevalence of 17 respiratory viruses, analysed their seasonality patterns using information-theoretic measures and agglomerative clustering, and analysed their propensity for dual infection using a new metric dubbed average coinfection exclusion score (ACES). Results: After initial data pre-processing, we retained 206,814 samples, corresponding to 1,408,657 performed tests. We found that Influenza viruses were reported for less than half of all infections and that they exhibited the highest degree of seasonality Coinfections of viruses are frequent, the most prevalent coinfection was rhinovirus/bocavirus and most of the virus pairs had a positive ACES indicating a tendency to exclude each other regarding infection. Conclusions: The analysis of respiratory viruses dynamics in monoinfection and coinfection contributes to the prevention, diagnostic, treatment, and development of new therapeutics. Data obtained from multiplex testing is fundamental for this analysis and should be prioritized over single pathogen testing.

Quantifiers in Natural Language: Efficient Communication and Degrees of Semantic Universals

While the languages of the world vary greatly, they exhibit systematic patterns, as well. Semantic universals are restrictions on the variation in meaning exhibit cross-linguistically (e.g., that, in all languages, expressions of a certain type can only denote meanings with a certain special property). This paper pursues an efficient communication analysis to explain the presence of semantic universals in a domain of function words: quantifiers. Two experiments measure how well languages do in optimally trading off between competing pressures of simplicity and informativeness. First, we show that artificial languages which more closely resemble natural languages are more optimal. Then, we introduce information-theoretic measures of degrees of semantic universals and show that these are not correlated with optimality in a random sample of artificial languages. These results suggest both that efficient communication shapes semantic typology in both content and function word domains, as well as that semantic universals may not stand in need of independent explanation.

Auditory word comprehension is less incremental in isolated words

Speech input is often understood to trigger rapid and automatic activation of successively higher-level representations for comprehension of words. Here we show evidence from magnetoencephalography that incremental processing of speech input is limited when words are heard in isolation as compared to continuous speech. This suggests a less unified and automatic process than is often assumed. We present evidence that neural effects of phoneme-by-phoneme lexical uncertainty, quantified by cohort entropy, occur in connected speech but not isolated words. In contrast, we find robust effects of phoneme probability, quantified by phoneme surprisal, during perception of both connected speech and isolated words. This dissociation rules out models of word recognition in which phoneme surprisal and cohort entropy are common indicators of a uniform process, even though these closely related information-theoretic measures both arise from the probability distribution of wordforms consistent with the input. We propose that phoneme surprisal effects reflect automatic access of a lower level of representation of the auditory input (e.g., wordforms) while cohort entropy effects are task-sensitive, driven by a competition process or a higher-level representation that is engaged late (or not at all) during the processing of single words.

Transport in Fusion Plasmas: Is the Tail Wagging the Dog?

Turbulent plasmas notably self-organize to higher energy states upon application of additional free energy sources or modification of edge operating conditions. Mechanisms whereby such bifurcations occur have been actively debated for decades, mostly on the basis of reduced models. Here we unravel a surprising causal chain of events in the onset of an improved confinement state, by applying generic entropy-based and information theoretic measures to the primitive kinetic equations. Interfacial contamination of a large, stable region (the ‘dog’) by locally-borne peripheral turbulent fluctuations (the ‘tail’) is found to be central to explaining transport properties, globally. These results, highly relevant to the quest for magnetic fusion advocate the use of such data-driven methods to many problems in fluids and plasmas where interfacial turbulent contamination is active.

On the complexity of assimilation in urban communities

Cities are microcosms representing a diversity of human experience. The complexity of urban systems arises from this diversity, where the services that cities offer to their inhabitants have to be tailored for their unique requirements. This paper studies the complexity of urban environments in terms of the assimilation of its communities. We examine the urban assimilation complexity with respect to the foreignness between communities and formalize the level of complexity using information-theoretic measures. Our findings contribute to a sociological perspective of the relationship between urban complex systems and the diversity of communities that make up urban systems.

Least kth-Order and Rényi Generative Adversarial Networks

We investigate the use of parameterized families of information-theoretic measures to generalize the loss functions of generative adversarial networks (GANs) with the objective of improving performance. A new generator loss function, least kth-order GAN (LkGAN), is introduced, generalizing the least squares GANs (LSGANs) by using a kth-order absolute error distortion measure with k≥1 (which recovers the LSGAN loss function when k=2). It is shown that minimizing this generalized loss function under an (unconstrained) optimal discriminator is equivalent to minimizing the kth-order Pearson-Vajda divergence. Another novel GAN generator loss function is next proposed in terms of Rényi cross-entropy functionals with order α>0, α≠1. It is demonstrated that this Rényi-centric generalized loss function, which provably reduces to the original GAN loss function as α→1, preserves the equilibrium point satisfied by the original GAN based on the Jensen-Rényi divergence, a natural extension of the Jensen-Shannon divergence. Experimental results indicate that the proposed loss functions, applied to the MNIST and CelebA data sets, under both DCGAN and StyleGAN architectures, confer performance benefits by virtue of the extra degrees of freedom provided by the parameters k and α, respectively. More specifically, experiments show improvements with regard to the quality of the generated images as measured by the Fréchet inception distance score and training stability. While it was applied to GANs in this study, the proposed approach is generic and can be used in other applications of information theory to deep learning, for example, the issues of fairness or privacy in artificial intelligence.

Dynamic Formant Trajectories in German Read Speech: Impact of Predictability and Prominence

Phonetic structures expand temporally and spectrally when they are difficult to predict from their context. To some extent, effects of predictability are modulated by prosodic structure. So far, studies on the impact of contextual predictability and prosody on phonetic structures have neglected the dynamic nature of the speech signal. This study investigates the impact of predictability and prominence on the dynamic structure of the first and second formants of German vowels. We expect to find differences in the formant movements between vowels standing in different predictability contexts and a modulation of this effect by prominence. First and second formant values are extracted from a large German corpus. Formant trajectories of peripheral vowels are modeled using generalized additive mixed models, which estimate nonlinear regressions between a dependent variable and predictors. Contextual predictability is measured as biphone and triphone surprisal based on a statistical German language model. We test for the effects of the information-theoretic measures surprisal and word frequency, as well as prominence, on formant movement, while controlling for vowel phonemes and duration. Primary lexical stress and vowel phonemes are significant predictors of first and second formant trajectory shape. We replicate previous findings that vowels are more dispersed in stressed syllables than in unstressed syllables. The interaction of stress and surprisal explains formant movement: unstressed vowels show more variability in their formant trajectory shape at different surprisal levels than stressed vowels. This work shows that effects of contextual predictability on fine phonetic detail can be observed not only in pointwise measures but also in dynamic features of phonetic segments.

Information Flow Between Heart Rhythm, Repolarization, and the Diastolic Interval Series for Healthy Individuals and LQTS1 Patients

Using information theoretic measures, relations between heart rhythm, repolarization in the tissue of the heart, and the diastolic interval time series are analyzed. These processes are a fragment of the cardiovascular physiological network. A comparison is made between the results for 84 (42 women) healthy individuals and 65 (45 women) long QT syndrome type 1 (LQTS1) patients. Self-entropy, transfer entropy, and joint transfer entropy are calculated for the three time series and their combinations. The results for self-entropy indicate the well-known result that regularity of heart rhythm for healthy individuals is larger than that of QT interval series. The flow of information depends on the direction with the flow from the heart rhythm to QT dominating. In LQTS1 patients, however, our results indicate that information flow in the opposite direction may occur—a new result. The information flow from the heart rhythm to QT dominates, which verifies the asymmetry seen by Porta et al. in the variable tilt angle experiment. The amount of new information and self-entropy for LQTS1 patients is smaller than that for healthy individuals. However, information transfers from RR to QT and from DI to QT are larger in the case of LQTS1 patients.

Disentangling the Information in Species Interaction Networks

Shannon’s entropy measure is a popular means for quantifying ecological diversity. We explore how one can use information-theoretic measures (that are often called indices in ecology) on joint ensembles to study the diversity of species interaction networks. We leverage the little-known balance equation to decompose the network information into three components describing the species abundance, specificity, and redundancy. This balance reveals that there exists a fundamental trade-off between these components. The decomposition can be straightforwardly extended to analyse networks through time as well as space, leading to the corresponding notions for alpha, beta, and gamma diversity. Our work aims to provide an accessible introduction for ecologists. To this end, we illustrate the interpretation of the components on numerous real networks. The corresponding code is made available to the community in the specialised Julia package EcologicalNetworks.jl.