scholarly journals Disentangling the Information in Species Interaction Networks

Entropy ◽  
2021 ◽  
Vol 23 (6) ◽  
pp. 703
Author(s):  
Michiel Stock ◽  
Laura Hoebeke ◽  
Bernard De Baets
Keyword(s):  
Species Abundance ◽  
Species Interaction ◽  
Interaction Networks ◽  
Entropy Measure ◽  
Ecological Diversity ◽  
Gamma Diversity ◽  
Information Theoretic ◽  
Network Information ◽  
Information Theoretic Measures ◽  
Beta And Gamma Diversity

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.

scholarly journals Effect of Localization on the Stability of Mutualistic Ecological Networks

2015 ◽  
Author(s):  
Samir Suweis ◽  
Jacopo Grilli ◽  
Jayanth Banavar ◽  
Stefano Allesina ◽  
Amos Maritan
Keyword(s):  
Species Abundance ◽  
Interaction Network ◽  
Species Interaction ◽  
Interaction Networks ◽  
Ecological Communities ◽  
Weighted Degree ◽  
Perturbation Propagation ◽  
The Stability ◽  
The Impact ◽  
The Relationship

The relationships between the core-periphery architecture of the species interaction network and the mechanisms ensuring the stability in mutualistic ecological communities are still unclear. In particular, most studies have focused their attention on asymptotic resilience or persistence, neglecting how perturbations propagate through the system. Here we develop a theoretical framework to evaluate the relationship between architecture of the interaction networks and the impact of perturbations by studying localization, a measure describing the ability of the perturbation to propagate through the network. We show that mutualistic ecological communities are localized, and localization reduces perturbation propagation and attenuates its impact on species abundance. Localization depends on the topology of the interaction networks, and it positively correlates with the variance of the weighted degree distribution, a signature of the network topological hetereogenity. Our results provide a different perspective on the interplay between the architecture of interaction networks in mutualistic communities and their stability.

scholarly journals Properties of Entropy-Based Topological Measures of Fullerenes

Mathematics ◽  
2020 ◽  
Vol 8 (5) ◽  
pp. 740 ◽  
Author(s):  
Modjtaba Ghorbani ◽  
Matthias Dehmer ◽  
Frank Emmert-Streib
Keyword(s):  
Present Article ◽  
Connected Graph ◽  
Entropy Measure ◽  
Topological Information ◽  
Information Theoretic ◽  
Relational Structures ◽  
Chemical Structures ◽  
Topological Measures ◽  
Information Theoretic Measures ◽  
Fullerene Graphs

A fullerene is a cubic three-connected graph whose faces are entirely composed of pentagons and hexagons. Entropy applied to graphs is one of the significant approaches to measuring the complexity of relational structures. Recently, the research on complex networks has received great attention, because many complex systems can be modelled as networks consisting of components as well as relations among these components. Information—theoretic measures have been used to analyze chemical structures possessing bond types and hetero-atoms. In the present article, we reviewed various entropy-based measures on fullerene graphs. In particular, we surveyed results on the topological information content of a graph, namely the orbit-entropy Ia(G), the symmetry index, a degree-based entropy measure Iλ(G), the eccentric-entropy Ifσ(G) and the Hosoya entropy H(G).

Large-sample confidence intervals of information-theoretic measures in linguistics

2020 ◽  
Vol 6 (1) ◽  
pp. 19-54
Author(s):  
Ryan Ka Yau Lai ◽  
Youngah Do
Keyword(s):  
Maximum Likelihood ◽  
Corpus Linguistics ◽  
Delta Method ◽  
Confidence Bounds ◽  
Likelihood Estimator ◽  
Information Theoretic ◽  
Leibler Divergence ◽  
Information Theoretic Measures ◽  
Data Points ◽  
Measure Of Uncertainty

This article explores a method of creating confidence bounds for information-theoretic measures in linguistics, such as entropy, Kullback-Leibler Divergence (KLD), and mutual information. We show that a useful measure of uncertainty can be derived from simple statistical principles, namely the asymptotic distribution of the maximum likelihood estimator (MLE) and the delta method. Three case studies from phonology and corpus linguistics are used to demonstrate how to apply it and examine its robustness against common violations of its assumptions in linguistics, such as insufficient sample size and non-independence of data points.

scholarly journals Optimized permutation testing for information theoretic measures of multi-gene interactions

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
James M. Kunert-Graf ◽  
Nikita A. Sakhanenko ◽  
David J. Galas
Keyword(s):  
Large Scale ◽  
Permutation Test ◽  
Association Studies ◽  
Genome Wide Association Studies ◽  
Permutation Testing ◽  
Exact Test ◽  
Information Theoretic ◽  
Information Theoretic Measures ◽  
Full Analysis ◽  
Computational Bottleneck

Abstract Background Permutation testing is often considered the “gold standard” for multi-test significance analysis, as it is an exact test requiring few assumptions about the distribution being computed. However, it can be computationally very expensive, particularly in its naive form in which the full analysis pipeline is re-run after permuting the phenotype labels. This can become intractable in multi-locus genome-wide association studies (GWAS), in which the number of potential interactions to be tested is combinatorially large. Results In this paper, we develop an approach for permutation testing in multi-locus GWAS, specifically focusing on SNP–SNP-phenotype interactions using multivariable measures that can be computed from frequency count tables, such as those based in Information Theory. We find that the computational bottleneck in this process is the construction of the count tables themselves, and that this step can be eliminated at each iteration of the permutation testing by transforming the count tables directly. This leads to a speed-up by a factor of over 103 for a typical permutation test compared to the naive approach. Additionally, this approach is insensitive to the number of samples making it suitable for datasets with large number of samples. Conclusions The proliferation of large-scale datasets with genotype data for hundreds of thousands of individuals enables new and more powerful approaches for the detection of multi-locus genotype-phenotype interactions. Our approach significantly improves the computational tractability of permutation testing for these studies. Moreover, our approach is insensitive to the large number of samples in these modern datasets. The code for performing these computations and replicating the figures in this paper is freely available at https://github.com/kunert/permute-counts.

Insights into codeswitching from online communication: Effects of language preference and conditions arising from vocabulary richness

2021 ◽  
pp. 1-7
Author(s):  
Laurie Beth Feldman ◽  
Vidhushini Srinivasan ◽  
Rachel B. Fernandes ◽  
Samira Shaikh
Keyword(s):  
Online Communication ◽  
Language Preference ◽  
Lexical Diversity ◽  
Information Theoretic ◽  
Vocabulary Richness ◽  
Twitter Data ◽  
Language Mixing ◽  
Communication Effects ◽  
Information Theoretic Measures ◽  
Spanish Bilinguals

Abstract Twitter data from a crisis that impacted many English–Spanish bilinguals show that the direction of codeswitches is associated with the statistically documented tendency of single speakers to prefer one language over another in their tweets, as gleaned from their tweeting history. Further, lexical diversity, a measure of vocabulary richness derived from information-theoretic measures of uncertainty in communication, is greater in proximity to a codeswitch than in productions remote from a switch. The prospects of a role for lexical diversity in characterizing the conditions for a language switch suggest that communicative precision may induce conditions that attenuate constraints against language mixing.

scholarly journals Information-Theoretic Measures and Modeling Stock Market Volatility: A Comparative Approach

Risks ◽  
2021 ◽  
Vol 9 (5) ◽  
pp. 89
Author(s):  
Muhammad Sheraz ◽  
Imran Nasir
Keyword(s):  
Stock Market ◽  
Stock Returns ◽  
Stock Exchange ◽  
Approximate Entropy ◽  
Market Volatility ◽  
Comparative Approach ◽  
Stock Market Volatility ◽  
Information Theoretic ◽  
Information Theoretic Measures ◽  
Garch Modeling

The volatility analysis of stock returns data is paramount in financial studies. We investigate the dynamics of volatility and randomness of the Pakistan Stock Exchange (PSX-100) and obtain insights into the behavior of investors during and before the coronavirus disease (COVID-19 pandemic). The paper aims to present the volatility estimations and quantification of the randomness of PSX-100. The methodology includes two approaches: (i) the implementation of EGARCH, GJR-GARCH, and TGARCH models to estimate the volatilities; and (ii) analysis of randomness in volatilities series, return series, and PSX-100 closing prices for pre-pandemic and pandemic period by using Shannon’s, Tsallis, approximate and sample entropies. Volatility modeling suggests the existence of the leverage effect in both the underlying periods of study. The results obtained using GARCH modeling reveal that the stock market volatility has increased during the pandemic period. However, information-theoretic results based on Shannon and Tsallis entropies do not suggest notable variation in the estimated volatilities series and closing prices. We have examined regularity and randomness based on the approximate entropy and sample entropy. We have noticed both entropies are extremely sensitive to choices of the parameters.

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