4,329 research outputs found
Unified functional network and nonlinear time series analysis for complex systems science: The pyunicorn package
We introduce the \texttt{pyunicorn} (Pythonic unified complex network and
recurrence analysis toolbox) open source software package for applying and
combining modern methods of data analysis and modeling from complex network
theory and nonlinear time series analysis. \texttt{pyunicorn} is a fully
object-oriented and easily parallelizable package written in the language
Python. It allows for the construction of functional networks such as climate
networks in climatology or functional brain networks in neuroscience
representing the structure of statistical interrelationships in large data sets
of time series and, subsequently, investigating this structure using advanced
methods of complex network theory such as measures and models for spatial
networks, networks of interacting networks, node-weighted statistics or network
surrogates. Additionally, \texttt{pyunicorn} provides insights into the
nonlinear dynamics of complex systems as recorded in uni- and multivariate time
series from a non-traditional perspective by means of recurrence quantification
analysis (RQA), recurrence networks, visibility graphs and construction of
surrogate time series. The range of possible applications of the library is
outlined, drawing on several examples mainly from the field of climatology.Comment: 28 pages, 17 figure
Complex networks analysis in socioeconomic models
This chapter aims at reviewing complex networks models and methods that were
either developed for or applied to socioeconomic issues, and pertinent to the
theme of New Economic Geography. After an introduction to the foundations of
the field of complex networks, the present summary adds insights on the
statistical mechanical approach, and on the most relevant computational aspects
for the treatment of these systems. As the most frequently used model for
interacting agent-based systems, a brief description of the statistical
mechanics of the classical Ising model on regular lattices, together with
recent extensions of the same model on small-world Watts-Strogatz and
scale-free Albert-Barabasi complex networks is included. Other sections of the
chapter are devoted to applications of complex networks to economics, finance,
spreading of innovations, and regional trade and developments. The chapter also
reviews results involving applications of complex networks to other relevant
socioeconomic issues, including results for opinion and citation networks.
Finally, some avenues for future research are introduced before summarizing the
main conclusions of the chapter.Comment: 39 pages, 185 references, (not final version of) a chapter prepared
for Complexity and Geographical Economics - Topics and Tools, P.
Commendatore, S.S. Kayam and I. Kubin Eds. (Springer, to be published
Inference of the genetic network regulating lateral root initiation in Arabidopsis thaliana
Regulation of gene expression is crucial for organism growth, and it is one of the challenges in Systems Biology to reconstruct the underlying regulatory biological networks from transcriptomic data. The formation of lateral roots in Arabidopsis thaliana is stimulated by a cascade of regulators of which only the interactions of its initial elements have been identified. Using simulated gene expression data with known network topology, we compare the performance of inference algorithms, based on different approaches, for which ready-to-use software is available. We show that their performance improves with the network size and the inclusion of mutants. We then analyse two sets of genes, whose activity is likely to be relevant to lateral root initiation in Arabidopsis, by integrating sequence analysis with the intersection of the results of the best performing methods on time series and mutants to infer their regulatory network. The methods applied capture known interactions between genes that are candidate regulators at early stages of development. The network inferred from genes significantly expressed during lateral root formation exhibits distinct scale-free, small world and hierarchical properties and the nodes with a high out-degree may warrant further investigation
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