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      Inference of partial colexifications from multilingual wordlists

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          Abstract

          The past years have seen a drastic rise in studies devoted to the investigation of colexification patterns in individual languages families in particular and the languages of the world in specific. Specifically computational studies have profited from the fact that colexification as a scientific construct is easy to operationalize, enabling scholars to infer colexification patterns for large collections of cross-linguistic data. Studies devoted to partial colexifications—colexification patterns that do not involve entire words, but rather various parts of words—, however, have been rarely conducted so far. This is not surprising, since partial colexifications are less easy to deal with in computational approaches and may easily suffer from all kinds of noise resulting from false positive matches. In order to address this problem, this study proposes new approaches to the handling of partial colexifications by (1) proposing new models with which partial colexification patterns can be represented, (2) developing new efficient methods and workflows which help to infer various types of partial colexification patterns from multilingual wordlists, and (3) illustrating how inferred patterns of partial colexifications can be computationally analyzed and interactively visualized.

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          Cytoscape: a software environment for integrated models of biomolecular interaction networks.

          Cytoscape is an open source software project for integrating biomolecular interaction networks with high-throughput expression data and other molecular states into a unified conceptual framework. Although applicable to any system of molecular components and interactions, Cytoscape is most powerful when used in conjunction with large databases of protein-protein, protein-DNA, and genetic interactions that are increasingly available for humans and model organisms. Cytoscape's software Core provides basic functionality to layout and query the network; to visually integrate the network with expression profiles, phenotypes, and other molecular states; and to link the network to databases of functional annotations. The Core is extensible through a straightforward plug-in architecture, allowing rapid development of additional computational analyses and features. Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
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            SciPy 1.0: fundamental algorithms for scientific computing in Python

            SciPy is an open-source scientific computing library for the Python programming language. Since its initial release in 2001, SciPy has become a de facto standard for leveraging scientific algorithms in Python, with over 600 unique code contributors, thousands of dependent packages, over 100,000 dependent repositories and millions of downloads per year. In this work, we provide an overview of the capabilities and development practices of SciPy 1.0 and highlight some recent technical developments.
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              Cytoscape 2.8: new features for data integration and network visualization

              Summary: Cytoscape is a popular bioinformatics package for biological network visualization and data integration. Version 2.8 introduces two powerful new features—Custom Node Graphics and Attribute Equations—which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities. Custom Node Graphics allow an image to be projected onto a node, including images generated dynamically or at remote locations. Attribute Equations provide Cytoscape with spreadsheet-like functionality in which the value of an attribute is computed dynamically as a function of other attributes and network properties. Availability and implementation: Cytoscape is a desktop Java application released under the Library Gnu Public License (LGPL). Binary install bundles and source code for Cytoscape 2.8 are available for download from http://cytoscape.org. Contact: msmoot@ucsd.edu
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                Author and article information

                Contributors
                Journal
                Front Psychol
                Front Psychol
                Front. Psychol.
                Frontiers in Psychology
                Frontiers Media S.A.
                1664-1078
                16 June 2023
                2023
                : 14
                : 1156540
                Affiliations
                [1] 1Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology , Leipzig, Germany
                [2] 2Chair of Multilingual Computational Linguistics, University of Passau , Passau, Germany
                Author notes

                Edited by: Gerd Carling, Goethe University Frankfurt, Germany

                Reviewed by: Søren Wichmann, University of Kiel, Germany; Hongshan Yin, Qingdao University of Science and Technology, China

                *Correspondence: Johann-Mattis List mattis.list@ 123456uni-passau.de
                Article
                10.3389/fpsyg.2023.1156540
                10312387
                37397315
                ee907286-9b38-41b0-8376-1ced9d5efa86
                Copyright © 2023 List.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 01 February 2023
                : 23 May 2023
                Page count
                Figures: 4, Tables: 1, Equations: 0, References: 45, Pages: 10, Words: 7686
                Funding
                Funded by: European Research Council, doi 10.13039/501100000781;
                Award ID: 101044282
                This research was supported by the Max Planck Society Research Grant CALC 3 (J-ML, https://digling.org/calc/) and the ERC Consolidator Grant ProduSemy (J-ML, Grant No. 101044282, see: https://doi.org/10.3030/101044282).
                Categories
                Psychology
                Methods
                Custom metadata
                Psychology of Language

                Clinical Psychology & Psychiatry
                partial colexification,loose colexification,colexification networks,computational comparative linguistics,computer-assisted language comparison

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