Dataset Information

SuperNoder: a tool to discover over-represented modular structures in networks.

ABSTRACT: BACKGROUND:Networks whose nodes have labels can seem complex. Fortunately, many have substructures that occur often ("motifs"). A societal example of a motif might be a household. Replacing such motifs by named supernodes reduces the complexity of the network and can bring out insightful features. Doing so repeatedly may give hints about higher level structures of the network. We call this recursive process Recursive Supernode Extraction. RESULTS:This paper describes algorithms and a tool to discover disjoint (i.e. non-overlapping) motifs in a network, replacing those motifs by new nodes, and then recursing. We show applications in food-web and protein-protein interaction (PPI) networks where our methods reduce the complexity of the network and yield insights. CONCLUSIONS:SuperNoder is a web-based and standalone tool which enables the simplification of big graphs based on the reduction of high frequency motifs. It applies various strategies for identifying disjoint motifs with the goal of enhancing the understandability of networks.

SUBMITTER: Dessi D

PROVIDER: S-EPMC6131773 | biostudies-literature | 2018 Sep

REPOSITORIES: biostudies-literature

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SuperNoder: a tool to discover over-represented modular structures in networks.

Dessì Danilo D Cirrone Jacopo J Recupero Diego Reforgiato DR Shasha Dennis D

BMC bioinformatics 20180910 1

<h4>Background</h4>Networks whose nodes have labels can seem complex. Fortunately, many have substructures that occur often ("motifs"). A societal example of a motif might be a household. Replacing such motifs by named supernodes reduces the complexity of the network and can bring out insightful features. Doing so repeatedly may give hints about higher level structures of the network. We call this recursive process Recursive Supernode Extraction.<h4>Results</h4>This paper describes algorithms an ...[more]

PMID: 30200901

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Project description:Citizen science platforms are quickly accumulating hundreds of millions of biodiversity observations around the world annually. Quantifying and correcting for the biases in citizen science datasets remains an important first step before these data are used to address ecological questions and monitor biodiversity. One source of potential bias among datasets is the difference between those citizen science programs that have unstructured protocols and those that have semi-structured or structured protocols for submitting observations. To quantify biases in an unstructured citizen science platform, we contrasted bird observations from the unstructured iNaturalist platform with that from a semi-structured citizen science platform-eBird-for the continental United States. We tested whether four traits of species (body size, commonness, flock size, and color) predicted if a species was under- or over-represented in the unstructured dataset compared with the semi-structured dataset. We found strong evidence that large-bodied birds were over-represented in the unstructured citizen science dataset; moderate evidence that common species were over-represented in the unstructured dataset; strong evidence that species in large groups were over-represented; and no evidence that colorful species were over-represented in unstructured citizen science data. Our results suggest that biases exist in unstructured citizen science data when compared with semi-structured data, likely as a result of the detectability of a species and the inherent recording process. Importantly, in programs like iNaturalist the detectability process is two-fold-first, an individual organism needs to be detected, and second, it needs to be photographed, which is likely easier for many large-bodied species. Our results indicate that caution is warranted when using unstructured citizen science data in ecological modelling, and highlight body size as a fundamental trait that can be used as a covariate for modelling opportunistic species occurrence records, representing the detectability or identifiability in unstructured citizen science datasets. Future research in this space should continue to focus on quantifying and documenting biases in citizen science data, and expand our research by including structured citizen science data to understand how biases differ among unstructured, semi-structured, and structured citizen science platforms.

Dataset Information

SuperNoder: a tool to discover over-represented modular structures in networks.

Publications

SuperNoder: a tool to discover over-represented modular structures in networks.

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