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Posts tagged ‘visualization’

New Euler toolkit diagnostics and visualizations of inconsistent and ambiguous input alignments

Novel Euler/X diagnostics for inconsistent input alignments.

Two taxonomies together with 9 input articulations are shown in the TAP (taxonomy alignment problem) on the left. It is not clear what the “combined taxonomy” looks like. For this example, calling Euler/X’s “check-consistency” command yields “No” – the TAP is inconsistent, i.e., self-contradictory. Even for the trained expert it is difficult to locate the error. Euler/X can execute a “black-box inconsistency analysis”, trying various combinations of articulations to see which subsets of articulations are consistent. The resulting diagnosis lattice has 2^9 = 512 nodes, and is therefore hard to navigate. Euler/X can extract from the 512 combinations 9 maximal consistent sets (i.e., the purple combinations in the lower right cannot be extended with any of the missing articulations without rendering the alignment inconsistent), and 2 minimal inconsistent sets (i.e., the red subsets are already inconsistent, but removing any articulation will yield a consistent subset). This allows the user to effectively explore and understand the consistency/inconsistency landscape, leading to efficient repair actions.

EulerNovelDiagnostics

Euler/X toolkit visualization of Maximal Consistent Sets (MCS) and Minimal Inconsistent Sets (MIS).

PathwayMatrix visualization software shows Euler/X taxonomy alignment products and ambiguities

This post serves as an update on a new Euler/X compatible visualization software called PathwayMatrix, and also as a mini-review of the Exploring Taxonomic Concepts (ETC) Information Visualization Workshop, held on May 11-13, 2015, at the National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign. The workshop was organized by Bertram Ludäscher of the Euler/X Project and ETC lead information scientist Hong Cui.

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Weekly reading: Mikó et al. 2012. On Dorsal Prothoracic Appendages in Treehoppers (Hemiptera: Membracidae) and the Nature of Morphological Evidence

Our next reading is a response to a 2011 article (that paper available here) interpreting the “prothoracic helmet” of treehoppers as serially homologous with wings. Mikó et al. showcase some modern techniques for visualizing morphology, such as confocal laser scanning microscopy (CLSM) and micro-computed tomography (μ-CT) to provide an alternate interpretation, and discuss the importance of having well-defined morphological concepts for interpreting complex morphological structures.

Mikó et al. 2012 is available online here.

New publication: Reasoning over taxonomic change – Perelleschus

The first, fleshed out use case of the Euler/X project was published yesterday in PLoS ONE. This paper is a companion to the phylogenetic revision of the acalyptine weevil genus Perelleschus sec. Franz & Cardona-Duque (2013), and translates the 54 taxonomic concepts and 75 RCC-5 articulations provided in that paper into 13 logically consistent alignments and visualizations, with additional inferred articulations.

Franz, N.M., M. Chen, S. Yu, P. Kianmajd, S. Bowers & B. Ludäscher. 2015. Reasoning over taxonomic change: exploring alignments for the Perelleschus use case. PLoS ONE 10(2): e0118247. doi:10.1371/journal.pone.0118247. Available on-line here.

Very glad to see this one published; at the same time there are other use case papers in the pipeline (Andropogon, Primates). The particular motivation for this paper was to resolve sets of several small-scale yet taxonomically and phylogenetically complex input trees with the RCC-5 concept alignment approach and Euler/X toolkit. The paper is written in a “how to?” style, successively exploring and explaining the connections between the user-provided input constraints and the over-, under-, or well-specified reasoning outcomes. It deals with issues of logical consistency, input sufficiency, ambiguity, and alternative ways to align (parent) concepts in reference to either (1) their intensionally circumscribed properties (which may include synapomorphies) or (2) the ostensively indicated members. This corresponds to the program outlined in Franz & Thau (2010).

One reviewer wrote: “With an exceptionally suited use case, the complexity of taxonomic reasoning and its translation to machine processing are depicted in unprecedented form.” Our ultimate goal is to develop a widely applicable reference and linkage system for taxonomic products that human users create but which is actually optimized for computational processing – without compromising the Linnaean system whose services to humans are profoundly valuable.

Overview of Euler/X toolkit commands

An overview of Euler/X toolkit commands, with examples of how and when to use. This post expands on the Euler/X introduction and demonstration video which show a linear pathway to producing a logically consistent multi-taxonomy alignment. Post in development.

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Alignment of two classifications of the Monotremata

Echidnas, platypus – monotremes are amazing. They are also subject of an exploratory project to align two highly influential classifications of mammals using the Euler/X toolkit. Of course we are talking about:

  1. Mammal Species of the World, 3rd Edition. 2005.
  2. Mammal Species of the World, 2nd Edition. 1993. [not or no longer available on-line; which relates to our project’s aims.]

The respective 1993 & 2005 monotreme classifications were authored by Colin Groves. Thanks to MSW Editor DeeAnn Reeder for enthusiasm and support. Below is an abbreviated representation of how we aligned the two classifications. Most critically, in 1998 Zaglossus sec. Flannery & Groves (1998) was revised, and a new species (concept) Z. attenboroughi was added. Let us see what else changed..

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Using the Euler/X toolkit to align taxonomies – introductory notes

Most recent update: July 15, 2014 (minor editing updates; link to video).

Our group is involved in promoting concept taxonomy. Here are some preliminary, and evolving, step-by-step instructions on how to employ the Euler/X toolkit to align two taxonomies or phylogenies. A short video is also available here.

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Initial alignment of two weevil classifications with the Euler toolkit

Linked here is an interim result of my attempt to align two influential weevil classifications by Thompson (1992) and Alonso-Zarazaga & Lyal (1999) with the Euler/X toolkit. For additional information see this link.

Update, February 18, 2014: Here is another alignment of two phylogenetic classifications of weevil families and subfamilies, according to Kuschel (1995) and Marvaldi & Morrone (2002).

  • Kuschel, G. 1995. A phylogenetic classification of Curculionoidea to families and subfamilies. Memoirs of the Entomological Society of Washington 14: 5-33.
  • Marvaldi, A.E. & J.J. Morrone. 2000. Phylogenetic systematics of weevils (Coleoptera: Curculionoidea): a reappraisal based on larval and adult morphology. Insect Systematics & Evolution 31: 43-58.