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@@ -39,19 +39,19 @@ physically-relevant information and symmetries. The features associated with
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these representations can be used for unsupervised machine learning
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applications, such as clustering or classification of the different structures,
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and high-throughput screening of database for specific properties [@Maier2007;
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@De2017; @Hautier2019]. Unfortunately, The dimensionality of these features (as
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@De2017; @Hautier2019]. Unfortunately, the dimensionality of these features (as
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well as most of other descriptors used in chemical and materials informatics) is
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very high, which makes the resulting classifications, clustering or mapping very
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hard to visualize. Additional dimensionality reduction algorithm
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hard to visualize. Additional dimensionality reduction algorithms
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[@Schlkopf1998; @Ceriotti2011; @McInnes2018] can reduce the number of relevant
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dimensions to a handful, creating 2D or 3D maps of the full database.
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![The Qm7b database [@Montavon2013] visualized with chemiscope](screenshot.png)
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Chemiscope is a graphical tool for the interactive exploration of materials and
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molecular databases, correlating local and global structural descriptors with
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the physical properties of the different systems. The interface is composed by
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two panels. The left panel consists of a 2D or 3D scatter plot, in which each
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the physical properties of the different systems. The interface consists of
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two panels. The left panel displays a 2D or 3D scatter plot, in which each
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point corresponds to a chemical entity. The axes, color, and style of each point
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can be set to represent a property or a structural descriptor to visualize
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structure-property relations directly. Structural descriptors are not computed
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was used with the Smooth Overlap of Atomic Positions representation [@Bartok2013] to
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generate the visualization in Figure 1. The right panel displays the
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three-dimensional structure of the chemical entities, possibly including
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periodic repetition for crystals. Visualizing the chemical structure can help to
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find an intuitive rationalization of the layout of the dataset and the
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periodic repetition for crystals. Visualizing the chemical structure can help
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in finding an intuitive rationalization of the layout of the dataset and the
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structure-property relations.
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Whereas similar tools [@Gong2013; @Gutlein2014; @Probst2017; @ISV] only allow
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# Implementation
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Chemiscope is implemented using the web platform: HTML5, CSS and WebGL to
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display graphical elements, and TypeScript (compiled to JavaScript) for the
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display graphical elements, and TypeScript (compiled to JavaScript) for
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interactivity. It uses [Plotly.js](https://plot.ly/javascript/) to render and
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animate 2D and 3D plots; and the JavaScript version of [Jmol](http://jmol.org/)
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to display atomic structures. The visualization is fast enough to be used with
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The use of web technologies makes chemiscope usable from different operating
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systems without the need to develop, maintain and package the code for each
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operating system. It also means that we can provide an online service at
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http://chemiscope.org allowing users to visualize their own dataset without any
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http://chemiscope.org that allows users to visualize their own dataset without any
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local installation. Chemiscope is implemented as a library of re-usable
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components linked together via callbacks. This makes it easy to modify the
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default interface to generate more elaborate visualizations, for example,

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