@@ -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
@@ -63,8 +63,8 @@ for easier visualization. For example the sketch-map algorithm [@Ceriotti2011]
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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
@@ -89,7 +89,7 @@ databases, and the mapping of structure-property relationships [@De2016;
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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
@@ -100,7 +100,7 @@ slower, while still handling 100k points easily.
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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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