Skip to content

Commit 2f76a6d

Browse files
authored
More minor changes to the paper (#55)
1 parent 8c11a56 commit 2f76a6d

File tree

1 file changed

+11
-11
lines changed

1 file changed

+11
-11
lines changed

paper/paper.md

Lines changed: 11 additions & 11 deletions
Original file line numberDiff line numberDiff line change
@@ -39,19 +39,19 @@ physically-relevant information and symmetries. The features associated with
3939
these representations can be used for unsupervised machine learning
4040
applications, such as clustering or classification of the different structures,
4141
and high-throughput screening of database for specific properties [@Maier2007;
42-
@De2017; @Hautier2019]. Unfortunately, The dimensionality of these features (as
42+
@De2017; @Hautier2019]. Unfortunately, the dimensionality of these features (as
4343
well as most of other descriptors used in chemical and materials informatics) is
4444
very high, which makes the resulting classifications, clustering or mapping very
45-
hard to visualize. Additional dimensionality reduction algorithm
46-
[@Schlkopf1998; @Ceriotti2011; @McInnes2018] can reduce the number of relevant
47-
dimensions to a handful, creating 2D or 3D maps of the full database.
45+
hard to visualize. Dimensionality reduction algorithms [@Schlkopf1998;
46+
@Ceriotti2011; @McInnes2018] can reduce the number of relevant dimensions to a
47+
handful, creating 2D or 3D maps of the full database.
4848

4949
![The Qm7b database [@Montavon2013] visualized with chemiscope](screenshot.png)
5050

5151
Chemiscope is a graphical tool for the interactive exploration of materials and
5252
molecular databases, correlating local and global structural descriptors with
53-
the physical properties of the different systems. The interface is composed by
54-
two panels. The left panel consists of a 2D or 3D scatter plot, in which each
53+
the physical properties of the different systems. The interface consists of
54+
two panels. The left panel displays a 2D or 3D scatter plot, in which each
5555
point corresponds to a chemical entity. The axes, color, and style of each point
5656
can be set to represent a property or a structural descriptor to visualize
5757
structure-property relations directly. Structural descriptors are not computed
@@ -63,8 +63,8 @@ for easier visualization. For example the sketch-map algorithm [@Ceriotti2011]
6363
was used with the Smooth Overlap of Atomic Positions representation [@Bartok2013] to
6464
generate the visualization in Figure 1. The right panel displays the
6565
three-dimensional structure of the chemical entities, possibly including
66-
periodic repetition for crystals. Visualizing the chemical structure can help to
67-
find an intuitive rationalization of the layout of the dataset and the
66+
periodic repetition for crystals. Visualizing the chemical structure can help
67+
in finding an intuitive rationalization of the layout of the dataset and the
6868
structure-property relations.
6969

7070
Whereas similar tools [@Gong2013; @Gutlein2014; @Probst2017; @ISV] only allow
@@ -78,7 +78,7 @@ machine-learning schemes that decompose properties into atom-centred
7878
contributions [@Behler2007; @Bartok2010].
7979

8080

81-
![Database of chemical shieldings [@Paruzzo2018] in chemiscope demonstrating the use of a 3D plot and atomic environments highlighting](./screenshot-3d.png)
81+
![Database of chemical shieldings [@Paruzzo2018] in chemiscope demonstrating the use of a 3D plot and highlighting of atomic environments](./screenshot-3d.png)
8282

8383
Chemiscope took strong inspiration from a previous similar graphical software,
8484
the interactive sketch-map visualizer [@ISV]. This previous software was used in
@@ -89,7 +89,7 @@ databases, and the mapping of structure-property relationships [@De2016;
8989
# Implementation
9090

9191
Chemiscope is implemented using the web platform: HTML5, CSS and WebGL to
92-
display graphical elements, and TypeScript (compiled to JavaScript) for the
92+
display graphical elements, and TypeScript (compiled to JavaScript) for
9393
interactivity. It uses [Plotly.js](https://plot.ly/javascript/) to render and
9494
animate 2D and 3D plots; and the JavaScript version of [Jmol](http://jmol.org/)
9595
to display atomic structures. The visualization is fast enough to be used with
@@ -100,7 +100,7 @@ slower, while still handling 100k points easily.
100100
The use of web technologies makes chemiscope usable from different operating
101101
systems without the need to develop, maintain and package the code for each
102102
operating system. It also means that we can provide an online service at
103-
http://chemiscope.org allowing users to visualize their own dataset without any
103+
http://chemiscope.org that allows users to visualize their own dataset without any
104104
local installation. Chemiscope is implemented as a library of re-usable
105105
components linked together via callbacks. This makes it easy to modify the
106106
default interface to generate more elaborate visualizations, for example,

0 commit comments

Comments
 (0)