<commit_before># JGI-PURE-Challenge
A competition to identify, analyse and visualise interdisciplinary research at UoB using the PURE dataset.

To run the CSharp solution:

```
git clone <EMAIL>:IRC-SPHERE/JGI-PURE-Challenge.git
cd JGI-PURE-Challenge/AVPTM
nuget restore
xbuild
(cd bin/Debug && mono AVPTM.exe)
```

# Visualizations

## Common publications between organizations

We counted how many times every research group has collaborated with another
one by counting the number of common publications. With this information we
created a Chord diagram from the years 2008 to 2013 that can be found in
[story/static_chord_diagram.html][1].

It is also possible to query one particular year by passing as a GET argument
the specific year (e.g. for 2008 go to the link
[story/static_chord_diagram.html?years=2008][2]).

The same argument accepts a list of years separated by comma (e.g. for years
2012 and 2013 follow the link [story/static_chord_diagram.html?years=2012,2013][3]).

[1]: https://intelligentsystemslaboratory.github.io/JGI-PURE-Challenge/story/static_chord_diagram.html
[2]: https://intelligentsystemslaboratory.github.io/JGI-PURE-Challenge/story/static_chord_diagram.html?years=2008
[3]: https://intelligentsystemslaboratory.github.io/JGI-PURE-Challenge/story/static_chord_diagram.html?years=2012,2013

## Topic Models

We use Latent Dirichlet Allocation Topic Models to cluster publications of each
year by their titles and abstracts .

The discovered topics are visualised in [story/static_scatterplot.html][4],
where the X coordinate represents how many researchers contributed to the
topic, the Y coordinate represents how many organisations contributed, the size
of a topic circle represents how many publications assigned to it. We also show
top words and top organisations of a topic.


[4]: https://intelligentsystemslaboratory.github.io/JGI-PURE-Challenge/story/static_scatterplot.html

## PURE Challenge slides

You can find the slides for a presentation on this link [intelligentsystemslaboratory.github.io/JGI-PURE-Challenge/story][5]

[5]: https://intelligentsystemslaboratory.github.io/JGI-PURE-Challenge/story/<commit_msg>Added link to new slides<commit_after># JGI-PURE-Challenge
A competition to identify, analyse and visualise interdisciplinary research at UoB using the PURE dataset.

To run the CSharp solution:

```
git clone git@github.com:IRC-SPHERE/JGI-PURE-Challenge.git
cd JGI-PURE-Challenge/AVPTM
nuget restore
xbuild
(cd bin/Debug && mono AVPTM.exe)
```

# Visualizations

## Common publications between organizations

We counted how many times every research group has collaborated with another
one by counting the number of common publications. With this information we
created a Chord diagram from the years 2008 to 2013 that can be found in
[story/static_chord_diagram.html][1].

It is also possible to query one particular year by passing as a GET argument
the specific year (e.g. for 2008 go to the link
[story/static_chord_diagram.html?years=2008][2]).

The same argument accepts a list of years separated by comma (e.g. for years
2012 and 2013 follow the link [story/static_chord_diagram.html?years=2012,2013][3]).

[1]: https://intelligentsystemslaboratory.github.io/JGI-PURE-Challenge/story/static_chord_diagram.html
[2]: https://intelligentsystemslaboratory.github.io/JGI-PURE-Challenge/story/static_chord_diagram.html?years=2008
[3]: https://intelligentsystemslaboratory.github.io/JGI-PURE-Challenge/story/static_chord_diagram.html?years=2012,2013

## Topic Models

We use Latent Dirichlet Allocation Topic Models to cluster publications of each
year by their titles and abstracts .

The discovered topics are visualised in [story/static_scatterplot.html][4],
where the X coordinate represents how many researchers contributed to the
topic, the Y coordinate represents how many organisations contributed, the size
of a topic circle represents how many publications assigned to it. We also show
top words and top organisations of a topic.


[4]: https://intelligentsystemslaboratory.github.io/JGI-PURE-Challenge/story/static_scatterplot.html

## PURE Challenge slides

You can find the slides for a presentation on this link [intelligentsystemslaboratory.github.io/JGI-PURE-Challenge/story][5]

And new slides with more bullet points and figures: [new slides][6]

[5]: https://intelligentsystemslaboratory.github.io/JGI-PURE-Challenge/story/
[6]: https://intelligentsystemslaboratory.github.io/JGI-PURE-Challenge/story/pure_presentation.html
{'fraction_non_alphanumeric': 0.07979551011335853, 'fraction_numerical': 0.02444987775061125, 'mean_word_length': 5.484149855907781, 'pattern_counts': {'":': 0, '<': 4, '<?xml version=': 0, '>': 4, 'https://': 11, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 1, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '1100759', 'n_tokens_mistral': 1450, 'n_tokens_neox': 1318, 'n_words': 460}