nathimel / citesim

Exploring citation-similarity relationships in scientific literature

Similarity to previous research optimizes for citations

This repository accompanies XXX.

N.B.: this readme will be more documented soon.

Data

All of the data and figures from our analysis can be found under the analysis_data folder.

Replicating experiments

To analyze the experiments we run, use the commands:

• Physics

  python src/analyze.py experiment.atlas.center=hafenLowredshiftLymanLimit2017 experiment.cartography.required_pub_conditions.fields_of_study="[Physics]"

• Linguistics

  python src/analyze.py experiment.atlas.center=Imeletal2022 experiment.cartography.required_pub_conditions.fields_of_study="[Linguistics]"

• Education

  python src/analyze.py experiment.atlas.center=Ololube2012 experiment.cartography.required_pub_conditions.fields_of_study="[Education]"

• Medicine

  python src/analyze.py experiment.atlas.center=Torres2013 experiment.cartography.required_pub_conditions.fields_of_study="[Medicine]"

• Economics

  python src/analyze.py experiment.atlas.center=West2003 experiment.cartography.required_pub_conditions.fields_of_study="[Economics]"

• Philosophy

  python src/analyze.py experiment.atlas.center=Bacon2019 experiment.cartography.required_pub_conditions.fields_of_study="[Philosophy]"

• Materials Science

  python src/analyze.py experiment.atlas.center=Miele2022 experiment.cartography.required_pub_conditions.fields_of_study="[Materials Science]"

• Geology

  python src/analyze.py experiment.atlas.center=ForeroOrtega2021 experiment.cartography.required_pub_conditions.fields_of_study="[Geology]"

• Mathematics

  python src/analyze.py experiment.atlas.center=Andre2018 experiment.cartography.required_pub_conditions.fields_of_study="[Mathematics]"

Usage

The relevant scripts to run are

python src/build_atlas.py

python src/analyze.py

For now, to replicate results, or continue expanding/analyzing, select the folder of results you want and look at the .hydra/overrides.yaml file. That will give you a list of commands (overrides) that need to be passed when calling the relevant script. For example outputs/librarian=S2/vectorizer=SciBERT/center=hafenLowredshiftLymanLimit2017/.hydra/overrides.yaml has no extra commands, because it is the default setting. Meanwhile, multirun/librarian=S2/vectorizer=SciBERT/center=Ololube2012/.hydra/overrides.yaml specifies a list of commands that should follow calling the script. That overrides.yaml file corresponds to the following command:

python src/build_atlas.py -m experiment.vectorizer.name=GPT2 experiment.atlas.center=Ololube2012 experiment.cartography.required_pub_conditions.fields_of_study="[Education]" experiment.cartography.target_size=30000 experiment.cartography.n_pubs_max=500

Notice the quotes around the list containing Medicine in one of the overrides.