Density, asymmetry and citation dynamics in scientific literature

This repository accompanies the following paper:

Imel, Nathaniel and Hafen, Zachary. Density, asymmetry and citation dynamics in scientific literature. https://arxiv.org/abs/2506.23366

Data

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

Reproducing 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]"

Requirements

Create a fresh conda environment and install the dependencies found in environment.yaml.

In addition, this repo depends centrally on the sciterra package. Follow the instructions at the linked repo for installation.

Usage

To run a new analysis, 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.

Further visualizations can be reproduced from the generate_figures.py script and the notebooks folder.

Citation

To cite this work, please use:

@misc{Imel2025Density,
  author       = {Imel, Nathaniel and Hafen, Zachary},
  title        = {Density, asymmetry and citation dynamics in scientific literature},
  year         = {2025},
  eprint       = {2506.23366},
  archivePrefix = {arXiv},
  primaryClass = {cs.DL},
  url          = {https://arxiv.org/abs/2506.23366},
}