This repo stores the codes for topic modeling on palliative care journals for the following paper:

Revelations from a Machine Learning Analysis of the Most Downloaded Articles Published in Journal of Palliative Medicine 1999–2018 (Journal of Palliative Medicine, 2023) by Suzanne Tamang, Zhijing Jin, Vyjeyanthi S Periyakoil.

First, download the journal papers. For convenience, you can check the papers_parsed/ folder, or you can also download the data on your own as follows.

bash 1_download_pdfs.sh # To download papers from the journal `jpm`
bash 1_download_pdfs_jwh.sh # To download papers from the journal `jwh`

Install all the necessary python packages.

bash 2_pdf2json_prep_env.sh

Run the topic modeling on the default journal jpm:

python 3_pdf2json2topics.py

Or you can also run the topic modeling on the other journal jwh:

python 3_pdf2json2topics.py -journal_name jwh

In addition, we also saved the text for word cloud generation in the outputs/ folder.

@article{tamang2023revelations,
    author = "Tamang, Suzanne and Jin, Zhijing and Periyakoil, Vyjeyanthi S.",
    title = "Revelations from a Machine Learning Analysis of the Most Downloaded Articles Published in Journal of Palliative Medicine 1999--2018",
    journal = "Journal of Palliative Medicine",
    volume = "26",
    number = "1",
    pages = "13-16",
    year = "2023",
    doi = "10.1089/jpm.2022.0574",
    note = "PMID: 36607778",
    URL = "https://doi.org/10.1089/jpm.2022.0574",
    eprint = "https://doi.org/10.1089/jpm.2022.0574"
}