ontology-pretraining's Introduction

Ontology Pretraining

Generalizing over Long Tail Concepts for Medical Term Normalization

This repository contains the source code used for the experimental session of the "Generalizing over Long Tail Concepts for Medical Term Normalization" paper.

⚠️ This code may produce some errors. The updated version will be released soon.

Datasets

The datasets used for the experimental session are in the data folder, except for PROP that cannot be publicly released.

In the train.csv and test.csv files the relevant columns refer to:

ae: the ADE in the original sample text
term: the preferred term PT
term_llt_or_pt: the original LLT/PT

We don't have permission to share MedDRA (or parts of it), so to perform the ontology pretraining (OP) you have to download it by yourself.

Models execution

To create an environment env and install all the requirements, run:

make venv

In each folder in models you can find a train_test.sh script to run an example.

TODO

Provide evaluation script
fix some paths

Cite

@inproceedings{portelli-etal-2022-generalizing,
    title = "Generalizing over Long Tail Concepts for Medical Term Normalization",
    author = "Portelli, Beatrice  and
      Scaboro, Simone  and
      Santus, Enrico  and
      Sedghamiz, Hooman  and
      Chersoni, Emmanuele  and
      Serra, Giuseppe",
    booktitle = "Proceedings of the 2022 Conference on Empirical Methods in Natural Language Processing",
    month = dec,
    year = "2022",
    address = "Abu Dhabi, United Arab Emirates",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2022.emnlp-main.588",
    pages = "8580--8591"
}

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