Official PyTorch implementation of the paper "Similarity-based Memory Enhanced Joint Entity and Relation Extraction" accepted on the International Conference on Computational Science 2023.

To set up an environment first create the python 3.10 environment using conda or virtualenv, activate it, and install poetry using pip:

pip install poetry==1.4.2

make setup

OR

To force the CUDA version of pytorch library run the following:

make setup-cuda

We built our solution based on wonderful work from JEREX repository. We also used the code from Edge-oriented Graph repository to process the CDR dataset. We used the code as git submodules which You can initialize by running the following:

git submodule init && git submodule update --recursive

Because we import some code from the JEREX It might be useful to add the ./submodules/jerex directory to PYTHONPATH.

Create the '.env' file based on '.env.example' examples and set the variables:

• PRETRAINED_MODELS_DIR - The directory where the pretrained huggingface 🤗 models are stored;
• WANDB_PROJECT_NAME - If you want to use Weights&Biases logging You can set the project name used by the logger;

You can download the datasets we used in our experiments in ready-to-use format:

./scripts/datasets/fetch_datasets.sh

You can download the datasets we used in our experiments in ready-to-use format:

./scripts/fetch_models.sh

We used Hydra to create a hierarchical configuration for running our experiments. The ./config directory contains all the .yaml file used to run the scripts.

You can make use of downloaded model checkpoint and run the inference on the CDR dataset using the following command:

python ./scripts/run.py --config-name memory_re/cdr/test

All the artifacts created during run will be logged into directory created in ./storage/runs. The script is configured to visualize predictions in .html file (using the code from JEREX) and visualize the memory activations for entities and mentions categories.

You can run training on the CDR dataset using the following command:

python ./scripts/run.py --config-name memory_re/cdr/train