Factuality check of the SemRep Predications
The project deals with a Transformer based Language Model to filter predications belonging to the following subset of predicates from SemMedDB, informally called the "Substance Interactions" group:
- INTERACTS_WITH
- STIMULATES
- INHIBITS
Md Rakibul Islam Prince Graduate Research Assistant Department of Electrical and Computer Engineering Indiana University-Purdue University Indianapolis Email: mdprin@iu.edu
To reproduse the results at first all the necessarry packages are needed to be installed. the "semrepenv.yml" YAML file encapsulates the conda environment I used.
run
conda env create -f semrepenv.yml
conda activate semrepenv
or,
pip install -r requirements.txt
to install the environment before running any scripts or notebook. Or, you can manually install the packages from the "requirements.txt" file
/semrep
├── /data
│ ├── substance_interactions.csv
│ └── substance_interactions_cleaned.csv
├── /logs
│ ├── bert_logfile.log
│ ├── biobert_logfile.log
│ └── ...
├── /models
│ ├── semrep_simple_bert_model
│ ├── semrep_simple_biobert_model
│ └── ...
├── /plots
│ ├── bert_cat_arg_dis_impact_all.png
│ ├── bert_cat_arg_dis_impact_verbal.png
│ ├── bert_cum_arg_dis_impact_all.png
│ ├── bert_cum_arg_dis_impact_verbal.png
│ ├── bert_precision_recall_curve_all.png
│ ├── bert_precision_recall_curve_verbal.png
│ ├── bert_roc_curve.png
│ ├── bert_sub_obj_heatmap_all.png
│ ├── bert_sub_obj_heatmap_verbal.png
│ └── ...
├── /results
│ ├── bert_test_set_0_results.csv
│ ├── val_bert_results.csv
│ ├── test_bert_results.csv
│ └── ...
├── /src
│ ├── semrep_model.ipynb
│ └── utils.py
├── README.txt
├── requirements.txt
└── semrepenv.yml
Below is an overview of the key files and folders in this project:
-
`data/': Directory where the raw and processed data files are stored.
-
`data/substance_interactions.csv': raw data file
-
`data/substance_interactions_cleaned.csv': processed and clean data file
-
logs/: Directory containing the logs for each model. -
logs/<model_name>_logfile.log: logfile for model <model_name> -
models/: Directory containing the finetuned checkpoints of the models. -
plots/: Directory containing all the generated plots during analysis. -
results/: Directory where the test and validation results are installed. -
src/: Directory containing the model notebooks and scripts. -
src/semrep_model.ipynb: Notebook detailing the full implimentation of the project -
src/utils.py: Scripts used for data analysis visualization tasks -
`README.txt': File detailing the description of the codebase.
-
`requirements.txt': File detailing necessarry packages.
-
`semrepenv.yml': File for recreating the environment.