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Explaing Peer Reviews

Using Machine Learning, Explainable AI and Causal Inference to determine "What Make a Scientific Paper Be Accepted for Publication". This work is part of my thesis for the degree of MSc Advanced Computing from Imperial College London.

Data Dependencies

PeerRead:

Collect the PeerRead dataset from https://github.com/allenai/PeerRead:

mkdir data
cd data/
git clone https://github.com/allenai/PeerRead.git
export DATA=$(pwd)

SciBERT

Be sure to save the SciBERT weights (from https://github.com/allenai/scibert) to the following path under the data root ($DATA).

Be sure to export the path to directory where PeerRead is in, as specified above. This is essential for reading the data from PeerRead.

Libraries Dependencies

The python libraries can be found in the requirements.txt file and can be installed by:

pip install -r requirements.txt

Also install spaCy dependencies:

python3 -m spacy download 'en_core_web_lg'

Executing the Files

The files can be executed by running, for instance, the following:

python src/lstm_att_classifier_per_review.py

Those scrips need to be executed from the ROOT directory of the project.

Overview of Main Utility Files

  • DataLoader.py : offers the functionality needed to read the data from PeerRead, perform Preprocessing and generate BERT embeddings. Depending on whether the data should be used by BERT-based or RNN classifiers different, different classes should be used.
  • helper_functions.py : contains the main functionality needed to train and test the models (e.g. training loops, cross-validation functions etc.)
  • models.py : contains the main PyTorch models used for our various classifiers.
  • abstract_classifier.py : trains a classifier to predict whether a paper is going to be accepted for publication solely based on the abstract.
  • length_hist.py : provides histograms and other information concerning the lengths of peer reviews and meta-reviews.
  • logistic_regression_curves_per_review.py : produces the logistic regression curves needed for benchmarking different explainability techniques. Before running this, the explanations must have been saved in appropriate files.
  • majority_baseline.py : prints the majority baseline for the prediction of the final acceptance decision.
  • majority_baseline_per_review.py : prints the majority baseline for the prediction of reviewer recommendations.

Main Classifiers

This are the files of the main classifier build for this project:

  • bert_meta_review_classifier.py : uses a BERT based model to classify the meta-reviews. In order to explain the predictions of that classifier generate_explanations.py must be run. This will take around 6 hours on a GPU (Be sure to modify the static variable accordingly). Afterwards, run bert_lime_explanations.py to produce the global explanations and metrics on those explanations (Be sure to modify the static variable accordingly).
  • bert_final_decision_classifier.py : uses a BERT based model to classify the peer reviews on a submission level. In order to explain the predictions of that classifier generate_explanations.py must be run. This will take around 12 hours on a GPU (Be sure to modify the static variable accordingly). Afterwards, run bert_lime_explanations.py to produce the global explanations and metrics on those explanations (Be sure to modify the static variable accordingly).
  • bert_classifier_per_review.py : uses a BERT based model to classify the peer reviews on a review level. In order to explain the predictions of that classifier generate_bert_per_review_explanations.py must be run. This will take around 12 hours on a GPU. Afterwards, run bert_lime_explanations_per_review.py to produce the global explanations and metrics on those explanations. Modify the config/BERT_classifier_per_review.yaml file to change hyperparameters, specify if a causal model must be trained, etc.
  • lstm_att_classifier.py : uses a RNN model to classify the meta-reviews. In order to explain the predictions of that classifier lstm_att_explanations.py must be run. Modify the config/lstm_att_classifier.yaml file to change hyperparameters, RNN type, specify if a causal model must be trained, etc.
  • lstm_att_classifier_per_review.py : uses a RNN model to classify the indiviudal peer reviews. In order to explain the predictions of that classifier lstm_att_explanations_per_review.py must be run. Modify the config/lstm_att_classifier_per_review.yaml file to change hyperparameters, RNN type, specify if a causal model must be trained, etc.
  • bow_classifier_per_review.py : uses a BoW model to classify the indiviudal peer reviews. Before running this model,, be sure to have saved one of the lexicons from the previous peer review models. In order to explain the predictions of that classifier bow_explanations_per_review.py must be run. Modify the config/BOW_classifier_per_review.yaml file to change hyperparameters, specify if a causal model must be trained, etc.