MS^2 is a dataset containing medical systematic reviews, their constituent studies, and a large amount of related markup. This repository contains code for attempting to produce summaries from this data.
All commands are assumed to be run in the same terminal session, so variables such as PYTHONPATH are assumed to be carried between components.
You might wish to create a conda env:
conda create -n ms2 python=3.8
# or conda create -p ms2 python=3.8
conda activate ms2
You will need to install these packages:
conda install pytorch torchvision torchaudio cudatoolkit=10.2 -c pytorch
pip install -r requirements.txt
wget https://ai2-s2-research.s3-us-west-2.amazonaws.com/longformer/longformer-encdec-base-16384.tar.gz
wget https://ai2-s2-research.s3-us-west-2.amazonaws.com/longformer/longformer-encdec-large-16384.tar.gz
You will need to download the data, either from https://ai2-s2-ms2.s3-us-west-2.amazonaws.com/ms_data_2021-04-12.zip or from the s3 bucket s3 aws cp s3://ai2-s2-ms2/ms_data_2021-04-12.zip ./
In either case, checksums should be:
sha1sum ms_data_2021-04-12.zip
6090fbea367c7c52a4c3a9418591792d8dea90e7 ms_data_2021-04-12.zip
md5sum ms_data_2021-04-12.zip
7cf243af2373ad496d948fc73d7dcf31 ms_data_2021-04-12.zip
The first step is to convert model inputs for the summarizer. This converts the review structure into tensorized versions of inputs and outputs; either text or table inputs or outputs. The primary versions of interest are the text-to-text version and the table-to-table versions. See sample.json for an example of the raw inputs.
This will need to be repeated for each subset:
input_subset=...
output_reviews_file=...
MAX_LENGTH="--max_length 500"
# Run from either the ms2 root or specify the path of the ms2 repository.
export PYTHONPATH=./
# text-text version
python scripts/modeling/summarizer_input_prep.py --input $input_subset --output $output_reviews_file --tokenizer facebook/bart-base $MAX_LENGTH"
# table-table version
python scripts/modeling/tabular_summarizer_input_prep.py --input $input_subset --output $output_reviews_file --tokenizer facebook/bart-base $MAX_LENGTH"
# text-table version
python scripts/modeling/text_to_table_input_prep.py --input $input_subset --output $output_reviews_file --tokenizer facebook/bart-base $MAX_LENGTH"
# table-text version
python scripts/modeling/table_to_text_summarizer_input.py --input $input_subset --output $output_reviews_file --tokenizer facebook/bart-base $MAX_LENGTH"
All model training uses the same script. Run with --help for all options. This requires at least one RTX8000 (users of just one will need to adjust GRAD_ACCUM appropriately).
training_reviews_file="result of input prep"
validation_reviews_file="result of input prep"
training_root="place to store model artificats"
EPOCHS=8 # more doesn't seem to do much
GRAD_ACCUM=16 # if using 2x RTX8000, otherwise set for batch sizes of 32
MODEL_NAME= # options are facebook/bart-base, facebook/bart-large, /path/to/longformer/base, /path/to/longformer/large
python litreviews/models/transformer_summarizer.py \
--train $training_reviews_file \
--val $validation_reviews_file \
--training_root $training_dir \
--epochs=$EPOCHS \
--grad_accum=$GRAD_ACCUM \
--fp16 \
--model_name $MODEL_NAME
Make predictions via:
INPUT=$validation_reviews_file
OUTPUT="well, you want this to go somewhere?"
CHECKPOINT="trained model"
NUM_BEAMS=6
MODEL_NAME="same as in modeling"
python scripts/modeling/decode.py --input $INPUT --output $OUTPUT --checkpoint $CHECKPOINT --num_beams=$NUM_BEAMS --model_name $MODEL_NAME
The tabular target settings should have the extra arguments: --min_length 2 --max_length 10
For tabular scoring:
f="$OUTPUT from above"
python scripts/modeling/f1_scorer.py --input $f --output $f.scores
For textual scoring (requires a GPU):
f="$OUTPUT from above"
evidence_inference_dir=...
evidence_inference_classifier_params=...
python scripts/modeling/consistency_scorer.py --model_outputs $f --output $f.scores --evidence_inference_dir $evidence_inference_dir --evidence_inference_classifier_params $evidence_inference_params &
This section uses a modified version of the evidence inference dataset that discards the comparator. Clone evidence inference fom the ms2 tag. Once installing the requirements.txt file, the models may be trained via:
python evidence_inference/models/pipeline.py --params params/sampling_abstracts/bert_pipeline_8samples.json --output_dir $evidence_inference_dir
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