BioSyn

Biomedical Entity Representations with Synonym Marginalization

We present BioSyn for learning biomedical entity representations. You can train BioSyn with the two main components described in our paper: 1) synonym marginalization and 2) iterative candidate retrieval. Once you train BioSyn, you can easily normalize any biomedical mentions or represent them into entity embeddings.

Updates

• [Mar 17, 2022] Checkpoints of BioSyn for normalizing gene type are released. The BC2GN data used for the gene type has been pre-processed by Tutubalina et al., 2020.
• [Oct 25, 2021] Trained models are uploaded in Huggingface Hub(Please check out here). Other than BioBERT, we also train our model using another pre-trained model SapBERT, and obtain better performance than as described in our paper.

Requirements

$ conda create -n BioSyn python=3.7
$ conda activate BioSyn
$ conda install numpy tqdm scikit-learn
$ conda install pytorch=1.8.0 cudatoolkit=10.2 -c pytorch
$ pip install transformers==4.11.3

Note that Pytorch has to be installed depending on the version of CUDA.

Datasets

Datasets consist of queries (train, dev, test, and traindev), and dictionaries (train_dictionary, dev_dictionary, and test_dictionary). Note that the only difference between the dictionaries is that test_dictionary includes train and dev mentions, and dev_dictionary includes train mentions to increase the coverage. The queries are pre-processed with lowercasing, removing punctuations, resolving composite mentions and resolving abbreviation (Ab3P). The dictionaries are pre-processed with lowercasing, removing punctuations (If you need the pre-processing codes, please let us know by openning an issue).

Note that we use development (dev) set to search the hyperparameters, and train on traindev (train+dev) set to report the final performance.

• ncbi-disease
• bc5cdr-disease
• bc5cdr-chemical

TAC2017ADR dataset cannot be shared because of the license issue. Please visit the website or see here for pre-processing scripts.

Train

The following example fine-tunes our model on NCBI-Disease dataset (train+dev) with BioBERTv1.1.

MODEL_NAME_OR_PATH=dmis-lab/biobert-base-cased-v1.1
OUTPUT_DIR=./tmp/biosyn-biobert-ncbi-disease
DATA_DIR=./datasets/ncbi-disease

CUDA_VISIBLE_DEVICES=1 python train.py \
    --model_name_or_path ${MODEL_NAME_OR_PATH} \
    --train_dictionary_path ${DATA_DIR}/train_dictionary.txt \
    --train_dir ${DATA_DIR}/processed_traindev \
    --output_dir ${OUTPUT_DIR} \
    --use_cuda \
    --topk 20 \
    --epoch 10 \
    --train_batch_size 16\
    --initial_sparse_weight 0\
    --learning_rate 1e-5 \
    --max_length 25 \
    --dense_ratio 0.5

Note that you can train the model on processed_train and evaluate it on processed_dev when you want to search for the hyperparameters. (the argument --save_checkpoint_all can be helpful. )

Evaluation

The following example evaluates our trained model with NCBI-Disease dataset (test).

MODEL_NAME_OR_PATH=./tmp/biosyn-biobert-ncbi-disease
OUTPUT_DIR=./tmp/biosyn-biobert-ncbi-disease
DATA_DIR=./datasets/ncbi-disease

python eval.py \
    --model_name_or_path ${MODEL_NAME_OR_PATH} \
    --dictionary_path ${DATA_DIR}/test_dictionary.txt \
    --data_dir ${DATA_DIR}/processed_test \
    --output_dir ${OUTPUT_DIR} \
    --use_cuda \
    --topk 20 \
    --max_length 25 \
    --save_predictions \
    --score_mode hybrid

Result

The predictions are saved in predictions_eval.json with mentions, candidates and accuracies (the argument --save_predictions has to be on). Following is an example.

{
  "queries": [
    {
      "mentions": [
        {
          "mention": "ataxia telangiectasia",
          "golden_cui": "D001260",
          "candidates": [
            {
              "name": "ataxia telangiectasia",
              "cui": "D001260|208900",
              "label": 1
            },
            {
              "name": "ataxia telangiectasia syndrome",
              "cui": "D001260|208900",
              "label": 1
            },
            {
              "name": "ataxia telangiectasia variant",
              "cui": "C566865",
              "label": 0
            },
            {
              "name": "syndrome ataxia telangiectasia",
              "cui": "D001260|208900",
              "label": 1
            },
            {
              "name": "telangiectasia",
              "cui": "D013684",
              "label": 0
            }]
        }]
    },
    ...
    ],
    "acc1": 0.9114583333333334,
    "acc5": 0.9385416666666667
}

Inference

We provide a simple script that can normalize a biomedical mention or represent the mention into an embedding vector with BioSyn.

Trained models

NCBI-Disease

Model	Acc@1/Acc@5
biosyn-biobert-ncbi-disease	91.1/93.9
biosyn-sapbert-ncbi-disease	92.4/95.8

BC5CDR-Disease

Model	Acc@1/Acc@5
biosyn-biobert-bc5cdr-disease	93.2/96.0
biosyn-sapbert-bc5cdr-disease	93.5/96.4

BC5CDR-Chemical

Model	Acc@1/Acc@5
biosyn-biobert-bc5cdr-chemical	96.6/97.2
biosyn-sapbert-bc5cdr-chemical	96.6/98.3

BC2GN-Gene

Model	Acc@1/Acc@5
biosyn-biobert-bc2gn	90.6/95.6
biosyn-sapbert-bc2gn	91.3/96.3

Predictions (Top 5)

The example below gives the top 5 predictions for a mention ataxia telangiectasia. Note that the initial run will take some time to embed the whole dictionary. You can download the dictionary file here.

MODEL_NAME_OR_PATH=dmis-lab/biosyn-biobert-ncbi-disease
DATA_DIR=./datasets/ncbi-disease

python inference.py \
    --model_name_or_path ${MODEL_NAME_OR_PATH} \
    --dictionary_path ${DATA_DIR}/test_dictionary.txt \
    --use_cuda \
    --mention "ataxia telangiectasia" \
    --show_predictions

Result

{
  "mention": "ataxia telangiectasia", 
  "predictions": [
    {"name": "ataxia telangiectasia", "id": "D001260|208900"},
    {"name": "ataxia telangiectasia syndrome", "id": "D001260|208900"}, 
    {"name": "telangiectasia", "id": "D013684"}, 
    {"name": "telangiectasias", "id": "D013684"}, 
    {"name": "ataxia telangiectasia variant", "id": "C566865"}
  ]
}

Embeddings

The example below gives an embedding of a mention ataxia telangiectasia.

MODEL_NAME_OR_PATH=dmis-lab/biosyn-biobert-ncbi-disease
DATA_DIR=./datasets/ncbi-disease

python inference.py \
    --model_name_or_path ${MODEL_NAME_OR_PATH} \
    --use_cuda \
    --mention "ataxia telangiectasia" \
    --show_embeddings

Result

{
  "mention": "ataxia telangiectasia", 
  "mention_sparse_embeds": array([0.05979538, 0., ..., 0., 0.], dtype=float32),
  "mention_dense_embeds": array([-7.14258850e-02, ..., -4.03847933e-01,],dtype=float32)
}

Demo

How to run web demo

Web demo is implemented on Tornado framework. If a dictionary is not yet cached, it will take about couple of minutes to create dictionary cache.

MODEL_NAME_OR_PATH=dmis-lab/biosyn-biobert-ncbi-disease

python demo.py \
  --model_name_or_path ${MODEL_NAME_OR_PATH} \
  --use_cuda \
  --dictionary_path ./datasets/ncbi-disease/test_dictionary.txt

Citations

@inproceedings{sung2020biomedical,
    title={Biomedical Entity Representations with Synonym Marginalization},
    author={Sung, Mujeen and Jeon, Hwisang and Lee, Jinhyuk and Kang, Jaewoo},
    booktitle={ACL},
    year={2020},
}