ArboEL

(NAACL 2022!) Entity Linking via Explicit Mention-Mention Coreference Modeling: https://aclanthology.org/2022.naacl-main.343/
Entity Linking & Discovery via Arborescence-based Supervised Clustering: https://arxiv.org/abs/2109.01242

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Overview

ArboEL is an entity linking and discovery system, which uses a directed MST (arborescence) supervised clustering objective to train BERT-based dual-encoders coupled with multiple inference routines, including a transductive graph partitioning procedure that makes predictions by jointly considering links between mentions as well as between mentions and entities. The repository additionally contains cross-encoder training and inference procedures that utilize the improved representations provided by the arborescence-based dual-encoders.

Citing

If you use ArboEL in your work, please cite the following paper:

@inproceedings{agarwal-etal-2022-entity,
    title = "Entity Linking via Explicit Mention-Mention Coreference Modeling",
    author = "Agarwal, Dhruv  and
      Angell, Rico  and
      Monath, Nicholas  and
      McCallum, Andrew",
    booktitle = "Proceedings of the 2022 Conference of the North American Chapter of the Association for Computational Linguistics: Human Language Technologies",
    month = jul,
    year = "2022",
    address = "Seattle, United States",
    publisher = "Association for Computational Linguistics",
    url = "https://aclanthology.org/2022.naacl-main.343",
    pages = "4644--4658",
    abstract = "Learning representations of entity mentions is a core component of modern entity linking systems for both candidate generation and making linking predictions. In this paper, we present and empirically analyze a novel training approach for learning mention and entity representations that is based on building minimum spanning arborescences (i.e., directed spanning trees) over mentions and entities across documents to explicitly model mention coreference relationships. We demonstrate the efficacy of our approach by showing significant improvements in both candidate generation recall and linking accuracy on the Zero-Shot Entity Linking dataset and MedMentions, the largest publicly available biomedical dataset. In addition, we show that our improvements in candidate generation yield higher quality re-ranking models downstream, setting a new SOTA result in linking accuracy on MedMentions. Finally, we demonstrate that our improved mention representations are also effective for the discovery of new entities via cross-document coreference.",
}

Setting up

• Install conda (we recommend miniconda)
• Create an environment and install dependencies

  conda create -n blink37 -y python=3.7 && conda activate blink37 && pip install -r requirements.txt && conda install cython pytorch==1.4.0 torchvision==0.5.0 cudatoolkit=10.1 -c pytorch

• Build cluster-linking special_partition function (from Cython)

  cd blink/biencoder/special_partition; python setup.py build_ext --inplace

• Our setup assumes GPU availability
  • The code for our paper was run using 2 NVIDIA Quadro RTX 8000

Datasets

• MedMentions (Full): The MedMentions corpus consists of 4,392 papers (Titles and Abstracts) randomly selected from among papers released on PubMed in 2016, that were in the biomedical field, published in the English language, and had both a Title and an Abstract.
• ZeShEL: The Zero Shot Entity Linking dataset was constructed using multiple sub-domains in Wikia from FANDOM with automatically extracted labeled mentions using hyper-links.

Download instructions

• ZeShEL:
  • Download the data files from the original ZeShEL repo (https://github.com/lajanugen/zeshel)
  • This should give you a directory called "zeshel" with 2 sub-directories - "documents" and "mentions"
  • Our pre-processing code (arboEL/blink/preprocess/zeshel_*) assumes you place this "zeshel" folder in $PROJECT_ROOT/data
• MedMentions:
  • Download the data files from https://drive.google.com/file/d/1qywgi4VkumB3dAtRx6aHWUX65XrCPGXL/view?usp=sharing
  • This should give you a directory called "medmentions" with 2 sub-directories - "documents" and "mentions"
  • Our pre-processing code (arboEL/blink/preprocess/medmentions_*) assumes you place this "medmentions" folder in $PROJECT_ROOT/data

Pre-processing

• For MedMentions

  # Create the entity dictionary
  python blink/preprocess/medmentions_dictionary.py
  # Pre-process the query mentions
  python blink/preprocess/medmentions_preprocess.py

• For ZeShEL

  # Create the entity dictionary
  python blink/preprocess/zeshel_dictionary.py
  # Pre-process the query mentions
  python blink/preprocess/zeshel_preprocess.py

---

The following are example commands for MedMentions. For brevity, and to reduce repetition, commands for ZeShEL are omitted but can be constructed by simply swapping path values in these commands.

Dual-encoder Training

Arborescence

python blink/biencoder/train_biencoder_mst.py --bert_model=models/biobert-base-cased-v1.1 --data_path=data/medmentions/processed --output_path=models/trained/medmentions_mst/pos_neg_loss/no_type --pickle_src_path=models/trained/medmentions --num_train_epochs=5 --train_batch_size=128 --gradient_accumulation_steps=4 --eval_interval=10000 --pos_neg_loss --force_exact_search --embed_batch_size=3500 --data_parallel

k-NN negatives

python blink/biencoder/train_biencoder_mult.py --bert_model=models/biobert-base-cased-v1.1 --data_path=data/medmentions/processed --output_path=models/trained/medmentions/pos_neg_loss/no_type --pickle_src_path=models/trained/medmentions --num_train_epochs=5 --train_batch_size=128 --gradient_accumulation_steps=4 --eval_interval=10000 --pos_neg_loss --force_exact_search --embed_batch_size=3500 --data_parallel

In-batch negatives

python blink/biencoder/train_biencoder.py --bert_model=models/biobert-base-cased-v1.1 --num_train_epochs=5 --data_path=data/medmentions/processed --output_path=models/trained/medmentions_blink --data_parallel --train_batch_size=128 --eval_batch_size=128 --eval_interval=10000

Dual-encoder Inference

Linking

python blink/biencoder/eval_cluster_linking.py --bert_model=models/biobert-base-cased-v1.1 --data_path=data/medmentions/processed --output_path=models/trained/medmentions_mst/eval/pos_neg_loss/no_type/wo_type --pickle_src_path=models/trained/medmentions/eval --path_to_model=models/trained/medmentions_mst/pos_neg_loss/no_type/epoch_best_5th/pytorch_model.bin --recall_k=64 --embed_batch_size=3500 --force_exact_search --data_parallel

Discovery

python blink/biencoder/eval_entity_discovery.py --bert_model=models/biobert-base-cased-v1.1 --data_path=data/medmentions/processed --output_path=models/trained/medmentions_mst/eval/pos_neg_loss/directed --pickle_src_path=models/trained/medmentions/eval --embed_data_path=models/trained/medmentions_mst/eval/pos_neg_loss --use_types --force_exact_search --graph_mode=directed --exact_threshold=127.87733985396665 --exact_knn=8 --data_parallel

Cross-encoder Training

We specify cross-encoder commands for the Arborescence dual-encoder only for brevity. Commands for other variants can be constructed by simply swapping path values in these commands.

(using Arborescence dual-encoder)

# Generate dual-encoder candidates
python blink/crossencoder/eval_cluster_linking.py --data_path=data/medmentions/processed --output_path=models/trained/medmentions/candidates/arbo --pickle_src_path=models/trained/medmentions --path_to_biencoder_model=models/trained/medmentions_mst/pos_neg_loss/no_type/epoch_best_5th/pytorch_model.bin --bert_model=models/biobert-base-cased-v1.1 --data_parallel --scoring_batch_size=64 --save_topk_result

# Run cross-encoder training
python blink/crossencoder/original/train_cross.py --data_path=data/medmentions/processed --pickle_src_path=models/trained/medmentions --output_path=models/trained/medmentions/crossencoder/arbo --bert_model=models/biobert-base-cased-v1.1 --learning_rate=2e-05 --num_train_epochs=5 --train_batch_size=2 --eval_batch_size=2 --biencoder_indices_path=models/trained/medmentions/candidates/arbo --add_linear --skip_initial_eval --eval_interval=-1 --data_parallel

Cross-encoder Inference

(using Arborescence dual-encoder)

Regular

python blink/crossencoder/original/train_cross.py --data_path=data/medmentions/processed --pickle_src_path=models/trained/medmentions --output_path=models/trained/medmentions/crossencoder/eval/arbo --eval_batch_size=2 --biencoder_indices_path=models/trained/medmentions/candidates/arbo --add_linear --only_evaluate --data_parallel --bert_model=models/biobert-base-cased-v1.1 --path_to_model=models/trained/medmentions/crossencoder/arbo/pytorch_model.bin

Oracle (Self Set)

python blink/crossencoder/original/train_cross.py --data_path=data/medmentions/processed --pickle_src_path=models/trained/medmentions --output_path=models/trained/medmentions/crossencoder/eval/arbo/oracle --eval_batch_size=2 --biencoder_indices_path=models/trained/medmentions/candidates/arbo --add_linear --only_evaluate --data_parallel --bert_model=models/biobert-base-cased-v1.1 --inject_eval_ground_truth=True --path_to_model=models/trained/medmentions/crossencoder/arbo/pytorch_model.bin

Oracle (Union Set)

python blink/crossencoder/original/train_cross.py --data_path=data/medmentions/processed --pickle_src_path=models/trained/medmentions --output_path=models/trained/medmentions/crossencoder/eval/arbo/oracle_union --eval_batch_size=2 --biencoder_indices_path=models/trained/medmentions/candidates --custom_cand_set=union --add_linear --only_evaluate --data_parallel --bert_model=models/biobert-base-cased-v1.1 --inject_eval_ground_truth=True --path_to_model=models/trained/medmentions/crossencoder/arbo/pytorch_model.bin

Questions / Feedback

If you have any questions, comments, or feedback on our work, please reach out at [email protected]! (or open a GitHub issue)

Licence

ArboEL is MIT licensed. See the LICENSE file for details.

Acknowledgements

We thank BLINK for the base infrastructure of this project.