The extraction of named entities (named entity recognition, NER) and their semantic relations (relation extraction, RE) are key tasks in information extraction and retrieval (IE & IR). Given a sequence of text (usually a sentence), the objective is to identify both the named entities and the relations between them. This information is useful in a variety of NLP tasks such as question answering, knowledge base population, and semantic search (Jiang, 2012). In the biomedical domain, NER and RE facilitate large-scale biomedical data analysis, such as network biology (Zhou et al., 2014), gene prioritization (Aerts et al., 2006), drug repositioning (Wang and Zhang, 2013) and the creation of curated databases (Li et al., 2015). In the clinical domain, NER and RE can aid in disease and treatment prediction, readmission prediction, de-identification, and patient cohort identification (Miotto et al., 2017).
Most commonly, the tasks of NER and RE are approached as a pipeline, with NER preceding RE. There are two main drawbacks to this approach: (1) Pipeline systems are prone to error propagation between the NER and RE systems. (2) One task is not able to exploit useful information from the other (e.g. the type of relation identified by the RE system may be useful to the NER system for determining the type of entities involved in the relation, and vice versa). More recently, joint models that simultaneously learn to extract entities and relations have been proposed, alleviating the aforementioned issues and achieving state-of-the-art performance (Miwa and Sasaki, 2014; Miwa and Bansal, 2016; Gupta et al., 2016; Li et al., 2016, 2017; Zhang et al., 2017; Adel and Schütze, 2017; Bekoulis et al., 2018b, a; Nguyen and Verspoor, 2019; Li et al., 2019).
Many of the proposed joint models for entity and relation extraction rely heavily on external natural language processing (NLP) tools such as dependency parsers. For instance, Miwa and Bansal (2016)
propose a recurrent neural network (RNN)-based joint model that uses a bidirectional long-short term memory network (BiLSTM) to model the entities and a tree-LSTM to model the relations between entities;Li et al. (2017) propose a similar model for biomedical text. The tree-LSTM uses dependency tree information extracted using an external dependency parser to model relations between entities. The use of these external NLP tools limits the effectiveness of a model to domains (e.g. news) where those NLP tools perform well. As a remedy to this problem, Bekoulis et al. (2018b) proposes a neural, end-to-end system that jointly learns to extract entities and relations without relying on external NLP tools. In Bekoulis et al. (2018a), they augment this model with adversarial training. Nguyen and Verspoor (2019) propose a different, albeit similar end-to-end neural model which makes use of deep biaffine attention (Dozat and Manning, 2016). Li et al. (2019) approach the problem with multi-turn question answering, posing templated queries to a BERT-based QA model (Devlin et al., 2018) whose answers constitute extracted entities and their relations and achieve state-of-the-art results on three popular benchmark datasets.
While demonstrating strong performance, end-to-end systems like Bekoulis et al. (2018b, a) and Nguyen and Verspoor (2019) suffer from two main drawbacks. The first is that most of the models parameters are trained from scratch. For large datasets, this can lead to long training times. For small datasets, which are common in the biomedical and clinical domains where it is particularly challenging to acquire labelled data, this can lead to poor performance and/or overfitting. The second is that these systems typically contain RNNs, which are sequential in nature and cannot be parallelized within training examples. The multi-pass QA model proposed in Li et al. (2019) alleviates these issues by incorporating a pre-trained language model, BERT (Devlin et al., 2018), which eschews recurrence for self-attention. The main limitation of their approach is that it relies on hand-crafted question templates to achieve maximum performance. This may become a limiting factor where domain expertise is required to craft such questions (e.g., for biomedical or clinical corpora). Additionally, one has to create a question template for each entity and relation type of interest.
In this study, we propose an end-to-end model for joint NER and RE which addresses all of these issues. Similar to past work, our model can be viewed as a mixture of a NER module and a RE module (Figure 1). Unlike most previous works, we include a pre-trained, transformer-based language model, specifically BERT (Devlin et al., 2018), which achieved state-of-the-art performance across many NLP tasks. The weights of the BERT model are fine-tuned during training, and the entire model is trained in an end-to-end fashion.
Our main contributions are as follows: (1) Our solution is truly end-to-end, relying on no hand-crafted features (e.g. templated questions) or external NLP tools (e.g. dependency parsers). (2) Our model is fast to train (e.g. under 10 minutes on a single GPU for the CoNLL04 corpus), as most of its parameters are pre-trained and we avoid recurrence. (3) We match or exceed state-of-the-art performance for joint NER and RE on 5 datasets across 3 domains.
2 The Model
Figure 1 illustrates the architecture of our approach. Our model is composed of an NER module and an RE module. The NER module is identical to the one proposed by Devlin et al. (2018). For a given input sequence of word tokens , , , , the pre-trained BERTBASE model first produces a sequence of vectors, , , ,
which are then fed to a feed-forward neural network (FFNN) for classification.
The output size of this layer is the number of BIOES-based NER labels in the training data, . In the BIOES tag scheme, each token is assigned a label, where the B- tag indicates the beginning of an entity span, I- the inside, E- the end and S- is used for any single-token entity. All other tokens are assigned the label O.
During training, a cross-entropy loss is computed for the NER objective,
where is the predicted score that token belongs to the ground-truth entity class and is the predicted score for token belonging to the entity class .
In the RE module, the predicted entity labels are obtained by taking the argmax of each score vector , , , . The predicted entity labels are then embedded to produce a sequence of fixed-length, continuous vectors, , , , which are concatenated with the hidden states from the final layer in the BERT model and learned jointly with the rest of the models parameters.
Following Miwa and Bansal (2016) and Nguyen and Verspoor (2019), we incrementally construct the set of relation candidates, , using all possible combinations of the last word tokens of predicted entities, i.e. words with E- or S- labels. An entity pair is assigned to a negative relation class (NEG) when the pair has no relation or when the predicted entities are not correct. Once relation candidates are constructed, classification is performed with a deep bilinear attention mechanism (Dozat and Manning, 2016), as proposed by Nguyen and Verspoor (2019).
To encode directionality, the mechanism uses FFNNs to project each into head and tail vector representations, corresponding to whether the word serves as head or tail argument of the relation.
These projections are then fed to a biaffine classifier,
where is an tensor, is a matrix, and
is a bias vector. Here,is the size of the output layers of and and is the set of all relation classes (including NEG). During training, a second cross-entropy loss is computed for the RE objective
where is the predicted score that relation candidate belongs to the ground-truth relation class and is the predicted score for relation belonging to the relation class .
The model is trained in an end-to-end fashion to minimize the sum of the NER and RE losses.
2.1 Entity Pretraining
In Miwa and Bansal (2016)
, entity pre-training is proposed as a solution to the problem of low-performance entity detection in the early stages of training. It is implemented by delaying the training of the RE module by some number of epochs, before training the entire model jointly.
Our implementation of entity pretraining is slightly different. Instead of delaying training of the RE module by some number of epochs, we weight the contribution of to the total loss during the first epoch of training
where is increased linearly from 0 to 1 during the first epoch and set to 1 for the remaining epochs. We chose this scheme because the NER module quickly achieves good performance for all datasets (i.e. within one epoch). In early experiments, we found this scheme to outperform a delay of a full epoch.
We implemented our model in PyTorch(Paszke et al., 2017) using the BERTBASE model from the PyTorch Transformers library111https://github.com/huggingface/pytorch-transformers. Our model is available at our GitHub repository222https://github.com/bowang-lab/joint-ner-and-re. Furthermore, we use NVIDIAs automatic mixed precision (AMP) library Apex333https://github.com/NVIDIA/apex to speed up training and reduce memory usage without affecting task-specific performance.
3 Experimental Setup
3.1 Datasets and evaluation
To demonstrate the generalizability of our model, we evaluate it on 5 commonly used benchmark corpora across 3 domains. All corpora are in English. Detailed corpus statistics are presented in Table A.1 of the appendix.
The Automatic Content Extraction (ACE04) corpus was introduced by Doddington et al. (2004), and is commonly used to benchmark NER and RE methods. There are 7 entity types and 7 relation types. ACE05 builds on ACE04, splitting the Physical relation into two classes (Physical and Part-Whole), removing the Discourse relation class and merging Employment-Membership-Subsidiary and Person-Organization-Affiliation into one class (Employment-Membership-Subsidiary).
For ACE04, we follow Miwa and Bansal (2016) by removing the Discourse relation and evaluating our model using 5-fold cross-validation on the bnews and nwire subsets, where 10% of the data was held out within each fold as a validation set. For ACE05, we use the same test split as Miwa and Bansal (2016)
. We use 5-fold cross-validation on the remaining data to choose the hyperparameters. Once hyperparameters are chosen, we train on the combined data from all the folds and evaluate on the test set. For both corpora, we report the micro-averaged F1 score. We obtained the pre-processing scripts from Miwa and Bansal (2016)444https://github.com/tticoin/LSTM-ER/tree/master/data.
The CoNLL04 corpus was introduced in Roth and Yih (2004) and consists of articles from the Wall Street Journal (WSJ) and Associated Press (AP). There are 4 entity types and 5 relation types.
We use the same test set split as Miwa and Sasaki (2014)555https://github.com/pgcool/TF-MTRNN/tree/master/data/CoNLL04. We use 5-fold cross-validation on the remaining data to choose hyperparameters. Once hyperparameters are chosen, we train on the combined data from all folds and evaluate on the test set, reporting the micro-averaged F1 score.
The adverse drug event corpus was introduced by Gurulingappa et al. (2012) to serve as a benchmark for systems that aim to identify adverse drug events from free-text. It consists of the abstracts of medical case reports retrieved from PubMed666https://www.ncbi.nlm.nih.gov/pubmed. There are two entity types, Drug and Adverse effect and one relation type, Adverse drug event.
Similar to previous work (Li et al., 2016, 2017; Bekoulis et al., 2018a), we remove 130 relations with overlapping entities and evaluate our model using 10-fold cross-validation, where 10% of the data within each fold was used as a validation set, 10% as a test set and the remaining data is used as a train set. We report the macro F1 score averaged across all folds.
The 2010 i2b2/VA dataset was introduced by Uzuner et al. (2011) for the 2010 i2b2/Va Workshop on Natural Language Processing Challenges for Clinical Records. The workshop contained an NER task focused on the extraction of 3 medical entity types (Problem, Treatment, Test) and an RE task for 8 relation types.
In the official splits, the test set contains roughly twice as many examples as the train set. To increase the number of training examples while maintaining a rigorous evaluation, we elected to perform 5-fold cross-validation on the combined data from both partitions. We used 10% of the data within each fold as a validation set, 20% as a test set and the remaining data was used as a train set. We report the micro F1 score averaged across all folds.
To the best of our knowledge, we are the first to evaluate a joint NER and RE model on the 2010 i2b2/VA dataset. Therefore, we decided to compare to scores obtained by independent NER and RE systems. We note, however, that the scores of independent RE systems are not directly comparable to the scores we report in this paper. This is because RE is traditionally framed as a sentence-level classification problem. During pre-processing, each example is permutated into processed examples containing two blinded entities and labelled for one relation class. E.g. the example: His PCP had recently started ciprofloxacinTREATMENT for a UTIPROBLEM becomes His PCP had recently started @TREATMENT$ for a @PROBLEM$, where the model is trained to predict the target relation type, Treatment is administered for medical problem (TrAP).
This task is inherently easier than the joint setup, for two reasons: relation predictions are made on ground-truth entities, as opposed to predicted entities (which are noisy) and the model is only required to make one classification decision per pre-processed sentence. In the joint setup, a model must identify any number of relations (or the lack thereof) between all unique pairs of predicted entities in a given input sentence. To control for the first of these differences, we report scores from our model in two settings, once when predicted entities are used as input to the RE module, and once when ground-truth entities are used.
Besides batch size, learning rate and number of training epochs, we used the same hyperparameters across all experiments (see Table A.2). Similar to Devlin et al. (2018), learning rate and batch size were selected for each dataset using a minimal grid search (see See Table A.3).
One hyperparameter selected by hand was the choice of the pre-trained weights used to initialize the BERTBASE model. For general domain corpora, we found the cased BERTBASE weights from Devlin et al. (2018) to work well. For biomedical corpora, we used the weights from BioBERT (Lee et al., 2019), which recently demonstrated state-of-the-art performance for biomedical NER, RE and QA. Similarly, for clinical corpora we use the weights provided by Peng et al. (2019), who pre-trained BERTBASE on PubMed abstracts and clinical notes from MIMIC-III777https://mimic.physionet.org/.
4.1 Jointly learning NER and RE
Table 1 shows our results in comparison to previously published results, grouped by the domain of the evaluated corpus. We find that on every dataset besides i2b2, our model improves NER performance, for an average improvement of 2%. This improvement is particularly large on the ACE04 and ACE05 corpora (3.98% and 2.41% respectively). On i2b2, our joint model performs within 0.29% of the best independent NER solution.
For relation extraction, we outperform previous methods on 2 datasets and come within 2% on both ACE05 and CoNLL04. In two cases, our performance improvement is substantial, with improvements of 4.59% and 10.25% on the ACE04 and ADE corpora respectively. For i2b2, our score is not directly comparable to previous systems (as discussed in section 3.1.4) but will facilitate future comparisons of joint NER and RE methods on this dataset. By comparing overall performance, we find that our approach achieves new state-of-the-art performance for 3 popular benchmark datasets (ACE04, ACE05, ADE) and comes within 0.2% for CoNLL04.
|General||ACE04||Miwa and Bansal (2016)||81.80||48.40||65.10||-5.69|
|Bekoulis et al. (2018a)||81.64||47.45||64.54||-6.25|
|Li et al. (2019)||83.60||49.40||66.50||-4.29|
|ACE05||Miwa and Bansal (2016)||83.40||55.60||69.50||-3.42|
|Zhang et al. (2017)||83.50||57.50||70.50||-2.42|
|Li et al. (2019)||84.80||60.20||72.50||-0.42|
|CoNLL04||Miwa and Sasaki (2014)||80.70||61.00||70.85||-7.30|
|Bekoulis et al. (2018a)||83.61||61.95||72.78||-5.37|
|Li et al. (2019)||87.80||68.90||78.35||0.20|
|Biomedical||ADE||Li et al. (2016)||79.50||63.40||71.45||-16.21|
|Li et al. (2017)||84.60||71.40||78.00||-9.66|
|Bekoulis et al. (2018a)||86.73||75.52||81.13||-6.53|
|Clinical||i2b2*||Si et al. (2019)**||89.55||–||–||–|
|Peng et al. (2019)||–||76.40||–||–|
To the best of our knowledge, there are no published joint NER and RE models that evaluate on the i2b2 2010 corpus. We compare our model to the state-of-the-art for each individual task (see section 3.1.4).
We compare to the scores achieved by their BERTBASE model.
). Bold: best scores. Subscripts denote standard deviation across three runs.: difference to our overall score.
|(a) w/o Entity pre-training||85.910.1||59.440.2||72.67||-0.63|
|(b) w/o Entity embeddings||86.070.1||59.520.2||72.80||-0.51|
|(c) Single FFNN||86.020.1||60.130.0||73.07||-0.23|
|(d) w/o Head/Tail||83.930.2||54.670.8||69.30||-4.00|
|(e) w/o Bilinear||86.350.1||59.600.0||72.98||-0.33|
4.2 Ablation Analysis
To determine which training strategies and components are responsible for our models performance, we conduct an ablation analysis on the CoNLL04 corpus (Table 2). We perform five different ablations: (a) Without entity pre-training (see section 2.1
), i.e. the loss function is given by equation9. (b) Without entity embeddings, i.e. equation 3 becomes . (c) Replacing the two feed-forward neural networks, FFNNhead and FFNNtail with a single FFNN (see equation 4 and 5). (d) Removing FFNNhead and FFNNtail entirely. (e) Without the bilinear operation, i.e. equation 7
becomes a simple linear transformation.
Removing FFNNhead and FFNNtail has, by far, the largest negative impact on performance. Interestingly, however, replacing FFNNhead and FFNNtail with a single FFNN has only a small negative impact. This suggests that while these layers are very important for model performance, using distinct FFNNs for the projection of head and tail entities (as opposed to the same FFNN) is relatively much less important. The next most impactful ablation was entity pre-training, suggesting that low-performance entity detection during the early stages of training is detrimental to learning (see section 2.1). Finally, we note that the importance of entity embeddings is surprising, as a previous study has found that entity embeddings did not help performance on the CoNLL04 corpus (Bekoulis et al., 2018b), although their architecture was markedly different. We conclude that each of our ablated components is necessary to achieve maximum performance.
4.3 Analysis of the word-level attention weights
One advantage of including a transformer-based language model is that we can easily visualize the attention weights with respect to some input. This visualization is useful, for example, in detecting model bias and locating relevant attention heads (Vig, 2019). Previous works have used such visualizations to demonstrate that specific attention heads mark syntactic dependency relations and that lower layers tend to learn more about syntax while higher layers tend to encode more semantics (Raganato and Tiedemann, 2018).
In Figure 2 we visualize the attention weights of select layers and attention heads from an instance of BERT fine-tuned within our model on the CoNLL04 corpus. We display four patterns that are easily interpreted: paying attention to the next and previous words, paying attention to the word itself, and paying attention to the end of the sentence. These same patterns have been found in pre-trained BERT models that have not been fine-tuned on a specific, supervised task (Vig, 2019; Raganato and Tiedemann, 2018), and therefore, are retained after our fine-tuning procedure.
To facilitate further analysis of our learned model, we make available Jupyter and Google Colaboratory notebooks on our GitHub repository888https://github.com/bowang-lab/joint-ner-and-re, where users can use multiple views to explore the learned attention weights of our models. We use the BertViz library (Vig, 2019) to render the interactive, HTML-based views and to access the attention weights used to plot the heat maps.
5 Discussion and Conclusion
In this paper, we introduced an end-to-end model for entity and relation extraction. Our key contributions are: (1) No reliance on any hand-crafted features (e.g. templated questions) or external NLP tools (e.g. dependency parsers). (2) Integration of a pre-trained, transformer-based language model. (3) State-of-the-art performance on 5 datasets across 3 domains. Furthermore, our model is inherently modular. One can easily initialize the language model with pre-trained weights better suited for a domain of interest (e.g. BioBERT for biomedical corpora) or swap BERT for a comparable language model (e.g. XLNet (Yang et al., 2019)). Finally, because of (2), our model is fast to train, converging in approximately 1 hour or less on a single GPU for all datasets used in this study.
Our model out-performed previous state-of-the-art performance on ADE by the largest margin (6.53%). While exciting, we believe this corpus was particularly easy to learn. The majority of sentences (68%) are annotated for two entities (drug and adverse effect, and one relation (adverse drug event). Ostensibly, a model should be able to exploit this pattern to get near-perfect performance on the majority of sentences in the corpus. As a test, we ran our model again, this time using ground-truth entities in the RE module (as opposed to predicted entities) and found that the model very quickly reached almost perfect performance for RE on the test set (98%). As such, high performance on the ADE corpus is not likely to transfer to real-world scenarios involving the large-scale annotation of diverse biomedical articles.
In our experiments, we consider only intra-sentence relations. However, the multiple entities within a document generally exhibit complex, inter-sentence relations. Our model is not currently capable of extracting such inter-sentence relations and therefore our restriction to intra-sentence relations will limit its usefulness for certain downstream tasks, such as knowledge base creation. We also ignore the problem of nested entities, which are common in biomedical corpora. In the future, we would like to extend our model to handle both nested entities and inter-sentence relations. Finally, given that multilingual, pre-trained weights for BERT exist, we would also expect our model’s performance to hold across multiple languages. We leave this question to future work.
Global normalization of convolutional neural networks for joint entity and relation classification. In Proceedings of the 2017 Conference on Empirical Methods in Natural Language Processing, Copenhagen, Denmark. Cited by: §1.
- Gene prioritization through genomic data fusion. Nature Biotechnology 24 (5), pp. 537–544. External Links: Cited by: §1.
- Adversarial training for multi-context joint entity and relation extraction. arXiv preprint arXiv:1808.06876. Cited by: §1, §1, §1, §3.1.3, Table 1.
- Joint entity recognition and relation extraction as a multi-head selection problem. Expert Systems with Applications 114, pp. 34–45. Cited by: §1, §1, §1, §4.2.
- Bert: pre-training of deep bidirectional transformers for language understanding. arXiv preprint arXiv:1810.04805. Cited by: Table A.3, §1, §1, §1, §2, §3.2, §3.2.
- The automatic content extraction (ACE) program – tasks, data, and evaluation. In Proceedings of the Fourth International Conference on Language Resources and Evaluation (LREC’04), Lisbon, Portugal. External Links: Cited by: §3.1.1.
- Deep biaffine attention for neural dependency parsing. arXiv preprint arXiv:1611.01734. Cited by: §1, §2.
- Table filling multi-task recurrent neural network for joint entity and relation extraction. In Proceedings of COLING 2016, the 26th International Conference on Computational Linguistics: Technical Papers, pp. 2537–2547. Cited by: §1.
- Development of a benchmark corpus to support the automatic extraction of drug-related adverse effects from medical case reports. Journal of Biomedical Informatics 45 (5), pp. 885 – 892. Note: Text Mining and Natural Language Processing in Pharmacogenomics External Links: Cited by: §3.1.3.
- Information extraction from text. In Mining Text Data, pp. 11–41. External Links: Cited by: §1.
- Biobert: pre-trained biomedical language representation model for biomedical text mining. arXiv preprint arXiv:1901.08746. Cited by: Table A.3, §3.2.
- A neural joint model for entity and relation extraction from biomedical text. BMC bioinformatics 18 (1), pp. 198. Cited by: §1, §1, §3.1.3, Table 1.
- Joint models for extracting adverse drug events from biomedical text.. In IJCAI, Vol. 2016, pp. 2838–2844. Cited by: §1, §3.1.3, Table 1.
- miRTex: a text mining system for miRNA-gene relation extraction. PLOS Computational Biology 11 (9), pp. e1004391. External Links: Cited by: §1.
- Entity-relation extraction as multi-turn question answering. arXiv preprint arXiv:1905.05529. Cited by: §1, §1, §1, Table 1.
- Fixing weight decay regularization in adam. CoRR abs/1711.05101. External Links: Cited by: Table A.2.
- Deep learning for healthcare: review, opportunities and challenges. Briefings in bioinformatics 19 (6), pp. 1236–1246. Cited by: §1.
- End-to-end relation extraction using lstms on sequences and tree structures. arXiv preprint arXiv:1601.00770. Cited by: §1, §1, §2.1, §2, §3.1.1, Table 1.
- Modeling joint entity and relation extraction with table representation. In Proceedings of the 2014 Conference on Empirical Methods in Natural Language Processing (EMNLP), pp. 1858–1869. Cited by: §1, §3.1.2, Table 1.
- End-to-end neural relation extraction using deep biaffine attention. In Advances in Information Retrieval, L. Azzopardi, B. Stein, N. Fuhr, P. Mayr, C. Hauff, and D. Hiemstra (Eds.), Cham, pp. 729–738. External Links: Cited by: §1, §1, §1, §2.
On the difficulty of training recurrent neural networks.
International Conference on Machine Learning, pp. 1310–1318. Cited by: Table A.2.
- Automatic differentiation in PyTorch. In NIPS Autodiff Workshop, Cited by: §2.2.
- Transfer learning in biomedical natural language processing: an evaluation of BERT and elmo on ten benchmarking datasets. CoRR abs/1906.05474. External Links: Cited by: Table A.3, §3.2, Table 1.
- An analysis of encoder representations in transformer-based machine translation. In Proceedings of the 2018 EMNLP Workshop BlackboxNLP: Analyzing and Interpreting Neural Networks for NLP, pp. 287–297. Cited by: §4.3, §4.3.
A linear programming formulation for global inference in natural language tasks. In Proceedings of the Eighth Conference on Computational Natural Language Learning (CoNLL-2004) at HLT-NAACL 2004, pp. 1–8. Cited by: §3.1.2.
- Enhancing clinical concept extraction with contextual embedding. CoRR abs/1902.08691. External Links: Cited by: Table 1.
- 2010 i2b2/va challenge on concepts, assertions, and relations in clinical text. Journal of the American Medical Informatics Association 18 (5), pp. 552–556. Cited by: §3.1.4.
- A multiscale visualization of attention in the transformer model. CoRR abs/1906.05714. External Links: Cited by: §4.3, §4.3, §4.3.
- Rational drug repositioning by medical genetics. Nature Biotechnology 31 (12), pp. 1080–1082. External Links: Cited by: §1.
- XLNet: generalized autoregressive pretraining for language understanding. arXiv preprint arXiv:1906.08237. Cited by: §5.
- End-to-end neural relation extraction with global optimization. In Proceedings of the 2017 Conference on Empirical Methods in Natural Language Processing, pp. 1730–1740. Cited by: §1, Table 1.
- Human symptoms–disease network. Nature Communications 5. External Links: Cited by: §1.
Appendix A Appendix
a.1 Corpus Statistics
Table A.1 lists detailed statistics for each corpus used in this study.
|Dataset||Entity classes (count)||Relation classes (count)|
|General||ACE04||Person (12508), Organization (4405), Geographical Entities (4425), Location (614), Facility (688), Weapon (119), and Vehicle (209)||Physical (1202), Person-Social (362), Employment-Membership-Subsidiary (1591), Agent-Artifact (212), Person-Organization-Affiliation (141), Geopolitical Entity-Affiliation (517)|
|ACE05||Person (20891), Organization (5627), Geographical Entities (7455), Location(1119), Facility (1461), Weapon (911), and Vehicle (919)||Physical (1612), Part-Whole (1060), Person-Social (615), Agent-Artifact (703), Employment-Membership-Subsidiary (1922), Geopolitical Entity-Affiliation (730)|
|CoNLL04||Location (4765), Organization (2499), People (3918), Other (3011)||Kill (268), Live in (521), Located in (406), OrgBased in (452), Work for (401)|
|Biomedical||ADE||Drug (4979), Adverse effect (5669)||Adverse drug event (6682)|
|Clinical||i2b2||Problem (19664), Test (13831), Treatment (14186)||PIP (2203), TeCP (504), TeRP (3053), TrAP (2617), TrCP (526), TrIP (203), TrNAP (174), TrWP (133)|
a.2 Hyperparameters and Model Details
|Tagging scheme||BIOES||Single token entities are tagged with an S- tag, the beginning of an entity span with a B- tag, the last token of an entity span with an E- tag, and tokens inside an entity span with an I- tag.|
|Dropout rate||0.1||Dropout rate applied to the output of all FFNNs and the attention heads of the BERT model.|
|Entity embeddings||128||Output dimension of the entity embedding layer.|
|FFNNhead / FFNNtail||512||Output dimension of the FFNNhead and FFNNtail layers|
|No. layers (NER module)||1||Number of layers used in the FFNN of the NER module.|
|No. layers (RE module)||2||Number of layers used in the FFNNs of the RE module.|
|Optimizer||AdamW||Adam with fixed weight decay regulatization (Loshchilov and Hutter, 2017).|
|Gradient normalization||Rescales the gradient whenever the norm goes over some threshold (Pascanu et al., 2013).|
|Weight decay||0.1||L2 weight decay.|
|Dataset||No. Epochs||Batch size||Learning rate||Initial BERT weights|
|ACE04||15||16||2e-5||BERT-Base (cased) (Devlin et al., 2018)|
|ADE||7||16||2e-5||BioBERT (cased) (Lee et al., 2019)|
|i2b2||12||16||2e-5||NCBI-BERT (uncased) (Peng et al., 2019)|