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Title: End-to-end named entity recognition and relation extraction using pre-trained language models

Paper content:
Named entity recognition (NER) and relation extraction (RE) are two important tasks in information extraction and retrieval (IE & IR).
Recent work has demonstrated that it is beneficial to learn these tasks jointly, which avoids the propagation of error inherent in pipeline-based systems and improves performance.
However, state-of-the-art joint models typically rely on external natural language processing (NLP) tools, such as dependency parsers, limiting their usefulness to domains (e.g. news) where those tools perform well.
The few neural, end-to-end models that have been proposed are trained almost completely from scratch.
In this paper, we propose a neural, end-to-end model for jointly extracting entities and their relations which does not rely on external NLP tools and which integrates a large, pre-trained language model.
Because the bulk of our model's parameters are pre-trained and we eschew recurrence for self-attention, our model is fast to train.
On 5 datasets across 3 domains, our model matches or exceeds state-of-the-art performance, sometimes by a large margin.
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 & 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 & Sasaki, 2014; Miwa & Bansal, 2016; Gupta et al., 2016; Li et al., 2016; Adel & Schütze, 2017; Bekoulis et al., 2018a; b; Nguyen & 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 & 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. (2018a) 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. (2018b) , they augment this model with adversarial training.
Nguyen & Verspoor (2019) propose a different, albeit similar end-to-end neural model which makes use of deep biaffine attention (Dozat & 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. (2018a; b) and Nguyen & 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 handcrafted 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 handcrafted 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.
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 s of N word tokens w 1 , w 2 , .
. ., w N , the pre-trained BERT BASE model first produces a sequence of vectors, x
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.

assistant: text: A novel, high-performing architecture for end-to-end named entity recognition and relation extraction that is fast to train.