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Register a new userHealthcare NER Models Using Language Model Pretraining
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Added by
Dattaraj Rao
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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In this paper, we present our approach to extracting structured information from unstructured Electronic Health Records (EHR) [2] which can be used to, for example, study adverse drug reactions in patients due to chemicals in their products. Our solution uses a combination of Natural Language Processing (NLP) techniques and a web-based annotation tool to optimize the performance of a custom Named Entity Recognition (NER) [1] model trained on a limited amount of EHR training data. This work was presented at the first Health Search and Data Mining Workshop (HSDM 2020) [26]. We showcase a combination of tools and techniques leveraging the recent advancements in NLP aimed at targeting domain shifts by applying transfer learning and language model pre-training techniques [3]. We present a comparison of our technique to the current popular approaches and show the effective increase in performance of the NER model and the reduction in time to annotate data.A key observation of the results presented is that the F1 score of model (0.734) trained with our approach with just 50% of available training data outperforms the F1 score of the blank spaCy model without language model component (0.704) trained with 100% of the available training data. We also demonstrate an annotation tool to minimize domain expert time and the manual effort required to generate such a training dataset. Further, we plan to release the annotated dataset as well as the pre-trained model to the community to further research in medical health records.
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Recent studies have demonstrated the efficiency of generative pretraining for English natural language understanding. In this work, we extend this approach to multiple languages and show the effectiveness of cross-lingual pretraining. We propose two methods to learn cross-lingual language models (XLMs): one unsupervised that only relies on monolingual data, and one supervised that leverages parallel data with a new cross-lingual language model objective. We obtain state-of-the-art results on cross-lingual classification, unsupervised and supervised machine translation. On XNLI, our approach pushes the state of the art by an absolute gain of 4.9% accuracy. On unsupervised machine translation, we obtain 34.3 BLEU on WMT16 German-English, improving the previous state of the art by more than 9 BLEU. On supervised machine translation, we obtain a new state of the art of 38.5 BLEU on WMT16 Romanian-English, outperforming the previous best approach by more than 4 BLEU. Our code and pretrained models will be made publicly available.
Recent studies have demonstrated a perceivable improvement on the performance of neural machine translation by applying cross-lingual language model pretraining (Lample and Conneau, 2019), especially the Translation Language Modeling (TLM). To alleviate the need for expensive parallel corpora by TLM, in this work, we incorporate the translation information from dictionaries into the pretraining process and propose a novel Bilingual Dictionary-based Language Model (BDLM). We evaluate our BDLM in Chinese, English, and Romanian. For Chinese-English, we obtained a 55.0 BLEU on WMT-News19 (Tiedemann, 2012) and a 24.3 BLEU on WMT20 news-commentary, outperforming the Vanilla Transformer (Vaswani et al., 2017) by more than 8.4 BLEU and 2.3 BLEU, respectively. According to our results, the BDLM also has advantages on convergence speed and predicting rare words. The increase in BLEU for WMT16 Romanian-English also shows its effectiveness in low-resources language translation.
While buying a product from the e-commerce websites, customers generally have a plethora of questions. From the perspective of both the e-commerce service provider as well as the customers, there must be an effective question answering system to provide immediate answers to the user queries. While certain questions can only be answered after using the product, there are many questions which can be answered from the product specification itself. Our work takes a first step in this direction by finding out the relevant product specifications, that can help answering the user questions. We propose an approach to automatically create a training dataset for this problem. We utilize recently proposed XLNet and BERT architectures for this problem and find that they provide much better performance than the Siamese model, previously applied for this problem. Our model gives a good performance even when trained on one vertical and tested across different verticals.
The newly emerged transformer technology has a tremendous impact on NLP research. In the general English domain, transformer-based models have achieved state-of-the-art performances on various NLP benchmarks. In the clinical domain, researchers also have investigated transformer models for clinical applications. The goal of this study is to systematically explore three widely used transformer-based models (i.e., BERT, RoBERTa, and XLNet) for clinical relation extraction and develop an open-source package with clinical pre-trained transformer-based models to facilitate information extraction in the clinical domain. We developed a series of clinical RE models based on three transformer architectures, namely BERT, RoBERTa, and XLNet. We evaluated these models using 2 publicly available datasets from 2018 MADE1.0 and 2018 n2c2 challenges. We compared two classification strategies (binary vs. multi-class classification) and investigated two approaches to generate candidate relations in different experimental settings. In this study, we compared three transformer-based (BERT, RoBERTa, and XLNet) models for relation extraction. We demonstrated that the RoBERTa-clinical RE model achieved the best performance on the 2018 MADE1.0 dataset with an F1-score of 0.8958. On the 2018 n2c2 dataset, the XLNet-clinical model achieved the best F1-score of 0.9610. Our results indicated that the binary classification strategy consistently outperformed the multi-class classification strategy for clinical relation extraction. Our methods and models are publicly available at https://github.com/uf-hobi-informatics-lab/ClinicalTransformerRelationExtraction. We believe this work will improve current practice on clinical relation extraction and other related NLP tasks in the biomedical domain.
This paper describes our submission to subtask a and b of SemEval-2020 Task 4. For subtask a, we use a ALBERT based model with improved input form to pick out the common sense statement from two statement candidates. For subtask b, we use a multiple choice model enhanced by hint sentence mechanism to select the reason from given options about why a statement is against common sense. Besides, we propose a novel transfer learning strategy between subtasks which help improve the performance. The accuracy scores of our system are 95.6 / 94.9 on official test set and rank 7$^{th}$ / 2$^{nd}$ on Post-Evaluation leaderboard.
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