Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in machine learning, extracting valuable information from biomedical literature has gained popularity among researchers, and deep learning has boosted the development of effective biomedical text mining models. However, as deep learning models require a large amount of training data, applying deep learning to biomedical text mining is often unsuccessful due to the lack of training data in biomedical fields. Recent researches on training contextualized language representation models on text corpora shed light on the possibility of leveraging a large number of unannotated biomedical text corpora. We introduce BioBERT (Bidirectional Encoder Representations from Transformers for Biomedical Text Mining), which is a domain specific language representation model pre-trained on large-scale biomedical corpora. Based on the BERT architecture, BioBERT effectively transfers the knowledge from a large amount of biomedical texts to biomedical text mining models with minimal task-specific architecture modifications. While BERT shows competitive performances with previous state-of-the-art models, BioBERT significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.51% absolute improvement), biomedical relation extraction (3.49% absolute improvement), and biomedical question answering (9.61% absolute improvement). We make the pre-trained weights of BioBERT freely available at https://github.com/naver/biobert-pretrained, and the source code for fine-tuning BioBERT available at https://github.com/dmis-lab/biobert.

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文本数据挖掘(Text Mining)是指从文本数据中抽取有价值的信息和知识的计算机处理技术。

Recent work pre-training Transformers with self-supervised objectives on large text corpora has shown great success when fine-tuned on downstream NLP tasks including text summarization. However, pre-training objectives tailored for abstractive text summarization have not been explored. Furthermore there is a lack of systematic evaluation across diverse domains. In this work, we propose pre-training large Transformer-based encoder-decoder models on massive text corpora with a new self-supervised objective. In PEGASUS, important sentences are removed/masked from an input document and are generated together as one output sequence from the remaining sentences, similar to an extractive summary. We evaluated our best PEGASUS model on 12 downstream summarization tasks spanning news, science, stories, instructions, emails, patents, and legislative bills. Experiments demonstrate it achieves state-of-the-art performance on all 12 downstream datasets measured by ROUGE scores. Our model also shows surprising performance on low-resource summarization, surpassing previous state-of-the-art results on 6 datasets with only 1000 examples. Finally we validated our results using human evaluation and show that our model summaries achieve human performance on multiple datasets.

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Increasing model size when pretraining natural language representations often results in improved performance on downstream tasks. However, at some point further model increases become harder due to GPU/TPU memory limitations, longer training times, and unexpected model degradation. To address these problems, we present two parameter-reduction techniques to lower memory consumption and increase the training speed of BERT. Comprehensive empirical evidence shows that our proposed methods lead to models that scale much better compared to the original BERT. We also use a self-supervised loss that focuses on modeling inter-sentence coherence, and show it consistently helps downstream tasks with multi-sentence inputs. As a result, our best model establishes new state-of-the-art results on the GLUE, RACE, and SQuAD benchmarks while having fewer parameters compared to BERT-large.

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Pre-trained language representation models, such as BERT, capture a general language representation from large-scale corpora, but lack domain-specific knowledge. When reading a domain text, experts make inferences with relevant knowledge. For machines to achieve this capability, we propose a knowledge-enabled language representation model (K-BERT) with knowledge graphs (KGs), in which triples are injected into the sentences as domain knowledge. However, too much knowledge incorporation may divert the sentence from its correct meaning, which is called knowledge noise (KN) issue. To overcome KN, K-BERT introduces soft-position and visible matrix to limit the impact of knowledge. K-BERT can easily inject domain knowledge into the models by equipped with a KG without pre-training by-self because it is capable of loading model parameters from the pre-trained BERT. Our investigation reveals promising results in twelve NLP tasks. Especially in domain-specific tasks (including finance, law, and medicine), K-BERT significantly outperforms BERT, which demonstrates that K-BERT is an excellent choice for solving the knowledge-driven problems that require experts.

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Entity and relation extraction is the necessary step in structuring medical text. However, the feature extraction ability of the bidirectional long short term memory network in the existing model does not achieve the best effect. At the same time, the language model has achieved excellent results in more and more natural language processing tasks. In this paper, we present a focused attention model for the joint entity and relation extraction task. Our model integrates well-known BERT language model into joint learning through dynamic range attention mechanism, thus improving the feature representation ability of shared parameter layer. Experimental results on coronary angiography texts collected from Shuguang Hospital show that the F1-score of named entity recognition and relation classification tasks reach 96.89% and 88.51%, which are better than state-of-the-art methods 1.65% and 1.22%, respectively.

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Relation classification is an important NLP task to extract relations between entities. The state-of-the-art methods for relation classification are primarily based on Convolutional or Recurrent Neural Networks. Recently, the pre-trained BERT model achieves very successful results in many NLP classification / sequence labeling tasks. Relation classification differs from those tasks in that it relies on information of both the sentence and the two target entities. In this paper, we propose a model that both leverages the pre-trained BERT language model and incorporates information from the target entities to tackle the relation classification task. We locate the target entities and transfer the information through the pre-trained architecture and incorporate the corresponding encoding of the two entities. We achieve significant improvement over the state-of-the-art method on the SemEval-2010 task 8 relational dataset.

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Language model pre-training has proven to be useful in learning universal language representations. As a state-of-the-art language model pre-training model, BERT (Bidirectional Encoder Representations from Transformers) has achieved amazing results in many language understanding tasks. In this paper, we conduct exhaustive experiments to investigate different fine-tuning methods of BERT on text classification task and provide a general solution for BERT fine-tuning. Finally, the proposed solution obtains new state-of-the-art results on eight widely-studied text classification datasets.

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Pre-trained language model representations have been successful in a wide range of language understanding tasks. In this paper, we examine different strategies to integrate pre-trained representations into sequence to sequence models and apply it to neural machine translation and abstractive summarization. We find that pre-trained representations are most effective when added to the encoder network which slows inference by only 14%. Our experiments in machine translation show gains of up to 5.3 BLEU in a simulated resource-poor setup. While returns diminish with more labeled data, we still observe improvements when millions of sentence-pairs are available. Finally, on abstractive summarization we achieve a new state of the art on the full text version of CNN/DailyMail.

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Intent classification and slot filling are two essential tasks for natural language understanding. They often suffer from small-scale human-labeled training data, resulting in poor generalization capability, especially for rare words. Recently a new language representation model, BERT (Bidirectional Encoder Representations from Transformers), facilitates pre-training deep bidirectional representations on large-scale unlabeled corpora, and has created state-of-the-art models for a wide variety of natural language processing tasks after simple fine-tuning. However, there has not been much effort on exploring BERT for natural language understanding. In this work, we propose a joint intent classification and slot filling model based on BERT. Experimental results demonstrate that our proposed model achieves significant improvement on intent classification accuracy, slot filling F1, and sentence-level semantic frame accuracy on several public benchmark datasets, compared to the attention-based recurrent neural network models and slot-gated models.

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Kernel methods have produced state-of-the-art results for a number of NLP tasks such as relation extraction, but suffer from poor scalability due to the high cost of computing kernel similarities between discrete natural language structures. A recently proposed technique, kernelized locality-sensitive hashing (KLSH), can significantly reduce the computational cost, but is only applicable to classifiers operating on kNN graphs. Here we propose to use random subspaces of KLSH codes for efficiently constructing an explicit representation of NLP structures suitable for general classification methods. Further, we propose an approach for optimizing the KLSH model for classification problems by maximizing a variational lower bound on mutual information between the KLSH codes (feature vectors) and the class labels. We evaluate the proposed approach on biomedical relation extraction datasets, and observe significant and robust improvements in accuracy w.r.t. state-of-the-art classifiers, along with drastic (orders-of-magnitude) speedup compared to conventional kernel methods.

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Transfer learning has revolutionized computer vision, but existing approaches in NLP still require task-specific modifications and training from scratch. We propose Fine-tuned Language Models (FitLaM), an effective transfer learning method that can be applied to any task in NLP, and introduce techniques that are key for fine-tuning a state-of-the-art language model. Our method significantly outperforms the state-of-the-art on five text classification tasks, reducing the error by 18-24% on the majority of datasets. We open-source our pretrained models and code to enable adoption by the community.

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