3,887 research outputs found

    BioBERT: a pre-trained biomedical language representation model for biomedical text mining

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    Biomedical text mining is becoming increasingly important as the number of biomedical documents rapidly grows. With the progress in natural language processing (NLP), 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, directly applying the advancements in NLP to biomedical text mining often yields unsatisfactory results due to a word distribution shift from general domain corpora to biomedical corpora. In this article, we investigate how the recently introduced pre-trained language model BERT can be adapted for biomedical 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. With almost the same architecture across tasks, BioBERT largely outperforms BERT and previous state-of-the-art models in a variety of biomedical text mining tasks when pre-trained on biomedical corpora. While BERT obtains performance comparable to that of previous state-of-the-art models, BioBERT significantly outperforms them on the following three representative biomedical text mining tasks: biomedical named entity recognition (0.62% F1 score improvement), biomedical relation extraction (2.80% F1 score improvement) and biomedical question answering (12.24% MRR improvement). Our analysis results show that pre-training BERT on biomedical corpora helps it to understand complex biomedical texts. 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.Comment: Bioinformatic

    Robust Layout-aware IE for Visually Rich Documents with Pre-trained Language Models

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    Many business documents processed in modern NLP and IR pipelines are visually rich: in addition to text, their semantics can also be captured by visual traits such as layout, format, and fonts. We study the problem of information extraction from visually rich documents (VRDs) and present a model that combines the power of large pre-trained language models and graph neural networks to efficiently encode both textual and visual information in business documents. We further introduce new fine-tuning objectives to improve in-domain unsupervised fine-tuning to better utilize large amount of unlabeled in-domain data. We experiment on real world invoice and resume data sets and show that the proposed method outperforms strong text-based RoBERTa baselines by 6.3% absolute F1 on invoices and 4.7% absolute F1 on resumes. When evaluated in a few-shot setting, our method requires up to 30x less annotation data than the baseline to achieve the same level of performance at ~90% F1.Comment: 10 pages, to appear in SIGIR 2020 Industry Trac

    ERNIE: Enhanced Language Representation with Informative Entities

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    Neural language representation models such as BERT pre-trained on large-scale corpora can well capture rich semantic patterns from plain text, and be fine-tuned to consistently improve the performance of various NLP tasks. However, the existing pre-trained language models rarely consider incorporating knowledge graphs (KGs), which can provide rich structured knowledge facts for better language understanding. We argue that informative entities in KGs can enhance language representation with external knowledge. In this paper, we utilize both large-scale textual corpora and KGs to train an enhanced language representation model (ERNIE), which can take full advantage of lexical, syntactic, and knowledge information simultaneously. The experimental results have demonstrated that ERNIE achieves significant improvements on various knowledge-driven tasks, and meanwhile is comparable with the state-of-the-art model BERT on other common NLP tasks. The source code of this paper can be obtained from https://github.com/thunlp/ERNIE.Comment: Accepted by ACL 201

    Transfer Learning for Scientific Data Chain Extraction in Small Chemical Corpus with BERT-CRF Model

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    Computational chemistry develops fast in recent years due to the rapid growth and breakthroughs in AI. Thanks for the progress in natural language processing, researchers can extract more fine-grained knowledge in publications to stimulate the development in computational chemistry. While the works and corpora in chemical entity extraction have been restricted in the biomedicine or life science field instead of the chemistry field, we build a new corpus in chemical bond field annotated for 7 types of entities: compound, solvent, method, bond, reaction, pKa and pKa value. This paper presents a novel BERT-CRF model to build scientific chemical data chains by extracting 7 chemical entities and relations from publications. And we propose a joint model to extract the entities and relations simultaneously. Experimental results on our Chemical Special Corpus demonstrate that we achieve state-of-art and competitive NER performance

    Exploring Contextualized Neural Language Models for Temporal Dependency Parsing

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    Extracting temporal relations between events and time expressions has many applications such as constructing event timelines and time-related question answering. It is a challenging problem which requires syntactic and semantic information at sentence or discourse levels, which may be captured by deep contextualized language models (LMs) such as BERT (Devlin et al., 2019). In this paper, we develop several variants of BERT-based temporal dependency parser, and show that BERT significantly improves temporal dependency parsing (Zhang and Xue, 2018a). We also present a detailed analysis on why deep contextualized neural LMs help and where they may fall short. Source code and resources are made available at https://github.com/bnmin/tdp_ranking

    An Empirical Study of Multi-Task Learning on BERT for Biomedical Text Mining

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    Multi-task learning (MTL) has achieved remarkable success in natural language processing applications. In this work, we study a multi-task learning model with multiple decoders on varieties of biomedical and clinical natural language processing tasks such as text similarity, relation extraction, named entity recognition, and text inference. Our empirical results demonstrate that the MTL fine-tuned models outperform state-of-the-art transformer models (e.g., BERT and its variants) by 2.0% and 1.3% in biomedical and clinical domains, respectively. Pairwise MTL further demonstrates more details about which tasks can improve or decrease others. This is particularly helpful in the context that researchers are in the hassle of choosing a suitable model for new problems. The code and models are publicly available at https://github.com/ncbi-nlp/bluebertComment: Accepted by BioNLP 202

    DisSent: Sentence Representation Learning from Explicit Discourse Relations

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    Learning effective representations of sentences is one of the core missions of natural language understanding. Existing models either train on a vast amount of text, or require costly, manually curated sentence relation datasets. We show that with dependency parsing and rule-based rubrics, we can curate a high quality sentence relation task by leveraging explicit discourse relations. We show that our curated dataset provides an excellent signal for learning vector representations of sentence meaning, representing relations that can only be determined when the meanings of two sentences are combined. We demonstrate that the automatically curated corpus allows a bidirectional LSTM sentence encoder to yield high quality sentence embeddings and can serve as a supervised fine-tuning dataset for larger models such as BERT. Our fixed sentence embeddings achieve high performance on a variety of transfer tasks, including SentEval, and we achieve state-of-the-art results on Penn Discourse Treebank's implicit relation prediction task.Comment: 13 pages, 4 figures. ACL 201

    Text-based Question Answering from Information Retrieval and Deep Neural Network Perspectives: A Survey

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    Text-based Question Answering (QA) is a challenging task which aims at finding short concrete answers for users' questions. This line of research has been widely studied with information retrieval techniques and has received increasing attention in recent years by considering deep neural network approaches. Deep learning approaches, which are the main focus of this paper, provide a powerful technique to learn multiple layers of representations and interaction between questions and texts. In this paper, we provide a comprehensive overview of different models proposed for the QA task, including both traditional information retrieval perspective, and more recent deep neural network perspective. We also introduce well-known datasets for the task and present available results from the literature to have a comparison between different techniques

    QuASE: Question-Answer Driven Sentence Encoding

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    Question-answering (QA) data often encodes essential information in many facets. This paper studies a natural question: Can we get supervision from QA data for other tasks (typically, non-QA ones)? For example, {\em can we use QAMR (Michael et al., 2017) to improve named entity recognition?} We suggest that simply further pre-training BERT is often not the best option, and propose the {\em question-answer driven sentence encoding (QuASE)} framework. QuASE learns representations from QA data, using BERT or other state-of-the-art contextual language models. In particular, we observe the need to distinguish between two types of sentence encodings, depending on whether the target task is a single- or multi-sentence input; in both cases, the resulting encoding is shown to be an easy-to-use plugin for many downstream tasks. This work may point out an alternative way to supervise NLP tasks

    Enriching Pre-trained Language Model with Entity Information for Relation Classification

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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.Comment: 6 page
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