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Register a new userConstructing Artificial Data for Fine-tuning for Low-Resource Biomedical Text Tagging with Applications in PICO Annotation
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Added by
Gaurav Singh
Publication date
2019
fields
Informatics Engineering
and research's language is
English
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Biomedical text tagging systems are plagued by the dearth of labeled training data. There have been recent attempts at using pre-trained encoders to deal with this issue. Pre-trained encoder provides representation of the input text which is then fed to task-specific layers for classification. The entire network is fine-tuned on the labeled data from the target task. Unfortunately, a low-resource biomedical task often has too few labeled instances for satisfactory fine-tuning. Also, if the label space is large, it contains few or no labeled instances for majority of the labels. Most biomedical tagging systems treat labels as indexes, ignoring the fact that these labels are often concepts expressed in natural language e.g. `Appearance of lesion on brain imaging. To address these issues, we propose constructing extra labeled instances using label-text (i.e. labels name) as input for the corresponding label-index (i.e. labels index). In fact, we propose a number of strategies for manufacturing multiple artificial labeled instances from a single label. The network is then fine-tuned on a combination of real and these newly constructed artificial labeled instances. We evaluate the proposed approach on an important low-resource biomedical task called textit{PICO annotation}, which requires tagging raw text describing clinical trials with labels corresponding to different aspects of the trial i.e. PICO (Population, Intervention/Control, Outcome) characteristics of the trial. Our empirical results show that the proposed method achieves a new state-of-the-art performance for PICO annotation with very significant improvements over competitive baselines.
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The massive growth of digital biomedical data is making biomedical text indexing and classification increasingly important. Accordingly, previous research has devised numerous deep learning techniques focused on using feedforward, convolutional or recurrent neural architectures. More recently, fine-tuned transformers-based pretrained models (PTMs) have demonstrated superior performance compared to such models in many natural language processing tasks. However, the direct use of PTMs in the biomedical domain is only limited to the target documents, ignoring the rich semantic information in the label descriptions. In this paper, we develop an improved label attention-based architecture to inject semantic label description into the fine-tuning process of PTMs. Results on two public medical datasets show that the proposed fine-tuning scheme outperforms the conventionally fine-tuned PTMs and prior state-of-the-art models. Furthermore, we show that fine-tuning with the label attention mechanism is interpretable in the interpretability study.
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Data augmentation techniques have been widely used to improve machine learning performance as they enhance the generalization capability of models. In this work, to generate high quality synthetic data for low-resource tagging tasks, we propose a novel augmentation method with language models trained on the linearized labeled sentences. Our method is applicable to both supervised and semi-supervised settings. For the supervised settings, we conduct extensive experiments on named entity recognition (NER), part of speech (POS) tagging and end-to-end target based sentiment analysis (E2E-TBSA) tasks. For the semi-supervised settings, we evaluate our method on the NER task under the conditions of given unlabeled data only and unlabeled data plus a knowledge base. The results show that our method can consistently outperform the baselines, particularly when the given gold training data are less.
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