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Register a new userImproving Biomedical Pretrained Language Models with Knowledge
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Added by
Zheng Yuan
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Pretrained language models have shown success in many natural language processing tasks. Many works explore incorporating knowledge into language models. In the biomedical domain, experts have taken decades of effort on building large-scale knowledge bases. For example, the Unified Medical Language System (UMLS) contains millions of entities with their synonyms and defines hundreds of relations among entities. Leveraging this knowledge can benefit a variety of downstream tasks such as named entity recognition and relation extraction. To this end, we propose KeBioLM, a biomedical pretrained language model that explicitly leverages knowledge from the UMLS knowledge bases. Specifically, we extract entities from PubMed abstracts and link them to UMLS. We then train a knowledge-aware language model that firstly applies a text-only encoding layer to learn entity representation and applies a text-entity fusion encoding to aggregate entity representation. Besides, we add two training objectives as entity detection and entity linking. Experiments on the named entity recognition and relation extraction from the BLURB benchmark demonstrate the effectiveness of our approach. Further analysis on a collected probing dataset shows that our model has better ability to model medical knowledge.
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Pre-trained language models (LMs) have become ubiquitous in solving various natural language processing (NLP) tasks. There has been increasing interest in what knowledge these LMs contain and how we can extract that knowledge, treating LMs as knowledge bases (KBs). While there has been much work on probing LMs in the general domain, there has been little attention to whether these powerful LMs can be used as domain-specific KBs. To this end, we create the BioLAMA benchmark, which is comprised of 49K biomedical factual knowledge triples for probing biomedical LMs. We find that biomedical LMs with recently proposed probing methods can achieve up to 18.51% Acc@5 on retrieving biomedical knowledge. Although this seems promising given the task difficulty, our detailed analyses reveal that most predictions are highly correlated with prompt templates without any subjects, hence producing similar results on each relation and hindering their capabilities to be used as domain-specific KBs. We hope that BioLAMA can serve as a challenging benchmark for biomedical factual probing.
How can pretrained language models (PLMs) learn factual knowledge from the training set? We investigate the two most important mechanisms: reasoning and memorization. Prior work has attempted to quantify the number of facts PLMs learn, but we present, using synthetic data, the first study that investigates the causal relation between facts present in training and facts learned by the PLM. For reasoning, we show that PLMs seem to learn to apply some symbolic reasoning rules correctly but struggle with others, including two-hop reasoning. Further analysis suggests that even the application of learned reasoning rules is flawed. For memorization, we identify schema conformity (facts systematically supported by other facts) and frequency as key factors for its success.
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.
This paper studies how to automatically generate a natural language text that describes the facts in knowledge graph (KG). Considering the few-shot setting, we leverage the excellent capacities of pretrained language models (PLMs) in language understanding and generation. We make three major technical contributions, namely representation alignment for bridging the semantic gap between KG encodings and PLMs, relation-biased KG linearization for deriving better input representations, and multi-task learning for learning the correspondence between KG and text. Extensive experiments on three benchmark datasets have demonstrated the effectiveness of our model on KG-to-text generation task. In particular, our model outperforms all comparison methods on both fully-supervised and few-shot settings. Our code and datasets are available at https://github.com/RUCAIBox/Few-Shot-KG2Text.
Recently, it has been found that monolingual English language models can be used as knowledge bases. Instead of structural knowledge base queries, masked sentences such as Paris is the capital of [MASK] are used as probes. We translate the established benchmarks TREx and GoogleRE into 53 languages. Working with mBERT, we investigate three questions. (i) Can mBERT be used as a multilingual knowledge base? Most prior work only considers English. Extending research to multiple languages is important for diversity and accessibility. (ii) Is mBERTs performance as knowledge base language-independent or does it vary from language to language? (iii) A multilingual model is trained on more text, e.g., mBERT is trained on 104 Wikipedias. Can mBERT leverage this for better performance? We find that using mBERT as a knowledge base yields varying performance across languages and pooling predictions across languages improves performance. Conversely, mBERT exhibits a language bias; e.g., when queried in Italian, it tends to predict Italy as the country of origin.
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