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Register a new userBoosting Low-Resource Biomedical QA via Entity-Aware Masking Strategies
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Added by
Gabriele Pergola
Publication date
2021
fields
Informatics Engineering
and research's language is
English
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Biomedical question-answering (QA) has gained increased attention for its capability to provide users with high-quality information from a vast scientific literature. Although an increasing number of biomedical QA datasets has been recently made available, those resources are still rather limited and expensive to produce. Transfer learning via pre-trained language models (LMs) has been shown as a promising approach to leverage existing general-purpose knowledge. However, finetuning these large models can be costly and time consuming, often yielding limited benefits when adapting to specific themes of specialised domains, such as the COVID-19 literature. To bootstrap further their domain adaptation, we propose a simple yet unexplored approach, which we call biomedical entity-aware masking (BEM). We encourage masked language models to learn entity-centric knowledge based on the pivotal entities characterizing the domain at hand, and employ those entities to drive the LM fine-tuning. The resulting strategy is a downstream process applicable to a wide variety of masked LMs, not requiring additional memory or components in the neural architectures. Experimental results show performance on par with state-of-the-art models on several biomedical QA datasets.
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Entity linking is an important problem with many applications. Most previous solutions were designed for settings where annotated training data is available, which is, however, not the case in numerous domains. We propose a light-weight and scalable entity linking method, Eigenthemes, that relies solely on the availability of entity names and a referent knowledge base. Eigenthemes exploits the fact that the entities that are truly mentioned in a document (the gold entities) tend to form a semantically dense subset of the set of all candidate entities in the document. Geometrically speaking, when representing entities as vectors via some given embedding, the gold entities tend to lie in a low-rank subspace of the full embedding space. Eigenthemes identifies this subspace using the singular value decomposition and scores candidate entities according to their proximity to the subspace. On the empirical front, we introduce multiple strong baselines that compare favorably to the existing state of the art. Extensive experiments on benchmark datasets from a variety of real-world domains showcase the effectiveness of our approach.
Despite the widespread success of self-supervised learning via masked language models (MLM), accurately capturing fine-grained semantic relationships in the biomedical domain remains a challenge. This is of paramount importance for entity-level tasks such as entity linking where the ability to model entity relations (especially synonymy) is pivotal. To address this challenge, we propose SapBERT, a pretraining scheme that self-aligns the representation space of biomedical entities. We design a scalable metric learning framework that can leverage UMLS, a massive collection of biomedical ontologies with 4M+ concepts. In contrast with previous pipeline-based hybrid systems, SapBERT offers an elegant one-model-for-all solution to the problem of medical entity linking (MEL), achieving a new state-of-the-art (SOTA) on six MEL benchmarking datasets. In the scientific domain, we achieve SOTA even without task-specific supervision. With substantial improvement over various domain-specific pretrained MLMs such as BioBERT, SciBERTand and PubMedBERT, our pretraining scheme proves to be both effective and robust.
Pre-trained language models induce dense entity representations that offer strong performance on entity-centric NLP tasks, but such representations are not immediately interpretable. This can be a barrier to model uptake in important domains such as biomedicine. There has been recent work on general interpretable representation learning (Onoe and Durrett, 2020), but these domain-agnostic representations do not readily transfer to the important domain of biomedicine. In this paper, we create a new entity type system and training set from a large corpus of biomedical texts by mapping entities to concepts in a medical ontology, and from these to Wikipedia pages whose categories are our types. From this mapping we derive Biomedical Interpretable Entity Representations(BIERs), in which dimensions correspond to fine-grained entity types, and values are predicted probabilities that a given entity is of the corresponding type. We propose a novel method that exploits BIERs final sparse and intermediate dense representations to facilitate model and entity type debugging. We show that BIERs achieve strong performance in biomedical tasks including named entity disambiguation and entity label classification, and we provide error analysis to highlight the utility of their interpretability, particularly in low-supervision settings. Finally, we provide our induced 68K biomedical type system, the corresponding 37 million triples of derived data used to train BIER models and our best performing model.
Entity Matching (EM) aims at recognizing entity records that denote the same real-world object. Neural EM models learn vector representation of entity descriptions and match entities end-to-end. Though robust, these methods require many resources for training, and lack of interpretability. In this paper, we propose a novel EM framework that consists of Heterogeneous Information Fusion (HIF) and Key Attribute Tree (KAT) Induction to decouple feature representation from matching decision. Using self-supervised learning and mask mechanism in pre-trained language modeling, HIF learns the embeddings of noisy attribute values by inter-attribute attention with unlabeled data. Using a set of comparison features and a limited amount of annotated data, KAT Induction learns an efficient decision tree that can be interpreted by generating entity matching rules whose structure is advocated by domain experts. Experiments on 6 public datasets and 3 industrial datasets show that our method is highly efficient and outperforms SOTA EM models in most cases. Our codes and datasets can be obtained from https://github.com/THU-KEG/HIF-KAT.
Distant supervision allows obtaining labeled training corpora for low-resource settings where only limited hand-annotated data exists. However, to be used effectively, the distant supervision must be easy to gather. In this work, we present ANEA, a tool to automatically annotate named entities in texts based on entity lists. It spans the whole pipeline from obtaining the lists to analyzing the errors of the distant supervision. A tuning step allows the user to improve the automatic annotation with their linguistic insights without labelling or checking all tokens manually. In six low-resource scenarios, we show that the F1-score can be increased by on average 18 points through distantly supervised data obtained by ANEA.
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