Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userBERT-GT: Cross-sentence n-ary relation extraction with BERT and Graph Transformer
142
0
0.0
(
0
)
Added by
Po-Ting Lai
Publication date
2021
fields
Informatics Engineering
and research's language is
English
Ask ChatGPT about the research
No Arabic abstract
A biomedical relation statement is commonly expressed in multiple sentences and consists of many concepts, including gene, disease, chemical, and mutation. To automatically extract information from biomedical literature, existing biomedical text-mining approaches typically formulate the problem as a cross-sentence n-ary relation-extraction task that detects relations among n entities across multiple sentences, and use either a graph neural network (GNN) with long short-term memory (LSTM) or an attention mechanism. Recently, Transformer has been shown to outperform LSTM on many natural language processing (NLP) tasks. In this work, we propose a novel architecture that combines Bidirectional Encoder Representations from Transformers with Graph Transformer (BERT-GT), through integrating a neighbor-attention mechanism into the BERT architecture. Unlike the original Transformer architecture, which utilizes the whole sentence(s) to calculate the attention of the current token, the neighbor-attention mechanism in our method calculates its attention utilizing only its neighbor tokens. Thus, each token can pay attention to its neighbor information with little noise. We show that this is critically important when the text is very long, as in cross-sentence or abstract-level relation-extraction tasks. Our benchmarking results show improvements of 5.44% and 3.89% in accuracy and F1-measure over the state-of-the-art on n-ary and chemical-protein relation datasets, suggesting BERT-GT is a robust approach that is applicable to other biomedical relation extraction tasks or datasets.
rate research
Read More
Past work in relation extraction has focused on binary relations in single sentences. Recent NLP inroads in high-value domains have sparked interest in the more general setting of extracting n-ary relations that span multiple sentences. In this paper, we explore a general relation extraction framework based on graph long short-term memory networks (graph LSTMs) that can be easily extended to cross-sentence n-ary relation extraction. The graph formulation provides a unified way of exploring different LSTM approaches and incorporating various intra-sentential and inter-sentential dependencies, such as sequential, syntactic, and discourse relations. A robust contextual representation is learned for the entities, which serves as input to the relation classifier. This simplifies handling of relations with arbitrary arity, and enables multi-task learning with related relations. We evaluate this framework in two important precision medicine settings, demonstrating its effectiveness with both conventional supervised learning and distant supervision. Cross-sentence extraction produced larger knowledge bases. and multi-task learning significantly improved extraction accuracy. A thorough analysis of various LSTM approaches yielded useful insight the impact of linguistic analysis on extraction accuracy.
The models of n-ary cross sentence relation extraction based on distant supervision assume that consecutive sentences mentioning n entities describe the relation of these n entities. However, on one hand, this assumption introduces noisy labeled data and harms the models performance. On the other hand, some non-consecutive sentences also describe one relation and these sentences cannot be labeled under this assumption. In this paper, we relax this strong assumption by a weaker distant supervision assumption to address the second issue and propose a novel sentence distribution estimator model to address the first problem. This estimator selects correctly labeled sentences to alleviate the effect of noisy data is a two-level agent reinforcement learning model. In addition, a novel universal relation extractor with a hybrid approach of attention mechanism and PCNN is proposed such that it can be deployed in any tasks, including consecutive and nonconsecutive sentences. Experiments demonstrate that the proposed model can reduce the impact of noisy data and achieve better performance on general n-ary cross sentence relation extraction task compared to baseline models.
Knowledge graphs are important resources for many artificial intelligence tasks but often suffer from incompleteness. In this work, we propose to use pre-trained language models for knowledge graph completion. We treat triples in knowledge graphs as textual sequences and propose a novel framework named Knowledge Graph Bidirectional Encoder Representations from Transformer (KG-BERT) to model these triples. Our method takes entity and relation descriptions of a triple as input and computes scoring function of the triple with the KG-BERT language model. Experimental results on multiple benchmark knowledge graphs show that our method can achieve state-of-the-art performance in triple classification, link prediction and relation prediction tasks.
Most information extraction methods focus on binary relations expressed within single sentences. In high-value domains, however, $n$-ary relations are of great demand (e.g., drug-gene-mutation interactions in precision oncology). Such relations often involve entity mentions that are far apart in the document, yet existing work on cross-sentence relation extraction is generally confined to small text spans (e.g., three consecutive sentences), which severely limits recall. In this paper, we propose a novel multiscale neural architecture for document-level $n$-ary relation extraction. Our system combines representations learned over various text spans throughout the document and across the subrelation hierarchy. Widening the systems purview to the entire document maximizes potential recall. Moreover, by integrating weak signals across the document, multiscale modeling increases precision, even in the presence of noisy labels from distant supervision. Experiments on biomedical machine reading show that our approach substantially outperforms previous $n$-ary relation extraction methods.
Relation prediction in knowledge graphs is dominated by embedding based methods which mainly focus on the transductive setting. Unfortunately, they are not able to handle inductive learning where unseen entities and relations are present and cannot take advantage of prior knowledge. Furthermore, their inference process is not easily explainable. In this work, we propose an all-in-one solution, called BERTRL (BERT-based Relational Learning), which leverages pre-trained language model and fine-tunes it by taking relation instances and their possible reasoning paths as training samples. BERTRL outperforms the SOTAs in 15 out of 18 cases in both inductive and transductive settings. Meanwhile, it demonstrates strong generalization capability in few-shot learning and is explainable.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
