Causal relation extraction of biomedical entities is one of the most complex tasks in biomedical text mining, which involves two kinds of information: entity relations and entity functions. One feasible approach is to take relation extraction and function detection as two independent sub-tasks. However, this separate learning method ignores the intrinsic correlation between them and leads to unsatisfactory performance. In this paper, we propose a joint learning model, which combines entity relation extraction and entity function detection to exploit their commonality and capture their inter-relationship, so as to improve the performance of biomedical causal relation extraction. Experimental results on the BioCreative-V Track 4 corpus show that our joint learning model outperforms the separate models in BEL statement extraction, achieving the F1 scores of 57.0% and 37.3% on the test set in Stage 2 and Stage 1 evaluations, respectively. This demonstrates that our joint learning system reaches the state-of-the-art performance in Stage 2 compared with other systems.

BACKGROUND: The COVID-19 pandemic has increasingly accelerated the publication pace of scientific literature. How to efficiently curate and index this large amount of biomedical literature under the current crisis is of great importance. Previous literature indexing is mainly performed by human experts using Medical Subject Headings (MeSH), which is labor-intensive and time-consuming. Therefore, to alleviate the expensive time consumption and monetary cost, there is an urgent need for automatic semantic indexing technologies for the emerging COVID-19 domain. RESULTS: In this research, to investigate the semantic indexing problem for COVID-19, we first construct the new COVID-19 Semantic Indexing dataset, which consists of more than 80 thousand biomedical articles. We then propose a novel semantic indexing framework based on the multi-probe attention neural network (MPANN) to address the COVID-19 semantic indexing problem. Specifically, we employ a k-nearest neighbour based MeSH masking approach to generate candidate topic terms for each input article. We encode and feed the selected candidate terms as well as other contextual information as probes into the downstream attention-based neural network. Each semantic probe carries specific aspects of biomedical knowledge and provides informatively discriminative features for the input article. After extracting the semantic features at both term-level and document-level through the attention-based neural network, MPANN adopts a linear multi-view classifier to conduct the final topic prediction for COVID-19 semantic indexing. CONCLUSION: The experimental results suggest that MPANN promises to represent the semantic features of biomedical texts and is effective in predicting semantic topics for COVID-19 related biomedical articles.

Jie Zhu, Junhui Li, Muhua Zhu, Longhua Qian, Min Zhang, Guodong Zhou. Proceedings of the 2019 Conference on Empirical Methods in Natural Language Processing and the 9th International Joint Conference on Natural Language Processing (EMNLP-IJCNLP). 2019.

BACKGROUND: Automatically understanding chemical-disease relations (CDRs) is crucial in various areas of biomedical research and health care. Supervised machine learning provides a feasible solution to automatically extract relations between biomedical entities from scientific literature, its success, however, heavily depends on large-scale biomedical corpora manually annotated with intensive labor and tremendous investment. RESULTS: We present an attention-based distant supervision paradigm for the BioCreative-V CDR extraction task. Training examples at both intra- and inter-sentence levels are generated automatically from the Comparative Toxicogenomics Database (CTD) without any human intervention. An attention-based neural network and a stacked auto-encoder network are applied respectively to induce learning models and extract relations at both levels. After merging the results of both levels, the document-level CDRs can be finally extracted. It achieves the precision/recall/F1-score of 60.3%/73.8%/66.4%, outperforming the state-of-the-art supervised learning systems without using any annotated corpus. CONCLUSION: Our experiments demonstrate that distant supervision is promising for extracting chemical disease relations from biomedical literature, and capturing both local and global attention features simultaneously is effective in attention-based distantly supervised learning.

Active learning (AL) has been proven effective to reduce human annotation efforts in NLP.However, previous studies on AL are limited to applications in a single language.This paper proposes a bilingual active learning paradigm for relation classification, where the unlabeled instances are first jointly chosen in terms of their prediction uncertainty scores in two languages and then manually labeled by an oracle.Instead of using a parallel corpus, labeled and unlabeled instances in one language are translated into ones in the other language and all instances in both languages are then fed into a bilingual active learning engine as pseudo parallel corpora.Experimental results on the ACE RDC 2005 Chinese and English corpora show that bilingual active learning for relation classification significantly outperforms monolingual active learning.

This article proposes a new approach to dynamically determine the tree span for tree kernel-based semantic relation extraction between named entities. The basic idea is to employ constituent dependency information in keeping the necessary nodes and their head children along the path connecting the two entities in the syntactic parse tree, while removing the noisy information from the tree, eventually leading to a dynamic syntactic parse tree. This article also explores various entity features and their possible combinations via a unified syntactic and semantic tree framework, which integrates both structural syntactic parse information and entity-related semantic information. Evaluation on the ACE RDC 2004 English and 2005 Chinese benchmark corpora shows that our dynamic syntactic parse tree much outperforms all previous tree spans, indicating its effectiveness in well representing the structural nature of relation instances while removing redundant information. Moreover, the unified parse and semantic tree significantly outperforms the single syntactic parse tree, largely due to the remarkable contributions from entity-related semantic features such as its type, subtype, mention-level as well as their bi-gram combinations. Finally, the best performance so far in semantic relation extraction is achieved via a composite kernel, which combines this tree kernel with a linear, state-of-the-art, feature-based kernel.