Automated relation extraction (RE) from biomedical literature is critical for many downstream text mining applications in both research and real-world settings. However, most existing benchmarking datasets for bio-medical RE only focus on relations of a single type (e.g., protein-protein interactions) at the sentence level, greatly limiting the development of RE systems in biomedicine. In this work, we first review commonly used named entity recognition (NER) and RE datasets. Then we present BioRED, a first-of-its-kind biomedical RE corpus with multiple entity types (e.g., gene/protein, disease, chemical) and relation pairs (e.g., gene-disease; chemical-chemical) at the document level, on a set of 600 PubMed abstracts. Further, we label each relation as describing either a novel finding or previously known background knowledge, enabling automated algorithms to differentiate between novel and background information. We assess the utility of BioRED by benchmarking several existing state-of-the-art methods, including BERT-based models, on the NER and RE tasks. Our results show that while existing approaches can reach high performance on the NER task (F-score of 89.3%), there is much room for improvement for the RE task, especially when extracting novel relations (F-score of 47.7%). Our experiments also demonstrate that such a rich dataset can successfully facilitate the development of more accurate, efficient, and robust RE systems for biomedicine. The BioRED dataset and annotation guideline are freely available at https://ftp.ncbi.nlm.nih.gov/pub/lu/BioRED/.
Natural language understanding's relation extraction makes innovative and encouraging novel business concepts possible and facilitates new digitilized decision-making processes. Current approaches allow the extraction of relations with a fixed number of entities as attributes. Extracting relations with an arbitrary amount of attributes requires complex systems and costly relation-trigger annotations to assist these systems. We introduce multi-attribute relation extraction (MARE) as an assumption-less problem formulation with two approaches, facilitating an explicit mapping from business use cases to the data annotations. Avoiding elaborated annotation constraints simplifies the application of relation extraction approaches. The evaluation compares our models to current state-of-the-art event extraction and binary relation extraction methods. Our approaches show improvement compared to these on the extraction of general multi-attribute relations.
Document-level entity-based extraction (EE), aiming at extracting entity-centric information such as entity roles and entity relations, is key to automatic knowledge acquisition from text corpora for various domains. Most document-level EE systems build extractive models, which struggle to model long-term dependencies among entities at the document level. To address this issue, we propose a generative framework for two document-level EE tasks: role-filler entity extraction (REE) and relation extraction (RE). We first formulate them as a template generation problem, allowing models to efficiently capture cross-entity dependencies, exploit label semantics, and avoid the exponential computation complexity of identifying N-ary relations. A novel cross-attention guided copy mechanism, TopK Copy, is incorporated into a pre-trained sequence-to-sequence model to enhance the capabilities of identifying key information in the input document. Experiments done on the MUC-4 and SciREX dataset show new state-of-the-art results on REE (+3.26%), binary RE (+4.8%), and 4-ary RE (+2.7%) in F1 score.
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.
Relation extraction aims to identify the target relations of entities in texts. Relation extraction is very important for knowledge base construction and text understanding. Traditional binary relation extraction, including supervised, semi-supervised and distant supervised ones, has been extensively studied and significant results are achieved. In recent years, many complex relation extraction tasks, i.e., the variants of simple binary relation extraction, are proposed to meet the complex applications in practice. However, there is no literature to fully investigate and summarize these complex relation extraction works so far. In this paper, we first report the recent progress in traditional simple binary relation extraction. Then we summarize the existing complex relation extraction tasks and present the definition, recent progress, challenges and opportunities for each task.
Named Entity Recognition (NER) and Relation Extraction (RE) are essential tools in distilling knowledge from biomedical literature. This paper presents our findings from participating in BioNLP Shared Tasks 2019. We addressed Named Entity Recognition including nested entities extraction, Entity Normalization and Relation Extraction. Our proposed approach of Named Entities can be generalized to different languages and we have shown it's effectiveness for English and Spanish text. We investigated linguistic features, hybrid loss including ranking and Conditional Random Fields (CRF), multi-task objective and token-level ensembling strategy to improve NER. We employed dictionary based fuzzy and semantic search to perform Entity Normalization. Finally, our RE system employed Support Vector Machine (SVM) with linguistic features. Our NER submission (team:MIC-CIS) ranked first in BB-2019 norm+NER task with standard error rate (SER) of 0.7159 and showed competitive performance on PharmaCo NER task with F1-score of 0.8662. Our RE system ranked first in the SeeDev-binary Relation Extraction Task with F1-score of 0.3738.
Binary relation extraction methods have been widely studied in recent years. However, few methods have been developed for higher n-ary relation extraction. One limiting factor is the effort required to generate training data. For binary relations, one only has to provide a few dozen pairs of entities per relation, as training data. For ternary relations (n=3), each training instance is a triplet of entities, placing a greater cognitive load on people. For example, many people know that Google acquired Youtube but not the dollar amount or the date of the acquisition and many people know that Hillary Clinton is married to Bill Clinton by not the location or date of their wedding. This makes higher n-nary training data generation a time consuming exercise in searching the Web. We present a resource for training ternary relation extractors. This was generated using a minimally supervised yet effective approach. We present statistics on the size and the quality of the dataset.