scholarly journals Full-Abstract Biomedical Relation Extraction with Keyword-Attentive Domain Knowledge Infusion

2021 ◽  
Vol 11 (16) ◽  
pp. 7318
Author(s):  
Xian Zhu ◽  
Lele Zhang ◽  
Jiangnan Du ◽  
Zhifeng Xiao
Keyword(s):  
Language Processing ◽  
Domain Knowledge ◽  
Learning Algorithm ◽  
State Of The Art ◽  
Relation Extraction ◽  
Text Representation ◽  
Upper Level ◽  
Document Level ◽  
Semantic Interaction ◽  
Biomedical Relation Extraction

Relation extraction (RE) is an essential task in natural language processing. Given a context, RE aims to classify an entity-mention pair into a set of pre-defined relations. In the biomedical field, building an efficient and accurate RE system is critical for the construction of a domain knowledge base to support upper-level applications. Recent advances have witnessed a focus shift from sentence to document-level RE problems, which are more challenging due to the need for inter- and intra-sentence semantic reasoning. This type of distant dependency is difficult to understand and capture for a learning algorithm. To address the challenge, prior efforts either attempted to improve the cross sentence text representation or infuse domain or local knowledge into the model. Both strategies demonstrated efficacy on various datasets. In this paper, a keyword-attentive knowledge infusion strategy is proposed and integrated into BioBERT. A domain keyword collection mechanism is developed to discover the most relation-suggestive word tokens for bio-entities in a given context. By manipulating the attention masks, the model can be guided to focus on the semantic interaction between bio-entities linked by the keywords. We validated the proposed method on the Biocreative V Chemical Disease Relation dataset with an F1 of 75.6%, outperforming the state-of-the-art by 5.6%.

scholarly journals Document-Level Biomedical Relation Extraction Leveraging Pretrained Self-Attention Structure and Entity Replacement: Algorithm and Pretreatment Method Validation Study

10.2196/17644 ◽  
2020 ◽  
Vol 8 (5) ◽  
pp. e17644
Author(s):  
Xiaofeng Liu ◽  
Jianye Fan ◽  
Shoubin Dong
Keyword(s):  
State Of The Art ◽  
Relation Extraction ◽  
Biomedical Literature ◽  
Long Distance ◽  
Replacement Method ◽  
Replacement Algorithm ◽  
Additional Noise ◽  
The Relationship ◽  
Document Level ◽  
Biomedical Relation Extraction

Background The most current methods applied for intrasentence relation extraction in the biomedical literature are inadequate for document-level relation extraction, in which the relationship may cross sentence boundaries. Hence, some approaches have been proposed to extract relations by splitting the document-level datasets through heuristic rules and learning methods. However, these approaches may introduce additional noise and do not really solve the problem of intersentence relation extraction. It is challenging to avoid noise and extract cross-sentence relations. Objective This study aimed to avoid errors by dividing the document-level dataset, verify that a self-attention structure can extract biomedical relations in a document with long-distance dependencies and complex semantics, and discuss the relative benefits of different entity pretreatment methods for biomedical relation extraction. Methods This paper proposes a new data preprocessing method and attempts to apply a pretrained self-attention structure for document biomedical relation extraction with an entity replacement method to capture very long-distance dependencies and complex semantics. Results Compared with state-of-the-art approaches, our method greatly improved the precision. The results show that our approach increases the F1 value, compared with state-of-the-art methods. Through experiments of biomedical entity pretreatments, we found that a model using an entity replacement method can improve performance. Conclusions When considering all target entity pairs as a whole in the document-level dataset, a pretrained self-attention structure is suitable to capture very long-distance dependencies and learn the textual context and complicated semantics. A replacement method for biomedical entities is conducive to biomedical relation extraction, especially to document-level relation extraction.

scholarly journals Bias Modeling for Distantly Supervised Relation Extraction

2015 ◽  
Vol 2015 ◽  
pp. 1-10 ◽  
Author(s):  
Yang Xiang ◽  
Yaoyun Zhang ◽  
Xiaolong Wang ◽  
Yang Qin ◽  
Wenying Han
Keyword(s):  
Language Processing ◽  
Learning Algorithm ◽  
State Of The Art ◽  
Relation Extraction ◽  
Knowledge Bases ◽  
Training Data ◽  
Free Text ◽  
Distant Supervision ◽  
Annotation Process ◽  
Noise Tolerant

Distant supervision (DS) automatically annotates free text with relation mentions from existing knowledge bases (KBs), providing a way to alleviate the problem of insufficient training data for relation extraction in natural language processing (NLP). However, the heuristic annotation process does not guarantee the correctness of the generated labels, promoting a hot research issue on how to efficiently make use of the noisy training data. In this paper, we model two types of biases to reduce noise: (1)bias-distto model the relative distance between points (instances) and classes (relation centers); (2)bias-rewardto model the possibility of each heuristically generated label being incorrect. Based on the biases, we propose three noise tolerant models:MIML-dist,MIML-dist-classify, andMIML-reward, building on top of a state-of-the-art distantly supervised learning algorithm. Experimental evaluations compared with three landmark methods on the KBP dataset validate the effectiveness of the proposed methods.

scholarly journals Document-level medical relation extraction via edge-oriented graph neural network based on document structure and external knowledge

2021 ◽  
Vol 21 (S7) ◽  
Author(s):  
Tao Li ◽  
Ying Xiong ◽  
Xiaolong Wang ◽  
Qingcai Chen ◽  
Buzhou Tang
Keyword(s):  
Neural Network ◽  
Language Processing ◽  
State Of The Art ◽  
Relation Extraction ◽  
Oriented Graph ◽  
Document Structure ◽  
External Knowledge ◽  
Novel Method ◽  
Public Datasets ◽  
Document Level

Abstract Objective Relation extraction (RE) is a fundamental task of natural language processing, which always draws plenty of attention from researchers, especially RE at the document-level. We aim to explore an effective novel method for document-level medical relation extraction. Methods We propose a novel edge-oriented graph neural network based on document structure and external knowledge for document-level medical RE, called SKEoG. This network has the ability to take full advantage of document structure and external knowledge. Results We evaluate SKEoG on two public datasets, that is, Chemical-Disease Relation (CDR) dataset and Chemical Reactions dataset (CHR) dataset, by comparing it with other state-of-the-art methods. SKEoG achieves the highest F1-score of 70.7 on the CDR dataset and F1-score of 91.4 on the CHR dataset. Conclusion The proposed SKEoG method achieves new state-of-the-art performance. Both document structure and external knowledge can bring performance improvement in the EoG framework. Selecting proper methods for knowledge node representation is also very important.

scholarly journals Document-Level Biomedical Relation Extraction Leveraging Pretrained Self-Attention Structure and Entity Replacement: Algorithm and Pretreatment Method Validation Study (Preprint)

2019 ◽  
Author(s):  
Xiaofeng Liu ◽  
Jianye Fan ◽  
Shoubin Dong
Keyword(s):  
State Of The Art ◽  
Relation Extraction ◽  
Biomedical Literature ◽  
Long Distance ◽  
Replacement Method ◽  
Replacement Algorithm ◽  
Additional Noise ◽  
The Relationship ◽  
Document Level ◽  
Biomedical Relation Extraction

BACKGROUND The most current methods applied for intrasentence relation extraction in the biomedical literature are inadequate for document-level relation extraction, in which the relationship may cross sentence boundaries. Hence, some approaches have been proposed to extract relations by splitting the document-level datasets through heuristic rules and learning methods. However, these approaches may introduce additional noise and do not really solve the problem of intersentence relation extraction. It is challenging to avoid noise and extract cross-sentence relations. OBJECTIVE This study aimed to avoid errors by dividing the document-level dataset, verify that a self-attention structure can extract biomedical relations in a document with long-distance dependencies and complex semantics, and discuss the relative benefits of different entity pretreatment methods for biomedical relation extraction. METHODS This paper proposes a new data preprocessing method and attempts to apply a pretrained self-attention structure for document biomedical relation extraction with an entity replacement method to capture very long-distance dependencies and complex semantics. RESULTS Compared with state-of-the-art approaches, our method greatly improved the precision. The results show that our approach increases the F1 value, compared with state-of-the-art methods. Through experiments of biomedical entity pretreatments, we found that a model using an entity replacement method can improve performance. CONCLUSIONS When considering all target entity pairs as a whole in the document-level dataset, a pretrained self-attention structure is suitable to capture very long-distance dependencies and learn the textual context and complicated semantics. A replacement method for biomedical entities is conducive to biomedical relation extraction, especially to document-level relation extraction.

scholarly journals Biomedical Relation Extraction Using Distant Supervision

2020 ◽  
Vol 2020 ◽  
pp. 1-9 ◽  
Author(s):  
Nada Boudjellal ◽  
Huaping Zhang ◽  
Asif Khan ◽  
Arshad Ahmad
Keyword(s):  
Big Data ◽  
Information Extraction ◽  
State Of The Art ◽  
Relation Extraction ◽  
Knowledge Bases ◽  
Structured Data ◽  
Distant Supervision ◽  
Future Challenges ◽  
Unstructured Information ◽  
Biomedical Relation Extraction

With the accelerating growth of big data, especially in the healthcare area, information extraction is more needed currently than ever, for it can convey unstructured information into an easily interpretable structured data. Relation extraction is the second of the two important tasks of relation extraction. This study presents an overview of relation extraction using distant supervision, providing a generalized architecture of this task based on the state-of-the-art work that proposed this method. Besides, it surveys the methods used in the literature targeting this topic with a description of different knowledge bases used in the process along with the corpora, which can be helpful for beginner practitioners seeking knowledge on this subject. Moreover, the limitations of the proposed approaches and future challenges were highlighted, and possible solutions were proposed.

scholarly journals Using Natural Language Processing and Artificial Intelligence to Explore the Nutrition and Sustainability of Recipes and Food

2021 ◽  
Vol 3 ◽  
Author(s):  
Marieke van Erp ◽  
Christian Reynolds ◽  
Diana Maynard ◽  
Alain Starke ◽  
Rebeca Ibáñez Martín ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Domain Knowledge ◽  
State Of The Art ◽  
Interdisciplinary Approach ◽  
Comprehensive Analysis ◽  
The State ◽  
Use Cases

In this paper, we discuss the use of natural language processing and artificial intelligence to analyze nutritional and sustainability aspects of recipes and food. We present the state-of-the-art and some use cases, followed by a discussion of challenges. Our perspective on addressing these is that while they typically have a technical nature, they nevertheless require an interdisciplinary approach combining natural language processing and artificial intelligence with expert domain knowledge to create practical tools and comprehensive analysis for the food domain.

scholarly journals Towards relation extraction from Arabic text: a review

2019 ◽  
Vol 5 (5) ◽  
pp. 212-215
Author(s):  
Abeer AlArfaj
Keyword(s):  
Language Processing ◽  
Question Answering ◽  
State Of The Art ◽  
Relation Extraction ◽  
Arabic Language ◽  
Extraction Methods ◽  
The State ◽  
Semantic Relations ◽  
Arabic Text ◽  
Taxonomic Relation

Semantic relation extraction is an important component of ontologies that can support many applications e.g. text mining, question answering, and information extraction. However, extracting semantic relations between concepts is not trivial and one of the main challenges in Natural Language Processing (NLP) Field. The Arabic language has complex morphological, grammatical, and semantic aspects since it is a highly inflectional and derivational language, which makes task even more challenging. In this paper, we present a review of the state of the art for relation extraction from texts, addressing the progress and difficulties in this field. We discuss several aspects related to this task, considering the taxonomic and non-taxonomic relation extraction methods. Majority of relation extraction approaches implement a combination of statistical and linguistic techniques to extract semantic relations from text. We also give special attention to the state of the work on relation extraction from Arabic texts, which need further progress.

scholarly journals Document-level Relation Extraction as Semantic Segmentation

2021 ◽  
Author(s):  
Ningyu Zhang ◽  
Xiang Chen ◽  
Xin Xie ◽  
Shumin Deng ◽  
Chuanqi Tan ◽  
...  
Keyword(s):  
Computer Vision ◽  
State Of The Art ◽  
Relation Extraction ◽  
Semantic Segmentation ◽  
Experimental Results ◽  
Context Information ◽  
Global Information ◽  
Benchmark Datasets ◽  
Segmentation Task ◽  
Document Level

Document-level relation extraction aims to extract relations among multiple entity pairs from a document. Previously proposed graph-based or transformer-based models utilize the entities independently, regardless of global information among relational triples. This paper approaches the problem by predicting an entity-level relation matrix to capture local and global information, parallel to the semantic segmentation task in computer vision. Herein, we propose a Document U-shaped Network for document-level relation extraction. Specifically, we leverage an encoder module to capture the context information of entities and a U-shaped segmentation module over the image-style feature map to capture global interdependency among triples. Experimental results show that our approach can obtain state-of-the-art performance on three benchmark datasets DocRED, CDR, and GDA.

scholarly journals A Hierarchical Multi-Task Approach for Learning Embeddings from Semantic Tasks

2019 ◽  
Vol 33 ◽  
pp. 6949-6956 ◽  
Author(s):  
Victor Sanh ◽  
Thomas Wolf ◽  
Sebastian Ruder
Keyword(s):  
Language Processing ◽  
Semantic Information ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
Relation Extraction ◽  
Entity Recognition ◽  
Inductive Bias ◽  
Named Entity ◽  
Task Learning ◽  
Hidden States

Much effort has been devoted to evaluate whether multi-task learning can be leveraged to learn rich representations that can be used in various Natural Language Processing (NLP) down-stream applications. However, there is still a lack of understanding of the settings in which multi-task learning has a significant effect. In this work, we introduce a hierarchical model trained in a multi-task learning setup on a set of carefully selected semantic tasks. The model is trained in a hierarchical fashion to introduce an inductive bias by supervising a set of low level tasks at the bottom layers of the model and more complex tasks at the top layers of the model. This model achieves state-of-the-art results on a number of tasks, namely Named Entity Recognition, Entity Mention Detection and Relation Extraction without hand-engineered features or external NLP tools like syntactic parsers. The hierarchical training supervision induces a set of shared semantic representations at lower layers of the model. We show that as we move from the bottom to the top layers of the model, the hidden states of the layers tend to represent more complex semantic information.

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