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 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 A Relation-Specific Attention Network for Joint Entity and Relation Extraction

2020 ◽  
Author(s):  
Yue Yuan ◽  
Xiaofei Zhou ◽  
Shirui Pan ◽  
Qiannan Zhu ◽  
Zeliang Song ◽  
...  
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
State Of The Art ◽  
Relation Extraction ◽  
Attention Mechanism ◽  
Important Task ◽  
Entity Recognition ◽  
Attention Network ◽  
Public Datasets

Joint extraction of entities and relations is an important task in natural language processing (NLP), which aims to capture all relational triplets from plain texts. This is a big challenge due to some of the triplets extracted from one sentence may have overlapping entities. Most existing methods perform entity recognition followed by relation detection between every possible entity pairs, which usually suffers from numerous redundant operations. In this paper, we propose a relation-specific attention network (RSAN) to handle the issue. Our RSAN utilizes relation-aware attention mechanism to construct specific sentence representations for each relation, and then performs sequence labeling to extract its corresponding head and tail entities. Experiments on two public datasets show that our model can effectively extract overlapping triplets and achieve state-of-the-art performance.

scholarly journals Enhancing the performance of cancer text classification model based on cancer hallmarks

2021 ◽  
Vol 10 (2) ◽  
pp. 316
Author(s):  
Noha Ali ◽  
Ahmed H. AbuEl-Atta ◽  
Hala H. Zayed
Keyword(s):  
Neural Network ◽  
Language Processing ◽  
Text Classification ◽  
State Of The Art ◽  
Classification Model ◽  
Biomedical Text ◽  
Cancer Hallmarks ◽  
Embedding Technique ◽  
Proposed Model ◽  
Biomedical Text Classification

<span id="docs-internal-guid-cb130a3a-7fff-3e11-ae3d-ad2310e265f8"><span>Deep learning (DL) algorithms achieved state-of-the-art performance in computer vision, speech recognition, and natural language processing (NLP). In this paper, we enhance the convolutional neural network (CNN) algorithm to classify cancer articles according to cancer hallmarks. The model implements a recent word embedding technique in the embedding layer. This technique uses the concept of distributed phrase representation and multi-word phrases embedding. The proposed model enhances the performance of the existing model used for biomedical text classification. The result of the proposed model overcomes the previous model by achieving an F-score equal to 83.87% using an unsupervised technique that trained on PubMed abstracts called PMC vectors (PMCVec) embedding. Also, we made another experiment on the same dataset using the recurrent neural network (RNN) algorithm with two different word embeddings Google news and PMCVec which achieving F-score equal to 74.9% and 76.26%, respectively.</span></span>

scholarly journals Edge-Nodes Representation Neural Machine for Link Prediction

Algorithms ◽  
2019 ◽  
Vol 12 (1) ◽  
pp. 12 ◽  
Author(s):  
Guangluan Xu ◽  
Xiaoke Wang ◽  
Yang Wang ◽  
Daoyu Lin ◽  
Xian Sun ◽  
...  
Keyword(s):  
Neural Network ◽  
Formation Mechanism ◽  
Link Prediction ◽  
State Of The Art ◽  
Prediction Methods ◽  
Topological Features ◽  
Novel Method ◽  
Fully Connected ◽  
Two Sides

Link prediction is a task predicting whether there is a link between two nodes in a network. Traditional link prediction methods that assume handcrafted features (such as common neighbors) as the link’s formation mechanism are not universal. Other popular methods tend to learn the link’s representation, but they cannot represent the link fully. In this paper, we propose Edge-Nodes Representation Neural Machine (ENRNM), a novel method which can learn abundant topological features from the network as the link’s representation to promote the formation of the link. The ENRNM learns the link’s formation mechanism by combining the representation of edge and the representations of nodes on the two sides of the edge as link’s full representation. To predict the link’s existence, we train a fully connected neural network which can learn meaningful and abundant patterns. We prove that the features of edge and two nodes have the same importance in link’s formation. Comprehensive experiments are conducted on eight networks, experiment results demonstrate that the method ENRNM not only exceeds plenty of state-of-the-art link prediction methods but also performs very well on diverse networks with different structures and characteristics.

scholarly journals Unsupervised Keyphrase Extraction for Web Pages

2019 ◽  
Vol 3 (3) ◽  
pp. 58 ◽  
Author(s):  
Tim Haarman ◽  
Bastiaan Zijlema ◽  
Marco Wiering
Keyword(s):  
Language Processing ◽  
State Of The Art ◽  
Structural Information ◽  
Extraction Methods ◽  
Web Pages ◽  
Keyphrase Extraction ◽  
Text Documents ◽  
Normal Text ◽  
Textual Data ◽  
Novel Method

Keyphrase extraction is an important part of natural language processing (NLP) research, although little research is done in the domain of web pages. The World Wide Web contains billions of pages that are potentially interesting for various NLP tasks, yet it remains largely untouched in scientific research. Current research is often only applied to clean corpora such as abstracts and articles from academic journals or sets of scraped texts from a single domain. However, textual data from web pages differ from normal text documents, as it is structured using HTML elements and often consists of many small fragments. These elements are furthermore used in a highly inconsistent manner and are likely to contain noise. We evaluated the keyphrases extracted by several state-of-the-art extraction methods and found that they did not transfer well to web pages. We therefore propose WebEmbedRank, an adaptation of a recently proposed extraction method that can make use of structural information in web pages in a robust manner. We compared this novel method to other baselines and state-of-the-art methods using a manually annotated dataset and found that WebEmbedRank achieved significant improvements over existing extraction methods on web pages.

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 Enhancing Label Representations with Relational Inductive Bias Constraint for Fine-Grained Entity Typing

2021 ◽  
Author(s):  
Jinqing Li ◽  
Xiaojun Chen ◽  
Dakui Wang ◽  
Yuwei Li
Keyword(s):  
State Of The Art ◽  
Phase 1 ◽  
Phase 2 ◽  
Two Phase ◽  
Inductive Bias ◽  
Fine Grained ◽  
Wide Range ◽  
Dynamic Experiments ◽  
Novel Method ◽  
Public Datasets

Fine-Grained Entity Typing (FGET) is a task that aims at classifying an entity mention into a wide range of entity label types. Recent researches improve the task performance by imposing the label-relational inductive bias based on the hierarchy of labels or label co-occurrence graph. However, they usually overlook explicit interactions between instances and labels which may limit the capability of label representations. Therefore, we propose a novel method based on a two-phase graph network for the FGET task to enhance the label representations, via imposing the relational inductive biases of instance-to-label and label-to-label. In the phase 1, instance features will be introduced into label representations to make the label representations more representative. In the phase 2, interactions of labels will capture dependency relationships among them thus make label representations more smooth. During prediction, we introduce a pseudo-label generator for the construction of the two-phase graph. The input instances differ from batch to batch so that the label representations are dynamic. Experiments on three public datasets verify the effectiveness and stability of our proposed method and achieve state-of-the-art results on their testing sets.

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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