Document-Level Biomedical Relation Extraction with Generative Adversarial Network and Dual-Attention Multi-Instance Learning

2021 ◽  
Author(s):  
Lishuang Li ◽  
Ruiyuan Lian ◽  
Hongbin Lu
Keyword(s):  
Relation Extraction ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Document Level ◽  
Biomedical Relation Extraction

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 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 (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.

ORGANIC (1).pdf

2017 ◽  
Author(s):  
Benjamin Sanchez-Lengeling ◽  
Carlos Outeiral ◽  
Gabriel L. Guimaraes ◽  
Alan Aspuru-Guzik
Keyword(s):  
Machine Learning ◽  
Learning Community ◽  
Chemical Species ◽  
Material Design ◽  
Organic Photovoltaic ◽  
Generative Adversarial Networks ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Adversarial Networks ◽  
Photovoltaic Material

Molecular discovery seeks to generate chemical species tailored to very specific needs. In this paper, we present ORGANIC, a framework based on Objective-Reinforced Generative Adversarial Networks (ORGAN), capable of producing a distribution over molecular space that matches with a certain set of desirable metrics. This methodology combines two successful techniques from the machine learning community: a Generative Adversarial Network (GAN), to create non-repetitive sensible molecular species, and Reinforcement Learning (RL), to bias this generative distribution towards certain attributes. We explore several applications, from optimization of random physicochemical properties to candidates for drug discovery and organic photovoltaic material design.

Role of General Adversarial Networks in Mammogram Analysis: A Review

2020 ◽  
Vol 16 (7) ◽  
pp. 863-877
Author(s):  
Annapoorani Gopal ◽  
Lathaselvi Gandhimaruthian ◽  
Javid Ali
Keyword(s):  
Breast Tumor ◽  
Deep Neural Networks ◽  
Training Data ◽  
Learning Technology ◽  
Breast Cancers ◽  
Generative Adversarial Network ◽  
Adversarial Network ◽  
Adversarial Networks ◽  
Tumor Extraction

The Deep Neural Networks have gained prominence in the biomedical domain, becoming the most commonly used networks after machine learning technology. Mammograms can be used to detect breast cancers with high precision with the help of Convolutional Neural Network (CNN) which is deep learning technology. An exhaustive labeled data is required to train the CNN from scratch. This can be overcome by deploying Generative Adversarial Network (GAN) which comparatively needs lesser training data during a mammogram screening. In the proposed study, the application of GANs in estimating breast density, high-resolution mammogram synthesis for clustered microcalcification analysis, effective segmentation of breast tumor, analysis of the shape of breast tumor, extraction of features and augmentation of the image during mammogram classification have been extensively reviewed.

scholarly journals Realistic Sonar Image Simulation Using Generative Adversarial Network

2019 ◽  
Vol 52 (21) ◽  
pp. 291-296 ◽  
Author(s):  
Minsung Sung ◽  
Jason Kim ◽  
Juhwan Kim ◽  
Son-Cheol Yu
Keyword(s):  
Image Simulation ◽  
Generative Adversarial Network ◽  
Sonar Image ◽  
Adversarial Network
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