scholarly journals A Graph Convolutional Network–Based Method for Chemical-Protein Interaction Extraction: Algorithm Development

10.2196/17643 ◽  
2020 ◽  
Vol 8 (5) ◽  
pp. e17643
Author(s):  
Erniu Wang ◽  
Fan Wang ◽  
Zhihao Yang ◽  
Lei Wang ◽  
Yin Zhang ◽  
...  
Keyword(s):  
Language Processing ◽  
Protein Interaction ◽  
State Of The Art ◽  
Significance Test ◽  
Biomedical Literature ◽  
Convolutional Network ◽  
Data Set ◽  
Dependency Structure ◽  
Syntactic Information ◽  
Biomedical Texts

Background Extracting the interactions between chemicals and proteins from the biomedical literature is important for many biomedical tasks such as drug discovery, medicine precision, and knowledge graph construction. Several computational methods have been proposed for automatic chemical-protein interaction (CPI) extraction. However, the majority of these proposed models cannot effectively learn semantic and syntactic information from complex sentences in biomedical texts. Objective To relieve this problem, we propose a method to effectively encode syntactic information from long text for CPI extraction. Methods Since syntactic information can be captured from dependency graphs, graph convolutional networks (GCNs) have recently drawn increasing attention in natural language processing. To investigate the performance of a GCN on CPI extraction, this paper proposes a novel GCN-based model. The model can effectively capture sequential information and long-range syntactic relations between words by using the dependency structure of input sentences. Results We evaluated our model on the ChemProt corpus released by BioCreative VI; it achieved an F-score of 65.17%, which is 1.07% higher than that of the state-of-the-art system proposed by Peng et al. As indicated by the significance test (P<.001), the improvement is significant. It indicates that our model is effective in extracting CPIs. The GCN-based model can better capture the semantic and syntactic information of the sentence compared to other models, therefore alleviating the problems associated with the complexity of biomedical literature. Conclusions Our model can obtain more information from the dependency graph than previously proposed models. Experimental results suggest that it is competitive to state-of-the-art methods and significantly outperforms other methods on the ChemProt corpus, which is the benchmark data set for CPI extraction.

scholarly journals A Graph Convolutional Network–Based Method for Chemical-Protein Interaction Extraction: Algorithm Development (Preprint)

2019 ◽  
Author(s):  
Erniu Wang ◽  
Fan Wang ◽  
Zhihao Yang ◽  
Lei Wang ◽  
Yin Zhang ◽  
...  
Keyword(s):  
Language Processing ◽  
Protein Interaction ◽  
State Of The Art ◽  
Significance Test ◽  
Biomedical Literature ◽  
Convolutional Network ◽  
Data Set ◽  
Dependency Structure ◽  
Syntactic Information ◽  
Biomedical Texts

BACKGROUND Extracting the interactions between chemicals and proteins from the biomedical literature is important for many biomedical tasks such as drug discovery, medicine precision, and knowledge graph construction. Several computational methods have been proposed for automatic chemical-protein interaction (CPI) extraction. However, the majority of these proposed models cannot effectively learn semantic and syntactic information from complex sentences in biomedical texts. OBJECTIVE To relieve this problem, we propose a method to effectively encode syntactic information from long text for CPI extraction. METHODS Since syntactic information can be captured from dependency graphs, graph convolutional networks (GCNs) have recently drawn increasing attention in natural language processing. To investigate the performance of a GCN on CPI extraction, this paper proposes a novel GCN-based model. The model can effectively capture sequential information and long-range syntactic relations between words by using the dependency structure of input sentences. RESULTS We evaluated our model on the ChemProt corpus released by BioCreative VI; it achieved an F-score of 65.17%, which is 1.07% higher than that of the state-of-the-art system proposed by Peng et al. As indicated by the significance test (<i>P</i>&lt;.001), the improvement is significant. It indicates that our model is effective in extracting CPIs. The GCN-based model can better capture the semantic and syntactic information of the sentence compared to other models, therefore alleviating the problems associated with the complexity of biomedical literature. CONCLUSIONS Our model can obtain more information from the dependency graph than previously proposed models. Experimental results suggest that it is competitive to state-of-the-art methods and significantly outperforms other methods on the ChemProt corpus, which is the benchmark data set for CPI extraction.

scholarly journals The 2019 n2c2/OHNLP Track on Clinical Semantic Textual Similarity: Overview (Preprint)

2020 ◽  
Author(s):  
Yanshan Wang ◽  
Sunyang Fu ◽  
Feichen Shen ◽  
Sam Henry ◽  
Ozlem Uzuner ◽  
...  
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
State Of The Art ◽  
Shared Task ◽  
Data Set ◽  
Clinical Text ◽  
Clinical Notes ◽  
Clinical Domain ◽  
Semantic Textual Similarity

BACKGROUND Semantic textual similarity is a common task in the general English domain to assess the degree to which the underlying semantics of 2 text segments are equivalent to each other. Clinical Semantic Textual Similarity (ClinicalSTS) is the semantic textual similarity task in the clinical domain that attempts to measure the degree of semantic equivalence between 2 snippets of clinical text. Due to the frequent use of templates in the Electronic Health Record system, a large amount of redundant text exists in clinical notes, making ClinicalSTS crucial for the secondary use of clinical text in downstream clinical natural language processing applications, such as clinical text summarization, clinical semantics extraction, and clinical information retrieval. OBJECTIVE Our objective was to release ClinicalSTS data sets and to motivate natural language processing and biomedical informatics communities to tackle semantic text similarity tasks in the clinical domain. METHODS We organized the first BioCreative/OHNLP ClinicalSTS shared task in 2018 by making available a real-world ClinicalSTS data set. We continued the shared task in 2019 in collaboration with National NLP Clinical Challenges (n2c2) and the Open Health Natural Language Processing (OHNLP) consortium and organized the 2019 n2c2/OHNLP ClinicalSTS track. We released a larger ClinicalSTS data set comprising 1642 clinical sentence pairs, including 1068 pairs from the 2018 shared task and 1006 new pairs from 2 electronic health record systems, GE and Epic. We released 80% (1642/2054) of the data to participating teams to develop and fine-tune the semantic textual similarity systems and used the remaining 20% (412/2054) as blind testing to evaluate their systems. The workshop was held in conjunction with the American Medical Informatics Association 2019 Annual Symposium. RESULTS Of the 78 international teams that signed on to the n2c2/OHNLP ClinicalSTS shared task, 33 produced a total of 87 valid system submissions. The top 3 systems were generated by IBM Research, the National Center for Biotechnology Information, and the University of Florida, with Pearson correlations of <i>r</i>=.9010, <i>r</i>=.8967, and <i>r</i>=.8864, respectively. Most top-performing systems used state-of-the-art neural language models, such as BERT and XLNet, and state-of-the-art training schemas in deep learning, such as pretraining and fine-tuning schema, and multitask learning. Overall, the participating systems performed better on the Epic sentence pairs than on the GE sentence pairs, despite a much larger portion of the training data being GE sentence pairs. CONCLUSIONS The 2019 n2c2/OHNLP ClinicalSTS shared task focused on computing semantic similarity for clinical text sentences generated from clinical notes in the real world. It attracted a large number of international teams. The ClinicalSTS shared task could continue to serve as a venue for researchers in natural language processing and medical informatics communities to develop and improve semantic textual similarity techniques for clinical text.

scholarly journals Transformer-Based Decoder Designs for Semantic Segmentation on Remotely Sensed Images

2021 ◽  
Vol 13 (24) ◽  
pp. 5100
Author(s):  
Teerapong Panboonyuen ◽  
Kulsawasd Jitkajornwanich ◽  
Siam Lawawirojwong ◽  
Panu Srestasathiern ◽  
Peerapon Vateekul
Keyword(s):  
Image Processing ◽  
Deep Learning ◽  
Natural Language Processing ◽  
Language Processing ◽  
State Of The Art ◽  
Semantic Segmentation ◽  
Landsat 8 ◽  
Convolutional Network ◽  
Image Labeling ◽  
Feature Pyramid

Transformers have demonstrated remarkable accomplishments in several natural language processing (NLP) tasks as well as image processing tasks. Herein, we present a deep-learning (DL) model that is capable of improving the semantic segmentation network in two ways. First, utilizing the pre-training Swin Transformer (SwinTF) under Vision Transformer (ViT) as a backbone, the model weights downstream tasks by joining task layers upon the pretrained encoder. Secondly, decoder designs are applied to our DL network with three decoder designs, U-Net, pyramid scene parsing (PSP) network, and feature pyramid network (FPN), to perform pixel-level segmentation. The results are compared with other image labeling state of the art (SOTA) methods, such as global convolutional network (GCN) and ViT. Extensive experiments show that our Swin Transformer (SwinTF) with decoder designs reached a new state of the art on the Thailand Isan Landsat-8 corpus (89.8% F1 score), Thailand North Landsat-8 corpus (63.12% F1 score), and competitive results on ISPRS Vaihingen. Moreover, both our best-proposed methods (SwinTF-PSP and SwinTF-FPN) even outperformed SwinTF with supervised pre-training ViT on the ImageNet-1K in the Thailand, Landsat-8, and ISPRS Vaihingen corpora.

scholarly journals Sentence Compression Using BERT and Graph Convolutional Networks

2021 ◽  
Vol 11 (21) ◽  
pp. 9910
Author(s):  
Yo-Han Park ◽  
Gyong-Ho Lee ◽  
Yong-Seok Choi ◽  
Kong-Joo Lee
Keyword(s):  
Language Processing ◽  
Large Scale ◽  
Convolutional Network ◽  
Convolutional Networks ◽  
Compression Model ◽  
Sentence Compression ◽  
Dependency Tree ◽  
Proposed Model ◽  
Syntactic Information ◽  
Input Sentence

Sentence compression is a natural language-processing task that produces a short paraphrase of an input sentence by deleting words from the input sentence while ensuring grammatical correctness and preserving meaningful core information. This study introduces a graph convolutional network (GCN) into a sentence compression task to encode syntactic information, such as dependency trees. As we upgrade the GCN to activate a directed edge, the compression model with the GCN layers can distinguish between parent and child nodes in a dependency tree when aggregating adjacent nodes. Furthermore, by increasing the number of GCN layers, the model can gradually collect high-order information of a dependency tree when propagating node information through the layers. We implement a sentence compression model for Korean and English, respectively. This model consists of three components: pre-trained BERT model, GCN layers, and a scoring layer. The scoring layer can determine whether a word should remain in a compressed sentence by relying on the word vector containing contextual and syntactic information encoded by BERT and GCN layers. To train and evaluate the proposed model, we used the Google sentence compression dataset for English and a Korean sentence compression corpus containing about 140,000 sentence pairs for Korean. The experimental results demonstrate that the proposed model achieves state-of-the-art performance for English. To the best of our knowledge, this sentence compression model based on the deep learning model trained with a large-scale corpus is the first attempt for Korean.

scholarly journals Cross-lingual Semantic Annotation of Biomedical Literature: Experiments in Spanish and English

2019 ◽  
Author(s):  
Naiara Perez ◽  
Pablo Accuosto ◽  
Àlex Bravo ◽  
Montse Cuadros ◽  
Eva Martínez-García ◽  
...  
Keyword(s):  
Language Processing ◽  
Text Processing ◽  
Semantic Annotation ◽  
Biomedical Literature ◽  
Supplementary Information ◽  
Sources Of Information ◽  
Language Resources ◽  
Combined System ◽  
Biomedical Texts ◽  
Cross Lingual

Abstract Motivation Biomedical literature is one of the most relevant sources of information for knowledge mining in the field of Bioinformatics. In spite of English being the most widely addressed language in the field, in recent years there has been a growing interest from the natural language processing community in dealing with languages other than English. However, the availability of language resources and tools for appropriate treatment of non-English texts is lacking behind. Our research is concerned with the semantic annotation of biomedical texts in the Spanish language, which can be considered an under-resourced language where biomedical text processing is concerned. Results We have carried out experiments to assess the effectiveness of several methods for the automatic annotation of biomedical texts in Spanish. One approach is based on the linguistic analysis of Spanish texts and their annotation using an information retrieval and concept disambiguation approach. A second method takes advantage of a Spanish-English machine translation process to annotate English documents and transfer annotations back to Spanish. A third method takes advantage of the combination of both procedures. Our evaluation shows that a combined system has competitive advantages over the two individual procedures. Availability UMLSmapper (https://snlt.vicomtech.org/umlsmapper) and the annotation transfer tool (http://scientmin.taln.upf.edu/anntransfer) are freely available for research purposes as web services and/or demos. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Augmenting Paraphrase Generation with Syntax Information Using Graph Convolutional Networks

Entropy ◽  
2021 ◽  
Vol 23 (5) ◽  
pp. 566
Author(s):  
Xiaoqiang Chi ◽  
Yang Xiang
Keyword(s):  
Language Processing ◽  
Neural Nets ◽  
Linguistic Knowledge ◽  
Convolutional Network ◽  
Tree Structures ◽  
Convolutional Networks ◽  
Sequence Modeling ◽  
Syntactic Information ◽  
Dependency Trees ◽  
Paraphrase Generation

Paraphrase generation is an important yet challenging task in natural language processing. Neural network-based approaches have achieved remarkable success in sequence-to-sequence learning. Previous paraphrase generation work generally ignores syntactic information regardless of its availability, with the assumption that neural nets could learn such linguistic knowledge implicitly. In this work, we make an endeavor to probe into the efficacy of explicit syntactic information for the task of paraphrase generation. Syntactic information can appear in the form of dependency trees, which could be easily acquired from off-the-shelf syntactic parsers. Such tree structures could be conveniently encoded via graph convolutional networks to obtain more meaningful sentence representations, which could improve generated paraphrases. Through extensive experiments on four paraphrase datasets with different sizes and genres, we demonstrate the utility of syntactic information in neural paraphrase generation under the framework of sequence-to-sequence modeling. Specifically, our graph convolutional network-enhanced models consistently outperform their syntax-agnostic counterparts using multiple evaluation metrics.

scholarly journals The 2019 n2c2/OHNLP Track on Clinical Semantic Textual Similarity: Overview

10.2196/23375 ◽  
2020 ◽  
Vol 8 (11) ◽  
pp. e23375 ◽  
Author(s):  
Yanshan Wang ◽  
Sunyang Fu ◽  
Feichen Shen ◽  
Sam Henry ◽  
Ozlem Uzuner ◽  
...  
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
State Of The Art ◽  
Shared Task ◽  
Data Set ◽  
Clinical Text ◽  
Clinical Notes ◽  
Clinical Domain ◽  
Semantic Textual Similarity

Background Semantic textual similarity is a common task in the general English domain to assess the degree to which the underlying semantics of 2 text segments are equivalent to each other. Clinical Semantic Textual Similarity (ClinicalSTS) is the semantic textual similarity task in the clinical domain that attempts to measure the degree of semantic equivalence between 2 snippets of clinical text. Due to the frequent use of templates in the Electronic Health Record system, a large amount of redundant text exists in clinical notes, making ClinicalSTS crucial for the secondary use of clinical text in downstream clinical natural language processing applications, such as clinical text summarization, clinical semantics extraction, and clinical information retrieval. Objective Our objective was to release ClinicalSTS data sets and to motivate natural language processing and biomedical informatics communities to tackle semantic text similarity tasks in the clinical domain. Methods We organized the first BioCreative/OHNLP ClinicalSTS shared task in 2018 by making available a real-world ClinicalSTS data set. We continued the shared task in 2019 in collaboration with National NLP Clinical Challenges (n2c2) and the Open Health Natural Language Processing (OHNLP) consortium and organized the 2019 n2c2/OHNLP ClinicalSTS track. We released a larger ClinicalSTS data set comprising 1642 clinical sentence pairs, including 1068 pairs from the 2018 shared task and 1006 new pairs from 2 electronic health record systems, GE and Epic. We released 80% (1642/2054) of the data to participating teams to develop and fine-tune the semantic textual similarity systems and used the remaining 20% (412/2054) as blind testing to evaluate their systems. The workshop was held in conjunction with the American Medical Informatics Association 2019 Annual Symposium. Results Of the 78 international teams that signed on to the n2c2/OHNLP ClinicalSTS shared task, 33 produced a total of 87 valid system submissions. The top 3 systems were generated by IBM Research, the National Center for Biotechnology Information, and the University of Florida, with Pearson correlations of r=.9010, r=.8967, and r=.8864, respectively. Most top-performing systems used state-of-the-art neural language models, such as BERT and XLNet, and state-of-the-art training schemas in deep learning, such as pretraining and fine-tuning schema, and multitask learning. Overall, the participating systems performed better on the Epic sentence pairs than on the GE sentence pairs, despite a much larger portion of the training data being GE sentence pairs. Conclusions The 2019 n2c2/OHNLP ClinicalSTS shared task focused on computing semantic similarity for clinical text sentences generated from clinical notes in the real world. It attracted a large number of international teams. The ClinicalSTS shared task could continue to serve as a venue for researchers in natural language processing and medical informatics communities to develop and improve semantic textual similarity techniques for clinical text.

scholarly journals Applying Citizen Science to Gene, Drug, Disease Relationship Extraction from Biomedical Abstracts

2019 ◽  
Author(s):  
Ginger Tsueng ◽  
Max Nanis ◽  
Jennifer T. Fouquier ◽  
Michael Mayers ◽  
Benjamin M. Good ◽  
...  
Keyword(s):  
Information Extraction ◽  
Citizen Science ◽  
Computational Methods ◽  
Language Processing ◽  
Named Entity Recognition ◽  
Biomedical Literature ◽  
Entity Recognition ◽  
Named Entity ◽  
Relationship Extraction ◽  
Biomedical Texts

AbstractBiomedical literature is growing at a rate that outpaces our ability to harness the knowledge contained therein. In order to mine valuable inferences from the large volume of literature, many researchers have turned to information extraction algorithms to harvest information in biomedical texts. Information extraction is usually accomplished via a combination of manual expert curation and computational methods. Advances in computational methods usually depends on the generation of gold standards by a limited number of expert curators. This process can be time consuming and represents an area of biomedical research that is ripe for exploration with citizen science. Citizen scientists have been previously found to be willing and capable of performing named entity recognition of disease mentions in biomedical abstracts, but it was uncertain whether or not the same could be said of relationship extraction. Relationship extraction requires training on identifying named entities as well as a deeper understanding of how different entity types can relate to one another. Here, we used the web-based application Mark2Cure (https://mark2cure.org) to demonstrate that citizen scientists can perform relationship extraction and confirm the importance of accurate named entity recognition on this task. We also discuss opportunities for future improvement of this system, as well as the potential synergies between citizen science, manual biocuration, and natural language processing.

scholarly journals Improving Biomedical Named Entity Recognition with Syntactic Information

2020 ◽  
Author(s):  
YUANHE TIAN ◽  
Wang Shen ◽  
Yan Song ◽  
Fei Xia ◽  
Min He ◽  
...  
Keyword(s):  
Domain Knowledge ◽  
Large Scale ◽  
State Of The Art ◽  
Named Entity Recognition ◽  
Training Data ◽  
Entity Recognition ◽  
Named Entity ◽  
Syntactic Information ◽  
Biomedical Texts ◽  
Biomedical Named Entity Recognition

Abstract Background Biomedical named entity recognition (BioNER) is an important task for understanding biomedical texts. The task can be challenging due to the lack of large-scale labeled training data and domain knowledge. Previous studies have shown that syntactic information can be useful for named entity recognition; however, most of them fail to weigh that information with respect to its contribution as they treat the syntactic information as gold reference. Results In this paper, we propose BioKMNER, a BioNER model for biomedical texts with key-value memory networks to incorporate syntactic information, which is extracted from syntactic structures automatically generated by existing toolkits. Our approach outperforms baselines without memories and achieves new state-of-the-art results on on four biomedical datasets compared with previous studies, i.e., 85.67% on BC2GM, 94.22% on BC5CDR-chemical, 90.11% on NCBI-diease, and 76.33% on Species-800. Conclusion Experimental results on four benchmark datasets demonstrate the effectiveness of our method, where the state-of-the-art performance is achieved on all of them.

scholarly journals An Overview of Biomolecular Event Extraction from Scientific Documents

2015 ◽  
Vol 2015 ◽  
pp. 1-19 ◽  
Author(s):  
Jorge A. Vanegas ◽  
Sérgio Matos ◽  
Fabio González ◽  
José L. Oliveira
Keyword(s):  
Natural Language ◽  
Language Processing ◽  
State Of The Art ◽  
Biomedical Literature ◽  
Event Extraction ◽  
Automatic Extraction ◽  
Biological Processes ◽  
Scientific Texts ◽  
Research Areas ◽  
Current State

This paper presents a review of state-of-the-art approaches to automatic extraction of biomolecular events from scientific texts. Events involving biomolecules such as genes, transcription factors, or enzymes, for example, have a central role in biological processes and functions and provide valuable information for describing physiological and pathogenesis mechanisms. Event extraction from biomedical literature has a broad range of applications, including support for information retrieval, knowledge summarization, and information extraction and discovery. However, automatic event extraction is a challenging task due to the ambiguity and diversity of natural language and higher-level linguistic phenomena, such as speculations and negations, which occur in biological texts and can lead to misunderstanding or incorrect interpretation. Many strategies have been proposed in the last decade, originating from different research areas such as natural language processing, machine learning, and statistics. This review summarizes the most representative approaches in biomolecular event extraction and presents an analysis of the current state of the art and of commonly used methods, features, and tools. Finally, current research trends and future perspectives are also discussed.

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