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RoBGP:A Chinese Nested Biomedical named entity recognition Model Based on RoBERTa and Global Pointer

Computers, Materials & Continua 2024年第3期78卷 3603-3618页

作者： Xiaohui Cui Chao Song Dongmei Li Xiaolong Qu Jiao Long Yu Yang Hanchao Zhang School of Information Science and Technology Beijing Forestry UniversityBeijing100083China Engineering Research Center for Forestry-Oriented Intelligent Information Processing of National Forestry and Grassland Administration Beijing100083China Division of Biostatistics Department of Population HealthGrossman School of MedicineNew York UniversityNew York10016USA

named entity recognition(NER)stands as a fundamental task within the field of biomedical text mining,aiming to extract specific types of entities such as genes,proteins,and diseases from complex biomedical texts and categorize them into predefined entity types.This process can provide basic support for the automatic construction of knowledge bases.In contrast to general texts,biomedical texts frequently contain numerous nested entities and local dependencies among these entities,presenting significant challenges to prevailing NER models.To address these issues,we propose a novel Chinese nested biomedical NER model based on RoBERTa and Global Pointer(RoBGP).Our model initially utilizes the RoBERTa-wwm-ext-large pretrained language model to dynamically generate word-level initial vectors.It then incorporates a Bidirectional Long Short-Term Memory network for capturing bidirectional semantic information,effectively addressing the issue of long-distance dependencies.Furthermore,the Global Pointer model is employed to comprehensively recognize all nested entities in the text.We conduct extensive experiments on the Chinese medical dataset CMeEE and the results demonstrate the superior performance of RoBGP over several baseline models.This research confirms the effectiveness of RoBGP in Chinese biomedical NER,providing reliable technical support for biomedical information extraction and knowledge base construction.

关键词： Biomedicine knowledge base named entity recognition pretrained language model global pointer

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SciCN:A Scientific Dataset for Chinese named entity recognition

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Computers, Materials & Continua 2024年第3期78卷 4303-4315页

作者： Jing Yang Bin Ji Shasha Li Jun Ma Jie Yu College of Computer National University of Defense TechnologyChangsha410073China

named entity recognition(NER)is a fundamental task of information extraction(IE),and it has attracted considerable research attention in recent years.The abundant annotated English NER datasets have significantly promoted the NER research in the English field.By contrast,much fewer efforts are made to the Chinese NER research,especially in the scientific domain,due to the scarcity of Chinese NER datasets.To alleviate this problem,we present aChinese scientificNER dataset–SciCN,which contains entity annotations of titles and abstracts derived from 3,500 scientific papers.We manually annotate a total of 62,059 entities,and these entities are classified into six types.Compared to English scientific NER datasets,SciCN has a larger scale and is more diverse,for it not only contains more paper abstracts but these abstracts are derived from more research fields.To investigate the properties of SciCN and provide baselines for future research,we adapt a number of previous state-of-theart Chinese NER models to evaluate SciCN.Experimental results show that SciCN is more challenging than other Chinese NER datasets.In addition,previous studies have proven the effectiveness of using lexicons to enhance Chinese NER models.Motivated by this fact,we provide a scientific domain-specific lexicon.Validation results demonstrate that our lexicon delivers better performance gains than lexicons of other domains.We hope that the SciCN dataset and the lexicon will enable us to benchmark the NER task regarding the Chinese scientific domain and make progress for future research.The dataset and lexicon are available at:https://***/yangjingla/SciCN.git.

关键词： named entity recognition dataset scientific information extraction lexicon

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Few-Shot named entity recognition with the Integration of Spatial Features

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Wuhan University Journal of Natural Sciences 2024年第2期29卷 125-133页

作者： LIU Zhiwei HUANG Bo XIA Chunming XIONG Yujie ZANG Zhensen ZHANG Yongqiang College of Electrical and Electronic Engineering Shanghai University of Engineering ScienceShanghai 201620China Shanghai Zhongyu Academy of Industrial Internet Shanghai 201620China AIoT Manufacturing Solutions Technology Co. Ltd.Hefei 230000AnhuiChina

The few-shot named entity recognition(NER)task aims to train a robust model in the source domain and transfer it to the target domain with very few annotated data.Currently,some approaches rely on the prototypical network for NER.However,these approaches often overlook the spatial relations in the span boundary matrix because entity words tend to depend more on adjacent words.We propose using a multidimensional convolution module to address this limitation to capture short-distance spatial dependencies.Additionally,we uti-lize an improved prototypical network and assign different weights to different samples that belong to the same class,thereby enhancing the performance of the few-shot NER task.Further experimental analysis demonstrates that our approach has significantly improved over baseline models across multiple datasets.

关键词： named entity recognition prototypical network spatial relation multidimensional convolution

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Decoupled Two-Phase Framework for Class-Incremental Few-Shot named entity recognition

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Tsinghua Science and Technology 2023年第5期28卷 976-987页

作者： Yifan Chen Zhen Huang Minghao Hu Dongsheng Li Changjian Wang Feng Liu Xicheng Lu College of Computer National University of Defense TechnologyChangsha 410073China Information Research Center of Military Science PLA Academy of Military ScienceBeijing 100091China

Class-Incremental Few-Shot named entity recognition(CIFNER)aims to identify entity categories that have appeared with only a few newly added(novel)class examples.However,existing class-incremental methods typically introduce new parameters to adapt to new classes and treat all information equally,resulting in poor generalization.Meanwhile,few-shot methods necessitate samples for all observed classes,making them difficult to transfer into a class-incremental setting.Thus,a decoupled two-phase framework method for the CIFNER task is proposed to address the above issues.The whole task is converted to two separate tasks named entity Span Detection(ESD)and entity Class Discrimination(ECD)that leverage parameter-cloning and label-fusion to learn different levels of knowledge separately,such as class-generic knowledge and class-specific knowledge.Moreover,different variants,such as the Conditional Random Field-based(CRF-based),word-pair-based methods in ESD module,and add-based,Natural Language Inference-based(NLI-based)and prompt-based methods in ECD module,are investigated to demonstrate the generalizability of the decoupled framework.Extensive experiments on the three named entity recognition(NER)datasets reveal that our method achieves the state-of-the-art performance in the CIFNER setting.

关键词： named entity recognition deep learning class-incremental learning few-shot learning

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Few-shot named entity recognition with Joint Token and Sentence Awareness

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Data Intelligence 2023年第3期5卷 767-785页

作者： Wen Wen Yongbin Liu Qiang Lin Chunping Ouyang Computer School University of South ChinaChina Hunan provincial base for scientific and technological innovation cooperation HunanChina

Few-shot learning has been proposed and rapidly emerging as a viable means for completing various tasks.Recently,few-shot models have been used for named entity recognition(NER).Prototypical network shows high efficiency on few-shot NER.However,existing prototypical methods only consider the similarity of tokens in query sets and support sets and ignore the semantic similarity among the sentences which contain these entities.We present a novel model,Few-shot named entity recognition with Joint Token and Sentence Awareness(JTSA),to address the issue.The sentence awareness is introduced to probe the semantic similarity among the sentences.The Token awareness is used to explore the similarity of the tokens.To further improve the robustness and results of the model,we adopt the joint learning scheme on the few-shot NER.Experimental results demonstrate that our model outperforms state-of-the-art models on two standard Fewshot NER datasets.

关键词： Few-shot Learning named entity recognition Prototypical Network

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A Federated named entity recognition Model with Explicit Relation for Power Grid

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Computers, Materials & Continua 2023年第5期75卷 4207-4216页

作者： Jingtang Luo Shiying Yao Changming Zhao Jie Xu Jim Feng State Grid Sichuan Economic Research Institute ChengduChina School of Computer Science Chengdu University of Information TechnologyChengduChina School of Information and Communication Engineering University of Electronic Science and Technology of China ChengduChina Amphenol Global Interconnect Systems San JoseCA 95131USA

The power grid operation process is complex,and many operation process data involve national security,business secrets,and user privacy.Meanwhile,labeled datasets may exist in many different operation platforms,but they cannot be directly shared since power grid data is highly privacysensitive.How to use these multi-source heterogeneous data as much as possible to build a power grid knowledge map under the premise of protecting privacy security has become an urgent problem in developing smart grid.Therefore,this paper proposes federated learning named entity recognition method for the power grid field,aiming to solve the problem of building a named entity recognition model covering the entire power grid process training by data with different security requirements.We decompose the named entity recognition(NER)model FLAT(Chinese NER Using Flat-Lattice Transformer)in each platform into a global part and a local part.The local part is used to capture the characteristics of the local data in each platform and is updated using locally labeled data.The global part is learned across different operation platforms to capture the shared NER knowledge.Its local gradients fromdifferent platforms are aggregated to update the global model,which is further delivered to each platform to update their global part.Experiments on two publicly available Chinese datasets and one power grid dataset validate the effectiveness of our method.

关键词： Power grid named entity recognition federal learning

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Corpus of Carbonate Platforms with Lexical Annotations for named entity recognition

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Computer Modeling in Engineering & Sciences 2023年第4期135卷 91-108页

作者： Zhichen Hu Huali Ren Jielin Jiang Yan Cui Xiumian Hu Xiaolong Xu School of Computer and Software Nanjing University of Information Science and TechnologyNanjing210044China Institution of Artificial Intelligence and Blockchain Guangzhou UniversityGuangzhou515021China School of Earth Sciences and Engineering Nanjing UniversityNanjing210023China College of Mathematics and Information Science Nanjing Normal University of Special EducationNanjing210023China

An obviously challenging problem in named entity recognition is the construction of the kind data set of entities.Although some research has been conducted on entity database construction,the majority of them are directed at Wikipedia or the minority at structured entities such as people,locations and organizational nouns in the news.This paper focuses on the identification of scientific entities in carbonate platforms in English literature,using the example of carbonate platforms in sedimentology.Firstly,based on the fact that the reasons for writing literature in key disciplines are likely to be provided by multidisciplinary experts,this paper designs a literature content extraction method that allows dealing with complex text structures.Secondly,based on the literature extraction content,we formalize the entity extraction task(lexicon and lexical-based entity extraction)for entity extraction.Furthermore,for testing the accuracy of entity extraction,three currently popular recognition methods are chosen to perform entity detection in this paper.Experiments show that the entity data set provided by the lexicon and lexical-based entity extraction method is of significant assistance for the named entity recognition task.This study presents a pilot study of entity extraction,which involves the use of a complex structure and specialized literature on carbonate platforms in English.

关键词： named entity recognition carbonate platform corpus entity extraction english literature detection

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Leveraging Continuous Prompt for Few-Shot named entity recognition in Electric Power Domain with Meta-Learning

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Data Intelligence 2023年第2期5卷 494-509页

作者： Yang Yu Wei He Yu-meng Kang You-lang Ji Metrology Center State Grid Jiangsu Market Service Center Nanjing Jiangsu 210019China

Conventional named entity recognition methods usually assume that the model can be trained with sufficient annotated data to obtain good recognition results.However,in Chinese named entity recognition in the electric power domain,existing methods still face the challenges of lack of annotated data and new entities of unseen types.To address these challenges,this paper proposes a meta-learning-based continuous cue adjustment method.A generative pre-trained language model is used so that it does not change its own model structure when dealing with new entity types.To guide the pre-trained model to make full use of its own latent knowledge,a vector of learnable parameters is set as a cue to compensate for the lack of training data.In order to further improve the model's few-shot learning capability,a meta-learning strategy is used to train the model.Experimental results show that the proposed approach achieves the best results in a few-shot electric Chinese power named entity recognition dataset compared to several traditional named entity approaches.

关键词： named entity recognition Pre-trained model Prompt-Tuning Meta-Learning Few-Shot

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Chinese Cyber Threat Intelligence named entity recognition via RoBERTa-wwm-RDCNN-CRF

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Computers, Materials & Continua 2023年第10期77卷 299-323页

作者： Zhen Zhen Jian Gao School of Information Network Security People’s Public Security University of ChinaBeijing100038China Key Laboratory of Safety Precautions and Risk Assessment Ministry of Public SecurityBeijing102623China

In recent years,cyber attacks have been intensifying and causing great harm to individuals,companies,and countries.The mining of cyber threat intelligence(CTI)can facilitate intelligence integration and serve well in combating cyber attacks.named entity recognition(NER),as a crucial component of text mining,can structure complex CTI text and aid cybersecurity professionals in effectively countering threats.However,current CTI NER research has mainly focused on studying English CTI.In the limited studies conducted on Chinese text,existing models have shown poor performance.To fully utilize the power of Chinese pre-trained language models(PLMs)and conquer the problem of lengthy infrequent English words mixing in the Chinese CTIs,we propose a residual dilated convolutional neural network(RDCNN)with a conditional random field(CRF)based on a robustly optimized bidirectional encoder representation from transformers pre-training approach with whole word masking(RoBERTa-wwm),abbreviated as RoBERTa-wwm-RDCNN-CRF.We are the first to experiment on the relevant open source dataset and achieve an F1-score of 82.35%,which exceeds the common baseline model bidirectional encoder representation from transformers(BERT)-bidirectional long short-term memory(BiLSTM)-CRF in this field by about 19.52%and exceeds the current state-of-the-art model,BERT-RDCNN-CRF,by about 3.53%.In addition,we conducted an ablation study on the encoder part of the model to verify the effectiveness of the proposed model and an in-depth investigation of the PLMs and encoder part of the model to verify the effectiveness of the proposed model.The RoBERTa-wwm-RDCNN-CRF model,the shared pre-processing,and augmentation methods can serve the subsequent fundamental tasks such as cybersecurity information extraction and knowledge graph construction,contributing to important applications in downstream tasks such as intrusion detection and advanced persistent threat(APT)attack detection.

关键词： Cybersecurity cyber threat intelligence named entity recognition

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Data Masking for Chinese Electronic Medical Records with named entity recognition

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Intelligent Automation & Soft Computing 2023年第6期36卷 3657-3673页

作者： Tianyu He Xiaolong Xu Zhichen Hu Qingzhan Zhao Jianguo Dai Fei Dai School of Computer Science Nanjing University of Information Science and TechnologyNanjing21000China Geospatial Information Engineering Research Center Xinjiang Production and Construction CorpsShihezi832003China College of Big Data and Intelligent Engineering Southwest Forestry UniversityKunming650224China

With the rapid development of information technology,the electronifi-cation of medical records has gradually become a trend.In China,the population base is huge and the supporting medical institutions are numerous,so this reality drives the conversion of paper medical records to electronic medical records.Electronic medical records are the basis for establishing a smart hospital and an important guarantee for achieving medical intelligence,and the massive amount of electronic medical record data is also an important data set for conducting research in the medical field.However,electronic medical records contain a large amount of private patient information,which must be desensitized before they are used as open resources.Therefore,to solve the above problems,data masking for Chinese electronic medical records with named entity recognition is proposed in this paper.Firstly,the text is vectorized to satisfy the required format of the model input.Secondly,since the input sentences may have a long or short length and the relationship between sentences in context is not negligible.To this end,a neural network model for named entity recognition based on bidirectional long short-term memory(BiLSTM)with conditional random fields(CRF)is constructed.Finally,the data masking operation is performed based on the named entity recog-nition results,mainly using regular expression filtering encryption and principal component analysis(PCA)word vector compression and replacement.In addi-tion,comparison experiments with the hidden markov model(HMM)model,LSTM-CRF model,and BiLSTM model are conducted in this paper.The experi-mental results show that the method used in this paper achieves 92.72%Accuracy,92.30%Recall,and 92.51%F1_score,which has higher accuracy compared with other models.

关键词： named entity recognition Chinese electronic medical records data masking principal component analysis regular expression

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