CHINERS

BackgroundThe unstructured data of Chinese cancer electronic health records (EHRs) contains valuable medical expertise. Accurate medical entity recognition is crucial for building a medical-assisted decision system. Named entity recognition (NER) in cancer EHRs typically uses general models designed for English medical records. There is a lack of specialized handling for cancer-specific records and limited application to Chinese medical records.ObjectiveThis study aims to propose a specific NER model to enhance the recognition of medical entities in Chinese cancer EHRs.MethodsDesensitized inpatient EHRs related to breast cancer were collected from a leading hospital in Beijing. Building upon the MC Bidirectional Encoder Representations from Transformers (BERT) foundation, the study further incorporated a Chinese cancer corpus for pretraining, resulting in the construction of the ChCancerBERT pretrained model. In conjunction with dilated-gated convolutional neural networks, bidirectional long short-term memory, multihead attention mechanism, and a conditional random field, this model forms a multimodel, multilevel integrated NER approach.ResultsThis approach effectively extracts medical entity features related to symptoms, signs, tests, treatments, and time in Chinese breast cancer EHRs. The entity recognition performance of the proposed model surpasses that of the baseline model and other models compared in the experiment. The F1-score reached 86.93%, precision reached 87.24%, and recall reached 86.61%. The model introduced in this study demonstrates exceptional performance on the CCKS2019 dataset, attaining a precision rate of 87.26%, a recall rate of 87.27%, and an impressive F1-score of 87.26%, surpassing that of existing models.ConclusionsThe experiments demonstrate that the approach proposed in this study exhibits excellent performance in NER within breast cancer EHRs. This advancement will further contribute to clinical decision support for cancer treatment and research. In addition, the study reveals that incorporating domain-specific corpora in clinical NER tasks can further enhance the performance of BERT models in specialized domains.

This paper reports development of Hindi named entity recognition (NER) system using various machine learning algorithms and their combination. Three machine learning algorithms namely simple K-nearest neighbour (KNN), weighted K-nearest neighbour and HMM have been used for developing three different Hindi NER systems which are finally combined through majority voting to develop an improved hybrid NER system. We have designed set of novel features which have been used for improving the performances of the KNN-based NER systems. A comparative study among our developed NER models has been made based on some standard data sets. This study reveals that performance of the weighted KNN-based NER system is comparable with that of the HMM-based NER system and performance of the hybrid system is significantly better than each individual base model. Our experimental results also show that performance of the hybrid NER system is better than some existing state-of-the art Hindi NER systems.

Social media texts are significant informa-tion sources for several application areas including trend analysis, event monitor-ing, and opinion mining. Unfortunately, existing solutions for tasks such as named entity recognition that perform well on formal texts usually perform poorly when applied to social media texts. In this pa-per, we report on experiments that have the purpose of improving named entity recog-nition on Turkish tweets, using two dif-ferent annotated data sets. In these ex-periments, starting with a baseline named entity recognition system, we adapt its recognition rules and resources to better fit Twitter language by relaxing its capital-ization constraint and by diacritics-based expansion of its lexical resources, and we employ a simplistic normalization scheme on tweets to observe the effects of these on the overall named entity recognition per-formance on Turkish tweets. The evalua-tion results of the system with these differ-ent settings are provided with discussions of these results. 1

Named entity recognition of building construction defect information from text with linguistic noise

Named Entity Recognition (NER) is a core task of NLP. State-of-art supervised NER models rely heavily on a large amount of high-quality annotated data, which is quite expensive to obtain. Various existing ways have been proposed to reduce the heavy reliance on large training data, but only with limited effect. In this paper, we propose a crowd-efficient learning approach for supervised NER learning by making full use of the online encyclopedia pages. In our approach, we first define three criteria (representativeness, informativeness, diversity) to help select a much smaller set of samples for crowd labeling. We then propose a data augmentation method, which could generate a lot more training data with the help of the structured knowledge of online encyclopedia to greatly augment the training effect. After conducting model training on the augmented sample set, we re-select some new samples for crowd labeling for model refinement. We perform the training and selection procedure iteratively until the model could not be further improved or the performance of the model meets our requirement. Our empirical study conducted on several real data collections shows that our approach could reduce 50% manual annotations with almost the same NER performance as the fully trained model.

In the rapidly evolving field of cybersecurity, the integration of multi-source, heterogeneous, and fragmented data into a coherent knowledge graph has garnered considerable attention. Such a graph elucidates semantic interconnections, thereby facilitating sophisticated analytical decision support. Central to the construction of a cybersecurity knowledge graph is Named Entity Recognition (NER), a critical technology that converts unstructured text into structured data. The efficacy of NER is pivotal, as it directly influences the integrity of the knowledge graph. The task of NER in cybersecurity, particularly within the Chinese linguistic context, presents distinct challenges. Chinese text lacks explicit space delimiters and features complex contextual dependencies, exacerbating the difficulty in discerning and categorizing named entities. These linguistic characteristics contribute to errors in word segmentation and semantic ambiguities, impeding NER accuracy. This paper introduces a novel NER methodology tailored for the Chinese cybersecurity corpus, termed CSBERT-IDCNN-BiLSTM-CRF. This approach harnesses Iterative Dilated Convolutional Neural Networks (IDCNN) for extracting local features, and Bi-directional Long Short-Term Memory networks (BiLSTM) for contextual understanding. It incorporates CSBERT, a pre-trained model adept at processing few-shot data, to derive input feature representations. The process culminates with Conditional Random Fields (CRF) for precise sequence labeling. To compensate for the scarcity of publicly accessible Chinese cybersecurity datasets, this paper synthesizes a bespoke dataset, authenticated by data from the China National Vulnerability Database, processed via the YEDDA annotation tool. Empirical analysis affirms that the proposed CSBERT-IDCNN-BiLSTM-CRF model surpasses existing Chinese NER frameworks, with an F1-score of 87.30% and a precision rate of 85.89%. This marks a significant advancement in the accurate identification of cybersecurity entities in Chinese text, reflecting the model’s robust capability to address the unique challenges presented by the language’s structural intricacies.

In digital libraries, the accessibility of digitized documents is directly related to the way they are indexed. Named entities are one of the main entry points used to search and retrieve digital documents. However, most digitized documents are indexed through their OCRed version and OCR errors may hinder their accessibility. This paper aims to quantitatively estimate the impact of OCR quality on the performance of named entity recognition (NER). We tested state-of-the-art NER techniques over several evaluation benchmarks, and experimented with various levels and types of synthesised OCR noise so as to estimate the impact of OCR noise on NER performance. We share all corresponding datasets. To the best of our knowledge, no other research work has systematically studied the impact of OCR on named entity recognition over datasets in multiple languages. The final outcome of this study is an evaluation over historical newspaper data of the national library of Finland, resulting in an increase of around 11% points in terms of F1-measure over the best-known results to this day.

Automatic Parts of Speech(POS) tagging is one of the most fundamental tasks for a language in Natural Language Processing(NLP), which acts as a feature for solving advanced NLP tasks. Named Entity Recognition(NER) is another essential task of NLP for information retrieval. Researchers could not find up to the mark solution yet on these two tasks for Bangla language compared to other languages, for instance, English, Ger-man. Moreover, many solutions heavily depend on handcrafted features that require strong linguistic expertise. As these two sequence labeling tasks are similar, In this work, two different datasets of POS tagging and NER were prepared, and different deep neural network approaches studied for solving these two tasks separately. All of the approaches were end to end and did not need any handcrafted feature like word suffixes or affixes, gazetteers, dictionary. This study came up with an end to end solution using deep neural network-based model consisting of Bi-directional Long short-term memory(BLSTM), Convolutional Neural Network(CNN) and Conditional Random Field(CRF). The proposed model trained on respected datasets achieved an accuracy of 93.86% on POS tagging and a strict f1 score of 0.6285 on NER on prepared datasets, respectively.

Disease associated gene discovery is a critical step to realize the future of personalized medicine. However empirical and clinical validation of disease associated genes are time consuming and expensive. In silico discovery of disease associated genes from literature is therefore becoming the first essential step for biomarker discovery to support hypothesis formulation and decision making. Completion of human genome project and advent of high-throughput technology have produced tremendous amount of data, which results in exponential growing of biomedical knowledge deposited in literature database. The sheer quantity of unexplored information causes information overflow for biomedical researchers, and poses big challenge for informatics researchers to address user's information extraction needs. This thesis focused on mining disease associated genes from PubMed literature database using machine learning and graph theory based information extraction (IE) methods. Mining disease associated genes is not trivial and requires pipelines of information extraction steps and methods. Beginning from named entity recognition (NER), the author introduced semantic concept type into feature space for conditional random fields machine learning and demonstrated the effectiveness of the concept feature for disease NER. The effects of domain specific POS tagging, domain specific dictionaries, and named entity encoding scheme on NER performance were also explored. Experimental results show that by combining knowledge base with concept feature space, it can significantly improve the overall disease NER performance. It has also shown that shallow linguistic features of global and local word sequence context can be used with string kernel based supporting vector machine (SVM) for efficient disease-gene relation extraction. Lastly, the disease-associated gene network was constructed by utilizing concept co-occurrence matrix computed from disease focused document collection, and subjected to systematic topology analysis. The gene network was then merged with a seed-gene expanded network to form heterogeneous disease-gene network. The author identified and prioritized disease-associated genes by graph centrality measurements. This novel approach provides a new mean for disease associated gene extraction from large corpora.

A complete inpatient electronic medical record contains a lot of information. In recent years, numerous researchers have carried out research on word segmentation of medical texts. Since the medical record text is written by free text, structuring the medical record text is an important part of the medical record intelligent analysis when these medical named entities are recognized. At present, named entity recognition methods are mainly divided into lexicographical and rule-based methods and machine learning-based methods. The machine learn-based approach takes the named entity recognition task as the annotation problem of sequence data, mainly considering the context information. The features commonly used in feature construction are contextual feature and dictionary features. BERT+LSTM+CRF were used to train the named entity recognition model. Open source CRF++ was adopted as the tool we relied on. We trained the LSTM+F model using the results of the original word segmentation and the information in the context as features. We carried out a 5-fold cross validation. The results showed that the overall F-1 score (MICRO-F) of named entity recognition reached 0.92, which confirmed that the model could accurately complete the task of medical named entity recognition.KeywordsWord segmentationNamed entity recognitionNatural language processing

In the field of Natural Language Processing, one of the very important research areas of Information Extraction (IE) comes in Named Entity Recognition (NER). NER is a subtask of IE that seeks to identify and classify the predefined categories of named entities in text documents. Considerable amount of work has been done on NER in recent years due to the increasing demand of automated texts and the wide availability of electronic corpora. While it is relatively easy and natural for a human reader to read and understand the context of a given article, getting a machine to understand and differentiate between words is a big challenge. For instance, the word ‘brown’ may refer to a person called Mr. Brown, or the colour of an item which is brown. Human readers can easily discern the meaning of the word by looking at the context of that particular sentence, but it would be almost impossible for a computer to interpret it without any additional information. To deal with the issue, researchers in NER field have proposed various rule-based systems (Wakao, Gaizauskas & Wilks, 1996; Krupka & Hausman, 1998; Maynard, Tablan, Ursu, Cunningham & Wilks, 2001). These systems are able to achieve high accuracy in recognition with the help of some lists of known named entities called gazetteers. The problem with rule-based approach is that it lacks the robustness and portability. It incurs steep maintenance cost especially when new rules need to be introduced for some new information or new domains. A better option is thus to use machine learning approach that is trainable and adaptable. Three wellknown machine learning approaches that have been used extensively in NER are Hidden Markov Model (HMM), Maximum Entropy Model (MEM) and Decision Tree. Many of the existing machine learning-based NER systems (Bikel, Schwartz & Weischedel, 1999; Zhou & Su, 2002; Borthwick, Sterling, Agichten & Grisham, 1998; Bender, Och & Ney, 2003; Chieu & Ng, 2002; Sekine, Grisham & Shinnou, 1998) are able to achieve near-human performance for named entity tagging, even though the overall performance is still about 2% short from the rule-based systems. There have also been many attempts to improve the performance of NER using a hybrid approach with the combination of handcrafted rules and statistical models (Mikheev, Moens & Grover, 1999; Srihari & Li, 2000; Seon, Ko, Kim & Seo, 2001). These systems can achieve relatively good performance in the targeted domains owing to the comprehensive handcrafted rules. Nevertheless, the portability problem still remains unsolved when it comes to dealing with NER in various domains. As such, this article presents a hybrid machine learning approach using MEM and HMM successively. The reason for using two statistical models in succession instead of one is due to the distinctive nature of the two models. HMM is able to achieve better performance than any other statistical models, and is generally regarded as the most successful one in machine learning approach. However, it suffers from sparseness problem, which means considerable amount of data is needed for it to achieve acceptable performance. On the other hand, MEM is able to maintain reasonable performance even when there is little data available for training purpose. The idea is therefore to walkthrough the testing corpus using MEM first in order to generate a temporary tagging result, while this procedure can be simultaneously used as a training process for HMM. During the second walkthrough, the corpus uses HMM for the final tagging. In this process, the temporary tagging result generated by MEM will be used as a reference for subsequent error checking and correction. In the case when there is little training data available, the final result can still be reliable based on the contribution of the initial MEM tagging result.

The paper presents a pipeline for building a high-quality, multi-layer annotated corpus for Kazakh NLP. The pipeline integrates large-scale web crawling, aggressive text cleaning, transformer-based pre-annotation, linguist-in-the-loop validation, and quality assurance via inter-annotator agreement (IAA). The final release contains 20,000 documents, 350,000 sentences, and 6.2 million tokens spanning 5 domains (news, politics, science, education, culture), annotated with POS, morphology, NER, and UD dependencies. The report IAA per layer and baseline model performance (POS, NER, parsing) to demonstrate utility. The study releases the corpus, code, and guidelines to support reproducible research. The proposed methodology includes the complete workflow from data acquisition through targeted web crawling of prominent Kazakh-language news outlets, to text cleaning, automated pre-annotation utilizing transformer-based language models, and manual validation via a custom-designed annotation interface. Particular emphasis is placed on the agglutinative characteristics of Kazakh and its extensive morphological variants, which present distinct challenges in annotation and model training. The generated corpus comprises comprehensive annotations for part-of-speech (POS), named entity recognition (NER), morphological characteristics, and syntactic dependencies, establishing a fundamental dataset for several downstream NLP applications. The research additionally examines significant obstacles in the annotation process, including maintaining consistency, assessing inter-annotator agreement, and evaluating the adaptability and functionality of the annotation tools. Baseline NLP models were employed and evaluated to determine the quality and utility of the corpus. This work provides a reproducible and flexible methodology for constructing corpora in low-resource and morphologically complex languages. Its objective is to promote additional study, tool creation, and technological progress in Kazakh language processing, hence advancing the overarching purpose of multilingual NLP inclusion.

Medical named entity recognition based on dilated convolutional neural network

Named entity recognition (NER) in Chinese is essential but difficult because of the lack of natural delimiters. Therefore, Chinese Word Segmentation (CWS) is usually considered as the first step for Chinese NER. However, models based on word-level embeddings and lexicon features often suffer from segmentation errors and out-of-vocabulary (OOV) words. In this paper, we investigate a Convolutional Attention Network called CAN for Chinese NER, which consists of a character-based convolutional neural network (CNN) with local-attention layer and a gated recurrent unit (GRU) with global self-attention layer to capture the information from adjacent characters and sentence contexts. Also, compared to other models, not depending on any external resources like lexicons and employing small size of char embeddings make our model more practical. Extensive experimental results show that our approach outperforms state-of-the-art methods without word embedding and external lexicon resources on different domain datasets including Weibo, MSRA and Chinese Resume NER dataset.

Named entity recognition (NER) in Chinese electronic medical records (EMRs) has become an important task of clinical natural language processing (NLP). However, limited studies have been performed on the clinical NER study in Chinese EMRs. Furthermore, when end-to-end neural network models have improved clinical NER performance, medical knowledge dictionaries such as various disease association dictionaries, which provide rich information of medical entities and relations among them, are rarely utilized in NER model. In this study, we investigate the problem of NER in Chinese EMRs and propose a clinical neural network NER model enhanced with medical knowledge attention by combining the entity mention information contained in external medical knowledge bases with EMR context together. Experimental results on the manually labeled dataset demonstrated that the proposed method can achieve better performance than the previous methods in most cases.