Cimind: A phonetic-based tool for multilingual named entity recognition in biomedical texts.

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.

Biomedical Named Entity Recognition (NER) is a fundamental task in biomedical text mining and is used to extract critical key information such as genes, proteins, diseases, and drugs. However, the complexity of biomedical terminology, including morphological variations, out-of-vocabulary terms, and complex relationships between entities, poses significant challenges for traditional NER systems. In this paper, we propose a novel hybrid deep learning architecture designed to capture complex representations of biomedical text data for a robust biomedical NER task. Our proposed GraphNet-BiLSTM combines bidirectional long short-term memory deep learning model with Graph Neural Network to explicitly capture structural dependencies, such as syntactic or co-occurrence relationships, between tokens. We evaluated our proposed GraphNet-BiLSTM model on six widely-used biomedical NER datasets: AnatEM, BC2GM, BC5CDR, ExPTM, linnaeus, and NCBI. Experimental results demonstrate that our proposed architecture achieves improved F1-scores compared to a strong baseline on five out of the six datasets, highlighting its effectiveness in capturing the intricate characteristics of biomedical text. Utilizing graph neural network component enables the model to leverage structural context, contributing to enhanced performance. Our work demonstrates that combining character, word, sequential BiLSTM, and structural graph-based representations with CRF decoding yields a powerful framework for biomedical NER, achieving improved results across diverse datasets and entity types.

Data augmentation is important in addressing data sparsity and low resources in NLP. Unlike data augmentation for other tasks such as sentence-level and sentence-pair ones, data augmentation for named entity recognition (NER) requires preserving the semantic of entities. To that end, in this paper we propose a simple semantic-based data augmentation method for biomedical NER. Our method leverages semantic information from pre-trained language models for both entity-level and sentence-level. Experimental results on two datasets: i2b2-2010 (English) and VietBioNER (Vietnamese) showed that the proposed method could improve NER performance.

In recent years, as cybersecurity threats have become increasingly severe and cyberattacks have occurred frequently, higher requirements have been put forward for cybersecurity protection. Therefore, the Named Entity Recognition (NER) technique, which is the cornerstone of Cyber Threat Intelligence (CTI) analysis, is particularly important. However, most existing NER studies are limited to recognizing single-layer flat entities, ignoring the possible nested entities in CTI. On the other hand, most of the existing studies focus on English CTIs, and the existing models performed poorly in a limited number of Chinese CTI studies. Given the above challenges, we propose in this paper a novel unified model, RBTG, which aims to identify flat and nested entities in Chinese CTI effectively. To overcome the difficult boundary recognition problem and the direction-dependent and distance-dependent properties in Chinese CTI NER, we use Global Pointer as the decoder and TENER as the encoder layer, respectively. Specifically, the Global Pointer layer solves the problem of the insensitivity of general NER methods to entity boundaries by utilizing the relative position information and the multiplicative attention mechanism. The TENER layer adapts to the Chinese CTI NER task by introducing an attention mechanism with direction awareness and distance awareness. Meanwhile, to cope with the complex feature capture of hierarchical structure and dependencies among Chinese CTI nested entities, the TENER layer solves the problem by following the structure of multiple self-attention layers and feed-forward network layers superimposed on each other in the Transformer. In addition, to fill the gap in the Chinese CTI nested entity dataset, we further apply the Large Language Modeling (LLM) technique and domain knowledge to construct a high-quality Chinese CTI nested entity dataset, CDTinee, which consists of six entity types selected from STIX, including nearly 4000 entity types extracted from more than 3000 threatening sentences. In the experimental session, we conduct extensive experiments on multiple datasets, and the results show that the proposed model RBTG outperforms the baseline model in both flat NER and nested NER.

Intent classification (IC) and Named Entity Recognition (NER) are arguably the two main components needed to build a Natural Language Understanding (NLU) engine, which is a main component of conversational agents. The IC and NER components are closely intertwined and the entities are often connected to the underlying intent. Current research has primarily focused to model IC and NER as two separate units, which results in error propagation, and thus, sub-optimal performance. In this paper, we propose a simple yet effective novel framework for NLU where the parameters of the IC and the NER models are jointly trained in a consolidated parameter space. Text semantic representations are obtained from popular pre-trained contextual language models, which are fine-tuned for our task, and these parameters are propagated to other deep neural layers in our framework leading to a faithful unified modelling of the IC and NER parameters. The overall framework results in a faithful parameter sharing when the training is underway, leading to a more coherent learning. Experiments on two public datasets, ATIS and SNIPS, show that our model outperforms other methods by a noticeable margin. On the SNIPS dataset, we obtain a 1.42% improvement in NER in terms of the F1 score, and 1% improvement in intent accuracy score. On ATIS, we achieve 1.54% improvement in intent accuracy score. We also present qualitative results to showcase the effectiveness of our model.

Few-shot nested named entity recognition

Named Entity Recognition (NER) is a vital task in natural language processing (NLP) that involves identifying and classifying named entities in text. This paper focuses on the comparison of four different algorithms of NER techniques in the context of India. The four different algorithms are CRF (Conditional Random Fields), Stanza, Spacy, and Nameparser. The accuracy will be compared with the expected accuracy of all four methods of NER. Accuracy will be obtained after running the method on a dataset or text. To calculate the accuracy of four algorithms a large dataset of Indian names will be used. A comparison graph was obtained to display the accuracy graph of all four algorithms. "NLP-Named Entity Recognition in India" which focuses on detecting person names, states, and districts, and suggesting names based on religion. Named Entity Recognition (NER) is a Natural Language Processing (NLP) task that identifies and classifies named entities in text. Named entities are typically proper nouns, such as person names, organization names, and location names. NER is a challenging task for Indian languages, due to the diversity of Indian languages and the lack of resources for training NER systems. The proposed system can be used to improve the accuracy and efficiency of a variety of NLP applications in India.

Named entity recognition (NER) is an important research problem in natural language processing. There are three types of NER tasks, including flat, nested and discontinuous entity recognition. Most previous sequential labeling models are task-specific, while recent years have witnessed the rising of generative models due to the advantage of unifying all NER tasks into the seq2seq model framework. Although achieving promising performance, our pilot studies demonstrate that existing generative models are ineffective at detecting entity boundaries and estimating entity types. This paper proposes a multi-task Transformer, which incorporates an entity boundary detection task into the named entity recognition task. More concretely, we achieve entity boundary detection by classifying the relations between tokens within the sentence. To improve the accuracy of entity-type mapping during decoding, we adopt an external knowledge base to calculate the prior entity-type distributions and then incorporate the information into the model via the self and cross-attention mechanisms. We perform experiments on an extensive set of NER benchmarks, including two flat, three nested, and three discontinuous NER datasets. Experimental results show that our approach considerably improves the generative NER model’s performance.

BackgroundIn biomedical text mining, named entity recognition (NER) is an important task used to extract information from biomedical articles. Previously proposed methods for NER are dictionary- or rule-based methods and machine learning approaches. However, these traditional approaches are heavily reliant on large-scale dictionaries, target-specific rules, or well-constructed corpora. These methods to NER have been superseded by the deep learning-based approach that is independent of hand-crafted features. However, although such methods of NER employ additional conditional random fields (CRF) to capture important correlations between neighboring labels, they often do not incorporate all the contextual information from text into the deep learning layers.ResultsWe propose herein an NER system for biomedical entities by incorporating n-grams with bi-directional long short-term memory (BiLSTM) and CRF; this system is referred to as a contextual long short-term memory networks with CRF (CLSTM). We assess the CLSTM model on three corpora: the disease corpus of the National Center for Biotechnology Information (NCBI), the BioCreative II Gene Mention corpus (GM), and the BioCreative V Chemical Disease Relation corpus (CDR). Our framework was compared with several deep learning approaches, such as BiLSTM, BiLSTM with CRF, GRAM-CNN, and BERT. On the NCBI corpus, our model recorded an F-score of 85.68% for the NER of diseases, showing an improvement of 1.50% over previous methods. Moreover, although BERT used transfer learning by incorporating more than 2.5 billion words, our system showed similar performance with BERT with an F-scores of 81.44% for gene NER on the GM corpus and a outperformed F-score of 86.44% for the NER of chemicals and diseases on the CDR corpus. We conclude that our method significantly improves performance on biomedical NER tasks.ConclusionThe proposed approach is robust in recognizing biological entities in text.

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.

Medical named entity recognition can assist doctors to quickly identifying key content and improving clinical work efficiency. Chinese named entity recognition methods based on pre-trained language models have achieved remarkable performance. However, most of these models have the following problems for medical named entity recognition: these models are designed for flat named entity recognition tasks but not for nested entities. Furthermore, the medical entities are hard to be recognized due to the lack of medical domain knowledge. To tackle these problems, we propose a Chinese medical nested named entity recognition model based on feature fusion and a bidirectional lattice embedding graph. The problem of poor recognition of medical entities due to the lack of medical domain knowledge is solved by introducing a medical lexicon. The problem of Chinese polyphonic characters with different meanings in the same form is solved by introducing pinyin information. The model considers the similarity between different entity types to improve the model’s effectiveness. The results on a Chinese medical nested named entity dataset CBLUE-CMeEE demonstrate the outperform performance and effectiveness of the model.

Developing Named Entity Recognition (NER) systems for Indian languages has been a long-standing challenge, mainly owing to the requirement of a large amount of annotated clean training instances. This paper proposes an end-to-end framework for NER for Indian languages in a low-resource setting by exploiting parallel corpora of English and Indian languages and an English NER dataset. The proposed framework includes an annotation projection method that combines word alignment score and NER tag prediction confidence score on source language (English) data to generate weakly labeled data in a target Indian language. We employ a variant of the Teacher-Student model and optimize it jointly on the pseudo labels of the Teacher model and predictions on the generated weakly labeled data. We also present manually annotated test sets for three Indian languages: Hindi, Bengali, and Gujarati. We evaluate the performance of the proposed framework on the test sets of the three Indian languages. Empirical results show a minimum 10% performance improvement compared to the zero-shot transfer learning model on all languages. This indicates that weakly labeled data generated using the proposed annotation projection method in target Indian languages can complement well-annotated source language data to enhance performance. Our code is publicly available at https://github.com/aksh555/CL-NERIL.

ADPG: Biomedical entity recognition based on Automatic Dependency Parsing Graph

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.

Text mining is increasingly used to manage the accelerating pace of the biomedical literature. Many text mining applications depend on accurate named entity recognition (NER) and normalization (grounding). While high performing machine learning methods trainable for many entity types exist for NER, normalization methods are usually specialized to a single entity type. NER and normalization systems are also typically used in a serial pipeline, causing cascading errors and limiting the ability of the NER system to directly exploit the lexical information provided by the normalization. We propose the first machine learning model for joint NER and normalization during both training and prediction. The model is trainable for arbitrary entity types and consists of a semi-Markov structured linear classifier, with a rich feature approach for NER and supervised semantic indexing for normalization. We also introduce TaggerOne, a Java implementation of our model as a general toolkit for joint NER and normalization. TaggerOne is not specific to any entity type, requiring only annotated training data and a corresponding lexicon, and has been optimized for high throughput. We validated TaggerOne with multiple gold-standard corpora containing both mention- and concept-level annotations. Benchmarking results show that TaggerOne achieves high performance on diseases (NCBI Disease corpus, NER f-score: 0.829, normalization f-score: 0.807) and chemicals (BioCreative 5 CDR corpus, NER f-score: 0.914, normalization f-score 0.895). These results compare favorably to the previous state of the art, notwithstanding the greater flexibility of the model. We conclude that jointly modeling NER and normalization greatly improves performance. The TaggerOne source code and an online demonstration are available at: http://www.ncbi.nlm.nih.gov/bionlp/taggerone zhiyong.lu@nih.gov Supplementary data are available at Bioinformatics online.