Biomedical Named Entity Recognition Tasks Research Articles

BioBBC: a multi-feature model that enhances the detection of biomedical entities

The rapid increase in biomedical publications necessitates efficient systems to automatically handle Biomedical Named Entity Recognition (BioNER) tasks in unstructured text. However, accurately detecting biomedical entities is quite challenging due to the complexity of their names and the frequent use of abbreviations. In this paper, we propose BioBBC, a deep learning (DL) model that utilizes multi-feature embeddings and is constructed based on the BERT-BiLSTM-CRF to address the BioNER task. BioBBC consists of three main layers; an embedding layer, a Long Short-Term Memory (Bi-LSTM) layer, and a Conditional Random Fields (CRF) layer. BioBBC takes sentences from the biomedical domain as input and identifies the biomedical entities mentioned within the text. The embedding layer generates enriched contextual representation vectors of the input by learning the text through four types of embeddings: part-of-speech tags (POS tags) embedding, char-level embedding, BERT embedding, and data-specific embedding. The BiLSTM layer produces additional syntactic and semantic feature representations. Finally, the CRF layer identifies the best possible tag sequence for the input sentence. Our model is well-constructed and well-optimized for detecting different types of biomedical entities. Based on experimental results, our model outperformed state-of-the-art (SOTA) models with significant improvements based on six benchmark BioNER datasets.

Transformer-based Named Entity Recognition for Clinical Cancer Drug Toxicity by Positive-unlabeled Learning and KL Regularizers

Background: With increasing rates of polypharmacy, the vigilant surveillance of clinical drug toxicity has emerged as an important concern. Named Entity Recognition (NER) stands as an indispensable undertaking, essential for the extraction of valuable insights regarding drug safety from the biomedical literature. In recent years, significant advancements have been achieved in the deep learning models on NER tasks. Nonetheless, the effectiveness of these NER techniques relies on the availability of substantial volumes of annotated data, which is labor-intensive and inefficient. background: With increasing rates of polypharmacy, clinical drug toxicity has been closely monitored. Named Entity Recognition (NER) is a vital task for extracting valuable drug safety information from biomedical literature. Recently, many deep learning models in biomedical domain have made great progress for NER, especially pre-trained language models. However, these NER methods require large amounts of high-quality manually annotated data with named entities, which is labor intensive and inefficient. Methods: This study introduces a novel approach that diverges from the conventional reliance on manually annotated data. It employs a transformer-based technique known as Positive-Unlabeled Learning (PULearning), which incorporates adaptive learning and is applied to the clinical cancer drug toxicity corpus. To improve the precision of prediction, we employ relative position embeddings within the transformer encoder. Additionally, we formulate a composite loss function that integrates two Kullback-Leibler (KL) regularizers to align with PULearning assumptions. The outcomes demonstrate that our approach attains the targeted performance for NER tasks, solely relying on unlabeled data and named entity dictionaries. objective: To improve the performance of prediction Conclusion: Our model achieves an overall NER performance with an F1 of 0.819. Specifically, it attains F1 of 0.841, 0.801 and 0.815 for DRUG, CANCER, and TOXI entities, respectively. A comprehensive analysis of the results validates the effectiveness of our approach in comparison to existing PULearning methods on biomedical NER tasks. Additionally, a visualization of the associations among three identified entities is provided, offering a valuable reference for querying their interrelationships. method: In this work, instead of relying on the manually labeled data, a transformer-based Positive-Unlabeled Learning (PULearning) is proposed with adaptive learning and applied on the clinical cancer drug toxicity corpus. To improve the precision of prediction, relative position embeddings are used in transformer encoder. And then, a mixed loss is designed with two Kullback-Leibler (KL) regularizers for PULearning assumptions. Through adaptive sampling, our approach meets the expected performance for NER task only using unlabeled data and named entity dictionaries. result: The overall NER performance of our model obtains 0.819 of F1-score, while 0.841, 0.801 and 0.815 of F1-score on DRUG, CANCER and TOXI, respectively. other: None

Transferring from Textual Entailment to Biomedical Named Entity Recognition.

Biomedical Named Entity Recognition (BioNER) aims at identifying biomedical entities such as genes, proteins, diseases, and chemical compounds in the given textual data. However, due to the issues of ethics, privacy, and high specialization of biomedical data, BioNER suffers from the more severe problem of lacking in quality labeled data than the general domain especially for the token-level. Facing the extremely limited labeled biomedical data, this work studies the problem of gazetteer-based BioNER, which aims at building a BioNER system from scratch. It needs to identify the entities in the given sentences when we have zero token-level annotations for training. Previous works usually use sequential labeling models to solve the NER or BioNER task and obtain weakly labeled data from gazetteers when we don't have full annotations. However, these labeled data are quite noisy since we need the labels for each token and the entity coverage of the gazetteers is limited. Here we propose to formulate the BioNER task as a Textual Entailment problem and solve the task via Textual Entailment with Dynamic Contrastive learning (TEDC). TEDC not only alleviates the noisy labeling issue, but also transfers the knowledge from pre-trained textual entailment models. Additionally, the dynamic contrastive learning framework contrasts the entities and non-entities in the same sentence and improves the model's discrimination ability. Experiments on two real-world biomedical datasets show that TEDC can achieve state-of-the-art performance for gazetteer-based BioNER.

Reinforcement learning based distantly supervised biomedical named entity recognition

Data used by current Biomedical named entity recognition (BioNER) systems has mostly been manually labelled for supervision. However, it might be difficult to find large amounts of annotated data, especially in fields with a high level of specialization, such as biomedical, bioinformatics, and so on. When dictionaries and ontologies are available, which are domain-specific knowledge resources, automatically tagged distantly supervised biomedical training data can be developed. However, any such distantly supervised NER result is normally noisy. The prevalence of false positives and false negatives with this type of autonomously generated data is the main problem that directly affects efficiency. This research investigates distant supervision to detect false positive occurrences in BioNER task. A reinforcement learning technique is employed that is modelled as a graphical processing unit (GPU) accelerated Markov decision process (MDP) with a neural network policy. To deal with false negative cases, we employ a partial annotation conditional random field (CRF) technique. Results on two benchmark datasets show a cutting-edge methodology that can enhance the functionality of the neural NER system. It goes on to show how the proposed approach cuts down on human annotated data for BioNER tasks in Natural Language Processing (NLP).

On the Use of Knowledge Transfer Techniques for Biomedical Named Entity Recognition

Biomedical named entity recognition (BioNER) is a preliminary task for many other tasks, e.g., relation extraction and semantic search. Extracting the text of interest from biomedical documents becomes more demanding as the availability of online data is increasing. Deep learning models have been adopted for biomedical named entity recognition (BioNER) as deep learning has been found very successful in many other tasks. Nevertheless, the complex structure of biomedical text data is still a challenging aspect for deep learning models. Limited annotated biomedical text data make it more difficult to train deep learning models with millions of trainable parameters. The single-task model, which focuses on learning a specific task, has issues in learning complex feature representations from a limited quantity of annotated data. Moreover, manually constructing annotated data is a time-consuming job. It is, therefore, vital to exploit other efficient ways to train deep learning models on the available annotated data. This work enhances the performance of the BioNER task by taking advantage of various knowledge transfer techniques: multitask learning and transfer learning. This work presents two multitask models (MTMs), which learn shared features and task-specific features by implementing the shared and task-specific layers. In addition, the presented trained MTM is also fine-tuned for each specific dataset to tailor it from a general features representation to a specialized features representation. The presented empirical results and statistical analysis from this work illustrate that the proposed techniques enhance significantly the performance of the corresponding single-task model (STM).

BioByGANS: biomedical named entity recognition by fusing contextual and syntactic features through graph attention network in node classification framework

BackgroundAutomatic and accurate recognition of various biomedical named entities from literature is an important task of biomedical text mining, which is the foundation of extracting biomedical knowledge from unstructured texts into structured formats. Using the sequence labeling framework and deep neural networks to implement biomedical named entity recognition (BioNER) is a common method at present. However, the above method often underutilizes syntactic features such as dependencies and topology of sentences. Therefore, it is an urgent problem to be solved to integrate semantic and syntactic features into the BioNER model.ResultsIn this paper, we propose a novel biomedical named entity recognition model, named BioByGANS (BioBERT/SpaCy-Graph Attention Network-Softmax), which uses a graph to model the dependencies and topology of a sentence and formulate the BioNER task as a node classification problem. This formulation can introduce more topological features of language and no longer be only concerned about the distance between words in the sequence. First, we use periods to segment sentences and spaces and symbols to segment words. Second, contextual features are encoded by BioBERT, and syntactic features such as part of speeches, dependencies and topology are preprocessed by SpaCy respectively. A graph attention network is then used to generate a fusing representation considering both the contextual features and syntactic features. Last, a softmax function is used to calculate the probabilities and get the results. We conduct experiments on 8 benchmark datasets, and our proposed model outperforms existing BioNER state-of-the-art methods on the BC2GM, JNLPBA, BC4CHEMD, BC5CDR-chem, BC5CDR-disease, NCBI-disease, Species-800, and LINNAEUS datasets, and achieves F1-scores of 85.15%, 78.16%, 92.97%, 94.74%, 87.74%, 91.57%, 75.01%, 90.99%, respectively.ConclusionThe experimental results on 8 biomedical benchmark datasets demonstrate the effectiveness of our model, and indicate that formulating the BioNER task into a node classification problem and combining syntactic features into the graph attention networks can significantly improve model performance.

Biomedical named entity recognition using BERT in the machine reading comprehension framework

Recognition of biomedical entities from literature is a challenging research focus, which is the foundation for extracting a large amount of biomedical knowledge existing in unstructured texts into structured formats. Using the sequence labeling framework to implement biomedical named entity recognition (BioNER) is currently a conventional method. This method, however, often cannot take full advantage of the semantic information in the dataset, and the performance is not always satisfactory. In this work, instead of treating the BioNER task as a sequence labeling problem, we formulate it as a machine reading comprehension (MRC) problem. This formulation can introduce more prior knowledge utilizing well-designed queries, and no longer need decoding processes such as conditional random fields (CRF). We conduct experiments on six BioNER datasets, and the experimental results demonstrate the effectiveness of our method. Our method achieves state-of-the-art (SOTA) performance on the BC4CHEMD, BC5CDR-Chem, BC5CDR-Disease, NCBI-Disease, BC2GM and JNLPBA datasets, achieving F1-scores of 92.92%, 94.19%, 87.83%, 90.04%, 85.48% and 78.93%, respectively.

Comparing general and specialized word embeddings for biomedical named entity recognition.

Increased interest in the use of word embeddings, such as word representation, for biomedical named entity recognition (BioNER) has highlighted the need for evaluations that aid in selecting the best word embedding to be used. One common criterion for selecting a word embedding is the type of source from which it is generated; that is, general (e.g., Wikipedia, Common Crawl), or specific (e.g., biomedical literature). Using specific word embeddings for the BioNER task has been strongly recommended, considering that they have provided better coverage and semantic relationships among medical entities. To the best of our knowledge, most studies have focused on improving BioNER task performance by, on the one hand, combining several features extracted from the text (for instance, linguistic, morphological, character embedding, and word embedding itself) and, on the other, testing several state-of-the-art named entity recognition algorithms. The latter, however, do not pay great attention to the influence of the word embeddings, and do not facilitate observing their real impact on the BioNER task. For this reason, the present study evaluates three well-known NER algorithms (CRF, BiLSTM, BiLSTM-CRF) with respect to two corpora (DrugBank and MedLine) using two classic word embeddings, GloVe Common Crawl (of the general type) and Pyysalo PM + PMC (specific), as unique features. Furthermore, three contextualized word embeddings (ELMo, Pooled Flair, and Transformer) are compared in their general and specific versions. The aim is to determine whether general embeddings can perform better than specialized ones on the BioNER task. To this end, four experiments were designed. In the first, we set out to identify the combination of classic word embedding, NER algorithm, and corpus that results in the best performance. The second evaluated the effect of the size of the corpus on performance. The third assessed the semantic cohesiveness of the classic word embeddings and their correlation with respect to several gold standards; while the fourth evaluates the performance of general and specific contextualized word embeddings on the BioNER task. Results show that the classic general word embedding GloVe Common Crawl performed better in the DrugBank corpus, despite having less word coverage and a lower internal semantic relationship than the classic specific word embedding, Pyysalo PM + PMC; while in the contextualized word embeddings the best results are presented in the specific ones. We conclude, therefore, when using classic word embeddings as features on the BioNER task, the general ones could be considered a good option. On the other hand, when using contextualized word embeddings, the specific ones are the best option.

Medical Text Entity Recognition Based on Deep Learning

Named entity recognition is a very important basic task in natural language processing, and a basic technology for many high-level applications of natural language processing. Traditional methods to solve named entity recognition are mainly based on rules and statistics. The rule-based method requires strong linguistic knowledge and is poor in generality. Based on the above background, the purpose of this paper is to recognize medical text entities based on deep learning. This paper proposes a new LSTM framework that integrates dual-channel and sentence-level reading control gates. In the input part, double channels are added to obtain two kinds of semantic information from static word vectors and fine-tuned word vectors. Then, the read-in control gate is integrated inside the neural network to determine the propagation of the sentence representation vector. Finally, the CRF model is used to fully consider the dependency relationship between the types of context words when outputting tags. The F1 value of 89.49% was achieved on the BioCreative II GM corpus. In summary, this article applies two deep learning methods to improve the performance of biomedical named entity recognition tasks. Finally, without adding any artificial features and post-processing operations, this article has achieved 89.94% F1 value on the BioCreative II GM corpus, and it is 0.89% higher than the F1 value of the current best system.

Multidimensional Self-Attention for Aspect Term Extraction and Biomedical Named Entity Recognition

Wide attention has been paid to named entity recognition (NER) in specific fields. Among the representative tasks are the aspect term extraction (ATE) in user online comments and the biomedical named entity recognition (BioNER) in medical documents. Existing methods only perform well in a particular field, and it is difficult to maintain an advantage in other fields. In this article, we propose a supervised learning method that can be used for much special domain NER tasks. The model consists of two parts, a multidimensional self-attention (MDSA) network and a CNN-based model. The multidimensional self-attention mechanism can calculate the importance of the context to the current word, select the relevance according to the importance, and complete the update of the word vector. This update mechanism allows the subsequent CNN model to have variable-length memory of sentence context. We conduct experiments on benchmark datasets of ATE and BioNER tasks. The results show that our model surpasses most baseline methods.

Biomedical named entity recognition based on Glove-BLSTM-CRF model

Named entity recognition is a fundamental task of natural language processing. The number of biomedical named entities is huge, the naming rules are not uniform, and the entity word formation is complex, which brings great difficulties to the biomedical named entity recognition. Traditional machine learning algorithms rely heavily on manual extraction of features. The quality of feature extraction directly affects the accuracy of entity recognition. In the biomedical domain, the cost of manually extracting features and annotating data sets is enormous. In recent years, deep learning methods that do not rely on artificial features have made great progress in many domains. This paper proposes a model based on Glove-BLSTM-CRF for biomedical named entity recognition. Firstly, the Glove model is used to train word vector with semantic features, and BLSTM is used to train word vector with character morphological features. The two are combined as the final representation of the word, then input into the BLSTM-CRF deep learning model to recognize the entity categories. The experimental results show that the model has achieved a better result in the JNLPBA 2004 biomedical named entity recognition task without relying on any artificial features and rules, and the F1 value reaches 75.62%.

A Boundary Assembling Method for Nested Biomedical Named Entity Recognition

Biomedical named entity recognition (BNER) is an important task in biomedical natural language processing, in which neologisms (new terms, words) are coined constantly. Most of the existing work can only identify biomedical named entities with flattened structures and ignore nested biomedical named entities and discontinuous biomedical named entities. Because biomedical domains often use nested structures to represent semantic information of named entities, existing methods fail to utilize abundant information when processing biomedical texts. This paper focuses on identifying nested biomedical named entities using a boundary assembly (BA) model, which is a cascading framework consisting of three steps. First, start and end named entity boundaries are identified and then assembled into named entity candidates. Finally, a classifier is implemented for filtering false named entities. Our approach is effective in handling nesting and discontinuous problems in biomedical named entity recognition tasks. It improves the performance considerably, achieving an F1-score of 81.34% on the GENIA dataset.

WCP-RNN: a novel RNN-based approach for Bio-NER in Chinese EMRs

Deep learning has achieved remarkable success in a wide range of domains. However, it has not been comprehensively evaluated as a solution for the task of Chinese biomedical named entity recognition (Bio-NER). The traditional deep-learning approach for the Bio-NER task is usually based on the structure of recurrent neural networks (RNN) and only takes word embeddings into consideration, ignoring the value of character-level embeddings to encode the morphological and shape information. We propose an RNN-based approach, WCP-RNN, for the Chinese Bio-NER problem. Our method combines word embeddings and character embeddings to capture orthographic and lexicosemantic features. In addition, POS tags are involved as a priori word information to improve the final performance. The experimental results show our proposed approach outperforms the baseline method; the highest F-scores for subject and lesion detection tasks reach 90.36 and 90.48% with an increase of 3.10 and 2.60% compared with the baseline methods, respectively.

GRAM-CNN: a deep learning approach with local context for named entity recognition in biomedical text.

MotivationBest performing named entity recognition (NER) methods for biomedical literature are based on hand-crafted features or task-specific rules, which are costly to produce and difficult to generalize to other corpora. End-to-end neural networks achieve state-of-the-art performance without hand-crafted features and task-specific knowledge in non-biomedical NER tasks. However, in the biomedical domain, using the same architecture does not yield competitive performance compared with conventional machine learning models.ResultsWe propose a novel end-to-end deep learning approach for biomedical NER tasks that leverages the local contexts based on n-gram character and word embeddings via Convolutional Neural Network (CNN). We call this approach GRAM-CNN. To automatically label a word, this method uses the local information around a word. Therefore, the GRAM-CNN method does not require any specific knowledge or feature engineering and can be theoretically applied to a wide range of existing NER problems. The GRAM-CNN approach was evaluated on three well-known biomedical datasets containing different BioNER entities. It obtained an F1-score of 87.26% on the Biocreative II dataset, 87.26% on the NCBI dataset and 72.57% on the JNLPBA dataset. Those results put GRAM-CNN in the lead of the biological NER methods. To the best of our knowledge, we are the first to apply CNN based structures to BioNER problems.Availability and implementationThe GRAM-CNN source code, datasets and pre-trained model are available online at: https://github.com/valdersoul/GRAM-CNN.Supplementary information Supplementary data are available at Bioinformatics online.

Evaluating word representation features in biomedical named entity recognition tasks.

Biomedical Named Entity Recognition (BNER), which extracts important entities such as genes and proteins, is a crucial step of natural language processing in the biomedical domain. Various machine learning-based approaches have been applied to BNER tasks and showed good performance. In this paper, we systematically investigated three different types of word representation (WR) features for BNER, including clustering-based representation, distributional representation, and word embeddings. We selected one algorithm from each of the three types of WR features and applied them to the JNLPBA and BioCreAtIvE II BNER tasks. Our results showed that all the three WR algorithms were beneficial to machine learning-based BNER systems. Moreover, combining these different types of WR features further improved BNER performance, indicating that they are complementary to each other. By combining all the three types of WR features, the improvements in F-measure on the BioCreAtIvE II GM and JNLPBA corpora were 3.75% and 1.39%, respectively, when compared with the systems using baseline features. To the best of our knowledge, this is the first study to systematically evaluate the effect of three different types of WR features for BNER tasks.

A composite kernel for named entity recognition

In this paper, we propose a novel kernel function for support vector machines (SVM) that can be used for sequential labeling tasks like named entity recognition (NER). Machine learning methods like support vector machines, maximum entropy, hidden Markov model and conditional random fields are the most widely used methods for implementing NER systems. The features used in machine learning algorithms for NER are mostly string based features. The proposed kernel is based on calculating a novel distance function between the string based features. In tasks like NER, the similarity between the contexts as well as the semantic similarity between the words play an important role. The goal is to capture the context and semantic information in NER like tasks. The proposed distance function makes use of certain statistics primarily derived from the training data and hierarchical clustering information. The kernel function is applied to the Hindi and biomedical NER tasks and the results are quite promising.

Classifier subset selection for biomedical named entity recognition

Classifier ensembling approach is considered for biomedical named entity recognition task. A vote-based classifier selection scheme having an intermediate level of search complexity between static classifier selection and real-valued and class-dependent weighting approaches is developed. Assuming that the reliability of the predictions of each classifier differs among classes, the proposed approach is based on selection of the classifiers by taking into account their individual votes. A wide set of classifiers, each based on a different set of features and modeling parameter setting are generated for this purpose. A genetic algorithm is developed so as to label the predictions of these classifiers as reliable or not. During testing, the votes that are labeled as being reliable are combined using weighted majority voting. The classifier ensemble formed by the proposed scheme surpasses the full object F-score of the best individual classifier by 2.75% and it is the highest score achieved on the data set considered.