Fast and Accurate Recognition of Chinese Clinical Named Entities with Residual Dilated Convolutions

Clinical Named Entity Recognition (CNER) aims to identify and classify clinical terms such as diseases, symptoms, treatments, exams, and body parts in electronic health records, which is a fundamental and crucial task for clinical and translation research. In recent years, deep learning methods have achieved significant success in CNER tasks. However, these methods depend greatly on Recurrent Neural Networks (RNNs), which maintain a vector of hidden activations that are propagated through time, thus causing too much time to train models. In this paper, we propose a Residual Dilated Convolutional Neural Network with Conditional Random Field (RD-CNN-CRF) to solve it. Specifically, Chinese characters and dictionary features are first projected into dense vector representations, then they are fed into the residual dilated convolutional neural network to capture contextual features. Finally, a conditional random field is employed to capture dependencies between neighboring tags. Computational results on the CCKS-2017 Task 2 benchmark dataset show that our proposed RD-CNN-CRF method competes favorably with state-of-the-art RNN-based methods both in terms of computational performance and training time.Comment: 8 pages, 3 figures. Accepted as regular paper by 2018 IEEE International Conference on Bioinformatics and Biomedicine. arXiv admin note: text overlap with arXiv:1804.0501

A Deep Learning Entity Extraction Model for Chinese Government Documents

In this paper, we propose a combined Whole-Word-Masking based Robustly Optimized BERT pretraining approach with dictionary embedding entities recognition model for Chinese documents. By using multiple feature vectors generated by such as Roberta and domain dictionaries as embedding layers, the contextual semantic information of the text is fully considered. Meanwhile, Bi-directional Long Short-Term Memory(BiLSTM) and a multi-head attention mechanism are used to learn the information of long-distance dependency of the text. We use conditional random field(CRF) to obtain the global optimal annotation sequence, which is expected to improve the performance of the model. In this paper, we conduct comparison experiments with five baseline-based methods in the official document dataset of government affairs domain. The Precision of the model is 91.8%, Recall is 90.5%, and F1 value is 91.1%, which are better than other baseline models, indicating that the proposed model is more accurate for recognizing named entities in government documents

A Named Entity Recognition Method Enhanced with Lexicon Information and Text Local Feature

At present, Named Entity Recognition (NER) is one of the fundamental tasks for extracting knowledge from traditional Chinese medicine (TCM) texts. The variability of the length of TCM entities and the characteristics of the language of TCM texts lead to ambiguity of TCM entity boundaries. In addition, better extracting and exploiting local features of text can improve the accuracy of named entity recognition. In this paper, we proposed a TCM NER model with lexicon information and text local feature enhancement of text. In this model, a lexicon is introduced to encode the characters in the text to obtain the context-sensitive global semantic representation of the text. The convolutional neural network (CNN) and gate joined collaborative attention network are used to form a text local feature extraction module to capture the important semantic features of local text. Experiments were conducted on two TCM domain datasets and the F1 values are 91.13% and 90.21% respectively

BERT Based Clinical Knowledge Extraction for Biomedical Knowledge Graph Construction and Analysis

Background : Knowledge is evolving over time, often as a result of new discoveries or changes in the adopted methods of reasoning. Also, new facts or evidence may become available, leading to new understandings of complex phenomena. This is particularly true in the biomedical field, where scientists and physicians are constantly striving to find new methods of diagnosis, treatment and eventually cure. Knowledge Graphs (KGs) offer a real way of organizing and retrieving the massive and growing amount of biomedical knowledge. Objective : We propose an end-to-end approach for knowledge extraction and analysis from biomedical clinical notes using the Bidirectional Encoder Representations from Transformers (BERT) model and Conditional Random Field (CRF) layer. Methods : The approach is based on knowledge graphs, which can effectively process abstract biomedical concepts such as relationships and interactions between medical entities. Besides offering an intuitive way to visualize these concepts, KGs can solve more complex knowledge retrieval problems by simplifying them into simpler representations or by transforming the problems into representations from different perspectives. We created a biomedical Knowledge Graph using using Natural Language Processing models for named entity recognition and relation extraction. The generated biomedical knowledge graphs (KGs) are then used for question answering. Results : The proposed framework can successfully extract relevant structured information with high accuracy (90.7% for Named-entity recognition (NER), 88% for relation extraction (RE)), according to experimental findings based on real-world 505 patient biomedical unstructured clinical notes. Conclusions : In this paper, we propose a novel end-to-end system for the construction of a biomedical knowledge graph from clinical textual using a variation of BERT models

Comparative Analysis of Contextual Relation Extraction based on Deep Learning Models

Contextual Relation Extraction (CRE) is mainly used for constructing a knowledge graph with a help of ontology. It performs various tasks such as semantic search, query answering, and textual entailment. Relation extraction identifies the entities from raw texts and the relations among them. An efficient and accurate CRE system is essential for creating domain knowledge in the biomedical industry. Existing Machine Learning and Natural Language Processing (NLP) techniques are not suitable to predict complex relations from sentences that consist of more than two relations and unspecified entities efficiently. In this work, deep learning techniques have been used to identify the appropriate semantic relation based on the context from multiple sentences. Even though various machine learning models have been used for relation extraction, they provide better results only for binary relations, i.e., relations occurred exactly between the two entities in a sentence. Machine learning models are not suited for complex sentences that consist of the words that have various meanings. To address these issues, hybrid deep learning models have been used to extract the relations from complex sentence effectively. This paper explores the analysis of various deep learning models that are used for relation extraction.Comment: This Paper Presented in the International Conference on FOSS Approaches towards Computational Intelligence and Language TTechnolog on February 2023, Thiruvananthapura