scholarly journals Identifying Chemical Reactions and Their Associated Attributes in Patents

2021 ◽  
Vol 6 ◽  
Author(s):  
Darshini Mahendran ◽  
Gabrielle Gurdin ◽  
Nastassja Lewinski ◽  
Christina Tang ◽  
Bridget T. McInnes
Keyword(s):  
Chemical Reactions ◽  
Chemical Reaction ◽  
Short Term Memory ◽  
Named Entity Recognition ◽  
Event Extraction ◽  
Entity Recognition ◽  
Automatic Identification ◽  
Named Entity ◽  
Long Short Term Memory ◽  
Source Of Information

Chemical patents are an essential source of information about novel chemicals and chemical reactions. However, with the increasing volume of such patents, mining information about these chemicals and chemical reactions has become a time-intensive and laborious endeavor. In this study, we present a system to extract chemical reaction events from patents automatically. Our approach consists of two steps: 1) named entity recognition (NER)—the automatic identification of chemical reaction parameters from the corresponding text, and 2) event extraction (EE)—the automatic classifying and linking of entities based on their relationships to each other. For our NER system, we evaluate bidirectional long short-term memory (BiLSTM)-based and bidirectional encoder representations from transformer (BERT)-based methods. For our EE system, we evaluate BERT-based, convolutional neural network (CNN)-based, and rule-based methods. We evaluate our NER and EE components independently and as an end-to-end system, reporting the precision, recall, and F1 score. Our results show that the BiLSTM-based method performed best at identifying the entities, and the CNN-based method performed best at extracting events.

scholarly journals Pengenalan Entitas Bernama Otomatis untuk Bahasa Indonesia dengan Pendekatan Pembelajaran Mesin

2018 ◽  
Author(s):  
Yudi Wibisono ◽  
Masayu Leylia Khodra
Keyword(s):  
Short Term Memory ◽  
Conditional Random Field ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Short Term ◽  
Term Memory ◽  
Named Entity ◽  
Long Short Term Memory ◽  
F Measure ◽  
Bahasa Indonesia

Pengenalan entitas bernama (named-entity recognition atau NER) adalah proses otomatis mengekstraksi entitas bernama yang dianggap penting di dalam sebuah teks dan menentukan kategorinya ke dalam kategori terdefinisi. Sebagai contoh, untuk teks berita, NER dapat mengekstraksi nama orang, nama organisasi, dan nama lokasi. NER bermanfaat dalam berbagai aplikasi analisis teks, misalnya pencarian, sistem tanya jawab, peringkasan teks dan mesin penerjemah. Tantangan utama NER adalah penanganan ambiguitas makna karena konteks kata pada kalimat, misalnya kata “Cendana” dapat merupakan nama lokasi (Jalan Cendana), atau nama organisasi (Keluarga Cendana), atau nama tanaman. Tantangan lainnya adalah penentuan batas entitas, misalnya “[Istora Senayan] [Jakarta]”. Berbagai kakas NER telah dikembangkan untuk berbagai bahasa terutama Bahasa Inggris dengan kinerja yang baik, tetapi kakas NER bahasa Indonesia masih memiliki kinerja yang belum baik. Makalah ini membahas pendekatan berbasis pembelajaran mesin untuk menghasilkan model NER bahasa Indonesia. Pendekatan ini sangat bergantung pada korpus yang menjadi sumber belajar, dan teknik pembelajaran mesin yang digunakan. Teknik yang akan digunakan adalah LSTM - CRF (Long Short Term Memory – Conditional Random Field). Hasil terbaik (F-measure = 0.72) didapatkan dengan menggunakan word embedding GloVe Wikipedia Bahasa Indonesia.

scholarly journals Biomedical named entity recognition using deep neural networks with contextual information

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Hyejin Cho ◽  
Hyunju Lee
Keyword(s):  
Deep Learning ◽  
Short Term Memory ◽  
Contextual Information ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Learning Approaches ◽  
Short Term ◽  
Term Memory ◽  
Named Entity ◽  
Long Short Term Memory

Abstract Background In 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. Results We 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. Conclusion The proposed approach is robust in recognizing biological entities in text.

scholarly journals Chinese Named Entity Recognition Method in History and Culture Field Based on BERT

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Shuang Liu ◽  
Hui Yang ◽  
Jiayi Li ◽  
Simon Kolmanič
Keyword(s):  
Short Term Memory ◽  
Conditional Random Field ◽  
Language Model ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Knowledge Graph ◽  
Recognition Method ◽  
Short Term ◽  
Named Entity ◽  
Long Short Term Memory

AbstractWith rapid development of the Internet, people have undergone tremendous changes in the way they obtain information. In recent years, knowledge graph is becoming a popular tool for the public to acquire knowledge. For knowledge graph of Chinese history and culture, most researchers adopted traditional named entity recognition methods to extract entity information from unstructured historical text data. However, the traditional named entity recognition method has certain defects, and it is easy to ignore the association between entities. To extract entities from a large amount of historical and cultural information more accurately and efficiently, this paper proposes one named entity recognition model combining Bidirectional Encoder Representations from Transformers and Bidirectional Long Short-Term Memory-Conditional Random Field (BERT-BiLSTM-CRF). First, a BERT pre-trained language model is used to encode a single character to obtain a vector representation corresponding to each character. Then one Bidirectional Long Short-Term Memory (BiLSTM) layer is applied to semantically encode the input text. Finally, the label with the highest probability is output through the Conditional Random Field (CRF) layer to obtain each character’s category. This model uses the Bidirectional Encoder Representations from Transformers (BERT) pre-trained language model to replace the static word vectors trained in the traditional way. In comparison, the BERT pre-trained language model can dynamically generate semantic vectors according to the context of words, which improves the representation ability of word vectors. The experimental results prove that the model proposed in this paper has achieved excellent results in the task of named entity recognition in the field of historical culture. Compared with the existing named entity identification methods, the precision rate, recall rate, and $$F_1$$ F 1 value have been significantly improved.

scholarly journals Chinese Clinical Named Entity Recognition in Electronic Medical Records: Development of a Lattice Long Short-Term Memory Model With Contextualized Character Representations (Preprint)

2020 ◽  
Author(s):  
Yongbin Li ◽  
Xiaohua Wang ◽  
Linhu Hui ◽  
Liping Zou ◽  
Hongjin Li ◽  
...  
Keyword(s):  
Electronic Medical Records ◽  
Medical Records ◽  
Short Term Memory ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Language Models ◽  
Short Term ◽  
Term Memory ◽  
Named Entity ◽  
Long Short Term Memory

BACKGROUND Clinical named entity recognition (CNER), whose goal is to automatically identify clinical entities in electronic medical records (EMRs), is an important research direction of clinical text data mining and information extraction. The promotion of CNER can provide support for clinical decision making and medical knowledge base construction, which could then improve overall medical quality. Compared with English CNER, and due to the complexity of Chinese word segmentation and grammar, Chinese CNER was implemented later and is more challenging. OBJECTIVE With the development of distributed representation and deep learning, a series of models have been applied in Chinese CNER. Different from the English version, Chinese CNER is mainly divided into character-based and word-based methods that cannot make comprehensive use of EMR information and cannot solve the problem of ambiguity in word representation. METHODS In this paper, we propose a lattice long short-term memory (LSTM) model combined with a variant contextualized character representation and a conditional random field (CRF) layer for Chinese CNER: the Embeddings from Language Models (ELMo)-lattice-LSTM-CRF model. The lattice LSTM model can effectively utilize the information from characters and words in Chinese EMRs; in addition, the variant ELMo model uses Chinese characters as input instead of the character-encoding layer of the ELMo model, so as to learn domain-specific contextualized character embeddings. RESULTS We evaluated our method using two Chinese CNER datasets from the China Conference on Knowledge Graph and Semantic Computing (CCKS): the CCKS-2017 CNER dataset and the CCKS-2019 CNER dataset. We obtained F1 scores of 90.13% and 85.02% on the test sets of these two datasets, respectively. CONCLUSIONS Our results show that our proposed method is effective in Chinese CNER. In addition, the results of our experiments show that variant contextualized character representations can significantly improve the performance of the model.

Sign in / Sign up

Export Citation Format

Share Document