scholarly journals Extracting Family History of Patients From Clinical Narratives: Exploring an End-to-End Solution With Deep Learning Models (Preprint)

2020 ◽  
Author(s):  
Xi Yang ◽  
Hansi Zhang ◽  
Xing He ◽  
Jiang Bian ◽  
Yonghui Wu
Keyword(s):  
Deep Learning ◽  
Family History ◽  
Information Extraction ◽  
Language Processing ◽  
Conditional Random Fields ◽  
Short Term Memory ◽  
Majority Voting ◽  
Learning Models ◽  
Concept Extraction ◽  
End To End

BACKGROUND Patients’ family history (FH) is a critical risk factor associated with numerous diseases. However, FH information is not well captured in the structured database but often documented in clinical narratives. Natural language processing (NLP) is the key technology to extract patients’ FH from clinical narratives. In 2019, the National NLP Clinical Challenge (n2c2) organized shared tasks to solicit NLP methods for FH information extraction. OBJECTIVE This study presents our end-to-end FH extraction system developed during the 2019 n2c2 open shared task as well as the new transformer-based models that we developed after the challenge. We seek to develop a machine learning–based solution for FH information extraction without task-specific rules created by hand. METHODS We developed deep learning–based systems for FH concept extraction and relation identification. We explored deep learning models including long short-term memory-conditional random fields and bidirectional encoder representations from transformers (BERT) as well as developed ensemble models using a majority voting strategy. To further optimize performance, we systematically compared 3 different strategies to use BERT output representations for relation identification. RESULTS Our system was among the top-ranked systems (3 out of 21) in the challenge. Our best system achieved micro-averaged F1 scores of 0.7944 and 0.6544 for concept extraction and relation identification, respectively. After challenge, we further explored new transformer-based models and improved the performances of both subtasks to 0.8249 and 0.6775, respectively. For relation identification, our system achieved a performance comparable to the best system (0.6810) reported in the challenge. CONCLUSIONS This study demonstrated the feasibility of utilizing deep learning methods to extract FH information from clinical narratives.

scholarly journals Extracting Family History of Patients From Clinical Narratives: Exploring an End-to-End Solution With Deep Learning Models

10.2196/22982 ◽  
2020 ◽  
Vol 8 (12) ◽  
pp. e22982
Author(s):  
Xi Yang ◽  
Hansi Zhang ◽  
Xing He ◽  
Jiang Bian ◽  
Yonghui Wu
Keyword(s):  
Deep Learning ◽  
Family History ◽  
Information Extraction ◽  
Language Processing ◽  
Conditional Random Fields ◽  
Short Term Memory ◽  
Majority Voting ◽  
Learning Models ◽  
Concept Extraction ◽  
End To End

Background Patients’ family history (FH) is a critical risk factor associated with numerous diseases. However, FH information is not well captured in the structured database but often documented in clinical narratives. Natural language processing (NLP) is the key technology to extract patients’ FH from clinical narratives. In 2019, the National NLP Clinical Challenge (n2c2) organized shared tasks to solicit NLP methods for FH information extraction. Objective This study presents our end-to-end FH extraction system developed during the 2019 n2c2 open shared task as well as the new transformer-based models that we developed after the challenge. We seek to develop a machine learning–based solution for FH information extraction without task-specific rules created by hand. Methods We developed deep learning–based systems for FH concept extraction and relation identification. We explored deep learning models including long short-term memory-conditional random fields and bidirectional encoder representations from transformers (BERT) as well as developed ensemble models using a majority voting strategy. To further optimize performance, we systematically compared 3 different strategies to use BERT output representations for relation identification. Results Our system was among the top-ranked systems (3 out of 21) in the challenge. Our best system achieved micro-averaged F1 scores of 0.7944 and 0.6544 for concept extraction and relation identification, respectively. After challenge, we further explored new transformer-based models and improved the performances of both subtasks to 0.8249 and 0.6775, respectively. For relation identification, our system achieved a performance comparable to the best system (0.6810) reported in the challenge. Conclusions This study demonstrated the feasibility of utilizing deep learning methods to extract FH information from clinical narratives.

scholarly journals A Tweet Sentiment Classification Approach Using a Hybrid Stacked Ensemble Technique

Information ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 374
Author(s):  
Babacar Gaye ◽  
Dezheng Zhang ◽  
Aziguli Wulamu
Keyword(s):  
Machine Learning ◽  
Logistic Regression ◽  
Deep Learning ◽  
Sentiment Analysis ◽  
Language Processing ◽  
Short Term Memory ◽  
State Of The Art ◽  
Accuracy Score ◽  
Learning Models ◽  
Proposed Model

With the extensive availability of social media platforms, Twitter has become a significant tool for the acquisition of peoples’ views, opinions, attitudes, and emotions towards certain entities. Within this frame of reference, sentiment analysis of tweets has become one of the most fascinating research areas in the field of natural language processing. A variety of techniques have been devised for sentiment analysis, but there is still room for improvement where the accuracy and efficacy of the system are concerned. This study proposes a novel approach that exploits the advantages of the lexical dictionary, machine learning, and deep learning classifiers. We classified the tweets based on the sentiments extracted by TextBlob using a stacked ensemble of three long short-term memory (LSTM) as base classifiers and logistic regression (LR) as a meta classifier. The proposed model proved to be effective and time-saving since it does not require feature extraction, as LSTM extracts features without any human intervention. We also compared our proposed approach with conventional machine learning models such as logistic regression, AdaBoost, and random forest. We also included state-of-the-art deep learning models in comparison with the proposed model. Experiments were conducted on the sentiment140 dataset and were evaluated in terms of accuracy, precision, recall, and F1 Score. Empirical results showed that our proposed approach manifested state-of-the-art results by achieving an accuracy score of 99%.

scholarly journals A Deep Learning Approach for the Romanized Tunisian Dialect Identification

2020 ◽  
Vol 17 (6) ◽  
pp. 935-946
Author(s):  
Jihene Younes ◽  
Hadhemi Achour ◽  
Emna Souissi ◽  
Ahmed Ferchichi
Keyword(s):  
Deep Learning ◽  
Language Processing ◽  
Conditional Random Fields ◽  
Short Term Memory ◽  
Learning Approach ◽  
Short Term ◽  
The Social ◽  
Long Short Term Memory ◽  
N Gram ◽  
Textual Content

Language identification is an important task in natural language processing that consists in determining the language of a given text. It has increasingly picked the interest of researchers for the past few years, especially for code-switching informal textual content. In this paper, we focus on the identification of the Romanized user-generated Tunisian dialect on the social web. We segment and annotate a corpus extracted from social media and propose a deep learning approach for the identification task. We use a Bidirectional Long Short-Term Memory neural network with Conditional Random Fields decoding (BLSTM-CRF). For word embeddings, we combine word-character BLSTM vector representation and Fast Text embeddings that takes into consideration character n-gram features. The overall accuracy obtained is 98.65%.

scholarly journals Deep learning models in detection of dietary supplement adverse event signals from Twitter

JAMIA Open ◽  
2021 ◽  
Vol 4 (4) ◽  
Author(s):  
Yefeng Wang ◽  
Yunpeng Zhao ◽  
Dalton Schutte ◽  
Jiang Bian ◽  
Rui Zhang
Keyword(s):  
Adverse Event ◽  
Deep Learning ◽  
Knowledge Base ◽  
Dietary Supplement ◽  
Relation Extraction ◽  
Learning Models ◽  
Concept Extraction ◽  
Annotation Guideline ◽  
End To End ◽  
Ae Signals

Abstract Objective The objective of this study is to develop a deep learning pipeline to detect signals on dietary supplement-related adverse events (DS AEs) from Twitter. Materials and Methods We obtained 247 807 tweets ranging from 2012 to 2018 that mentioned both DS and AE. We designed a tailor-made annotation guideline for DS AEs and annotated biomedical entities and relations on 2000 tweets. For the concept extraction task, we fine-tuned and compared the performance of BioClinical-BERT, PubMedBERT, ELECTRA, RoBERTa, and DeBERTa models with a CRF classifier. For the relation extraction task, we fine-tuned and compared BERT models to BioClinical-BERT, PubMedBERT, RoBERTa, and DeBERTa models. We chose the best-performing models in each task to assemble an end-to-end deep learning pipeline to detect DS AE signals and compared the results to the known DS AEs from a DS knowledge base (ie, iDISK). Results DeBERTa-CRF model outperformed other models in the concept extraction task, scoring a lenient microaveraged F1 score of 0.866. RoBERTa model outperformed other models in the relation extraction task, scoring a lenient microaveraged F1 score of 0.788. The end-to-end pipeline built on these 2 models was able to extract DS indication and DS AEs with a lenient microaveraged F1 score of 0.666. Conclusion We have developed a deep learning pipeline that can detect DS AE signals from Twitter. We have found DS AEs that were not recorded in an existing knowledge base (iDISK) and our proposed pipeline can as sist DS AE pharmacovigilance.

ASA: A framework for Arabic sentiment analysis

2019 ◽  
Vol 46 (4) ◽  
pp. 544-559 ◽  
Author(s):  
Ahmed Oussous ◽  
Fatima-Zahra Benjelloun ◽  
Ayoub Ait Lahcen ◽  
Samir Belfkih
Keyword(s):  
Deep Learning ◽  
Sentiment Analysis ◽  
Language Processing ◽  
Opinion Mining ◽  
Short Term Memory ◽  
Research Area ◽  
Support Vector ◽  
Learning Models ◽  
Arabic Natural Language Processing ◽  
Arabic Sentiment Analysis

Sentiment analysis (SA), also known as opinion mining, is a growing important research area. Generally, it helps to automatically determine if a text expresses a positive, negative or neutral sentiment. It enables to mine the huge increasing resources of shared opinions such as social networks, review sites and blogs. In fact, SA is used by many fields and for various languages such as English and Arabic. However, since Arabic is a highly inflectional and derivational language, it raises many challenges. In fact, SA of Arabic text should handle such complex morphology. To better handle these challenges, we decided to provide the research community and Arabic users with a new efficient framework for Arabic Sentiment Analysis (ASA). Our primary goal is to improve the performance of ASA by exploiting deep learning while varying the preprocessing techniques. For that, we implement and evaluate two deep learning models namely convolutional neural network (CNN) and long short-term memory (LSTM) models. The framework offers various preprocessing techniques for ASA (including stemming, normalisation, tokenization and stop words). As a result of this work, we first provide a new rich and publicly available Arabic corpus called Moroccan Sentiment Analysis Corpus (MSAC). Second, the proposed framework demonstrates improvement in ASA. In fact, the experimental results prove that deep learning models have a better performance for ASA than classical approaches (support vector machines, naive Bayes classifiers and maximum entropy). They also show the key role of morphological features in Arabic Natural Language Processing (NLP).

scholarly journals End-to-End Speech Recognition Using Recurrent Neural Network (RNN)

2021 ◽  
Author(s):  
Rene Avalloni de Morais ◽  
Baidya Nath Saha
Keyword(s):  
Deep Learning ◽  
Speech Recognition ◽  
Language Processing ◽  
High Performance ◽  
Short Term Memory ◽  
Learning Algorithms ◽  
Recognition System ◽  
End To End ◽  
Performance Computing

Deep learning algorithms have received dramatic progress in the area of natural language processing and automatic human speech recognition. However, the accuracy of the deep learning algorithms depends on the amount and quality of the data and training deep models requires high-performance computing resources. In this backdrop, this paper adresses an end-to-end speech recognition system where we finetune Mozilla DeepSpeech architecture using two different datasets: LibriSpeech clean dataset and Harvard speech dataset. We train Long Short Term Memory (LSTM) based deep Recurrent Neural Netowrk (RNN) models in Google Colab platform and use their GPU resources. Extensive experimental results demonstrate that Mozilla DeepSpeech model could be fine-tuned for different audio datasets to recognize speeches successfully.

scholarly journals Performance Analysis of Hybrid Deep Learning Models with Attention Mechanism Positioning and Focal Loss for Text Classification

2021 ◽  
Vol 2021 ◽  
pp. 1-12
Author(s):  
Sunil Kumar Prabhakar ◽  
Harikumar Rajaguru ◽  
Dong-Ok Won
Keyword(s):  
Deep Learning ◽  
Hybrid Model ◽  
Language Processing ◽  
Text Classification ◽  
Classification Accuracy ◽  
Short Term Memory ◽  
Learning Algorithm ◽  
Attention Mechanism ◽  
Learning Models ◽  
High Classification Accuracy

Over the past few decades, text classification problems have been widely utilized in many real time applications. Leveraging the text classification methods by means of developing new applications in the field of text mining and Natural Language Processing (NLP) is very important. In order to accurately classify tasks in many applications, a deeper insight into deep learning methods is required as there is an exponential growth in the number of complex documents. The success of any deep learning algorithm depends on its capacity to understand the nonlinear relationships of the complex models within data. Thus, a huge challenge for researchers lies in the development of suitable techniques, architectures, and models for text classification. In this paper, hybrid deep learning models, with an emphasis on positioning of attention mechanism analysis, are considered and analyzed well for text classification. The first hybrid model proposed is called convolutional Bidirectional Long Short-Term Memory (Bi-LSTM) with attention mechanism and output (CBAO) model, and the second hybrid model is called convolutional attention mechanism with Bi-LSTM and output (CABO) model. In the first hybrid model, the attention mechanism is placed after the Bi-LSTM, and then the output Softmax layer is constructed. In the second hybrid model, the attention mechanism is placed after convolutional layer and followed by Bi-LSTM and the output Softmax layer. The proposed hybrid models are tested on three datasets, and the results show that when the proposed CBAO model is implemented for IMDB dataset, a high classification accuracy of 92.72% is obtained and when the proposed CABO model is implemented on the same dataset, a high classification accuracy of 90.51% is obtained.

scholarly journals Compression of Deep Learning Models for Text: A Survey

2022 ◽  
Vol 16 (4) ◽  
pp. 1-55
Author(s):  
Manish Gupta ◽  
Puneet Agrawal
Keyword(s):  
Deep Learning ◽  
Language Processing ◽  
Short Term Memory ◽  
Response Times ◽  
Tensor Decomposition ◽  
Learning Models ◽  
Knowledge Distillation ◽  
Gated Recurrent Units ◽  
Work Done ◽  
Small Models

In recent years, the fields of natural language processing (NLP) and information retrieval (IR) have made tremendous progress thanks to deep learning models like Recurrent Neural Networks (RNNs), Gated Recurrent Units (GRUs) and Long Short-Term Memory (LSTMs) networks, and Transformer [ 121 ] based models like Bidirectional Encoder Representations from Transformers (BERT) [ 24 ], Generative Pre-training Transformer (GPT-2) [ 95 ], Multi-task Deep Neural Network (MT-DNN) [ 74 ], Extra-Long Network (XLNet) [ 135 ], Text-to-text transfer transformer (T5) [ 96 ], T-NLG [ 99 ], and GShard [ 64 ]. But these models are humongous in size. On the other hand, real-world applications demand small model size, low response times, and low computational power wattage. In this survey, we discuss six different types of methods (Pruning, Quantization, Knowledge Distillation (KD), Parameter Sharing, Tensor Decomposition, and Sub-quadratic Transformer-based methods) for compression of such models to enable their deployment in real industry NLP projects. Given the critical need of building applications with efficient and small models, and the large amount of recently published work in this area, we believe that this survey organizes the plethora of work done by the “deep learning for NLP” community in the past few years and presents it as a coherent story.

scholarly journals Clinical concept extraction using transformers

2020 ◽  
Vol 27 (12) ◽  
pp. 1935-1942
Author(s):  
Xi Yang ◽  
Jiang Bian ◽  
William R Hogan ◽  
Yonghui Wu
Keyword(s):  
Open Source ◽  
Language Processing ◽  
Conditional Random Fields ◽  
Short Term Memory ◽  
Concept Extraction ◽  
Clinical Models ◽  
Long Short Term Memory ◽  
Medical Domain ◽  
Public Datasets ◽  
Clinical Concept

Abstract Objective The goal of this study is to explore transformer-based models (eg, Bidirectional Encoder Representations from Transformers [BERT]) for clinical concept extraction and develop an open-source package with pretrained clinical models to facilitate concept extraction and other downstream natural language processing (NLP) tasks in the medical domain. Methods We systematically explored 4 widely used transformer-based architectures, including BERT, RoBERTa, ALBERT, and ELECTRA, for extracting various types of clinical concepts using 3 public datasets from the 2010 and 2012 i2b2 challenges and the 2018 n2c2 challenge. We examined general transformer models pretrained using general English corpora as well as clinical transformer models pretrained using a clinical corpus and compared them with a long short-term memory conditional random fields (LSTM-CRFs) mode as a baseline. Furthermore, we integrated the 4 clinical transformer-based models into an open-source package. Results and Conclusion The RoBERTa-MIMIC model achieved state-of-the-art performance on 3 public clinical concept extraction datasets with F1-scores of 0.8994, 0.8053, and 0.8907, respectively. Compared to the baseline LSTM-CRFs model, RoBERTa-MIMIC remarkably improved the F1-score by approximately 4% and 6% on the 2010 and 2012 i2b2 datasets. This study demonstrated the efficiency of transformer-based models for clinical concept extraction. Our methods and systems can be applied to other clinical tasks. The clinical transformer package with 4 pretrained clinical models is publicly available at https://github.com/uf-hobi-informatics-lab/ClinicalTransformerNER. We believe this package will improve current practice on clinical concept extraction and other tasks in the medical domain.

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