Entity recognition from clinical texts via recurrent neural network

Word embeddings have become the predominant representation scheme on a token-level for various clinical natural language processing (NLP) tasks. More recently, character-level neural language models, exploiting recurrent neural networks, have again received attention, because they achieved similar performance against various NLP benchmarks. We investigated to what extent character-based language models can be applied to the clinical domain and whether they are able to capture reasonable lexical semantics using this maximally fine-grained representation scheme. We trained a long short-term memory network on an excerpt from a table of de-identified 50-character long problem list entries in German, each of which assigned to an ICD-10 code. We modelled the task as a time series of one-hot encoded single character inputs. After the training phase we accessed the top 10 most similar character-induced word embeddings related to a clinical concept via a nearest neighbour search and evaluated the expected interconnected semantics. Results showed that traceable semantics were captured on a syntactic level above single characters, addressing the idiosyncratic nature of clinical language. The results support recent work on general language modelling that raised the question whether token-based representation schemes are still necessary for specific NLP tasks.

Evaluation of clinical named entity recognition methods for Serbian electronic health records

This article methodically reviews the literature on deep learning (DL) for natural language processing (NLP) in the clinical domain, providing quantitative analysis to answer 3 research questions concerning methods, scope, and context of current research. We searched MEDLINE, EMBASE, Scopus, the Association for Computing Machinery Digital Library, and the Association for Computational Linguistics Anthology for articles using DL-based approaches to NLP problems in electronic health records. After screening 1,737 articles, we collected data on 25 variables across 212 papers. DL in clinical NLP publications more than doubled each year, through 2018. Recurrent neural networks (60.8%) and word2vec embeddings (74.1%) were the most popular methods; the information extraction tasks of text classification, named entity recognition, and relation extraction were dominant (89.2%). However, there was a "long tail" of other methods and specific tasks. Most contributions were methodological variants or applications, but 20.8% were new methods of some kind. The earliest adopters were in the NLP community, but the medical informatics community was the most prolific. Our analysis shows growing acceptance of deep learning as a baseline for NLP research, and of DL-based NLP in the medical community. A number of common associations were substantiated (eg, the preference of recurrent neural networks for sequence-labeling named entity recognition), while others were surprisingly nuanced (eg, the scarcity of French language clinical NLP with deep learning). Deep learning has not yet fully penetrated clinical NLP and is growing rapidly. This review highlighted both the popular and unique trends in this active field.

ObjectivePituitary adenomas are the most common type of pituitary disorders, which usually occur in young adults and often affect the patient’s physical development, labor capacity and fertility. Clinical free texts noted in electronic medical records (EMRs) of pituitary adenomas patients contain abundant diagnosis and treatment information. However, this information has not been well utilized because of the challenge to extract information from unstructured clinical texts. This study aims to enable machines to intelligently process clinical information, and automatically extract clinical named entity for pituitary adenomas from Chinese EMRs.MethodsThe clinical corpus used in this study was from one pituitary adenomas neurosurgery treatment center of a 3A hospital in China. Four types of fine-grained texts of clinical records were selected, which included notes from present illness, past medical history, case characteristics and family history of 500 pituitary adenoma inpatients. The dictionary-based matching, conditional random fields (CRF), bidirectional long short-term memory with CRF (BiLSTM-CRF), and bidirectional encoder representations from transformers with BiLSTM-CRF (BERT-BiLSTM-CRF) were used to extract clinical entities from a Chinese EMRs corpus. A comprehensive dictionary was constructed based on open source vocabularies and a domain dictionary for pituitary adenomas to conduct the dictionary-based matching method. We selected features such as part of speech, radical, document type, and the position of characters to train the CRF-based model. Random character embeddings and the character embeddings pretrained by BERT were used respectively as the input features for the BiLSTM-CRF model and the BERT-BiLSTM-CRF model. Both strict metric and relaxed metric were used to evaluate the performance of these methods.ResultsExperimental results demonstrated that the deep learning and other machine learning methods were able to automatically extract clinical named entities, including symptoms, body regions, diseases, family histories, surgeries, medications, and disease courses of pituitary adenomas from Chinese EMRs. With regard to overall performance, BERT-BiLSTM-CRF has the highest strict F1 value of 91.27% and the highest relaxed F1 value of 95.57% respectively. Additional evaluations showed that BERT-BiLSTM-CRF performed best in almost all entity recognition except surgery and disease course. BiLSTM-CRF performed best in disease course entity recognition, and performed as well as the CRF model for part of speech, radical and document type features, with both strict and relaxed F1 value reaching 96.48%. The CRF model with part of speech, radical and document type features performed best in surgery entity recognition with relaxed F1 value of 95.29%.ConclusionsIn this study, we conducted four entity recognition methods for pituitary adenomas based on Chinese EMRs. It demonstrates that the deep learning methods can effectively extract various types of clinical entities with satisfying performance. This study contributed to the clinical named entity extraction from Chinese neurosurgical EMRs. The findings could also assist in information extraction in other Chinese medical texts.

Chinese clinical named entity recognition via multi-head self-attention based BiLSTM-CRF

BackgroundClinical entity recognition as a fundamental task of clinical text processing has been attracted a great deal of attention during the last decade. However, most studies focus on clinical text in English rather than other languages. Recently, a few researchers have began to study entity recognition in Chinese clinical text.MethodsIn this paper, a novel deep neural network, called attention-based CNN-LSTM-CRF, is proposed to recognize entities in Chinese clinical text. Attention-based CNN-LSTM-CRF is an extension of LSTM-CRF by introducing a CNN (convolutional neural network) layer after the input layer to capture local context information of words of interest and an attention layer before the CRF layer to select relevant words in the same sentence.ResultsIn order to evaluate the proposed method, we compare it with other two currently popular methods, CRF (conditional random field) and LSTM-CRF, on two benchmark datasets. One of the datasets is publically available and only contains contiguous clinical entities, and the other one is constructed by us and contains contiguous and discontiguous clinical entities. Experimental results show that attention-based CNN-LSTM-CRF outperforms CRF and LSTM-CRF.ConclusionsCNN and attention mechanism are individually beneficial to LSTM-CRF-based Chinese clinical entity recognition system, no matter whether contiguous clinical entities are considered. The conribution of attention mechanism is greater than CNN.

Sequence Classification is one of the on-demand research projects in the field of Natural Language Processing (NLP). Classifying a set of images or text into an appropriate category or class is a complex task that a lot of Machine Learning (ML) models fail to accomplish accurately and end up under-fitting the given dataset. Some of the ML algorithms used in text classification are KNN, Naïve Bayes, Support Vector Machines, Convolutional Neural Networks (CNNs), Recursive CNNs, Recurrent Neural Networks (RNNs), Long Short Term Memory (LSTM), etc. For this experimental study, LSTM and a few other algorithms were chosen for a more comparative study. The dataset used is the SMS Spam Collection Dataset from Kaggle and 150 more entries were additionally added from different sources. Two possible class labels for the data points are spam and ham. Each entry consists of the class label, a few sentences of text followed by a few useless features that are eliminated. After converting the text to the required format, the models are run and then evaluated using various metrics. In experimental studies, the LSTM gives much better classification accuracy than the other machine learning models. F1-Scores in the high nineties were achieved using LSTM for classifying the text. The other models showed very low F1-Scores and Cosine Similarities indicating that they had underperformed on the dataset. Another interesting observation is that the LSTM had reduced the number of false positives and false negatives than any other model.

The Army Rapid Capabilities Office (RCO) sponsored a Blind Signal Classification Competition seeking algorithms to automatically identify the modulation schemes of RF signal from complex-valued IQ (in-phase quadrature) samples. Traditional spectrum sensing technology uses energy detection to detect the existence of RF signals but the RCO competition further aimed to detect the modulation scheme of signals without prior information. Machine Learning (ML) technologies have been widely used for blind signal classification problem. Traditional ML methods usually have two stages where the first stage is to manually extract the features of the IQ symbols by subject matter experts and the second stage is to feed the features to an ML algorithm (e.g., a support vector machine) to develop the classifier. The state-of-art technology is to apply deep learning technologies such as Convolutional Neural Network (CNN) or Recurrent Neural Network (RNN) directly to the complex-value IQ symbols to train a multi-class classifier. Our team, dubbed Deep Dreamers, participated in the RCO competition and placed 3rd out of 42 active teams across industry, academia, and government. In this work we share our experience and lessons learned from the competition. Deep learning methods such as CNN, Residual Neural Network (ResNet), and Long Short-Term Memory (LSTM) are the fundamental neural network layers we used to develop a multi-class classifier. None of our individual models were able to achieve a competitively high ranking in the competition. The key to our success was to use ensemble learning to average the outputs of multiple diverse classifiers. In order for ensemble methods to be more accurate than any of its base models; the base learners have to be as accurate as possible. We found that while ResNet was more accurate than the LSTM; the LSTM was less sensitive to deviations in the test set.

Machine Learning (ML) technologies have been widely used for blind signal classification problem (Modulation Classification) to automatically identify the modulation schemes of Radio Frequency (RF) signal from complex- valued IQ (In-phase Quadrature) samples. Traditional ML methods usually have two stages where the first stage is to manually extract the features of the IQ symbols by subject matter experts and the second stage is to feed the features to an ML algorithm (e.g., a support vector machine) to develop the classifier. The state- of-art technology is to apply Deep Learning (DL) technologies such as Convolutional Neural Network (CNN) or Recurrent Neural Network (RNN) directly to the complex-value IQ symbols to train a multi-class classifier. In this effort we are focused on the modulation and coding rate classification problems for multi-carrier Orthogonal Frequency-Division Multiplexing (OFDM) signals. The generated OFDM data set consists of over 480k instances across four different modulations and three different coding rates which include BPSK + 1=2, BPSK+3=4, QPSK+1=2, QPSK+3=4, QAM16+1=2, QAM16+3=4, QAM64+2=3 and QAM64+3=4. Deep Learning (DL) models can successfully catch the features of OFDM modulations and identify the modulation scheme from the baseband IQ symbols. Four DL models including Residual Neural Network 34(Resnet34), Resnet18, Squeezenet and Long Short-Term Memory (LSTM) trained over the data set can achieve over 94% overall accuracy for signals across 􀀀10dB to 10dB with step size of 4dB. Among them, Squeezenet and LSTM models have much smaller model sizes which can be easily loaded in resource-limited edge computing platforms. To the best of our knowledge, coding rate classification of OFDM signals has not been studied in previous works. Therefore, three different DL models including a single-stage coding rate classifier, a combination of modulation and coding rate classifier, and a two-stage coding rate classifier are developed to identify the coding rate. However, coding rates can only be identified for low-order modulation schemes BPSK and QPSK but not for high-order modulation schemes QAM16 and QAM64. Further investigation is needed to understand the coding rate classification for high-order QAM signals.

Protein lysine acetylation is an important post- translational modification (PTM) that takes an important part in many cellular processes, such as metabolism, differentiation and replication. However, the current lysine acetylation site identification mainly adopts experimental detection methods which are time-consuming and inefficient. Therefore, several shallow machine learning algorithms were applied for protein lysine acetylation site prediction. However, traditional machine learning algorithms are not as accurate as deep learning algorithms. As a special kind of recurrent neural network (RNN), long short-term memory (LSTM) can not only process sequence data but also solve the vanishing gradient problem. Therefore, this paper proposes a method based on LSTM to predict lysine acetylation sites. In addition, two traditional machine learning algorithms k-nearest neighbors (KNN) and support vector machine (SVM) were adopted for training as comparison. Through experimental verification, the prediction method based on LSTM is superior to the other two based on traditional machine learning algorithms, and the final prediction accuracy of LSTM model can reach up to 81.52%.

Detecting previously unseen named entities in text is a challenging task. The paper describes how three initial classifier models were built using Conditional Random Fields (CRFs), Support Vector Machines (SVMs) and a Long Short-Term Memory (LSTM) recurrent neural network. The outputs of these three classifiers were then used as features to train another CRF classifier working as an ensemble. 5-fold cross-validation based on training and development data for the emerging and rare named entity recognition shared task showed precision, recall and F1-score of 66.87%, 46.75% and 54.97%, respectively. For surface form evaluation, the CRF ensemble-based system achieved precision, recall and F1 scores of 65.18%, 45.20% and 53.30%. When applied to unseen test data, the model reached 47.92% precision, 31.97% recall and 38.55% F1-score for entity level evaluation, with the corresponding surface form evaluation values of 44.91%, 30.47% and 36.31%.

Chunks play an important role in applied linguistics, such as Teaching English as a Second Language (TESL) and Computer-Aided Translation (CAT). Although corpora have already been widely used in the areas mentioned above, annotation and recognition of chunks are mainly done manually. Computer- and linguistic-based chunk recognition is significant in natural language processing (NLP). This paper briefly introduced the intelligent recognition of English chunks and applied the Recurrent Neural Network (RNN) to recognise chunks. To strengthen the RNN, it was improved by Long Short Term Memory (LSTM) for recognising English chunk. The LSTM-RNN was compared with support vector machine (SVM) and RNN in simulation experiments. The results suggested that the performance of the LSTM-RNN was always the highest when dealing with English texts, no matter whether it was trained using a general corpus or a corpus of specialised domain knowledge.

Artificial Intelligence (AI) has recently emerged as a powerful tool with versatile applications spanning various domains. AI replicates human intelligence processes through machinery and computer systems, finding utility in expert systems, image and speech recognition, machine vision, and natural language processing (NLP). One notable area with limited exploration pertains to using deep learning models, specifically Recurrent Neural Networks (RNNs), for predicting water quality in wastewater treatment plants (WWTPs). RNNs are purpose-built for handling sequential data, featuring a feedback mechanism. However, standard RNNs may exhibit limitations in accommodating both short-term and long-term dependencies when addressing intricate time series problems. The solution to this challenge lies in adopting Long Short-Term Memory (LSTM) cells, known for their inherent memory management through a ‘forget gate’ mechanism. In general, LSTM architecture demonstrates superior performance. WWTP data represent a historical series influenced by fluctuating environmental conditions. This study employs simple RNNs and LSTM architecture to construct prediction models for effluent parameters, systematically assessing their performance through various training data scenarios and model architectures. The primary objective was to determine the most suitable WWTP dataset model. The study revealed that an epoch setting of 50 and a batch size of 100 yielded the lowest training time and root mean square error (RMSE) values for both RNN and LSTM models. Furthermore, when these models are applied to predict effluent parameters, they exhibit precise RMSE values for all parameters. The study results can be applied to detect potential upsets in WWTP operations.

Prediction of volatile composition of coal pyrolysis under various swelling and catalytic conditions based on recurrent neural network

Prediction concept needs human-like thinking and ideas. ANN helps make a program for describing the solutions to the prediction problems. To gain accurate prediction, there is a need for deep thinking in the knowledge system discovered. Deep learning helps form such next-level type of ANN thinking. Deep learning models do not require humans for programming the problems. It can determine the prediction by itself by learning the dataset. This paper describes the prediction by considering sequential model for continuous accessing of data with the help of multi-layers. Deep learning is very helpful for predicting larger dataset. This paper proposes an algorithmic model known as a Comprehensive Deep Recurrent Artificial Neural Networks (CDRANN) by hybridizing LSTM (long short-term memory) with RNN (recurrent neural network) backtrack solver for better future stock prediction. This paper also explains the need for hybridizing evolutionary model CDRANN to create a novel change in future prediction.KeywordsCDRANN (Comprehensive Deep Recurrent Artificial Neural Networks)LSTM (long short-term memory)RNN (recurrent neural network)Stock marketPrediction