scholarly journals UMLS-based data augmentation for natural language processing of clinical research literature

2020 ◽  
Author(s):  
Tian Kang ◽  
Adler Perotte ◽  
Youlan Tang ◽  
Casey Ta ◽  
Chunhua Weng
Keyword(s):  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Data Augmentation ◽  
Training Data ◽  
Entity Recognition ◽  
Classification Model ◽  
Learning Models ◽  
Sentence Classification

Abstract Objective The study sought to develop and evaluate a knowledge-based data augmentation method to improve the performance of deep learning models for biomedical natural language processing by overcoming training data scarcity. Materials and Methods We extended the easy data augmentation (EDA) method for biomedical named entity recognition (NER) by incorporating the Unified Medical Language System (UMLS) knowledge and called this method UMLS-EDA. We designed experiments to systematically evaluate the effect of UMLS-EDA on popular deep learning architectures for both NER and classification. We also compared UMLS-EDA to BERT. Results UMLS-EDA enables substantial improvement for NER tasks from the original long short-term memory conditional random fields (LSTM-CRF) model (micro-F1 score: +5%, + 17%, and +15%), helps the LSTM-CRF model (micro-F1 score: 0.66) outperform LSTM-CRF with transfer learning by BERT (0.63), and improves the performance of the state-of-the-art sentence classification model. The largest gain on micro-F1 score is 9%, from 0.75 to 0.84, better than classifiers with BERT pretraining (0.82). Conclusions This study presents a UMLS-based data augmentation method, UMLS-EDA. It is effective at improving deep learning models for both NER and sentence classification, and contributes original insights for designing new, superior deep learning approaches for low-resource biomedical domains.

scholarly journals Obtaining Knowledge in Pathology Reports Through a Natural Language Processing Approach With Classification, Named-Entity Recognition, and Relation-Extraction Heuristics

2019 ◽  
pp. 1-8 ◽  
Author(s):  
Tomasz Oliwa ◽  
Steven B. Maron ◽  
Leah M. Chase ◽  
Samantha Lomnicki ◽  
Daniel V.T. Catenacci ◽  
...  
Keyword(s):  
Machine Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Classification Model ◽  
Supervised Machine Learning ◽  
Named Entity ◽  
Pathology Reports

PURPOSE Robust institutional tumor banks depend on continuous sample curation or else subsequent biopsy or resection specimens are overlooked after initial enrollment. Curation automation is hindered by semistructured free-text clinical pathology notes, which complicate data abstraction. Our motivation is to develop a natural language processing method that dynamically identifies existing pathology specimen elements necessary for locating specimens for future use in a manner that can be re-implemented by other institutions. PATIENTS AND METHODS Pathology reports from patients with gastroesophageal cancer enrolled in The University of Chicago GI oncology tumor bank were used to train and validate a novel composite natural language processing-based pipeline with a supervised machine learning classification step to separate notes into internal (primary review) and external (consultation) reports; a named-entity recognition step to obtain label (accession number), location, date, and sublabels (block identifiers); and a results proofreading step. RESULTS We analyzed 188 pathology reports, including 82 internal reports and 106 external consult reports, and successfully extracted named entities grouped as sample information (label, date, location). Our approach identified up to 24 additional unique samples in external consult notes that could have been overlooked. Our classification model obtained 100% accuracy on the basis of 10-fold cross-validation. Precision, recall, and F1 for class-specific named-entity recognition models show strong performance. CONCLUSION Through a combination of natural language processing and machine learning, we devised a re-implementable and automated approach that can accurately extract specimen attributes from semistructured pathology notes to dynamically populate a tumor registry.

scholarly journals Enhancing Natural Language Inference Using New and Expanded Training Data Sets and New Learning Models

2020 ◽  
Vol 34 (05) ◽  
pp. 8504-8511
Author(s):  
Arindam Mitra ◽  
Ishan Shrivastava ◽  
Chitta Baral
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Question Answering ◽  
Training Data ◽  
Data Sets ◽  
Learning Models ◽  
New Learning ◽  
Word Attention ◽  
Attention Function

Natural Language Inference (NLI) plays an important role in many natural language processing tasks such as question answering. However, existing NLI modules that are trained on existing NLI datasets have several drawbacks. For example, they do not capture the notion of entity and role well and often end up making mistakes such as “Peter signed a deal” can be inferred from “John signed a deal”. As part of this work, we have developed two datasets that help mitigate such issues and make the systems better at understanding the notion of “entities” and “roles”. After training the existing models on the new dataset we observe that the existing models do not perform well on one of the new benchmark. We then propose a modification to the “word-to-word” attention function which has been uniformly reused across several popular NLI architectures. The resulting models perform as well as their unmodified counterparts on the existing benchmarks and perform significantly well on the new benchmarks that emphasize “roles” and “entities”.

scholarly journals Automatic ICD-10 Coding and Training System: Deep Neural Network Based on Supervised Learning

10.2196/23230 ◽  
2021 ◽  
Vol 9 (8) ◽  
pp. e23230
Author(s):  
Pei-Fu Chen ◽  
Ssu-Ming Wang ◽  
Wei-Chih Liao ◽  
Lu-Cheng Kuo ◽  
Kuan-Chih Chen ◽  
...  
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Deep Neural Network ◽  
University Hospital ◽  
Classification Model ◽  
Icd 10 ◽  
And Training

Background The International Classification of Diseases (ICD) code is widely used as the reference in medical system and billing purposes. However, classifying diseases into ICD codes still mainly relies on humans reading a large amount of written material as the basis for coding. Coding is both laborious and time-consuming. Since the conversion of ICD-9 to ICD-10, the coding task became much more complicated, and deep learning– and natural language processing–related approaches have been studied to assist disease coders. Objective This paper aims at constructing a deep learning model for ICD-10 coding, where the model is meant to automatically determine the corresponding diagnosis and procedure codes based solely on free-text medical notes to improve accuracy and reduce human effort. Methods We used diagnosis records of the National Taiwan University Hospital as resources and apply natural language processing techniques, including global vectors, word to vectors, embeddings from language models, bidirectional encoder representations from transformers, and single head attention recurrent neural network, on the deep neural network architecture to implement ICD-10 auto-coding. Besides, we introduced the attention mechanism into the classification model to extract the keywords from diagnoses and visualize the coding reference for training freshmen in ICD-10. Sixty discharge notes were randomly selected to examine the change in the F1-score and the coding time by coders before and after using our model. Results In experiments on the medical data set of National Taiwan University Hospital, our prediction results revealed F1-scores of 0.715 and 0.618 for the ICD-10 Clinical Modification code and Procedure Coding System code, respectively, with a bidirectional encoder representations from transformers embedding approach in the Gated Recurrent Unit classification model. The well-trained models were applied on the ICD-10 web service for coding and training to ICD-10 users. With this service, coders can code with the F1-score significantly increased from a median of 0.832 to 0.922 (P<.05), but not in a reduced interval. Conclusions The proposed model significantly improved the F1-score but did not decrease the time consumed in coding by disease coders.

scholarly journals Towards a scientific workflow featuring Natural Language Processing for the digitisation of natural history collections

2020 ◽  
Vol 6 ◽  
Author(s):  
David Owen ◽  
Laurence Livermore ◽  
Quentin Groom ◽  
Alex Hardisty ◽  
Thijs Leegwater ◽  
...  
Keyword(s):  
Deep Learning ◽  
Natural Language Processing ◽  
Natural History ◽  
Natural Language ◽  
Language Processing ◽  
Scientific Workflow ◽  
Entity Recognition ◽  
Research Activities ◽  
Handwritten Text ◽  
Segmented Images

We describe an effective approach to automated text digitisation with respect to natural history specimen labels. These labels contain much useful data about the specimen including its collector, country of origin, and collection date. Our approach to automatically extracting these data takes the form of a pipeline. Recommendations are made for the pipeline's component parts based on some of the state-of-the-art technologies. Optical Character Recognition (OCR) can be used to digitise text on images of specimens. However, recognising text quickly and accurately from these images can be a challenge for OCR. We show that OCR performance can be improved by prior segmentation of specimen images into their component parts. This ensures that only text-bearing labels are submitted for OCR processing as opposed to whole specimen images, which inevitably contain non-textual information that may lead to false positive readings. In our testing Tesseract OCR version 4.0.0 offers promising text recognition accuracy with segmented images. Not all the text on specimen labels is printed. Handwritten text varies much more and does not conform to standard shapes and sizes of individual characters, which poses an additional challenge for OCR. Recently, deep learning has allowed for significant advances in this area. Google's Cloud Vision, which is based on deep learning, is trained on large-scale datasets, and is shown to be quite adept at this task. This may take us some way towards negating the need for humans to routinely transcribe handwritten text. Determining the countries and collectors of specimens has been the goal of previous automated text digitisation research activities. Our approach also focuses on these two pieces of information. An area of Natural Language Processing (NLP) known as Named Entity Recognition (NER) has matured enough to semi-automate this task. Our experiments demonstrated that existing approaches can accurately recognise location and person names within the text extracted from segmented images via Tesseract version 4.0.0. Potentially, NER could be used in conjunction with other online services, such as those of the Biodiversity Heritage Library to map the named entities to entities in the biodiversity literature (https://www.biodiversitylibrary.org/docs/api3.html). We have highlighted the main recommendations for potential pipeline components. The document also provides guidance on selecting appropriate software solutions. These include automatic language identification, terminology extraction, and integrating all pipeline components into a scientific workflow to automate the overall digitisation process.

Leveraging Natural Language Processing Applications Using Machine Learning

2020 ◽  
pp. 338-360
Author(s):  
Janjanam Prabhudas ◽  
C. H. Pradeep Reddy
Keyword(s):  
Machine Learning ◽  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Text Summarization ◽  
Feature Representation ◽  
Learning Models ◽  
Primary Focus ◽  
And Performance

The enormous increase of information along with the computational abilities of machines created innovative applications in natural language processing by invoking machine learning models. This chapter will project the trends of natural language processing by employing machine learning and its models in the context of text summarization. This chapter is organized to make the researcher understand technical perspectives regarding feature representation and their models to consider before applying on language-oriented tasks. Further, the present chapter revises the details of primary models of deep learning, its applications, and performance in the context of language processing. The primary focus of this chapter is to illustrate the technical research findings and gaps of text summarization based on deep learning along with state-of-the-art deep learning models for TS.

scholarly journals Using distant supervision to augment manually annotated data for relation extraction

2019 ◽  
Author(s):  
Peng Su ◽  
Gang Li ◽  
Cathy Wu ◽  
K. Vijay-Shanker
Keyword(s):  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Relation Extraction ◽  
Biomedical Literature ◽  
Training Data ◽  
Distant Supervision ◽  
Large Size ◽  
Domain Expertise

AbstractSignificant progress has been made in applying deep learning on natural language processing tasks recently. However, deep learning models typically require a large amount of annotated training data while often only small labeled datasets are available for many natural language processing tasks in biomedical literature. Building large-size datasets for deep learning is expensive since it involves considerable human effort and usually requires domain expertise in specialized fields. In this work, we consider augmenting manually annotated data with large amounts of data using distant supervision. However, data obtained by distant supervision is often noisy, we first apply some heuristics to remove some of the incorrect annotations. Then using methods inspired from transfer learning, we show that the resulting models outperform models trained on the original manually annotated sets.

Detection of Pneumothorax with Deep Learning Models: Learning From Radiologist Labels vs Natural Language Processing Model Generated Labels

2021 ◽  
Author(s):  
James Thomas Patrick Decourcy Hallinan ◽  
Mengling Feng ◽  
Dianwen Ng ◽  
Soon Yiew Sia ◽  
Vincent Tze Yang Tiong ◽  
...  
Keyword(s):  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Learning Models

scholarly journals Automatic Diagnosis of Spinal Disorders on Radiographic Images: Leveraging Existing Unstructured Datasets With Natural Language Processing

2021 ◽  
pp. 219256822110269
Author(s):  
Fabio Galbusera ◽  
Andrea Cina ◽  
Tito Bassani ◽  
Matteo Panico ◽  
Luca Maria Sconfienza
Keyword(s):  
Artificial Intelligence ◽  
Deep Learning ◽  
Natural Language Processing ◽  
Lumbar Spine ◽  
Natural Language ◽  
Language Processing ◽  
Large Set ◽  
Learning Models ◽  
Radiological Findings ◽  
Radiographic Images

Study Design: Retrospective study. Objectives: Huge amounts of images and medical reports are being generated in radiology departments. While these datasets can potentially be employed to train artificial intelligence tools to detect findings on radiological images, the unstructured nature of the reports limits the accessibility of information. In this study, we tested if natural language processing (NLP) can be useful to generate training data for deep learning models analyzing planar radiographs of the lumbar spine. Methods: NLP classifiers based on the Bidirectional Encoder Representations from Transformers (BERT) model able to extract structured information from radiological reports were developed and used to generate annotations for a large set of radiographic images of the lumbar spine (N = 10 287). Deep learning (ResNet-18) models aimed at detecting radiological findings directly from the images were then trained and tested on a set of 204 human-annotated images. Results: The NLP models had accuracies between 0.88 and 0.98 and specificities between 0.84 and 0.99; 7 out of 12 radiological findings had sensitivity >0.90. The ResNet-18 models showed performances dependent on the specific radiological findings with sensitivities and specificities between 0.53 and 0.93. Conclusions: NLP generates valuable data to train deep learning models able to detect radiological findings in spine images. Despite the noisy nature of reports and NLP predictions, this approach effectively mitigates the difficulties associated with the manual annotation of large quantities of data and opens the way to the era of big data for artificial intelligence in musculoskeletal radiology.

scholarly journals Deep Learning-Based Natural Language Processing in Radiology: The Impact of Report Complexity, Disease Prevalence, Dataset Size, and Algorithm Type on Model Performance

2021 ◽  
Vol 45 (10) ◽  
Author(s):  
A. W. Olthof ◽  
P. M. A. van Ooijen ◽  
L. J. Cornelissen
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Predictive Value ◽  
Training Data ◽  
Radiology Reports ◽  
Dataset Size ◽  
The Impact

AbstractIn radiology, natural language processing (NLP) allows the extraction of valuable information from radiology reports. It can be used for various downstream tasks such as quality improvement, epidemiological research, and monitoring guideline adherence. Class imbalance, variation in dataset size, variation in report complexity, and algorithm type all influence NLP performance but have not yet been systematically and interrelatedly evaluated. In this study, we investigate these factors on the performance of four types [a fully connected neural network (Dense), a long short-term memory recurrent neural network (LSTM), a convolutional neural network (CNN), and a Bidirectional Encoder Representations from Transformers (BERT)] of deep learning-based NLP. Two datasets consisting of radiologist-annotated reports of both trauma radiographs (n = 2469) and chest radiographs and computer tomography (CT) studies (n = 2255) were split into training sets (80%) and testing sets (20%). The training data was used as a source to train all four model types in 84 experiments (Fracture-data) and 45 experiments (Chest-data) with variation in size and prevalence. The performance was evaluated on sensitivity, specificity, positive predictive value, negative predictive value, area under the curve, and F score. After the NLP of radiology reports, all four model-architectures demonstrated high performance with metrics up to > 0.90. CNN, LSTM, and Dense were outperformed by the BERT algorithm because of its stable results despite variation in training size and prevalence. Awareness of variation in prevalence is warranted because it impacts sensitivity and specificity in opposite directions.

scholarly journals Deep learning in clinical natural language processing: a methodical review

2019 ◽  
Vol 27 (3) ◽  
pp. 457-470 ◽  
Author(s):  
Stephen Wu ◽  
Kirk Roberts ◽  
Surabhi Datta ◽  
Jingcheng Du ◽  
Zongcheng Ji ◽  
...  
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Computational Linguistics ◽  
Language Processing ◽  
Recurrent Neural Networks ◽  
Named Entity Recognition ◽  
Entity Recognition ◽  
Named Entity

Abstract Objective 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. Materials and Methods 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. Results 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. Discussion 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). Conclusion 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.

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