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.

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

2020 ◽  
Vol 6 ◽  
Author(s):  
David Owen ◽  
Quentin Groom ◽  
Alex Hardisty ◽  
Thijs Leegwater ◽  
Laurence Livermore ◽  
...  
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 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. We have highlighted the main recommendations for potential pipeline components. The paper 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.

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.

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.

Speech Master: Natural Language Processing and Deep Learning Approach for Automated Speech Evaluation

2021 ◽  
Author(s):  
K.G.C.M Kooragama ◽  
L.R.W.D. Jayashanka ◽  
J.A. Munasinghe ◽  
K.W. Jayawardana ◽  
Muditha Tissera ◽  
...  
Keyword(s):  
Deep Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Learning Approach ◽  
Speech Evaluation

Probing Patient Messages Enhanced by Natural Language Processing: A Top-Down Message Corpus Analysis

2021 ◽  
Vol 2021 ◽  
pp. 1-10
Author(s):  
George Mastorakos ◽  
Aditya Khurana ◽  
Ming Huang ◽  
Sunyang Fu ◽  
Ahmad P. Tafti ◽  
...  
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Named Entity Recognition ◽  
Corpus Analysis ◽  
Entity Recognition ◽  
Message Content ◽  
Named Entity ◽  
Medical Concepts ◽  
Insight Into

Background. Patients increasingly use asynchronous communication platforms to converse with care teams. Natural language processing (NLP) to classify content and automate triage of these messages has great potential to enhance clinical efficiency. We characterize the contents of a corpus of portal messages generated by patients using NLP methods. We aim to demonstrate descriptive analyses of patient text that can contribute to the development of future sophisticated NLP applications. Methods. We collected approximately 3,000 portal messages from the cardiology, dermatology, and gastroenterology departments at Mayo Clinic. After labeling these messages as either Active Symptom, Logistical, Prescription, or Update, we used NER (named entity recognition) to identify medical concepts based on the UMLS library. We hierarchically analyzed the distribution of these messages in terms of departments, message types, medical concepts, and keywords therewithin. Results. Active Symptom and Logistical content types comprised approximately 67% of the message cohort. The “Findings” medical concept had the largest number of keywords across all groupings of content types and departments. “Anatomical Sites” and “Disorders” keywords were more prevalent in Active Symptom messages, while “Drugs” keywords were most prevalent in Prescription messages. Logistical messages tended to have the lower proportions of “Anatomical Sites,”, “Disorders,”, “Drugs,”, and “Findings” keywords when compared to other message content types. Conclusions. This descriptive corpus analysis sheds light on the content and foci of portal messages. The insight into the content and differences among message themes can inform the development of more robust NLP models.

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