ARGO, Automatic Record Generator for Oncology: a natural language process-based tool to capture pathology features from onco-hematological reports (Preprint)

2021 ◽  
Author(s):  
Gian Maria Zaccaria ◽  
Vito Colella ◽  
Simona Colucci ◽  
Felice Clemente ◽  
Fabio Pavone ◽  
...  
Keyword(s):  
Natural Language ◽  
Translational Research ◽  
Language Processing ◽  
Character Recognition ◽  
Web Application ◽  
Optical Character Recognition ◽  
Anatomical Site ◽  
Cell Of Origin ◽  
Molecular Features ◽  
Clinical And Translational Research

BACKGROUND The unstructured nature of medical data from Real-World (RW) patients and the scarce accessibility for researchers to integrated systems restrain the use of RW information for clinical and translational research purposes. Natural Language Processing (NLP) might help in transposing unstructured reports in electronic health records (EHR), thus prompting their standardization and sharing. OBJECTIVE We aimed at designing a tool to capture pathological features directly from hemo-lymphopathology reports and automatically record them into electronic case report forms (eCRFs). METHODS We exploited Optical Character Recognition and NLP techniques to develop a web application, named ARGO (Automatic Record Generator for Oncology), that recognizes unstructured information from diagnostic paper-based reports of diffuse large B-cell lymphomas (DLBCL), follicular lymphomas (FL), and mantle cell lymphomas (MCL). ARGO was programmed to match data with standard diagnostic criteria of the National Institute of Health, automatically assign diagnosis and, via Application Programming Interface, populate specific eCRFs on the REDCap platform, according to the College of American Pathologists templates. A selection of 239 reports (n. 106 DLBCL, n.79 FL, and n. 54 MCL) from the Pathology Unit at the IRCCS - Istituto Tumori “Giovanni Paolo II” of Bari (Italy) was used to assess ARGO performance in terms of accuracy, precision, recall and F1-score. RESULTS By applying our workflow, we successfully converted 233 paper-based reports into corresponding eCRFs incorporating structured information about diagnosis, tissue of origin and anatomical site of the sample, major molecular markers and cell-of-origin subtype. Overall, ARGO showed high performance (nearly 90% of accuracy, precision, recall and F1-score) in capturing identification report number, biopsy date, specimen type, diagnosis, and additional molecular features. CONCLUSIONS We developed and validated an easy-to-use tool that converts RW paper-based diagnostic reports of major lymphoma subtypes into structured eCRFs. ARGO is cheap, feasible, and easily transferable into the daily practice to generate REDCap-based EHR for clinical and translational research purposes.

scholarly journals Image Spam Detection Using Machine Learning and Natural Language Processing

2020 ◽  
Vol 55 (2) ◽  
Author(s):  
Yaseen Khather Yaseen ◽  
Alaa Khudhair Abbas ◽  
Ahmed M. Sana
Keyword(s):  
Machine Learning ◽  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Character Recognition ◽  
Optical Character Recognition ◽  
Learning Algorithm ◽  
Machine Learning Algorithm ◽  
Optical Character ◽  
Harmful Content

Today, images are a part of communication between people. However, images are being used to share information by hiding and embedding messages within it, and images that are received through social media or emails can contain harmful content that users are not able to see and therefore not aware of. This paper presents a model for detecting spam on images. The model is a combination of optical character recognition, natural language processing, and the machine learning algorithm. Optical character recognition extracts the text from images, and natural language processing uses linguistics capabilities to detect and classify the language, to distinguish between normal text and slang language. The features for selected images are then extracted using the bag-of-words model, and the machine learning algorithm is run to detect any kind of spam that may be on it. Finally, the model can predict whether or not the image contains any harmful content. The results show that the proposed method using a combination of the machine learning algorithm, optical character recognition, and natural language processing provides high detection accuracy compared to using machine learning alone.

A Finding Aid for The Equity

2018 ◽  
Author(s):  
Jeff Blackadar
Keyword(s):  
Language Processing ◽  
Character Recognition ◽  
Optical Character Recognition ◽  
Large Collection ◽  
Digital History ◽  
R Language ◽  
Potential Value ◽  
Optical Character ◽  
Text Searching ◽  
Person Location

Bibliothèque et Archives Nationales du Québec digitally scanned and converted to text a large collection of newspapers to create a resource of tremendous potential value to historians. Unfortunately, the text files are difficult to search reliably due to many errors caused by the optical character recognition (OCR) text conversion process. This digital history project applied natural language processing in an R language computer program to create a new and useful index of this corpus of digitized content despite OCR related errors. The project used editions of The Equity, published in Shawville, Quebec since 1883. The program extracted the names of all the person, location and organization entities that appeared in each edition. Each of the entities was cataloged in a database and related to the edition of the newspaper it appeared in. The database was published to a public website to allow other researchers to use it. The resulting index or finding aid allows researchers to access The Equity in a different way than just full text searching. People, locations and organizations appearing in the Equity are listed on the website and each entity links to a page that lists all of the issues that entity appeared in as well as the other entities that may be related to it. Rendering the text files of each scanned newspaper into entities and indexing them in a database allows the content of the newspaper to be interacted with by entity name and type rather than just a set of large text files. Website: http://www.jeffblackadar.ca/graham_fellowship/corpus_entities_equity/

scholarly journals MELHISSA: a multilingual entity linking architecture for historical press articles

2021 ◽  
Author(s):  
Elvys Linhares Pontes ◽  
Luis Adrián Cabrera-Diego ◽  
Jose G. Moreno ◽  
Emanuela Boros ◽  
Ahmed Hamdi ◽  
...  
Keyword(s):  
Language Processing ◽  
Digital Libraries ◽  
Character Recognition ◽  
Optical Character Recognition ◽  
Historical Documents ◽  
Entity Linking ◽  
Named Entities ◽  
European Languages ◽  
Meta Information ◽  
The Impact

AbstractDigital libraries have a key role in cultural heritage as they provide access to our culture and history by indexing books and historical documents (newspapers and letters). Digital libraries use natural language processing (NLP) tools to process these documents and enrich them with meta-information, such as named entities. Despite recent advances in these NLP models, most of them are built for specific languages and contemporary documents that are not optimized for handling historical material that may for instance contain language variations and optical character recognition (OCR) errors. In this work, we focused on the entity linking (EL) task that is fundamental to the indexation of documents in digital libraries. We developed a Multilingual Entity Linking architecture for HIstorical preSS Articles that is composed of multilingual analysis, OCR correction, and filter analysis to alleviate the impact of historical documents in the EL task. The source code is publicly available. Experimentation has been done over two historical documents covering five European languages (English, Finnish, French, German, and Swedish). Results have shown that our system improved the global performance for all languages and datasets by achieving an F-score@1 of up to 0.681 and an F-score@5 of up to 0.787.

scholarly journals EventEpi–A Natural Language Processing Framework for Event-Based Surveillance

2019 ◽  
Author(s):  
Auss Abbood ◽  
Alexander Ullrich ◽  
Rüdiger Busche ◽  
Stéphane Ghozzi
Keyword(s):  
Natural Language Processing ◽  
Natural Language ◽  
Language Processing ◽  
Web Application ◽  
Fine Tuning ◽  
Entity Recognition ◽  
World Health ◽  
Support Vector ◽  
Event Based ◽  
Processing Framework

AbstractAccording to the World Health Organization (WHO), around 60% of all outbreaks are detected using informal sources. In many public health institutes, including the WHO and the Robert Koch Institute (RKI), dedicated groups of epidemiologists sift through numerous articles and newsletters to detect relevant events. This media screening is one important part of event-based surveillance (EBS). Reading the articles, discussing their relevance, and putting key information into a database is a time-consuming process. To support EBS, but also to gain insights into what makes an article and the event it describes relevant, we developed a natural-language-processing framework for automated information extraction and relevance scoring. First, we scraped relevant sources for EBS as done at RKI (WHO Disease Outbreak News and ProMED) and automatically extracted the articles’ key data: disease, country, date, and confirmed-case count. For this, we performed named entity recognition in two steps: EpiTator, an open-source epidemiological annotation tool, suggested many different possibilities for each. We trained a naive Bayes classifier to find the single most likely one using RKI’s EBS database as labels. Then, for relevance scoring, we defined two classes to which any article might belong: The article is relevant if it is in the EBS database and irrelevant otherwise. We compared the performance of different classifiers, using document and word embeddings. Two of the tested algorithms stood out: The multilayer perceptron performed best overall, with a precision of 0.19, recall of 0.50, specificity of 0.89, F1 of 0.28, and the highest tested index balanced accuracy of 0.46. The support-vector machine, on the other hand, had the highest recall (0.88) which can be of higher interest for epidemiologists. Finally, we integrated these functionalities into a web application called EventEpi where relevant sources are automatically analyzed and put into a database. The user can also provide any URL or text, that will be analyzed in the same way and added to the database. Each of these steps could be improved, in particular with larger labeled datasets and fine-tuning of the learning algorithms. The overall framework, however, works already well and can be used in production, promising improvements in EBS. The source code is publicly available at https://github.com/aauss/EventEpi.

scholarly journals Which OCR toolset is good and why? A comparative study

2021 ◽  
Vol 48 (2) ◽  
Author(s):  
Pooja Jain ◽  
◽  
Dr. Kavita Taneja ◽  
Dr. Harmunish Taneja ◽  
◽  
...  
Keyword(s):  
Comparative Study ◽  
Language Processing ◽  
Character Recognition ◽  
Optical Character Recognition ◽  
Research Area ◽  
Real World Applications ◽  
Banking Education ◽  
Active Research ◽  
Active Research Area ◽  
Computational Technology

Optical Character Recognition (OCR) is a very active research area in many challenging fields like pattern recognition, natural language processing (NLP), computer vision, biomedical informatics, machine learning (ML), and artificial intelligence (AI). This computational technology extracts the text in an editable format (MS Word/Excel, text files, etc.) from PDF files, scanned or hand-written documents, images (photographs, advertisements, and alike), etc. for further processing and has been utilized in many real-world applications including banking, education, insurance, finance, healthcare and keyword-based search in documents, etc. Many OCR toolsets are available under various categories, including open-source, proprietary, and online services. This research paper provides a comparative study of various OCR toolsets considering a variety of parameters.

Machine Learning Techniques Application

2021 ◽  
pp. 1396-1417
Author(s):  
Karthikeyan P. ◽  
Karunakaran Velswamy ◽  
Pon Harshavardhanan ◽  
Rajagopal R. ◽  
JeyaKrishnan V. ◽  
...  
Keyword(s):  
Machine Learning ◽  
Language Processing ◽  
Character Recognition ◽  
Optical Character Recognition ◽  
Supervised Machine Learning ◽  
Machine Learning Techniques ◽  
Modern World ◽  
Interdisciplinary Field ◽  
Sound Image ◽  
Learning Techniques

Machine learning is the part of artificial intelligence that makes machines learn without being expressly programmed. Machine learning application built the modern world. Machine learning techniques are mainly classified into three techniques: supervised, unsupervised, and semi-supervised. Machine learning is an interdisciplinary field, which can be joined in different areas including science, business, and research. Supervised techniques are applied in agriculture, email spam, malware filtering, online fraud detection, optical character recognition, natural language processing, and face detection. Unsupervised techniques are applied in market segmentation and sentiment analysis and anomaly detection. Deep learning is being utilized in sound, image, video, time series, and text. This chapter covers applications of various machine learning techniques, social media, agriculture, and task scheduling in a distributed system.

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