A Void Type for Medical Language Disambiguation

2004 ◽  
pp. 142-155 ◽  
Author(s):  
Christian Jacquelinet
Keyword(s):  
Medical Language

A Medical Text Analysis System for German - Syntax Analysis

1991 ◽  
Vol 30 (04) ◽  
pp. 275-283 ◽  
Author(s):  
P. M. Pietrzyk
Keyword(s):  
Text Analysis ◽  
Free Text ◽  
New Approach ◽  
Syntax Analysis ◽  
Medical Text ◽  
Medical Language ◽  
Computerized Processing ◽  
Language Data ◽  
Analysis System ◽  
German Syntax

Abstract:Much information about patients is stored in free text. Hence, the computerized processing of medical language data has been a well-known goal of medical informatics resulting in different paradigms. In Gottingen, a Medical Text Analysis System for German (abbr. MediTAS) has been under development for some time, trying to combine and to extend these paradigms. This article concentrates on the automated syntax analysis of German medical utterances. The investigated text material consists of 8,790 distinct utterances extracted from the summary sections of about 18,400 cytopathological findings reports. The parsing is based upon a new approach called Left-Associative Grammar (LAG) developed by Hausser. By extending considerably the LAG approach, most of the grammatical constructions occurring in the text material could be covered.

Towards the Use of a Tree Branching Logic in the Environment of a Hospital Information System

1980 ◽  
Vol 19 (04) ◽  
pp. 187-194
Author(s):  
J.-Ph. Berney ◽  
R. Baud ◽  
J.-R. Scherrer
Keyword(s):  
Syntactic Structure ◽  
Large Data ◽  
Selection System ◽  
Frame Selection ◽  
Knowing That ◽  
Medical Language ◽  
Selection Systems ◽  
Definition Of ◽  
Man Machine Dialogue ◽  
Oriented System

It is well known that Frame Selection Systems (FFS) have proved both popular and effective in physician-machine and patient-machine dialogue. A formal algorithm for definition of a Frame Selection System for handling man-machine dialogue is presented here. Besides, it is shown how the natural medical language can be handled using the approach of a tree branching logic. This logic appears to be based upon ordered series of selections which enclose a syntactic structure. The external specifications are discussed with regard to convenience and efficiency. Knowing that all communication between the user and the application programmes is handled only by FSS software, FSS contributes to achieving modularity and, therefore, also maintainability in a transaction-oriented system with a large data base and concurrent accesses.

scholarly journals Transformers-sklearn: a toolkit for medical language understanding with transformer-based models

2021 ◽  
Vol 21 (S2) ◽  
Author(s):  
Feihong Yang ◽  
Xuwen Wang ◽  
Hetong Ma ◽  
Jiao Li
Keyword(s):  
Language Processing ◽  
Pearson Correlation ◽  
Fine Tuning ◽  
Entity Recognition ◽  
Training Dataset ◽  
Training Methods ◽  
Code Size ◽  
Model Framework ◽  
Language Understanding ◽  
Medical Language

Abstract Background Transformer is an attention-based architecture proven the state-of-the-art model in natural language processing (NLP). To reduce the difficulty of beginning to use transformer-based models in medical language understanding and expand the capability of the scikit-learn toolkit in deep learning, we proposed an easy to learn Python toolkit named transformers-sklearn. By wrapping the interfaces of transformers in only three functions (i.e., fit, score, and predict), transformers-sklearn combines the advantages of the transformers and scikit-learn toolkits. Methods In transformers-sklearn, three Python classes were implemented, namely, BERTologyClassifier for the classification task, BERTologyNERClassifier for the named entity recognition (NER) task, and BERTologyRegressor for the regression task. Each class contains three methods, i.e., fit for fine-tuning transformer-based models with the training dataset, score for evaluating the performance of the fine-tuned model, and predict for predicting the labels of the test dataset. transformers-sklearn is a user-friendly toolkit that (1) Is customizable via a few parameters (e.g., model_name_or_path and model_type), (2) Supports multilingual NLP tasks, and (3) Requires less coding. The input data format is automatically generated by transformers-sklearn with the annotated corpus. Newcomers only need to prepare the dataset. The model framework and training methods are predefined in transformers-sklearn. Results We collected four open-source medical language datasets, including TrialClassification for Chinese medical trial text multi label classification, BC5CDR for English biomedical text name entity recognition, DiabetesNER for Chinese diabetes entity recognition and BIOSSES for English biomedical sentence similarity estimation. In the four medical NLP tasks, the average code size of our script is 45 lines/task, which is one-sixth the size of transformers’ script. The experimental results show that transformers-sklearn based on pretrained BERT models achieved macro F1 scores of 0.8225, 0.8703 and 0.6908, respectively, on the TrialClassification, BC5CDR and DiabetesNER tasks and a Pearson correlation of 0.8260 on the BIOSSES task, which is consistent with the results of transformers. Conclusions The proposed toolkit could help newcomers address medical language understanding tasks using the scikit-learn coding style easily. The code and tutorials of transformers-sklearn are available at https://doi.org/10.5281/zenodo.4453803. In future, more medical language understanding tasks will be supported to improve the applications of transformers_sklearn.

Leveraging the UMLS As a Data Standard for Rare Disease Data Normalization and Harmonization

2020 ◽  
Author(s):  
Qian Zhu ◽  
Dac-Trung Nguyen ◽  
Eric Sid ◽  
Anne Pariser
Keyword(s):  
Rare Disease ◽  
Rare Diseases ◽  
Mendelian Inheritance ◽  
Data Normalization ◽  
Community Settings ◽  
Unified Medical Language System ◽  
Data Standard ◽  
Medical Language ◽  
Disease Concepts ◽  
High Level

Abstract Objective In this study, we aimed to evaluate the capability of the Unified Medical Language System (UMLS) as one data standard to support data normalization and harmonization of datasets that have been developed for rare diseases. Through analysis of data mappings between multiple rare disease resources and the UMLS, we propose suggested extensions of the UMLS that will enable its adoption as a global standard in rare disease. Methods We analyzed data mappings between the UMLS and existing datasets on over 7,000 rare diseases that were retrieved from four publicly accessible resources: Genetic And Rare Diseases Information Center (GARD), Orphanet, Online Mendelian Inheritance in Men (OMIM), and the Monarch Disease Ontology (MONDO). Two types of disease mappings were assessed, (1) curated mappings extracted from those four resources; and (2) established mappings generated by querying the rare disease-based integrative knowledge graph developed in the previous study. Results We found that 100% of OMIM concepts, and over 50% of concepts from GARD, MONDO, and Orphanet were normalized by the UMLS and accurately categorized into the appropriate UMLS semantic groups. We analyzed 58,636 UMLS mappings, which resulted in 3,876 UMLS concepts across these resources. Manual evaluation of a random set of 500 UMLS mappings demonstrated a high level of accuracy (99%) of developing those mappings, which consisted of 414 mappings of synonyms (82.8%), 76 are subtypes (15.2%), and five are siblings (1%). Conclusion The mapping results illustrated in this study that the UMLS was able to accurately represent rare disease concepts, and their associated information, such as genes and phenotypes, and can effectively be used to support data harmonization across existing resources developed on collecting rare disease data. We recommend the adoption of the UMLS as a data standard for rare disease to enable the existing rare disease datasets to support future applications in a clinical and community settings.

Healing Society: Medical Language in American Eugenics

1995 ◽  
Vol 8 (1) ◽  
pp. 175-196 ◽  
Author(s):  
Debora Kamrat-Lang
Keyword(s):  
United States ◽  
The United States ◽  
Judicial System ◽  
Cultural Tradition ◽  
Medical Language ◽  
The Individual

The ArgumentAmerican eugenics developed out of a cultural tradition independent of medicine. However, the eugenicist Harry Hamilton Laughlin and some legal experts involved in eugenic practice in the United States used medical language in discussing and evaluating enforced eugenic sterilizations. They built on medicine as a model for healing, while at the same time playing down medicine's concern with its traditional client: the individual patient. Laughlin's attitude toward medicine was ambivalent because he wanted expert eugenicists, rather than medical experts, to control eugenic practice. In contrast, legal experts saw eugenics as an integral part of medicine, though one expert challenged basing the judicial system on eugenically minded medicine. All in all, the medicalization of American eugenics involved expanding the scope of medicine to include the mutilation of individuals for the benefit of society. The judicial system was medicalized in that an expanded medicine became the basis of legislation in the thirty states that permitted eugenic sterilizations

Book review: Medical Language Processing

1988 ◽  
Vol 20 (1) ◽  
pp. 70-71 ◽  
Author(s):  
Jon L. Schlossberg
Keyword(s):  
Language Processing ◽  
Medical Language ◽  
Medical Language Processing
Sign in / Sign up

Export Citation Format

Share Document