Constructing co-occurrence network embeddings to assist association extraction for COVID-19 and other coronavirus infectious diseases.
J Am Med Inform Assoc
; 27(8): 1259-1267, 2020 08 01.
Article
in English
| MEDLINE | ID: covidwho-381884
ABSTRACT
OBJECTIVE:
As coronavirus disease 2019 (COVID-19) started its rapid emergence and gradually transformed into an unprecedented pandemic, the need for having a knowledge repository for the disease became crucial. To address this issue, a new COVID-19 machine-readable dataset known as the COVID-19 Open Research Dataset (CORD-19) has been released. Based on this, our objective was to build a computable co-occurrence network embeddings to assist association detection among COVID-19-related biomedical entities. MATERIALS ANDMETHODS:
Leveraging a Linked Data version of CORD-19 (ie, CORD-19-on-FHIR), we first utilized SPARQL to extract co-occurrences among chemicals, diseases, genes, and mutations and build a co-occurrence network. We then trained the representation of the derived co-occurrence network using node2vec with 4 edge embeddings operations (L1, L2, Average, and Hadamard). Six algorithms (decision tree, logistic regression, support vector machine, random forest, naïve Bayes, and multilayer perceptron) were applied to evaluate performance on link prediction. An unsupervised learning strategy was also developed incorporating the t-SNE (t-distributed stochastic neighbor embedding) and DBSCAN (density-based spatial clustering of applications with noise) algorithms for case studies.RESULTS:
The random forest classifier showed the best performance on link prediction across different network embeddings. For edge embeddings generated using the Average operation, random forest achieved the optimal average precision of 0.97 along with a F1 score of 0.90. For unsupervised learning, 63 clusters were formed with silhouette score of 0.128. Significant associations were detected for 5 coronavirus infectious diseases in their corresponding subgroups.CONCLUSIONS:
In this study, we constructed COVID-19-centered co-occurrence network embeddings. Results indicated that the generated embeddings were able to extract significant associations for COVID-19 and coronavirus infectious diseases.Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Pneumonia, Viral
/
Algorithms
/
Neural Networks, Computer
/
Coronavirus Infections
/
Pandemics
Type of study:
Experimental Studies
/
Prognostic study
/
Randomized controlled trials
Limits:
Humans
Language:
English
Journal:
J Am Med Inform Assoc
Journal subject:
Medical Informatics
Year:
2020
Document Type:
Article
Affiliation country:
Jamia
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