Augmented curation of clinical notes from a massive EHR system reveals symptoms of impending COVID-19 diagnosis
This article has been Reviewed by the following groups
Listed in
- Evaluated articles (ScreenIT)
Abstract
Understanding temporal dynamics of COVID-19 symptoms could provide fine-grained resolution to guide clinical decision-making. Here, we use deep neural networks over an institution-wide platform for the augmented curation of clinical notes from 77,167 patients subjected to COVID-19 PCR testing. By contrasting Electronic Health Record (EHR)-derived symptoms of COVID-19-positive (COVID pos ; n = 2,317) versus COVID-19-negative (COVID neg ; n = 74,850) patients for the week preceding the PCR testing date, we identify anosmia/dysgeusia (27.1-fold), fever/chills (2.6-fold), respiratory difficulty (2.2-fold), cough (2.2-fold), myalgia/arthralgia (2-fold), and diarrhea (1.4-fold) as significantly amplified in COVID pos over COVID neg patients. The combination of cough and fever/chills has 4.2-fold amplification in COVID pos patients during the week prior to PCR testing, in addition to anosmia/dysgeusia, constitutes the earliest EHR-derived signature of COVID-19. This study introduces an Augmented Intelligence platform for the real-time synthesis of institutional biomedical knowledge. The platform holds tremendous potential for scaling up curation throughput, thus enabling EHR-powered early disease diagnosis.
Article activity feed
-
-
SciScore for 10.1101/2020.04.19.20067660: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources SciBERT differs from other domain-adapted BERT architectures as it is trained de novo on a biomedical corpus, whereas BioBERT is initialized with the BERT base vocabulary and fine- tuned with PubMed abstracts and PMC articles. BioBERTsuggested: (BioBERT, RRID:SCR_017547)PubMedsuggested: (PubMed, RRID:SCR_004846)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:There are a …
SciScore for 10.1101/2020.04.19.20067660: (What is this?)
Please note, not all rigor criteria are appropriate for all manuscripts.
Table 1: Rigor
NIH rigor criteria are not applicable to paper type.Table 2: Resources
Software and Algorithms Sentences Resources SciBERT differs from other domain-adapted BERT architectures as it is trained de novo on a biomedical corpus, whereas BioBERT is initialized with the BERT base vocabulary and fine- tuned with PubMed abstracts and PMC articles. BioBERTsuggested: (BioBERT, RRID:SCR_017547)PubMedsuggested: (PubMed, RRID:SCR_004846)Results from OddPub: We did not detect open data. We also did not detect open code. Researchers are encouraged to share open data when possible (see Nature blog).
Results from LimitationRecognizer: We detected the following sentences addressing limitations in the study:There are a few caveats that must be considered when relying solely on EHR inference to track symptoms preceding the PCR testing date. In addition to concerns regarding testing accuracy, there is an inherent delay in PCR testing, which arises because both the patient and physician must decide the symptoms warrant PCR testing. More specifically, to be tested, the patient must first consider the symptoms serious enough to visit the clinic and then the physician must determine the symptoms present a possibility of COVID infection. The length of this delay could also be influenced by how well-informed the public is of COVID-19 signs and symptoms, the availability of PCR testing, and the hospital protocols used to determine which patients get tested. Each of these factors would be absent or limited at the beginning of a pandemic but would increase or improve over time. However, this makes synchronization across patients difficult because the delay between symptom onset and PCR testing changes over time. For example, patients infected early in the pandemic would be less inclined to visit the clinic with mild symptoms, while those infected later have more information and more cause to get tested earlier. Similarly, in the early stages of the COVID-19 pandemic when PCR testing was limited, physicians were forced to reserve tests for more severe cases or for those who were in direct contact with a COVIDpos individual, whereas now PCR testing is more widespread. In each case, the delay...
Results from TrialIdentifier: No clinical trial numbers were referenced.
Results from Barzooka: We did not find any issues relating to the usage of bar graphs.
Results from JetFighter: We did not find any issues relating to colormaps.
Results from rtransparent:- Thank you for including a conflict of interest statement. Authors are encouraged to include this statement when submitting to a journal.
- No funding statement was detected.
- No protocol registration statement was detected.
-
