detect_medical_entities and phi should handle character vector #22

antoine-sachet · 2020-01-28T13:02:55Z

detect_medical_entities can only handle a scalar string. It should handle a character vector, like all other detect_* functions. Example code can be found in R/detect_entity.R.

Note that right now the medical stuff in the "medical" branch. Install with remotes::install_github("cloudyr/aws.comprehend", ref = "medical").

library("aws.comprehend")
medical_txt <- "Pt is 40yo mother, highschool teacher. HPI : Sleeping trouble on present dosage of Clonidine."
detect_medical_entities(medical_txt)
#>   Index BeginOffset                     Category EndOffset Id     Score
#> 1     1           6 PROTECTED_HEALTH_INFORMATION        10  0 0.9982511
#> 2     1          19 PROTECTED_HEALTH_INFORMATION        37  1 0.4113526
#> 3     1          45            MEDICAL_CONDITION        61  3 0.7587468
#> 4     1          83                   MEDICATION        92  2 0.9932888
#>                 Text                    Traits         Type
#> 1               40yo                      NULL          AGE
#> 2 highschool teacher                      NULL   PROFESSION
#> 3   Sleeping trouble SYMPTOM, 0.52603405714035      DX_NAME
#> 4          Clonidine                      NULL GENERIC_NAME

# This should work
detect_medical_entities(c(medical_txt, medical_txt))
#> Warning in comprehendHTTP(action = operation, body = bod, service =
#> "comprehendmedical"): Bad Request (HTTP 400).
#>      Index
#> [1,]     1

^{Created on 2020-01-28 by the reprex package (v0.3.0)}

Making sure indices are consistent with the input even when no entities are found...
detect_medical_entities(c(medical_txt, "No medical entity in here", medical_txt))

@dkincaid

antoine-sachet · 2020-03-05T15:46:36Z

My bad, AWS does not provide batch operations for Comprehend Medical. This is a good reason not to implement batch processing for the detect_medical_* functions.

One can always loop on detect_medical_* to process multiple documents, taking rate limits into account.

antoine-sachet added enhancement help wanted good first issue labels Jan 28, 2020

antoine-sachet mentioned this issue Jan 28, 2020

Merge Medical #21

Merged

antoine-sachet closed this Mar 5, 2020

cloudyr / aws.comprehend

detect_medical_entities and phi should handle character vector #22

detect_medical_entities and phi should handle character vector #22

antoine-sachet commented Jan 28, 2020 •

edited

antoine-sachet commented Mar 5, 2020

cloudyr / aws.comprehend

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detect_medical_entities and phi should handle character vector #22

detect_medical_entities and phi should handle character vector #22

Comments

antoine-sachet commented Jan 28, 2020 • edited

antoine-sachet commented Mar 5, 2020

antoine-sachet commented Jan 28, 2020 •

edited