We use PhenotypeR to help assess the research readiness of a set of study cohorts. To help make such assessments it can help to have an explicit set of expectations to compare our results. For example, is the age of our study cohort similar to what would be expected? Is the proportion of the cohort that is male vs female similar to what would be expected based on what we know about the phenotype of interest?
We can define a set of expectations about what we expect to see in
our phenotype diagnostic results. So that we can visualise these easily
using the tableCohortExpectations()
function, we will
create a tibble with the following columns: cohort_name (so we know
which expectation corresponds to which cohort), estimate (the estimate
for which our expectation is associated with), value (our expectation on
the value we should see in our results). As an example, say we have one
cohort called “knee_osteoarthritis” and another called
“knee_replacement”. We could create expectations about median age and
the proportion that is male for each cohort like so.
library(dplyr)
library(PhenotypeR)
knee_oa <- tibble(cohort_name = "knee_osteoarthritis",
estimate = c("Median age", "Proportion male"),
value = c("60 to 65", "45%"),
source = "Clinician")
knee_replacement <- tibble(cohort_name = "knee_replacement",
estimate = c("Median age", "Proportion male"),
value = c("65 to 70", "50%"),
source = "Clinician")
expectations <- bind_rows(knee_oa, knee_replacement)
Now we have our structured expectations, we can quickly create a summary of them (we’ll see in the next vignette how we can then also include them in our shiny app).
Note as long as we make sure to include our four required columns we can create any set of expectations that is relevant for our cohorts.
The custom expectations created above might be based on our (or a friendly colleagues’) clinical knowledge. This though requires access to the requisite clinical knowledge and is often time-consuming, especially if we have many cohorts and start considering the many different estimates from phenotype diagnostics.
To speed up the process we can use an LLM to help us draft our expectations. We could use this to create a custom set. Here for example we’ll use Google Gemini to populate our expectations.
Notice that you may need first to create a Gemini API to run the example. You can do that following this link: https://aistudio.google.com/app/apikey. And then add the API in your R environment:
usethis::edit_r_environ()
# Add your API in your R environment:
GEMINI_API_KEY = "your API"
# Restrart R
library(ellmer)
chat <- chat("google_gemini")
llm_expectation <- chat$chat(
interpolate("What are the typical characteristics we can expect to see in our real-world data for a cohort of people with an ankle sprain (average age, proportion male vs female, subsequent medications, etc)? Be brief and provide summar with a few sentences."))
tibble(cohort_name = "diagnosis_of_ankle_sprain",
estimate = "General summary",
value = llm_expectation,
source = "llm") |>
tableCohortExpectations()
To help us create a consistent set of phenotype expectations from
LLMs, PhenotypeR provides the getCohortExpectations()
. This
function will generate a set of expectations that are associated with
the various cohort diagnostic function results.
getCohortExpectations(chat = chat,
phenotypes = c("diagnosis_of_ankle_sprain",
"diagnosis_of_prostate_cancer",
"new_user_of_morphine")) |>
tableCohortExpectations()
Instead of passing our cohort names, we could instead pass our
results set from phenotypeDiagnostics()
instead. In this
case we’ll automatically get expectations for each of the study cohorts
in our results.
library(DBI)
library(duckdb)
library(CDMConnector)
library(CohortConstructor)
con <- dbConnect(duckdb(), dbdir = eunomiaDir())
cdm <- cdmFromCon(
con = con, cdmSchema = "main", writeSchema = "main", cdmName = "Eunomia"
)
codes <- list("diagnosis_of_ankle_sprain" = 81151,
"diagnosis_of_prostate_cancer" = 4163261,
"new_user_of_morphine" = c(1110410L, 35605858L, 40169988L))
cdm$my_cohort <- conceptCohort(cdm = cdm,
conceptSet = codes,
exit = "event_end_date",
name = "my_cohort")
diag_results <- phenotypeDiagnostics(cdm$my_cohort)
getCohortExpectations(chat = chat,
phenotypes = diag_results) |>
tableCohortExpectations()
Instead of Google Gemini we could use Mistral instead.
chat <- ellmer::chat("mistral")
diag_results <- phenotypeDiagnostics(cdm$my_cohort)
getCohortExpectations(chat = chat,
phenotypes = diag_results) |>
tableCohortExpectations()
It is important to note the importance of a descriptive cohort name. These are the names passed to the LLM and so the more informative the name, the better we can expect the LLM to do when generating our expectations. In general to make them amenable to the LLM workflow when naming cohorts we should:
It should also go without saying that we should not treat the output of the LLM as the unequivocal truth. While LLM expectations may well prove a useful starting point, clinical judgement and knowledge of the data source at hand will still be vital in appropriately interpreting our results. Our typical workflow may well be using LLMs to help generate phenotype expectations for review by a clinical expert which should save them time while ensuring we have an appropriate set to compare our results against.