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Cohort Tracking

The use of non-representative samples of a population when doing research on health questions gives raise to serious issues, importantly:

• conclusions drawn on subgroups (by age, gender, race, …) may not generalize to other subgroups

• underrepresented group’s characteristics may be hidden by the overrepresented group’s data

• models, such as clinical algorithms, trained on such samples may pick up, or even further amplify, biases in e.g. clinical decision making

For studies addressing medical questions, it is necessary to define exclusion and inclusion criteria. To detect, track and monitor the effects of such criteria on the composition of the study cohort, Ellen et al. propose a visual aid in the form of a flowchart diagram.

Here, we show how ehrapy can help to track and visualize key demographics of interest during filtering steps.

Environment setup

import ehrapy as ep
from tableone import TableOne

Load the data

We load the Diabetes 130-Hospitals dataset, which comes with a convenience loader in ehrapy.

More information on the dataset can be found here. We use a preprocessed version by fairlearn, from which more information can be found here.

adata = ep.dt.diabetes_130_fairlearn(
    columns_obs_only=["gender", "race", "time_in_hospital", "medicaid"]
)

2024-03-28 22:22:49,189 - root INFO - Transformed passed DataFrame into an AnnData object with n_obs x n_vars = `101766` x `20`.

Inspecting the dataset with tableone

tableone generates summary statistics for a patient population including the proportion of missing values (if any). tableone works on pandas.DataFrame objects, and hence interacts seamlessly with the .obs field of the AnnData object:

TableOne(adata.obs, categorical=["gender", "race", "medicaid"])

		Missing	Overall
n			101766
gender, n (%)	Female	0	54708 (53.8)
	Male		47055 (46.2)
	Unknown/Invalid		3 (0.0)
race, n (%)	AfricanAmerican	0	19210 (18.9)
	Asian		641 (0.6)
	Caucasian		76099 (74.8)
	Hispanic		2037 (2.0)
	Other		1506 (1.5)
	Unknown		2273 (2.2)
time_in_hospital, mean (SD)		0	4.4 (3.0)
medicaid, n (%)	False	0	98234 (96.5)
	True		3532 (3.5)

In the following, we show how this view can be complemented in ehrapy with a graphical representation

Inspecting the dataset with CohortTracker

Instead of generating a “Table 1”, ehrapy can generate a graphical representation: We create a CohortTracker object, which we can simply call on the AnnData object from above. The plot_cohort_barplot method then can plot the state of our cohort:

# instantiate the cohort tracker
ct = ep.tl.CohortTracker(adata, categorical=["gender", "race", "medicaid"])

# track the initial state of the dataset
ct(adata, label="Initial cohort")

# plot the change of the cohort
ct.plot_cohort_barplot()

Tracking the processing and filtering of a dataset with CohortTracker

Ellen et al. advocate to integrate a detailed participant flow diagram into the workflow of data reporting to track the changes in sociodemographic and clinical characteristics of each phase of a study.

The CohortTracker allows logging filtering steps with optional comments to recover such a filtering flow.

# instantiate the cohort tracker
ct = ep.tl.CohortTracker(adata, categorical=["gender", "race", "medicaid"])

# track the initial state of the dataset
ct(adata, label="Initial cohort")

# do a filtering step
adata = adata[adata.obs.medicaid]

# track the filtered dataset
ct(
    adata,
    label="Medicaid Cohort",
    operations_done="Include patients in medicaid program only",
)

# plot the change of the cohort
ct.plot_cohort_barplot()

# plot a flowchart
ct.plot_flowchart()

As we can see, focusing on the Medicaid cohort actually drastically shifts other demographics as well: The over-representation of the “Caucasian” population decreased and the imbalance between the representation of the genders is pronounced much more in this cohort.

Customizing plots

ct.plot_cohort_barplot(
    subfigure_title=True,
    yticks_labels={
        "time_in_hospital": "Time in hospital (days)",
        "race": "Race",
        "gender": "Gender",
    },
    color_palette="tab20",
    legend_labels={
        "time_in_hospital": "Time in hospital (days)",
        "AfricanAmerican": "African American",
    },
    legend_kwargs={"title": "Variables", "bbox_to_anchor": (1, 1)},
)

ct.plot_flowchart(
    title="Cohort flowchart",
    arrow_size=0.75,
    bbox_kwargs={"fc": "lightgreen"},
    arrowprops_kwargs={"color": "black"},
)