equiflow

EquiFlow - Equity-Focused Cohort Flow Diagrams

Visualize and quantify selection bias in clinical ML/research cohorts. Based on Ellen et al. (2024) J Biomed Inform.

When to Use This Skill

• Building patient cohorts from MIMIC-IV or eICU
• Documenting inclusion/exclusion criteria with CONSORT-style diagrams
• Detecting disproportionate exclusion of vulnerable groups
• Quantifying selection bias via Standardized Mean Difference (SMD)

Default Equity Variables

When no variables are specified, CohortFlow automatically tracks:

Category	Variables	Column Aliases
Demographics	gender	gender, sex
	race	race, ethnicity
	age	anchor_age, age, admission_age
Socioeconomic	insurance	insurance, insurance_type, payer
	language	language, primary_language
	marital_status	marital_status, marital
Clinical	los	los, length_of_stay, icu_los
Outcome	mortality	hospital_expire_flag, mortality, death

SMD Interpretation

| |SMD| | Interpretation | Action | |-------|----------------|--------| | < 0.1 | Negligible | OK | | 0.1-0.2 | Small | Monitor | | > 0.2 | Meaningful | Investigate | | > 0.5 | Large | Serious concern |

See references/smd_interpretation.md for detailed guidance.

Critical Implementation Notes

1. Auto-detection: CohortFlow scans DataFrame columns for known aliases. Override with use_defaults=False if you want full control.

2. SMD > 0.2 is the default threshold for flagging potential bias. This follows established covariate balance literature.

3. Missing data: Exclusion steps that remove patients with missing values can introduce systematic bias. Always check SMD after such steps.

Example Queries

Full workflow with MIMIC-IV

from cohort_flow import CohortFlow

# Step 1: Query MIMIC-IV
query = """
SELECT
    p.subject_id, p.gender, p.anchor_age,
    a.race, a.insurance, a.language, a.marital_status,
    a.hospital_expire_flag,
    i.los
FROM mimiciv_hosp.patients p
JOIN mimiciv_hosp.admissions a USING (subject_id)
JOIN mimiciv_icu.icustays i ON a.hadm_id = i.hadm_id
"""
df = execute_query(query)

# Step 2: Build cohort with equity tracking
cf = CohortFlow(df)  # Auto-detects equity variables

cf.exclude(df['anchor_age'] >= 18, "Age < 18", "Adults")
cf.exclude(df['los'] >= 24, "ICU < 24h", "ICU >= 24h")
cf.exclude(df['anchor_age'] <= 90, "Age > 90", "Age 18-90")

# Step 3: Check for bias
print(cf.check_bias())  # Flags variables with SMD > 0.2

# Step 4: Generate diagram
cf.plot("sepsis_cohort_flow")