De-identifying clinical free text

import re

# Synthetic note: every name, number and place below is invented
note = ("Mrs Asha Verma (MRN 00482913), DOB 04/02/1958, seen on 12/03/2026 at Lakeside Clinic. "
        "Accompanied by her son Ravi. Phone 98765 43210, email asha.verma@example.org. "
        "Dr Lee reviewed her foot ulcer. Lives at 14 Hill Road, PIN 999999. Retired school principal.")

# The identifiers a careful human reviewer marked in this note
GOLD = ["Asha Verma", "00482913", "04/02/1958", "12/03/2026", "Lakeside Clinic", "Ravi",
        "98765 43210", "asha.verma@example.org", "Lee", "14 Hill Road", "999999"]

PATTERNS = [
    ("NAME", r"\b(?:Mr|Mrs|Ms|Dr)\.?\s+((?:[A-Z][a-z]+)(?:\s+[A-Z][a-z]+)?)"),
    ("ID", r"\bMRN\s*(\d{6,})"),
    ("DATE", r"\b(\d{1,2}/\d{1,2}/\d{2,4})\b"),
    ("PHONE", r"\b(\d{5}\s?\d{5})\b"),
    ("EMAIL", r"\b([\w.+-]+@[\w-]+\.[\w.]+)\b"),
    ("POSTCODE", r"\bPIN\s*(\d{6})\b"),
]

def find_phi(text):
    spans = []
    for label, pattern in PATTERNS:
        for m in re.finditer(pattern, text):
            spans.append((m.start(1), m.end(1), label, m.group(1)))
    return sorted(spans)

found = [s[3] for s in find_phi(note)]
missed = [g for g in GOLD if not any(g in f or f in g for f in found)]
print(f"Found {len(GOLD) - len(missed)} of {len(GOLD)} identifiers (recall {1 - len(missed) / len(GOLD):.0%})")
print("Missed:", missed)

# Found 8 of 11 identifiers (recall 73%)
# Missed: ['Lakeside Clinic', 'Ravi', '14 Hill Road']

from datetime import datetime, timedelta

SHIFT = timedelta(days=-37)        # one random offset per patient, kept secret
def surrogate(label, value):
    if label == "DATE":
        d = datetime.strptime(value, "%d/%m/%Y") + SHIFT
        return d.strftime("%d/%m/%Y")
    return f"[{label}]"

def redact(text):
    for start, end, label, value in reversed(find_phi(text)):
        text = text[:start] + surrogate(label, value) + text[end:]
    return text

print(redact(note))

# Mrs [NAME] (MRN [ID]), DOB 29/12/1957, seen on 03/02/2026 at Lakeside Clinic. Accompanied by her son Ravi. Phone [PHONE], email [EMAIL]. Dr [NAME] reviewed her foot ulcer. Lives at 14 Hill Road, PIN [POSTCODE]. Retired school principal.