annotating-variants
Annotates VCF variants and normalizes HGVS nomenclature with public, license-free annotators…
Adversarially scan already-de-identified clinical text for residual identifiers and emit a leakage report that blocks release on any hit. Use after OpenMed de-identification when the user asks to verify a redaction, prove no PHI/PII leaked, gate a dataset before sharing, or run
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/auditing-deid-leakageContext preview
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Adversarially scan already-de-identified clinical text for residual identifiers and emit a leakage report that blocks release on any hit. Use after OpenMed de-identification when the user asks to verify a redaction, prove no PHI/PII leaked, gate a dataset before sharing, or run
name: auditing-deid-leakage description: "Adversarially scan already-de-identified clinical text for residual identifiers and emit a leakage report that blocks release on any hit. Use after OpenMed de-identification when the user asks to verify a redaction, prove no PHI/PII leaked, gate a dataset before sharing, or run a second-pass detector. Covers format and checksum detectors (SSN, Luhn for card numbers, MRN/account patterns, emails, phones, dates), entropy heuristics for high-randomness tokens, severity scoring, and a hard block-on-leak rule. This is the verification half of OpenMed's leakage-first ethos. Hand-off: re-run openmed.extract_pii on the de-id output and diff against expectations. License-free, local-first. Pairs after deidentifying-clinical-text." license: Apache-2.0 metadata: project: OpenMed category: de-identification pairs: after version: "1.0"
De-identification is **verified, not assumed**. A model-driven redaction can miss a structured identifier (an SSN typo'd with spaces, an account number in a footer, a date in an odd format) — and a single residual identifier defeats the whole release. This skill is the adversarial second pass: scan the *output* of de-identification for anything that still looks like an identifier, score it, and **block release on any leak**. It is the verification half of OpenMed's leakage-first ethos — gate on leakage, not on F1.
a trust boundary (export, share, train, publish).
that fails the build if any identifier survives.
redaction — a deterministic checker catches different failures than the NER.
Run this on the **de-identified** text, not the original. The original is expected to be full of identifiers.
Two complementary passes — a deterministic structural scan plus a model second-pass diff:
import re
import openmed
# Synthetic — the de-identified OUTPUT we are auditing for residual leaks.
deid_text = "Patient [NAME] seen on [DATE]. Backup contact 415-555-0184; acct 4111111111111111."
def luhn_ok(digits: str) -> bool:
nums = [int(d) for d in digits]
nums[-2::-2] = [(2 * d - 9 if 2 * d > 9 else 2 * d) for d in nums[-2::-2]]
return sum(nums) % 10 == 0
DETECTORS = {
"SSN": (r"\b\d{3}-\d{2}-\d{4}\b", "critical", None),
"EMAIL": (r"\b[\w.+-]+@[\w-]+\.[\w.-]+\b", "high", None),
"PHONE": (r"\b(?:\+?1[-.\s]?)?\(?\d{3}\)?[-.\s]?\d{3}[-.\s]?\d{4}\b", "high", None),
"DATE": (r"\b\d{1,2}[/-]\d{1,2}[/-]\d{2,4}\b", "medium", None),
"MRN": (r"\bMRN[:#\s]*\d{5,}\b", "high", None),
"CARD": (r"\b(?:\d[ -]?){13,19}\b", "critical", luhn_ok), # checksum-gated
}
findings = []
for label, (pattern, severity, checksum) in DETECTORS.items():
for m in re.finditer(pattern, deid_text, flags=re.IGNORECASE):
token = m.group()
if checksum and not checksum(re.sub(r"\D", "", token)):
continue # fails Luhn -> not a real card number, skip
findings.append({"label": label, "severity": severity,
"start": m.start(), "end": m.end()}) # offsets, not text
# Second-pass model detector: re-run PII extraction on the de-id output.
residual = openmed.extract_pii(deid_text) # PredictionResult
for ent in residual.entities:
findings.append({"label": ent.label, "severity": "high",
"start": ent.start, "end": ent.end})
leaked = bool(findings)
print({"leak": leaked, "count": len(findings)}) # report carries NO plaintext
assert not leaked, "Release BLOCKED: residual identifiers detected."Note what the report records: **labels, severities, and offsets — never the leaked plaintext**. Echoing the leaked identifier into a report or log re-creates the exact PHI exposure you are auditing for.
1. **Run deterministic format + checksum detectors** on the de-identified text: SSN, email, phone, dates, MRN/account/ID patterns, and card numbers gated by the **Luhn checksum** so random 16-digit strings don't false-positive. These catch structured identifiers a model may skip. 2. **Add an entropy heuristic** for high-randomness tokens (long base36/base64 strings, hex blobs) that match no known format but look like keys, tokens, or record locators. Flag for review rather than auto-block; entropy is noisy. 3. **Run a model second-pass:** re-run `openmed.extract_pii` on the *output* and treat any returned entity as a residual leak. Because it's a different detector than the one that did the redaction, it catches different misses. 4. **Score severity.** critical (SSN, card, full DOB+name co-occurrence) > high (email, phone, MRN, names) > medium (partial dates) > low (entropy-only). 5. **Block on any leak.** The gate is binary for release: if `findings` is non-empty at high/critical, fail the export. Surface a no-PHI report (counts + offsets + severities) so a reviewer can locate and re-redact.
`result.deidentified_text`. Never audit `result.original_text`.
on the de-id output and diff. Equivalent MCP/REST surfaces detect PII spans for the same purpose. Any span returned on already-de-identified text is a leak.
necessary but not sufficient — quasi-identifiers (age + ZIP + date) can still re-identify. Hand a clean-on-leakage dataset to QI risk scoring next.
a leakage regression fails CI, not just an F1 drop.
Local-first healthcare AI: clinical NER and HIPAA PII de-identification on hardware you control. 2,200+ medical models, 35 model-backed PII languages, and Python, MLX, Android and browser runtimes. Apache-2.0 SDK.
Repo: maziyarpanahi/openmed
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