Medical codes & tokenizers

PyHealth ships utilities for working with medical coding systems directly — no external API, just bundled mappings.

InnerMap: lookup within a coding system

InnerMap lets you look up code descriptions and traverse the code hierarchy (parents/ancestors).

from pyhealth.medcode import InnerMap

icd9cm = InnerMap.load("ICD9CM")
icd9cm.lookup("428.0")
# → 'Congestive heart failure, unspecified'

icd9cm.get_ancestors("428.0")
# → ['428', '420-429.99', '390-459.99', '001-999.99']

Supported coding systems:

atc = InnerMap.load("ATC")
atc.lookup("M01AE51")
# → 'ibuprofen, combinations'

CrossMap: translate between systems

CrossMap converts codes from one system to another. Many mappings are one-to-many — the result is always a list.

from pyhealth.medcode import CrossMap

# Diagnoses: ICD-9-CM → CCS (rolls fine-grained codes up to ~280 categories)
cm = CrossMap.load("ICD9CM", "CCSCM")
cm.map("428.0")
# → ['108']

# Drugs: NDC → RxNorm (normalized drug name)
cm = CrossMap.load("NDC", "RxNorm")
cm.map("50580049698")
# → ['209387']

Common cross-mappings:

• ICD9CM ↔ ICD10CM — ICD version conversion
• ICD9CM → CCSCM, ICD10CM → CCSCM — dimensionality reduction (~14k → 280 codes)
• NDC → RxNorm — drug normalization
• NDC → ATC — pharmacology grouping
• RxNorm → ATC — drug therapeutic classification

When to use cross-mapping: when the user has codes in one system but wants to predict or feature-engineer in another (e.g., training on ICD-9 from MIMIC-III but evaluating on ICD-10 from MIMIC-IV).

Tokenizer

pyhealth.tokenizer.Tokenizer converts code lists to integer indices and back. Most pipelines don't need to call it directly — set_task and the models handle tokenization internally — but it's exposed when you need batch encoding for custom models.

from pyhealth.tokenizer import Tokenizer

vocab = ['A01A', 'A02A', 'A02B', 'A03C', 'A03D', 'A04A']
tok = Tokenizer(tokens=vocab, special_tokens=["<pad>", "<unk>"])

# 2D = batch of code lists, one per sample
tokens = [['A03C', 'A03D'], ['A04A', 'B035']]   # 'B035' is OOV
indices = tok.batch_encode_2d(tokens)
# → [[5, 6], [7, 1]]    (1 = <unk>)

# 3D = batch of visits, each with code lists
tokens = [[['A03C', 'A03D'], ['A04A']], [['B035']]]
indices = tok.batch_encode_3d(tokens)

# Decode is symmetric
tok.batch_decode_2d(indices)

Reserved indices: 0 = <pad>, 1 = <unk> when both special tokens are passed (in that order).

When to surface this to the user

• Reduce label cardinality: ICD-9 → CCS turns 14,000 sparse labels into 280 — drug-rec and ICD-coding tasks often benefit.
• Cross-version compatibility: training on MIMIC-III (ICD-9) and inferring on MIMIC-IV (ICD-10) requires a cross-map.
• Drug normalization: NDC codes are vendor-specific; map to RxNorm or ATC for stable features.
• Interpretability: after a prediction, use InnerMap.lookup to render code IDs as human-readable descriptions in the output.