Datasets:
| -- FHIR-SQL fine-tuning study: frozen core clinical schema. | |
| -- | |
| -- This is the benchmark-facing schema shown to models in every prompt (benchmark | |
| -- authoring, SFT prompt format, RL reward execution). It is a deliberately curated | |
| -- subset of the full flattened data -- see METHODOLOGY_LOG.md for the two-layer | |
| -- rationale (full fidelity in the database, curated scope in what models see) and | |
| -- the token-cost/scope reasoning. | |
| -- | |
| -- Generated from the actual column types DuckDB inferred when loading | |
| -- data/train.duckdb, not hand-assumed -- see scripts/flatten_to_duckdb.py for | |
| -- the extraction logic that produces this shape. | |
| -- | |
| -- Version stamp: | |
| -- Date frozen: 2026-08-02 | |
| -- Synthea build: v3.4.0-18-ga07a65555 (git-describe string embedded in | |
| -- generated Patient resources; downloaded from the | |
| -- GitHub v4.0.0 release page -- see methodology log) | |
| -- Train population: 18,999 patients (target was ~15,000; see log for | |
| -- per-batch seed/state/age-bracket design) | |
| -- Held-out population: 6,383 patients (target was ~5,000) | |
| -- Populations verified disjoint: 0 patient_id overlap between train and held-out | |
| -- | |
| -- Every number produced downstream (benchmark accuracy, cost tables, etc.) is | |
| -- relative to this artifact. Do not modify this file without a note on what | |
| -- changed and why. | |
| -- | |
| -- Provider attribution: Synthea generates exactly one participant per encounter, | |
| -- typed "primary performer" only -- it does not distinguish admitting/attending/ | |
| -- consulting roles, so those remain unanswerable regardless of schema design. | |
| -- Procedure.performer is never populated by this Synthea version (0/29,947 in a | |
| -- full batch) -- procedure-level provider attribution is not available at all. | |
| -- | |
| -- Naming convention: columns are named to match FHIR element names directly, | |
| -- so a model's clinical-language understanding maps onto the schema with as | |
| -- little translation as possible: | |
| -- - Primary key: `id` (matches every FHIR resource's own `id` element). | |
| -- - Foreign keys: `patient_id`, `encounter_id` (SQL join-key convention; | |
| -- not itself a literal FHIR field name, since FHIR expresses this via | |
| -- subject/patient/encounter *reference* elements, but resolving those | |
| -- references to a flat join key needs a name, and `<type>_id` is the | |
| -- clearest SQL-side compromise). | |
| -- - Primary coding triple on each table: `code`, `system`, `display` | |
| -- (matches FHIR Coding.code/.system/.display exactly). | |
| -- - Where a resource's own field name differs from the generic "code" | |
| -- (Encounter.type, Encounter.class, Immunization.vaccineCode, | |
| -- CarePlan.category), the coding triple is prefixed with that field name | |
| -- instead: `type_code/type_system/type_display`, `class_code`, | |
| -- `vaccineCode/vaccineCode_system/vaccineCode_display`, | |
| -- `category_code/category_system/category_display`. | |
| -- - Status/descriptive fields: exact camelCase FHIR element names | |
| -- (clinicalStatus, verificationStatus, intent, criticality). | |
| -- - Dates: exact FHIR element names (birthDate, deceasedDateTime, | |
| -- onsetDateTime, abatementDateTime, recordedDate, effectiveDateTime, | |
| -- authoredOn, performedDateTime, occurrenceDateTime); Period-typed | |
| -- start/end kept as `period_start`/`period_end` (Period.start/.end). | |
| -- - value[x]: `valueQuantity`, `unit` (Quantity.unit), `valueCodeableConcept` | |
| -- (+ `valueCodeableConcept_system`), `valueString`. | |
| -- - Provider-reference columns match the FHIR field they were extracted | |
| -- from: `requester_npi`/`requester_name` on medication_request (from | |
| -- MedicationRequest.requester), `participant_npi`/`participant_name` on | |
| -- encounter (from Encounter.participant). | |
| -- - `race`/`ethnicity` on patient (US-Core extensions -- see | |
| -- scripts/flatten_to_duckdb.py's us_core_ext_text macro). | |
| -- - `imaging_study` (ImagingStudy resource) makes radiology-volume questions | |
| -- answerable (department-level radiology questions remain unanswerable -- | |
| -- no department/service-line concept exists anywhere in Synthea's FHIR | |
| -- output). | |
| -- | |
| -- Indexes: secondary (ART) indexes are added directly to train.duckdb and | |
| -- heldout.duckdb (not a change to this file -- no column/table/logical change, | |
| -- only a physical one) on the coding-triple columns (condition.code, | |
| -- observation.code, medication_request.code, encounter.class_code, | |
| -- encounter.type_code, procedure.code, immunization.vaccineCode, allergy.code, | |
| -- careplan.category_code, diagnostic_report.code, imaging_study.procedureCode, | |
| -- imaging_study.modality), to support the RL execution-efficiency reward term. | |
| -- patient_id/encounter_id deliberately NOT indexed -- DuckDB's ART index isn't | |
| -- used by the optimizer to accelerate joins, only point/highly-selective | |
| -- (<0.1% of rows) filters. See METHODOLOGY_LOG.md for the full verification | |
| -- history of this schema and its indexes. | |
| CREATE TABLE patient ( | |
| id VARCHAR PRIMARY KEY, | |
| gender VARCHAR, | |
| birthDate DATE, | |
| deceasedDateTime TIMESTAMP, | |
| maritalStatus VARCHAR, | |
| state VARCHAR, -- address[0].state | |
| city VARCHAR, -- address[0].city | |
| postalCode VARCHAR, -- address[0].postalCode | |
| race VARCHAR, -- US-Core race extension, ombCategory text | |
| ethnicity VARCHAR -- US-Core ethnicity extension, ombCategory text | |
| ); | |
| CREATE TABLE condition ( | |
| id VARCHAR PRIMARY KEY, | |
| patient_id VARCHAR, -- join key -> patient.id | |
| encounter_id VARCHAR, -- join key -> encounter.id | |
| code VARCHAR, | |
| system VARCHAR, -- kept alongside code deliberately: code-system confusion (SNOMED vs ICD-10 vs LOINC) is a failure mode to observe | |
| display VARCHAR, | |
| clinicalStatus VARCHAR, | |
| verificationStatus VARCHAR, | |
| onsetDateTime TIMESTAMP, | |
| abatementDateTime TIMESTAMP, | |
| recordedDate TIMESTAMP | |
| ); | |
| CREATE TABLE observation ( | |
| id VARCHAR PRIMARY KEY, | |
| patient_id VARCHAR, -- join key -> patient.id | |
| encounter_id VARCHAR, -- join key -> encounter.id | |
| code VARCHAR, | |
| system VARCHAR, | |
| display VARCHAR, | |
| category VARCHAR, | |
| status VARCHAR, | |
| effectiveDateTime TIMESTAMP, | |
| valueQuantity DOUBLE, -- value[x] flattened per plan design rule | |
| unit VARCHAR, | |
| valueCodeableConcept VARCHAR, | |
| valueCodeableConcept_system VARCHAR, -- code-system pairing for the value itself, when value[x] is coded | |
| valueString VARCHAR | |
| ); | |
| CREATE TABLE medication_request ( | |
| id VARCHAR PRIMARY KEY, | |
| patient_id VARCHAR, -- join key -> patient.id | |
| encounter_id VARCHAR, -- join key -> encounter.id | |
| code VARCHAR, | |
| system VARCHAR, | |
| display VARCHAR, | |
| status VARCHAR, | |
| intent VARCHAR, | |
| authoredOn TIMESTAMP, | |
| requester_npi VARCHAR, -- prescribing physician's NPI (from MedicationRequest.requester) | |
| requester_name VARCHAR | |
| ); | |
| CREATE TABLE encounter ( | |
| id VARCHAR PRIMARY KEY, | |
| patient_id VARCHAR, -- join key -> patient.id | |
| class_code VARCHAR, -- Encounter.class.code (AMB/EMER/IMP/HH/VR) | |
| type_code VARCHAR, -- Encounter.type[0].coding[0] | |
| type_system VARCHAR, | |
| type_display VARCHAR, | |
| status VARCHAR, | |
| period_start TIMESTAMP, | |
| period_end TIMESTAMP, | |
| reasonCode VARCHAR, | |
| participant_npi VARCHAR, -- primary-performer physician's NPI (Synthea models only one role per encounter, not admitting/attending/etc separately) | |
| participant_name VARCHAR | |
| ); | |
| CREATE TABLE procedure ( | |
| id VARCHAR PRIMARY KEY, | |
| patient_id VARCHAR, -- join key -> patient.id | |
| encounter_id VARCHAR, -- join key -> encounter.id | |
| code VARCHAR, | |
| system VARCHAR, | |
| display VARCHAR, | |
| status VARCHAR, | |
| performedDateTime TIMESTAMP | |
| -- Note: Procedure.performer (physician who performed it) is never populated | |
| -- by this Synthea version (confirmed 0/29,947) -- not available at all. | |
| ); | |
| CREATE TABLE immunization ( | |
| id VARCHAR PRIMARY KEY, | |
| patient_id VARCHAR, -- join key -> patient.id | |
| encounter_id VARCHAR, -- join key -> encounter.id | |
| vaccineCode VARCHAR, | |
| vaccineCode_system VARCHAR, | |
| vaccineCode_display VARCHAR, | |
| status VARCHAR, | |
| occurrenceDateTime TIMESTAMP | |
| ); | |
| CREATE TABLE allergy ( | |
| id VARCHAR PRIMARY KEY, | |
| patient_id VARCHAR, -- join key -> patient.id | |
| code VARCHAR, | |
| system VARCHAR, | |
| display VARCHAR, | |
| clinicalStatus VARCHAR, | |
| verificationStatus VARCHAR, | |
| category VARCHAR, | |
| criticality VARCHAR, | |
| recordedDate TIMESTAMP | |
| ); | |
| CREATE TABLE careplan ( | |
| id VARCHAR PRIMARY KEY, | |
| patient_id VARCHAR, -- join key -> patient.id | |
| encounter_id VARCHAR, -- join key -> encounter.id | |
| category_code VARCHAR, -- CarePlan.category[0].coding[0] | |
| category_system VARCHAR, | |
| category_display VARCHAR, | |
| status VARCHAR, | |
| period_start TIMESTAMP, | |
| period_end TIMESTAMP | |
| ); | |
| CREATE TABLE diagnostic_report ( | |
| id VARCHAR PRIMARY KEY, | |
| patient_id VARCHAR, -- join key -> patient.id | |
| encounter_id VARCHAR, -- join key -> encounter.id | |
| code VARCHAR, | |
| system VARCHAR, | |
| display VARCHAR, | |
| category VARCHAR, | |
| status VARCHAR, | |
| effectiveDateTime TIMESTAMP | |
| ); | |
| CREATE TABLE imaging_study ( | |
| id VARCHAR PRIMARY KEY, | |
| patient_id VARCHAR, -- join key -> patient.id | |
| encounter_id VARCHAR, -- join key -> encounter.id | |
| status VARCHAR, | |
| started TIMESTAMP, | |
| numberOfSeries INTEGER, | |
| numberOfInstances INTEGER, | |
| procedureCode VARCHAR, -- the imaging procedure performed, e.g. "Plain X-ray of ankle region" | |
| procedureCode_system VARCHAR, | |
| procedureCode_display VARCHAR, | |
| modality VARCHAR, -- DICOM modality code, e.g. "DX" = Digital Radiography (from series[0]) | |
| modality_system VARCHAR, | |
| modality_display VARCHAR, | |
| bodySite VARCHAR, -- from series[0] | |
| bodySite_display VARCHAR | |
| ); | |