recode-scenario

Creation of clinical scenario for medical documents generation

Create prompts to guide LLM in generation of clinical discharge report. Prompts are made by the association of :

• clinical scenario = medico-economic data sampled from french national hospitalization claims data (Base nationale PMSI)
• documents templates
• instruction for the model

The script describe an example of utilisation with Mistral API to generate a complete clinical report.

How to

• Config file : you need a file name config.py with de variables

api_key = "xxxx" # Mistral API key

path_results = "/path/to/result/"

• A data repository containing files with data extracted from claims data.

Variables definition

Variables dictionary :

• drg_code
• drg_description
• drg_parent_code
• drg_parent_code_description
• icd_code
• icd_code_description
• icd_parent_code
• icd_parent_code_description
• icd_primary_code : digonstic principal
• icd_primary_code_definition : digonstic principal
• icd_secondary : related diagnosis
• cage : age classes [0-1[, [1-5[,[15-18[, [5-10[, [10-15[, [30-40[, [50-60[, [18-30[, [40-50[, [60-70[, [70-80[, [80-[
• cage2 : age classes [0-1[ , [1-5[ , [5-10[ , [10-15[ , [15-18[, [18-50[ , [50-[
• sexe : 1/2 (F)
• admission_mode
• discharge_disposition
• admission_type

Table classification_profile

• drg_parent_code
• icd_primary_code
• icd_primary_parent_code
• case_management_type
• cage
• cage2
• sexe

Table secondary_diagnosis

• drg_parent_code
• icd_primary_parent_code
• cage2
• sexe

For cancer, we use a synthetic treatment recommandation table :

• primary_site
• histological_type
• Stage
• TNM_score
  • T : tumor (TNM)
  • N : nodes (TNM)
  • M : metastasis (TNM)
• biomarkers
• treatment_recommandation
• chemotherapy_regimen

Use the col_names options when import files in the load function of the project to align the columns names of your files with this dictionary.

French PMSI term	English equivalent	Notes / Context
Résumé PMSI	Patient-level coded abstract / Discharge abstract	Structured data for each hospitalization, includes ICD diagnoses, procedures, demographics.
Code diagnostic principal (DP)	Primary diagnosis (ICD code)	Main reason for hospitalization.
Codes diagnostics associés (DAS)	Secondary diagnoses (ICD codes)	Comorbidities or complications during the stay.
Actes	Procedures / ICD procedure codes	Coded interventions performed during hospitalization.
GHM (Groupe Homogène de Malades)	DRG (Diagnosis-Related Group)	Classification for resource use / reimbursement purposes.
CMD (Catégorie maejeure de diagnsotic)	MDC (Major Diagnostic Category)	Top-level DRG grouping by body system or disease category.
Données de séjour vs Données de patient	Case-level data vs Patient-level data`	Individual hospitalization record used for DRG assignment or analysis.
Mode entrée	Admission mode	How the patient was admitted to the hospital.
Mode de sortie	Discharge disposition	How the patient was discharged from the hospital, including deceased.
Mode d'hospitalisation	Type of admission	Inpatient admission vs Outpatient admission
Variables normalisées	Normalized variables / Standardized coded fields	Coded fields derived from the patient record (ICD, procedures, demographics).

Hospitalization management type

Hospitalization management type – a clinical abstraction derived from the combination of the principal diagnosis (DP) and the linked diagnosis (DR). This combination determines the DRG assignment and reflects the patient’s management mode during the hospital stay.

Hospitalization management type are inhéreted from ATIH coding rules : cf recap table Guide Situations cliniques.

Hospitalization management type for chronic diseases

Cancer	Diabetis	Other chronic diseases
Hospital admission with initial diagnosis of the cancer	Hospital admission with initial diagnosis of diabetes	Hospital admission with initial diagnosis of the disease
Hospital admission for cancer workup	Hospital admission for diabetes initial workup	Hospital admission for diagnostic workup
Hospital admission for initiation of treatment	Hospital admission for initiation of treatment of the diabetes	Hospital admission for initiation of treatment
Hospital admission for relapse or recurrence of the cancer	Hospital admission for change in therapeutic strategy	Hospital admission for acute exacerbation of the disease
Hospital admission for surgery

TODO

• Referentials
  • Transfrom all referentials into config files
• ATIH rules :
  • Review delivery recommandations