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Update README with cohort diagnostics and phenotype validation #20

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rkboyce merged 1 commit into from
Mar 17, 2026
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Update README with cohort diagnostics and phenotype validation #20

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16 changes: 13 additions & 3 deletions README.md
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Expand Up @@ -204,6 +204,16 @@ Below is a set of planned study agent services, organized by category. For each
**Output:** Directed acyclic graph of known causal/associative relations (LLM + literature discovery).
**Validation:** Consistency with cited relations and domain plausibility.

#### `explain_cohort_diagnostics`
**Input:** The user's study intent statement and cohort diagnostics output including code to run and the results files
**Output:** narrative summary / report of the analysis.
**Validation:** Correctly reported summary of the methods and results.

#### `explain_incidence/estimation/characterization_results`
**Input:** The user's study intent statement and cohort diagnostics and a completed analysis with strategus output folders with code to run and the results files (incidence/estimation/characterization).
**Output:** narrative summary / report of the analysis.
**Validation:** Correctly reported summary of the methods and results.

### High Level Operational

#### `strategus_*`
Expand Down Expand Up @@ -266,9 +276,9 @@ Below is a set of planned study agent services, organized by category. For each
**Validation:** Reproducible execution outputs; summary tied to diagnostics.

#### `phenotype_validation_review`
**Input:** Selected phenotype definition(s).
**Output:** Code to sample cases for validation and compare to known phenotype performance.
**Validation:** Sampling logic review; user confirmation before running.
**Input:** Selected phenotype definition (usually for an outcome cohort) and a narrative clinical description with differential diagnoses and known associated factors for validation and to compare to known phenotype performance.
**Output:** code to extract sample cases based on the clinical description and LLM-assessment of a sample (user-specified or random) of cohort records stripped of PHI.
**Validation:** Sampling logic review; user confirmation.

#### `cohort_definition_build`
**Input:** Phenotype/covariate intent without a cohort definition.
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