Index

A

ancestor_chain_ids() (in module phenoforge.engine.expansion)

assemble() (in module phenoforge.agent.nodes)

B

baseline_hierarchical_score (phenoforge.eval.models.DecompositionCaseResult attribute) BenchmarkReport (class in phenoforge.eval.models)

BM25Retriever (class in phenoforge.engine.retrieval) build_graph() (in module phenoforge.agent.graph)

C

check_curated() (in module phenoforge.agent.nodes) cohort_id (phenoforge.eval.decomposition.DecompositionTestCase attribute) (phenoforge.eval.models.CohortEvalResult attribute) (phenoforge.eval.models.DecompositionCaseResult attribute) cohort_name (phenoforge.eval.models.CohortEvalResult attribute) (phenoforge.eval.models.DecompositionCaseResult attribute) CohortAssemblyState (class in phenoforge.agent.state) CohortEvalResult (class in phenoforge.eval.models) Concept (class in phenoforge.engine.models) concept (phenoforge.agent.state.PendingCandidate attribute) concept_code (phenoforge.engine.curated.CuratedCohortConceptItem attribute) (phenoforge.engine.explain.InclusionExplanation attribute) (phenoforge.engine.models.Concept attribute) concept_id (phenoforge.engine.curated.CuratedCohortConceptItem attribute) (phenoforge.engine.models.Concept attribute)

concept_name (phenoforge.engine.explain.InclusionExplanation attribute) (phenoforge.engine.models.Concept attribute) concepts (phenoforge.engine.models.ConceptSet attribute) ConceptSet (class in phenoforge.engine.models) ConceptWithProvenance (class in phenoforge.engine.models) configure() (in module phenoforge.mcp.server) confirm() (in module phenoforge.agent.nodes) confirmed_codes (phenoforge.agent.state.CohortAssemblyState attribute) connect() (in module phenoforge.engine.db) coverage (phenoforge.eval.models.CohortEvalResult attribute) curated (phenoforge.agent.state.SeedTermResult attribute) CURATED (phenoforge.engine.models.ProvenanceTier attribute) CuratedCohortConceptItem (class in phenoforge.engine.curated)

D

decompose() (in module phenoforge.agent.nodes) decomposed_hierarchical_score (phenoforge.eval.models.DecompositionCaseResult attribute) DecomposedTerms (class in phenoforge.agent.nodes) DecompositionCaseResult (class in phenoforge.eval.models) DecompositionReport (class in phenoforge.eval.models) DecompositionTestCase (class in phenoforge.eval.decomposition)

default_decomposer() (in module phenoforge.agent.nodes) default_embedder() (in module phenoforge.engine.dense) DEFAULT_TEST_CASES (in module phenoforge.eval.decomposition) DenseRetriever (class in phenoforge.engine.dense) distance_weighted_score() (in module phenoforge.eval.metrics) domain_id (phenoforge.engine.models.Concept attribute)

E

evidence (phenoforge.engine.explain.InclusionPath attribute) expand_ancestors() (in module phenoforge.engine.expansion) expand_descendants() (in module phenoforge.engine.expansion)

expand_hierarchy() (in module phenoforge.mcp.server) explain_inclusion() (in module phenoforge.engine.explain) (in module phenoforge.mcp.server)

F

final_concept_set (phenoforge.agent.state.CohortAssemblyState attribute) find_curated_definition() (in module phenoforge.engine.curated) (in module phenoforge.mcp.server)

find_high_fanout_snomed_concepts() (in module phenoforge.engine.curated)

G

gap (phenoforge.eval.models.DecompositionCaseResult attribute) generate() (in module phenoforge.agent.nodes)

GENERATED (phenoforge.engine.models.ProvenanceTier attribute) ground_truth_codes (phenoforge.eval.models.CohortEvalResult attribute)

H

hierarchical_score (phenoforge.eval.models.CohortEvalResult attribute)

hierarchical_score() (in module phenoforge.eval.metrics) hybrid_search() (in module phenoforge.engine.hybrid)

I

include_descendants (phenoforge.engine.curated.CuratedCohortConceptItem attribute) InclusionExplanation (class in phenoforge.engine.explain)

InclusionPath (class in phenoforge.engine.explain) is_excluded (phenoforge.engine.curated.CuratedCohortConceptItem attribute)

L

load_cohort_concept_items() (in module phenoforge.engine.curated) load_curated_concept_set() (in module phenoforge.engine.curated)

lookup_by_code() (in module phenoforge.engine.lookup) lookup_concept() (in module phenoforge.mcp.server)

M

main() (in module phenoforge.mcp.server) match_scores() (in module phenoforge.eval.harness) mean_coverage_by_method (phenoforge.eval.models.BenchmarkReport attribute) mean_gap (phenoforge.eval.models.DecompositionReport attribute) mean_hierarchical_score_by_method (phenoforge.eval.models.BenchmarkReport attribute) mean_over_inclusion_by_method (phenoforge.eval.models.BenchmarkReport attribute) method (phenoforge.eval.models.CohortEvalResult attribute) model_config (phenoforge.agent.nodes.DecomposedTerms attribute) (phenoforge.agent.state.CohortAssemblyState attribute) (phenoforge.agent.state.PendingCandidate attribute) (phenoforge.agent.state.SeedTermResult attribute) (phenoforge.engine.curated.CuratedCohortConceptItem attribute) (phenoforge.engine.explain.InclusionExplanation attribute) (phenoforge.engine.explain.InclusionPath attribute) (phenoforge.engine.models.Concept attribute) (phenoforge.engine.models.ConceptSet attribute) (phenoforge.engine.models.ConceptWithProvenance attribute) (phenoforge.engine.models.UnmappableTerm attribute) (phenoforge.eval.decomposition.DecompositionTestCase attribute) (phenoforge.eval.models.BenchmarkReport attribute) (phenoforge.eval.models.CohortEvalResult attribute) (phenoforge.eval.models.DecompositionCaseResult attribute) (phenoforge.eval.models.DecompositionReport attribute)

module phenoforge.agent.graph phenoforge.agent.nodes phenoforge.agent.state phenoforge.engine.curated phenoforge.engine.db phenoforge.engine.dense phenoforge.engine.expansion phenoforge.engine.explain phenoforge.engine.hybrid phenoforge.engine.lookup phenoforge.engine.models phenoforge.engine.retrieval phenoforge.eval.decomposition phenoforge.eval.harness phenoforge.eval.metrics phenoforge.eval.models phenoforge.mcp.server

O

over_inclusion_penalty (phenoforge.eval.models.CohortEvalResult attribute)

over_inclusion_penalty() (in module phenoforge.eval.metrics)

P

paths (phenoforge.engine.explain.InclusionExplanation attribute) pending_candidates (phenoforge.agent.state.CohortAssemblyState attribute) PendingCandidate (class in phenoforge.agent.state) phenoforge.agent.graph module phenoforge.agent.nodes module phenoforge.agent.state module phenoforge.engine.curated module phenoforge.engine.db module phenoforge.engine.dense module phenoforge.engine.expansion module phenoforge.engine.explain module phenoforge.engine.hybrid module

phenoforge.engine.lookup module phenoforge.engine.models module phenoforge.engine.retrieval module phenoforge.eval.decomposition module phenoforge.eval.harness module phenoforge.eval.metrics module phenoforge.eval.models module phenoforge.mcp.server module population_description (phenoforge.agent.state.CohortAssemblyState attribute) (phenoforge.eval.decomposition.DecompositionTestCase attribute) (phenoforge.eval.models.DecompositionCaseResult attribute) predicted_codes (phenoforge.eval.models.CohortEvalResult attribute) ProvenanceTier (class in phenoforge.engine.models) PUBLISHED (phenoforge.engine.models.ProvenanceTier attribute)

R

reason (phenoforge.engine.models.UnmappableTerm attribute) reciprocal_rank_fusion() (in module phenoforge.engine.hybrid) resolve_curated_concepts() (in module phenoforge.engine.curated)

resolved (phenoforge.agent.state.SeedTermResult attribute) results (phenoforge.eval.models.BenchmarkReport attribute) (phenoforge.eval.models.DecompositionReport attribute) run_benchmark() (in module phenoforge.eval.harness)

S

score_cohort() (in module phenoforge.eval.harness) score_decomposition() (in module phenoforge.eval.decomposition) search() (phenoforge.engine.dense.DenseRetriever method) (phenoforge.engine.retrieval.BM25Retriever method) search_concepts() (in module phenoforge.mcp.server) seed_terms (phenoforge.agent.state.CohortAssemblyState attribute) (phenoforge.eval.models.DecompositionCaseResult attribute)

SeedTermResult (class in phenoforge.agent.state) set_coverage() (in module phenoforge.eval.metrics) source (phenoforge.engine.explain.InclusionPath attribute) (phenoforge.engine.models.ConceptWithProvenance attribute) (phenoforge.eval.decomposition.DecompositionTestCase attribute)

T

term (phenoforge.agent.state.PendingCandidate attribute) (phenoforge.agent.state.SeedTermResult attribute) (phenoforge.engine.models.UnmappableTerm attribute) term_results (phenoforge.agent.state.CohortAssemblyState attribute)

terms (phenoforge.agent.nodes.DecomposedTerms attribute) tier (phenoforge.engine.explain.InclusionPath attribute) (phenoforge.engine.models.ConceptWithProvenance attribute) tree_distance() (in module phenoforge.eval.metrics)

U

unmappable (phenoforge.agent.state.CohortAssemblyState attribute) (phenoforge.engine.models.ConceptSet attribute)

UnmappableTerm (class in phenoforge.engine.models) unresolvable_ground_truth (phenoforge.eval.models.CohortEvalResult attribute)

V

vocabulary_id (phenoforge.engine.curated.CuratedCohortConceptItem attribute) (phenoforge.engine.models.Concept attribute)