Crate clinlat 

clinlat — Clinical Lattice Types

A Rust substrate for symbolic clinical decision-making based on refinable hypothesis lattices and sound deduction operators.

Overview

The clinlat crate provides:

• Hyp: A partially ordered set (poset) of clinical hypotheses, ordered by refinement.
• Outcome<H, A>: A sum type for operator results (refined hypothesis or abstention).
• Deduction operators: Sound functions that refine hypotheses using clinical evidence (e.g., sofa::SofaRespOperator for respiratory dysfunction severity).

Architecture

Hypotheses and Refinement

A Hyp represents a set of clinical atoms at some level of specificity. Hypotheses are ordered by refinement: h1 ⊑ h2 (h1 refines h2) means h1 is more specific.

let unknown = Hyp::unknown();  // Top element: no information.
let atom = Atom {
    system: OntologySystem::SNOMED,
    code: "67822003".to_string(),
    preferred_term: "Hypoxemia".to_string(),
    version: "2026-01-31".to_string(),
};
let specific = Hyp::new(vec![atom]);  // More specific.
assert!(specific < unknown);  // Refinement ordering.

Operators

An Operator takes a hypothesis and evidence, producing an Outcome:

impl Operator for MyOperator {
    fn apply(&self, h: &Hyp, e: &Evidence) -> Outcome<Hyp, AbstainReason> {
        // Refine h using evidence e, or abstain with a reason.
    }
}

Operators are sound by construction: they satisfy three properties (DEF-PS-08):

1. Refinement monotonicity: Hypothesis specificity never decreases.
2. No spurious refinement: Output never exceeds evidence justification.
3. Abstention purity: Abstention is structural, not error handling.

SOFA-3 Respiratory Scoring

The sofa module implements one operator: SOFA-3 respiratory severity (PaO₂/FiO₂ ratio).

let evidence = SofaRespEvidence::new(350.0, 1.0, false);
let ratio = evidence.pao2_fio2_ratio().unwrap();
let score = score_from_ratio(ratio, false);  // Maps to SOFA score.
assert_eq!(score, Some(1));

v0.2.0-alpha Status

Shipped (Phases 0–3 of the M1 milestone):

• Atom replaces the v0.1.0 &'static str AtomId; resolved through four OntologyAdapter implementations (SNOMED CT, RxNorm, LOINC, ICD-11).
• operator::Evidence is a typed struct carrying Observations and a Provenance carrier (DEF-PS-12, DEF-PS-13).
• Provenance is a typed carrier with origin, timestamp, operator version, metadata, and optional derives_from hashes (DEF-MP-14, OBL-PS-04).
• sofa::SofaRespOperator enforces the version-respecting derivation chain invariant (INV-PS-05) by abstaining on version mismatch rather than silently producing refined output.
• Galois connection: operator::abstract_evidence (α_PS) and operator::is_consistent_with (the γ_PS predicate) are property-tested for the adjunction laws, discharging OBL-PS-02.

Deferred to later phases of the v0.2.0 cut:

• OperatorSet formalization (Phase 4).
• KDIGO AKI, Wells/PE, CURB-65 operators (Phase 5).
• SOFA-respiratory property-test tier upgrade (Phase 6).

References

• Position: Substrate-First Clinical AI (NOTE.md § 4A–4D).
• Formalization: SPEC.md § 2 (patient-state substrate).
• SOFA-3: Vincent et al. (1996), Singer et al. (2016, Sepsis-3).

Re-exports

pub use abstain::AbstainReason;

pub use curb65::Curb65Operator;

pub use hyp::Hyp;

pub use kdigo_aki::KdigoAkiOperator;

pub use lattice_search::LatticeSearchProposer;

pub use llm_proposer::LlmProposer;

pub use llm_proposer_config::LlmProposerConfig;

pub use llm_proposer_config::LlmProvider;

pub use ontology::Atom;

pub use ontology::CacheMode;

pub use ontology::Icd11Adapter;

pub use ontology::LoincAdapter;

pub use ontology::OntologyAdapter;

pub use ontology::OntologyError;

pub use ontology::OntologySystem;

pub use ontology::RxNormAdapter;

pub use ontology::SNOMEDAdapter;

pub use operator::Evidence;

pub use operator::Observation;

pub use operator::Operator;

pub use operator::abstract_evidence;

pub use operator::is_consistent_with;

pub use operator_set::OperatorMetadata;

pub use operator_set::OperatorSet;

pub use operator_set::SetOutcome;

pub use outcome::Outcome;

pub use proposer::CandidateSet;

pub use proposer::ConstraintError;

pub use proposer::FilterResult;

pub use proposer::ProposerConstraint;

pub use proposer::RefinementProposer;

pub use proposer::VerifyResult;

pub use proposer::propose_and_filter;

pub use proposer::propose_verify;

pub use provenance::Provenance;

pub use provenance::ProvenanceOrigin;

pub use sofa::SofaRespEvidence;

pub use sofa::SofaRespHypothesis;

pub use sofa::SofaRespOperator;

pub use version::Ver;

pub use wells_pe::WellsPeOperator;

Modules

abstain

Abstention reasons for deduction operators.

curb65

CURB-65 operator for community-acquired pneumonia disposition.

hyp

Clinical hypotheses as a refinable poset.

kdigo_aki

KDIGO AKI staging operator.

lattice_search

Exhaustive lattice-search proposer.

llm_proposer

LLM-based refinement proposer adapter (task 10.2).

llm_proposer_config

Configuration for LLM-based refinement proposer.

ontology

Ontology adapter infrastructure for binding clinical atoms to external ontology systems.

operator

Deduction operators on hypotheses.

operator_set

Composition of multiple deduction operators.

outcome

Operator outcome types: refined hypothesis or abstention.

proposer

Refinement proposers: black-box candidate generators per DEF-PS-14 / DEF-PS-15.

provenance

Provenance carrier for tracking evidence source, timestamp, and version through operator derivations.

sofa

SOFA-3 respiratory component (PaO₂/FiO₂ ratio) deduction operator.

version

Version tuple for tracking operator and build versions in provenance chains.

wells_pe

Wells score operator for pulmonary embolism risk stratification.