Generated from results/phase1/summary.json, semantic_benchmark.json, results/reproducibility.json, and results/tests.xml; not from assumed physiological outcomes. Regenerate with python scripts/generate_report.py after executing the experiments and tests.
The question is whether biomedical semantics can improve reliable model composition. This milestone tests a narrow part of it: an independently implemented, fixed-topology cardiovascular model plus annotated output-port equivalence checks. It does not establish arbitrary model composition, clinical reliability, patient-specific validity or improved human productivity.
The numerical core operates without an LLM. Three role-separated workstreams supplied physiology, semantic engineering and independent verification. The source/license review and equations are documented in ecosystem.md, physiology.md and ontology.md; the independent executed checks are in independent_verification.md. Earlier verification_protocol.md is a prospective plan, not a statement that every proposed criterion passed.
All physiological parameters are explicitly exploratory and unfitted. The baseline is an elevated-pressure computational reference, not a normal healthy adult. Each scenario starts from identical initial compartment volumes. Reduced contractility halves LV Emax alone; partial restoration multiplies the impaired Emax by 1.5. Neither intervention is a drug-dose model, and these are separate parameter runs, not a timed treatment-response series.
| Scenario | LV Emax (mmHg/mL) | CO (L/min) | Forward SV (mL) | Mean systemic P (mmHg) | LV EDV (mL) | LV ESV (mL) | Mean PV P (mmHg) |
|---|---|---|---|---|---|---|---|
| baseline | 2.500 | 7.6993 | 102.658 | 133.499 | 177.735 | 75.135 | 10.938 |
| reduced_contractility | 1.250 | 6.6993 | 89.325 | 116.434 | 214.082 | 124.705 | 12.999 |
| partial_contractility_restoration | 1.875 | 7.3310 | 97.746 | 127.282 | 190.919 | 93.136 | 11.685 |
Values are computed from the final complete beat. Forward SV integrates aortic flow; EDV/ESV are sampled extrema. PV pressure is a lumped pulmonary venous reservoir pressure, not an atrial measurement or a diagnosis of edema. For this parameter set, reduced LV Emax lowered output and increased ESV and PV pressure. This is a conditional mechanistic result, not a universal monotonicity theorem.
summary_equal=True). This is same-host/same-dependency determinism, not cross-platform proof.The canonical CLI uses tighter settings than the core API default. Independent verification locates the default-versus-tight 0.3153 mL maximum discrepancy at 28.856 s in the systemic arterial compartment, not just during initialization. Tight solution accuracy, temporal settling and output quadrature are distinct questions; successful conservation alone proves none of them.
Independent refinement found a roughly 0.057–0.059% change in forward SV when sampling the same solution at 400 versus 1600 points per beat. Displayed digits are retained for reproducibility, not claimed physiological or quadrature precision. Trapezoidal integration at native adaptive nodes leaves whole-run local flow-balance residuals of about 6.76 mL (baseline) and 4.47 mL (reduced) even at the finest tested ODE settings. Those postprocessing failures coexist with nearly exact global state-volume conservation; stronger cumulative-flow claims are explicitly withheld.
The tight baseline fails the independent final-three-beat 1e-4 mL criterion (residuals about 2.33e-4, 7.37e-5 and 2.29e-5 mL); finer integration passes for baseline and reduced conditions. This does not invalidate the declared 0.1 mL milestone, but it leaves the stronger prospective convergence requirement incomplete.
There are 34 registered variables. Exact external labels are checked against retained source evidence; aggregate compartments and several physical quantities are clearly marked local extensions. The current RDF export separates source-verified labels from project assertions.
The following 12-fixture synthetic fault-injection benchmark is not a user study. The manual condition is scripted acceptance without a validator. The units-only condition checks dimensions and explicit scaling. The semantic condition also checks anatomy, property, reference, time context, bearer and direction. Ground-truth labels are hand-assigned, not independent held-out clinical evidence.
| Condition | Correct accepts | Correct rejects | Unsafe accepts | Incorrect rejects |
|---|---|---|---|---|
| manual | 3 | 0 | 9 | 0 |
| units_only | 3 | 3 | 6 | 0 |
| semantic | 3 | 8 | 1 | 0 |
The semantic layer rejects wrong-anatomy pressure connections that dimensions alone accept. Explicit mmHg-to-Pa and mL/s-to-L/min conversion is supported and actually applied to numeric values. The integration tests verify that the report's semantically transferred cardiac output agrees with the direct numerical metric within floating-point roundoff.
Known failure: correct-looking LV metadata attached to actual RV pressure is accepted. The unsafe transfer was exercised with computed arrays; its maximum error against the intended LV pressure was 129.793 mmHg. This is an output-port corruption experiment, not a modified ODE integration. It demonstrates why metadata provenance and executable field binding need independent review.
The independent reviewer also found that two endpoints with equally missing anatomy identifiers or references could be accepted. A regression test first reproduced the bug, then required-field and flow-orientation checks were added. The original review snapshot remains unchanged; results/independent/c_verify_results.json records the post-fix rerun. Equation strings and free-text source contexts still do not establish mathematical/model-assumption compatibility.
Human integration effort was not measured. Changes in solver stability or conservation under dynamically composed models were not measured, because the model topology is fixed. General semantic connection accuracy and automatic anatomical equivalence remain unestablished.
Open ../results/phase1/index.html for plots, parameters and annotations. CSV, JSON and TriG exports plus output/source checksums are in that directory. results/tests.xml and results/reproducibility.json record executable evidence. requirements.lock pins the dependency environment and dist/ contains the built wheel.
No external reference trajectory has been reproduced; no physiological parameter estimation, patient data, confidence intervals, identifiability analysis or clinical validation are claimed. Numerical domain checks are not physiological range validation. The model omits separate atria, nonlinear passive ventricular mechanics, septal/pericardial interaction, valve inertia, baroreflex, respiratory and renal feedback, and drug pharmacology. The entire prospective verification plan is not complete.
The existing external cardiac simulator was accessible and reviewed, but no external engine was executed or incorporated. Its eight-state architecture is not silently treated as equivalent to this six-state model. Artifact-specific license restrictions are documented. The Smith 2004 CellML captures fall under the Physiome Model Repository CC BY 3.0 statement and may be redistributed with the attribution recorded in physiology.md; the originally parsed workspace-267 capture lacks all parameter and initial values, so only the canonical exposure file can serve as a reference simulation input.