biomedical software engineers

Abstract: When the parameter of a PDE surrogate is the flow domain itself, the key/value set of an attention model must encode that domain. We present CARS (Coronary Artery Rapid Surrogate), a learned surrogate for the finite-volume solution map of the steady incompressible Navier-Stokes equations on coronary lumens built from image-derived centerlines. CARS maps a centerline with per-point lumen radius and a scalar inlet flow rate to pressure and velocity at arbitrary query points. The attention focal set is the case's own centerline, so geometry fusion costs $O(N n_f)$ rather than $O(N^2)$ in the number of evaluation points. Trained per territory on $2{,}700$ OpenFOAM solutions with synthetic focal lesions, CARS reaches relative $\ell_2$ errors of $0.120/0.149$ (pressure/velocity) on left-coronary and $0.063/0.119$ on right-coronary test sets, in $87$~ms per case against a solver wall-clock of $572$-$1{,}063$~s. It outperforms four parameter-matched neural operators, and accuracy saturates eightfold below the operating focal count. Fractional flow reserve derived from the predicted pressure matches the CFD label at Pearson $r = 0.941/0.993$ and reproduces the $\mathrm{FFR}\le 0.8$ decision in $97.7\%/96.3\%$ of held-out cases. The predicted velocity does not satisfy continuity closely enough for derived quantities, and the weights are territory-specific.

Abstract: Traditional Chinese medicine (TCM) research connects classical texts, medicinal entities, molecular assays, computational predictions, and clinical studies. An autonomous research agent must preserve the inferential boundaries between these evidence types while coordinating analysis across heterogeneous resources. We introduce TCMScience, a scientific knowledge-discovery agent that separates language-model proposals from execution and release authority. Its architecture combines a trusted kernel, a scientific compiler, and claim-support contracts: plans are compiled into typed operations, execution is bounded by explicit permissions, and candidate findings are checked against source provenance, study design, and claim scope before release. The full capability registry contains 117 public-source connectors with 444 typed operations across 29 domains and 150 native tools across 12 domains; the TCM data hub catalogs 136 databases, 76 dataset specifications, and 84,294 formula-source records. These resources support model-independent workflows through browser and local execution interfaces. In a network-pharmacology analysis of Gegen Qinlian Tang, replacing the whole-proteome background with the assayed-protein background changed the number of significant pathways from 66 to zero; incorporating inactive screening records identified nine pathways, including drug-metabolism signals retained as mechanistic hypotheses. A governance ablation over 121 constructed erroneous outputs spanning 26 classes released 121 errors without governance, 57 with the domain layer, seven with the kernel, and zero with both layers. All 10 compliant controls were retained. These results establish complementary control of known failure modes and show how explicit evidence contracts change the conclusions an agent is permitted to report.