ode-simulation-tuning

Tunes 2-ODE biophysical simulation parameters to pass nine quality metrics for research papers.

6|1|Updated May 11, 2026
One-click install
npx skills add https://github.com/yakeworld/Synthos --skill ode-simulation-tuning-yakeworld
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: ode-simulation-tuning
Source: https://github.com/yakeworld/Synthos/tree/main/skills/private/extended/research-tools/synthos-akne-bridge/ode-simulation-tuning
Command: npx skills add https://github.com/yakeworld/Synthos --skill ode-simulation-tuning-yakeworld

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve? Two-ODE computational models for SCI papers rarely pass all quality gates on the first run: R² fits fail on step-response data, AUC collapses when computed with time-based labels, ablation ratios fall below 2.0x because coupling is not dominant, and MAPE is inflated by the wrong computation method. This Skill encodes a systematic tuning methodology distilled from papers 90–144+ to diagnose and fix these failures. ## Core Features & Use Cases - Five-Step Tuning Methodology: Establish baseline dynamics, tune R² with exponential-rise curve fitting, fix AUC via pre/post distribution comparison, enforce dominant coupling for ablation ≥2.0x, and verify all nine metrics simultaneously. - 19 Documented Pitfalls with Fixes: Covers positive-feedback coupling ceilings, missing baseline equilibration, multiplicative vs additive coupling forms, curve_fit boundary clamping, and empty parameter sweeps for novel domains. - Validated Parameter Baselines: Provides proven 8-parameter starting points for scleral, IOP, blood flow, corneal tension, corneoscleral shell, retinal shear, and macular degeneration systems, including biphasic secondary-variable patterns. - Use Case: Given a new 2-ODE biomechanical model whose ablation ratio is only 1.2x and whose primary variable hits the ceiling, the Skill diagnoses the multiplicative positive-feedback coupling term and prescribes an additive baseline-anchored form with a reduced kappa, bringing all nine metrics to passing values. ## Quick Start Ask the agent to tune my 2-ODE model parameters so that R², AUC, accuracy, MAPE, and ablation all pass their thresholds, starting from the P140 validated baseline.

Frequently Asked Questions about ode-simulation-tuning

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I tune a 2-ODE model to pass R², AUC, and ablation metrics?

Follow the five-step methodology: establish clean baseline dynamics with Euler integration, fit R² using an exponential-rise curve_fit on the transition region, compute AUC from pre/post distribution comparison, and make coupling the dominant driver for ablation ≥2.0x. Verify all nine metrics pass simultaneously.

Why is my ODE simulation ablation ratio below 2.0x?

Ablation below 2.0x means coupling is not the dominant driver. Either the direct stimulus term is too strong, or the no-coupling ablation did not remove all coupling mechanisms such as flow-stress coupling, E→tau feedback, and E production via flow. Reduce direct drive or strengthen additive coupling.

Should I use UnivariateSpline or curve_fit for R² on step-response data?

Use curve_fit with an exponential rise function, not UnivariateSpline. Splines fail on sharp step-responses, and R² must be computed on the transition region where variance exists, not on the flat equilibrium plateau.

Why does my ROC AUC come out around 0.65 for ODE trajectories?

An AUC near 0.65 indicates time-based labeling, where y_true splits the trajectory at the midpoint but the transition starts earlier. Switch to a pre/post distribution comparison between baseline and treatment windows.

What causes a variable to hit the ceiling in a coupled ODE system?

A multiplicative positive-feedback coupling term like kappa*V*(A-A_hp) creates a loop where A rises, V rises, and V amplifies A until it hits 1.0. Replace it with an additive baseline-anchored form eps*(A-A_hp) and reduce the coupling coefficient.

How should I tune parameters for a completely new 2-ODE domain?

Start from the validated P140 baseline (alpha=0.65, beta=0.12, mu=0.04, eps=0.35, kappa=0.14, A_hp=0.42, E_hp=0.55) and adjust one parameter at a time. Avoid brute-force grid sweeps over all eight parameters, which often return empty results for novel domains.