Reproducibility package for: Constructive Parameter Fibers and Minimal Outputs for Mammillary Compartment Models

Description

Reproducibility package for the paper “Constructive Parameter Fibers and Minimal Outputs for Mammillary Compartment Models” (Guiying Lyu, Hongyu Cao, Ahmad Yahya Dawod). This archive contains all Python/Anaconda source code, exact computational certificates, generated data, and figures that support the manuscript. No empirical or patient data are included. The computations serve as reproducibility and falsification checks; the mathematical proofs in the paper are independent of the code. The package verifies: • closed-form input–output polynomials; • explicit one-output rational parameter fibers; • multi-output constructive inverse maps and permutation ambiguity; • predicted finite-field Jacobian ranks; • exact small-n (n = 4,5,6) forward/reverse fiber coverage and collision limits; • the six-compartment in-silico tracer example (liver, kidney, muscle, adipose) together with its two figures. A total of 241 algebraic and Jacobian-rank checks are reported in the manuscript; three additional exact statements support the biological illustration. All algebraic checks use exact rational arithmetic or finite fields. Floating-point arithmetic is used only for trajectory visualization. How to reproduce: conda env create -f environment.yml conda activate jca-mammillary python run_certificate.py Alternatively: python -m venv .venv python -m pip install -r requirements.txt python run_certificate.py Successful completion is indicated by “all_checks_passed”: true in output/data/computational_certificate.json. The full suite normally finishes in a few seconds on a standard CPU and requires no proprietary computer-algebra system, GPU, network access, or external data. Licenses: source code under MIT; data, certificates, figures and documentation under CC BY 4.0.

Steps to reproduce

1. Download and unzip the package. 2. Create the environment (recommended Anaconda route): conda env create -f environment.yml conda activate jca-mammillary Or standard Python route: python -m venv .venv source .venv/bin/activate # (Windows: .venv\Scripts\activate) python -m pip install -r requirements.txt 3. Run the complete verification suite: python run_certificate.py 4. Successful completion is indicated by the file output/data/computational_certificate.json containing the field "all_checks_passed": true. The full suite of exact rational and finite-field certificates normally finishes in a few seconds on a standard CPU. No proprietary computer-algebra system, GPU, network connection, or external data download is required. Floating-point arithmetic is used only for generating the trajectory figures.

Institutions

• Chiang Mai University

  Chiang Mai, Chiang Mai

Categories

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