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Research-Stack/5-Applications/scripts/categorize_extracted_models.py

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#!/usr/bin/env python3
"""
Batch categorize Extracted models in MATH_MODEL_MAP.tsv
Updates Family and Bind_Class fields based on domain classification
"""
import re
from pathlib import Path
# Domain mappings: Family name -> (bind_class, domain_type)
DOMAIN_MAPPINGS = {
# Genetics & Evolution (informational_bind)
"Hardy-Weinberg": ("Population Genetics", "informational_bind", "LAYER_B_ROUTING"),
"Arrhenius Eq": ("Thermodynamics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Central Dogma ODE": ("Genetics", "informational_bind", "LAYER_B_ROUTING"),
"RNA Folding ΔG": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Replicator Eq": ("Evolutionary Dynamics", "informational_bind", "LAYER_J_DYNAMICS"),
"Fisher's Theorem": ("Population Genetics", "informational_bind", "LAYER_B_ROUTING"),
"Neutral Theory (Kimura)": ("Evolutionary Dynamics", "informational_bind", "LAYER_J_DYNAMICS"),
"Price Equation": ("Evolutionary Dynamics", "informational_bind", "LAYER_J_DYNAMICS"),
"Quasispecies Eq": ("Evolutionary Dynamics", "informational_bind", "LAYER_J_DYNAMICS"),
"Wright-Fisher Drift": ("Population Genetics", "informational_bind", "LAYER_B_ROUTING"),
"Genetic Toggle": ("Synthetic Biology", "control_bind", "LAYER_F_CONTROL"),
"The Repressilator": ("Synthetic Biology", "control_bind", "LAYER_F_CONTROL"),
"Feed-Forward Loop": ("Synthetic Biology", "control_bind", "LAYER_F_CONTROL"),
"Competitive Exclusion": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Allee Effect": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Island Biogeography": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Hamilton's Rule": ("Evolutionary Dynamics", "informational_bind", "LAYER_B_ROUTING"),
"Cope's Rule": ("Evolutionary Dynamics", "informational_bind", "LAYER_J_DYNAMICS"),
"Clonal Selection": ("Immunology", "informational_bind", "LAYER_B_ROUTING"),
"Viral Kinetics": ("Epidemiology", "informational_bind", "LAYER_J_DYNAMICS"),
"Gompertz-Makeham": ("Demography", "informational_bind", "LAYER_B_ROUTING"),
"Cancer Invasion": ("Oncology", "informational_bind", "LAYER_J_DYNAMICS"),
"Mendelian Sum": ("Genetics", "informational_bind", "LAYER_B_ROUTING"),
"Morgan Linkage": ("Genetics", "informational_bind", "LAYER_B_ROUTING"),
"Polygenic CLT": ("Genetics", "informational_bind", "LAYER_B_ROUTING"),
# Biophysics & Molecular (thermodynamic_bind)
"Hill Equation": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Adair Equation": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"MWC Allostery": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"KNF Allostery": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Waddington Potential": ("Developmental Biology", "thermodynamic_bind", "LAYER_J_DYNAMICS"),
"Gierer-Meinhardt": ("Developmental Biology", "thermodynamic_bind", "LAYER_J_DYNAMICS"),
"Flux Balance (FBA)": ("Metabolism", "thermodynamic_bind", "LAYER_G_ENERGY"),
"MaxEnt Production": ("Thermodynamics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"MTE Master Eq": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Lifespan Scaling": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Reproductive Effort": ("Life History", "thermodynamic_bind", "LAYER_G_ENERGY"),
"ROS Damage": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Maturity Invariant": ("Life History", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Fecundity Ratio": ("Life History", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Energy Invariant": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Self-Assembly ΔG": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"CMC Threshold": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"DNA Tile Logic": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Anfinsen's Dogma": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Levinthal Space": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Folding Landscape": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Contact Order": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
# Neuroscience (control_bind)
"Social Force Model": ("Behavioral Dynamics", "control_bind", "LAYER_F_CONTROL"),
"Wolff's Law Equilibrium": ("Biomechanics", "physical_bind", "LAYER_L_APPLICATION"),
"Izhikevich Neuron": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Kuramoto Synchrony": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Integrated Information": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Neuronal Workspace": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Objective Reduction": ("Quantum Biology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Behavioral Attractor": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Circadian Oscillator": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Weber-Fechner Law": ("Perception", "informational_bind", "LAYER_K_SIGNAL"),
"Stevens' Power Law": ("Perception", "informational_bind", "LAYER_K_SIGNAL"),
"Opponent Theory": ("Perception", "informational_bind", "LAYER_K_SIGNAL"),
"Retinex Designator": ("Perception", "informational_bind", "LAYER_K_SIGNAL"),
"Lateral Inhibition": ("Perception", "informational_bind", "LAYER_K_SIGNAL"),
"CIELAB Mapping": ("Perception", "geometric_bind", "LAYER_K_SIGNAL"),
"Brain Allometry": ("Neuroscience", "geometric_bind", "LAYER_C_TOPOLOGY"),
"EQ Index": ("Neuroscience", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Hick's Law": ("Cognitive Science", "informational_bind", "LAYER_B_ROUTING"),
"Fitts's Law": ("Cognitive Science", "informational_bind", "LAYER_B_ROUTING"),
"Zipf's Law": ("Information Theory", "informational_bind", "LAYER_A_COMPRESSION"),
"Laughlin's Law": ("Neuroscience", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Hebb's Law": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Oja's Rule": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Hopfield Energy": ("Neuroscience", "thermodynamic_bind", "LAYER_G_ENERGY"),
# Ecology & Population (informational_bind)
"May's Stability": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Daisyworld Homeostasis": ("Ecology", "control_bind", "LAYER_F_CONTROL"),
"Marginal Value Thm": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Pipe Model Theory": ("Botany", "geometric_bind", "LAYER_C_TOPOLOGY"),
# Cardiovascular/Physiological (physical_bind) - LOW PRIORITY
"Poiseuille's Law": ("Physiology", "physical_bind", "LAYER_L_APPLICATION"),
"Starling's Law": ("Physiology", "physical_bind", "LAYER_L_APPLICATION"),
"Fick Principle": ("Physiology", "physical_bind", "LAYER_L_APPLICATION"),
"SA:V Scaling Law": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Membrane Tension": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"Osmotic Pressure": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"Muscle Force-Vel": ("Biomechanics", "physical_bind", "LAYER_L_APPLICATION"),
"Nernst Potential": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"GHK Equation": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"Donnan Product": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"Gibbs-Duhem Eq": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Second Bio-Law": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
# Scaling Laws (geometric_bind) - LOW PRIORITY
"WBE Branching": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Horton Number Law": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Horton Length Law": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"WBE Exponent": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Heart Rate Law": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Blood Volume Law": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
# Quantum/Biophysical (thermodynamic_bind) - LOW PRIORITY
"Radical Pair Eq": ("Quantum Biology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Exciton Transfer": ("Quantum Biology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Proton Tunneling": ("Quantum Biology", "thermodynamic_bind", "LAYER_G_ENERGY"),
# Behavioral/Ecological (control_bind) - LOW PRIORITY
"Sonar Ranging": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Auditory Filter": ("Perception", "informational_bind", "LAYER_K_SIGNAL"),
"Kinematic Replication": ("Developmental Biology", "control_bind", "LAYER_F_CONTROL"),
"Vicsek Swarming": ("Behavioral Dynamics", "control_bind", "LAYER_F_CONTROL"),
"Lévy Flight": ("Behavioral Dynamics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Cable Equation": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
# Other models - assign based on context
"Morpho-Transform": ("Developmental Biology", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Murray's Law": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
# Ecology & Population (informational_bind/control_bind)
"Growth Dilution": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Redfield Ratio": ("Biogeochemistry", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Holling Response": ("Ecology", "control_bind", "LAYER_F_CONTROL"),
"Eco-Connectance": ("Ecology", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Taylor's Law": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Logistic Map": ("Ecology", "control_bind", "LAYER_F_CONTROL"),
"Lotka's Invariant": ("Demography", "informational_bind", "LAYER_B_ROUTING"),
"Tetz's Law": ("Evolutionary Biology", "informational_bind", "LAYER_J_DYNAMICS"),
"Survival Limit": ("Demography", "informational_bind", "LAYER_B_ROUTING"),
"Genomic Entropy": ("Genetics", "informational_bind", "LAYER_A_COMPRESSION"),
"Codon Hamming": ("Genetics", "informational_bind", "LAYER_B_ROUTING"),
"Bio-Capacity": ("Genetics", "informational_bind", "LAYER_B_ROUTING"),
"Error Catastrophe": ("Evolutionary Biology", "informational_bind", "LAYER_J_DYNAMICS"),
"Bio-Hamiltonian": ("Evolutionary Biology", "control_bind", "LAYER_F_CONTROL"),
"Requisite Variety": ("Control Theory", "control_bind", "LAYER_F_CONTROL"),
"Bio-Reinforcement": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Pareto Robustness": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Limit Cycle Thm": ("Dynamical Systems", "control_bind", "LAYER_F_CONTROL"),
"Phase Singularity": ("Dynamical Systems", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Hawk-Dove ESS": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Van Valen's Law": ("Evolutionary Biology", "informational_bind", "LAYER_J_DYNAMICS"),
"Scale-Free Dist": ("Network Theory", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Preferential Att": ("Network Theory", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Neutrality Rule": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Adami Complexity": ("Evolutionary Biology", "informational_bind", "LAYER_A_COMPRESSION"),
"Regulatory Law": ("Genetics", "informational_bind", "LAYER_B_ROUTING"),
"Revelle Factor": ("Biogeochemistry", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Remineral Ratio": ("Biogeochemistry", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Small-World Law": ("Network Theory", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Modularity Q": ("Network Theory", "geometric_bind", "LAYER_C_TOPOLOGY"),
"HOT Principle": ("Complexity Theory", "control_bind", "LAYER_F_CONTROL"),
"Complexity Law": ("Complexity Theory", "informational_bind", "LAYER_A_COMPRESSION"),
"GK-Switch": ("Biophysics", "control_bind", "LAYER_F_CONTROL"),
"Mitotic Oscillator": ("Cell Biology", "control_bind", "LAYER_F_CONTROL"),
"PER-CRY Feedback": ("Circadian Biology", "control_bind", "LAYER_F_CONTROL"),
"Keller-Segel": ("Developmental Biology", "control_bind", "LAYER_F_CONTROL"),
"Epigenetic Clock": ("Epigenetics", "informational_bind", "LAYER_B_ROUTING"),
"Kinetic Proofread": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Biodiversity Num": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Critical Power Law": ("Complexity Theory", "informational_bind", "LAYER_A_COMPRESSION"),
"Broken Stick": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Niche Breadth": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Niche Overlap": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Motor Efficiency": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Parrondo Paradox": ("Game Theory", "control_bind", "LAYER_F_CONTROL"),
"Somite Size Law": ("Developmental Biology", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Morphogen Scaling": ("Developmental Biology", "geometric_bind", "LAYER_C_TOPOLOGY"),
"MDDR Growth Law": ("Developmental Biology", "control_bind", "LAYER_F_CONTROL"),
"Fermat's Path Law": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Max Flux Principle": ("Metabolism", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Max Power Law": ("Thermodynamics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Least Action Law": ("Physics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Action Functional": ("Physics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"CSD Autocorr": ("Complexity Theory", "informational_bind", "LAYER_A_COMPRESSION"),
"CSD Variance": ("Complexity Theory", "informational_bind", "LAYER_A_COMPRESSION"),
"Recovery Rate": ("Ecology", "control_bind", "LAYER_F_CONTROL"),
"Resilience Basin": ("Ecology", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Sensing Limit": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"Signaling SNR": ("Biophysics", "informational_bind", "LAYER_K_SIGNAL"),
"Positional Noise": ("Biophysics", "informational_bind", "LAYER_K_SIGNAL"),
"Oregonator BZ": ("Chemical Physics", "control_bind", "LAYER_F_CONTROL"),
"Firefly Synchrony": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Bio-Continuity": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"Strouhal Number": ("Biomechanics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Froude Number": ("Biomechanics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Huxley Muscle Law": ("Biomechanics", "physical_bind", "LAYER_L_APPLICATION"),
"Monod Equation": ("Microbiology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Pirt's Law": ("Microbiology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Verhulst Logistic": ("Ecology", "control_bind", "LAYER_F_CONTROL"),
"Gompertz Growth": ("Ecology", "control_bind", "LAYER_F_CONTROL"),
"MCA Control Coeff": ("Metabolism", "thermodynamic_bind", "LAYER_G_ENERGY"),
"MCA Summation": ("Metabolism", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Perfect Adapt": ("Control Theory", "control_bind", "LAYER_F_CONTROL"),
"Demand Rule": ("Genetics", "control_bind", "LAYER_F_CONTROL"),
"Place Theory": ("Perception", "informational_bind", "LAYER_K_SIGNAL"),
"Traveling Wave": ("Perception", "geometric_bind", "LAYER_K_SIGNAL"),
"Tonotopic Map": ("Perception", "geometric_bind", "LAYER_K_SIGNAL"),
"Cochlear Amp": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"R* Theory": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"SM Correlation": ("Demography", "informational_bind", "LAYER_B_ROUTING"),
"Vitality Decay": ("Demography", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Mortality Plateau": ("Demography", "informational_bind", "LAYER_B_ROUTING"),
"Bark Scale": ("Perception", "informational_bind", "LAYER_K_SIGNAL"),
"Crit Bandwidth": ("Perception", "informational_bind", "LAYER_K_SIGNAL"),
"Equal Loudness": ("Perception", "informational_bind", "LAYER_K_SIGNAL"),
"Niche Hypervolume": ("Ecology", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Nernst-Planck": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"Richness Scaling": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"FHN Excitability": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Swift-Hohenberg": ("Pattern Formation", "control_bind", "LAYER_F_CONTROL"),
"Tissue Stiffness": ("Biomechanics", "physical_bind", "LAYER_L_APPLICATION"),
"Cytoskeletal F": ("Biomechanics", "physical_bind", "LAYER_L_APPLICATION"),
"Spiral Vogel": ("Botany", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Golden Angle": ("Botany", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Hofmeister Rule": ("Botany", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Muller's Ratchet": ("Evolutionary Biology", "informational_bind", "LAYER_J_DYNAMICS"),
"Neutral Diversity": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Reynolds Number": ("Fluid Dynamics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Peclet Number": ("Fluid Dynamics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Darcy's Law": ("Fluid Dynamics", "physical_bind", "LAYER_L_APPLICATION"),
"Starling Eq": ("Physiology", "physical_bind", "LAYER_L_APPLICATION"),
"Handicap Principle": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Honesty Condition": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Honest Equilibrium": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Schwan Equation": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"Cole-Cole Eq": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"Dispersion Law": ("Physics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"RNA Combinators": ("Synthetic Biology", "control_bind", "LAYER_F_CONTROL"),
"BioBrick Logic": ("Synthetic Biology", "control_bind", "LAYER_F_CONTROL"),
"Genetic Load": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Critical Depth": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Particle Sinking": ("Oceanography", "physical_bind", "LAYER_L_APPLICATION"),
"Q10 Rule": ("Biophysics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Base Saturation": ("Biogeochemistry", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Hyphal Flow": ("Mycology", "physical_bind", "LAYER_L_APPLICATION"),
"Terraced Barrel": ("Botany", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Reliability Law": ("Engineering", "informational_bind", "LAYER_B_ROUTING"),
"Reaction Prop": ("Chemistry", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Gillespie Step": ("Stochastic Processes", "control_bind", "LAYER_F_CONTROL"),
"Master Equation": ("Statistical Mechanics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Masking Slope": ("Perception", "informational_bind", "LAYER_K_SIGNAL"),
"SMR Priority": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Specific Loudness": ("Perception", "informational_bind", "LAYER_K_SIGNAL"),
"STDP Law": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Trophic 10% Rule": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Slender-Body F": ("Fluid Dynamics", "physical_bind", "LAYER_L_APPLICATION"),
"DVM Fitness": ("Marine Biology", "informational_bind", "LAYER_B_ROUTING"),
"Swim Response": ("Marine Biology", "control_bind", "LAYER_F_CONTROL"),
"Turbulent Encounter": ("Fluid Dynamics", "physical_bind", "LAYER_L_APPLICATION"),
"Patch Residence": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Input Matching": ("Foraging Theory", "informational_bind", "LAYER_B_ROUTING"),
"Fitness Equi": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"V-Formation Upwash": ("Aerodynamics", "physical_bind", "LAYER_L_APPLICATION"),
"Induced Drag Law": ("Aerodynamics", "physical_bind", "LAYER_L_APPLICATION"),
"Flight Efficiency": ("Aerodynamics", "physical_bind", "LAYER_L_APPLICATION"),
"Reproduction Num": ("Demography", "informational_bind", "LAYER_B_ROUTING"),
"Herd Immunity": ("Epidemiology", "informational_bind", "LAYER_B_ROUTING"),
"SIR Dynamics": ("Epidemiology", "control_bind", "LAYER_F_CONTROL"),
"NDZ Model": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Root Uptake": ("Plant Physiology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Root Fractal": ("Plant Physiology", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Constructal Law": ("Physics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Muscle Mechanics": ("Biomechanics", "physical_bind", "LAYER_L_APPLICATION"),
"Square-Cube Law": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Fung's Law": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Alveolar Laplace": ("Physiology", "physical_bind", "LAYER_L_APPLICATION"),
"Ventricular Wall": ("Physiology", "physical_bind", "LAYER_L_APPLICATION"),
"Process S": ("Metabolism", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Process C": ("Metabolism", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Aschoff's Rule": ("Chronobiology", "control_bind", "LAYER_F_CONTROL"),
"Lack's Principle": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Smith-Fretwell": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Repro Scaling": ("Evolutionary Biology", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Dunbar's Law": ("Social Neuroscience", "informational_bind", "LAYER_B_ROUTING"),
"Relationship Law": ("Social Science", "informational_bind", "LAYER_B_ROUTING"),
"Brain Curvature": ("Neuroscience", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Glottal Bernoulli": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"Source-Filter": ("Speech Science", "informational_bind", "LAYER_K_SIGNAL"),
"Pitch Scaling": ("Speech Science", "informational_bind", "LAYER_K_SIGNAL"),
"VTL Scaling": ("Speech Science", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Tissue Fluence": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"Luciferase Law": ("Molecular Biology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Beer-Lambert": ("Chemistry", "physical_bind", "LAYER_L_APPLICATION"),
"Cole's Paradox": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Maturity Ratio": ("Life History", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Allocation Law": ("Life History", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Euler-Lotka Eq": ("Demography", "informational_bind", "LAYER_B_ROUTING"),
"Rescorla-Wagner": ("Psychology", "control_bind", "LAYER_F_CONTROL"),
"Cognitive Lévy": ("Cognitive Science", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Cognitive MVT": ("Foraging Theory", "informational_bind", "LAYER_B_ROUTING"),
"SAM Probability": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Gouy-Stodola": ("Thermodynamics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"MinEnt Prod": ("Thermodynamics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"MaxEnt Prod": ("Thermodynamics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Useful Work": ("Thermodynamics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Corner's Law": ("Ecology", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Pipe Model": ("Botany", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Cavitation Law": ("Fluid Dynamics", "physical_bind", "LAYER_L_APPLICATION"),
"Species-Area Law": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Cell Prestress": ("Biomechanics", "physical_bind", "LAYER_L_APPLICATION"),
"Reciprocal Yield": ("Agriculture", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Noble Model": ("Cardiac Physiology", "control_bind", "LAYER_F_CONTROL"),
"Gating Dynamics": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Inward Rectifier": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"Stevens' 3/2 Law": ("Perception", "informational_bind", "LAYER_K_SIGNAL"),
"White Matter Law": ("Neuroscience", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Rall's 3/2 Law": ("Neuroscience", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Synaptic Invariant": ("Neuroscience", "informational_bind", "LAYER_B_ROUTING"),
"Multi-Hit Law": ("Radiation Biology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"MCA Elasticity": ("Metabolism", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Connectivity Thm": ("Network Theory", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Price Selection": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Reichardt Detect": ("Vision Science", "informational_bind", "LAYER_K_SIGNAL"),
"ACO Transition": ("Chemistry", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Pheromone Law": ("Chemical Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Donachie Rule": ("Cell Biology", "control_bind", "LAYER_F_CONTROL"),
"Cell Size Law": ("Cell Biology", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Adder Principle": ("Cell Biology", "informational_bind", "LAYER_B_ROUTING"),
"Wright's Gradient": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Mean Fitness": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"SBT Drift": ("Evolutionary Biology", "informational_bind", "LAYER_J_DYNAMICS"),
"Amari Neural Field": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Mexican Hat Kernel": ("Neuroscience", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Sigmoid Activity": ("Neuroscience", "control_bind", "LAYER_F_CONTROL"),
"Shell Spiral Law": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Mass Action Law": ("Chemistry", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Equilibrium Invariant": ("Thermodynamics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Malthusian Law": ("Demography", "control_bind", "LAYER_F_CONTROL"),
"Hayflick Limit": ("Cell Biology", "informational_bind", "LAYER_B_ROUTING"),
"Senescence Rule": ("Gerontology", "informational_bind", "LAYER_B_ROUTING"),
"Sheldon Spectrum": ("Oceanography", "informational_bind", "LAYER_B_ROUTING"),
"Inverse Mass N": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Productivity Law": ("Ecology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Fisher FGM Potential": ("Evolutionary Biology", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Beneficial Prob": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Small Mutation Law": ("Evolutionary Biology", "informational_bind", "LAYER_J_DYNAMICS"),
"Complexity Cost": ("Evolutionary Biology", "informational_bind", "LAYER_A_COMPRESSION"),
"Gene Family Law": ("Genetics", "informational_bind", "LAYER_B_ROUTING"),
"Functional Scale": ("Evolutionary Biology", "geometric_bind", "LAYER_C_TOPOLOGY"),
"BDIM Dynamics": ("Evolutionary Biology", "control_bind", "LAYER_F_CONTROL"),
"Margalef Index": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Shannon Index": ("Ecology", "informational_bind", "LAYER_A_COMPRESSION"),
"Info-Stability": ("Information Theory", "informational_bind", "LAYER_A_COMPRESSION"),
"Info-Shedding": ("Information Theory", "informational_bind", "LAYER_A_COMPRESSION"),
"Drake's Rule": ("Evolutionary Biology", "informational_bind", "LAYER_B_ROUTING"),
"Minimal Genome": ("Genetics", "informational_bind", "LAYER_B_ROUTING"),
"Effective Info": ("Information Theory", "informational_bind", "LAYER_A_COMPRESSION"),
"Constrained TEE": ("Thermodynamics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Metabolic Ceiling": ("Metabolism", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Metabolic Scope": ("Metabolism", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Droop Equation": ("Microbiology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Herbert's Law": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Quota Dynamics": ("Ecology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Homeostatic Eq": ("Physiology", "control_bind", "LAYER_F_CONTROL"),
"Damuth's Law": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Unified Metab": ("Metabolism", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Minimum Volume": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Locomotion Speed": ("Biomechanics", "physical_bind", "LAYER_L_APPLICATION"),
"Movement Freq": ("Biomechanics", "physical_bind", "LAYER_L_APPLICATION"),
"Diffusion Speed": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"Rubisco Limit": ("Plant Physiology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"RuBP Regen": ("Plant Physiology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Ball-Berry Law": ("Plant Physiology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Intrinsic WUE": ("Plant Physiology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Light Response": ("Plant Physiology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Reed-Frost Law": ("Epidemiology", "control_bind", "LAYER_F_CONTROL"),
"Trophic Wave": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Trophic Kinetic": ("Ecology", "control_bind", "LAYER_F_CONTROL"),
"Movement Freq": ("Biomechanics", "physical_bind", "LAYER_L_APPLICATION"),
"Diffusion Speed": ("Biophysics", "physical_bind", "LAYER_L_APPLICATION"),
"Rubisco Limit": ("Plant Physiology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"RuBP Regen": ("Plant Physiology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Ball-Berry Law": ("Plant Physiology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Intrinsic WUE": ("Plant Physiology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Light Response": ("Plant Physiology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Boltzmann State Weighting": ("Statistical Mechanics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Rubric-as-Reward (RaR)": ("Machine Learning", "agent_bind", "LAYER_M_LEAN_SEMANTICS"),
"Global Metric Learning (GML)": ("Machine Learning", "metric_bind", "LAYER_M_LEAN_SEMANTICS"),
"Equation Chain (YEC)": ("Logic", "logic_bind", "LAYER_M_LEAN_SEMANTICS"),
"Differential Spectral Correction (DSC)": ("Signal Processing", "signal_bind", "LAYER_K_SIGNAL"),
"Autogenetic Update Rule": ("Agent Logic", "agent_bind", "LAYER_M_LEAN_SEMANTICS"),
"Autogenetic_Update_Rule": ("Agent Logic", "agent_bind", "LAYER_M_LEAN_SEMANTICS"),
"Liebig's Law": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"Shelford Tolerance": ("Ecology", "informational_bind", "LAYER_B_ROUTING"),
"French Flag Model": ("Developmental Biology", "control_bind", "LAYER_F_CONTROL"),
"SDD Gradient": ("Developmental Biology", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Lewis's Law": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Aboav-Weaire Law": ("Biophysics", "geometric_bind", "LAYER_C_TOPOLOGY"),
"Drift-Barrier": ("Evolutionary Biology", "informational_bind", "LAYER_J_DYNAMICS"),
"Drift_Barrier": ("Evolutionary Biology", "informational_bind", "LAYER_J_DYNAMICS"),
"Fick's Law": ("Thermodynamics", "thermodynamic_bind", "LAYER_G_ENERGY"),
"Jarzynski Equality": ("Thermodynamics", "thermodynamic_bind", "LAYER_G_ENERGY"),
}
def main():
tsv_path = Path(__file__).resolve().parent.parent.parent / "3-Mathematical-Models" / "MATH_MODEL_MAP.tsv"
with open(tsv_path, 'r') as f:
lines = f.readlines()
updated_count = 0
still_extracted = 0
for i, line in enumerate(lines):
if i == 0: # Skip header
continue
# Split by tab, handling potential edge cases
parts = line.rstrip('\n').split('\t')
if len(parts) < 11:
continue
# Column indices (0-based):
# 0: ID, 1: Model_Name, 2: Family, 3: Equation, 4: Variables
# 5: Purpose, 6: Location, 7: Implemented, 8: Status
# 9: Cross_Refs, 10: Domain_Type, 11: Bind_Class
model_name = parts[1]
family = parts[2]
bind_class = parts[11] if len(parts) > 11 else ""
domain_type = parts[10] if len(parts) > 10 else ""
# Debug: print first few lines
if i < 5:
print(f"Line {i}: model={model_name}, family={family}, bind={bind_class}")
# Only process "Extracted" models
if family == "Extracted":
if model_name in DOMAIN_MAPPINGS:
new_family, new_bind, new_domain = DOMAIN_MAPPINGS[model_name]
parts[2] = new_family
parts[11] = new_bind
# Also update Domain_Type if it's missing or generic
if domain_type == "" or domain_type == "unknown":
parts[10] = new_domain
lines[i] = '\t'.join(parts) + '\n'
updated_count += 1
print(f"Updated: {model_name} -> {new_family} ({new_bind})")
else:
still_extracted += 1
with open(tsv_path, 'w') as f:
f.writelines(lines)
print(f"\nSummary:")
print(f" Updated: {updated_count} models")
print(f" Still unmapped: {still_extracted} models")
if __name__ == "__main__":
main()
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