Biofirm

A framework for ecological system control using Active Inference agents.

Overview

Biofirm consists of two main components:

1. Ecosystem Control System

   • Active Inference-based multi-agent control framework
   • Homeostatic regulation of ecological parameters
   • Comparative analysis between random and controlled dynamics

2. BioPerplexity Analysis

   • California county-level bioregion research using Perplexity.ai API
   • Business case generation and pitch development
   • Cross-document visualization and analysis

System Architecture

Active Inference Framework

• Multi-agent POMDP (Partially Observable Markov Decision Process) implementation
• Each agent controls one ecological modality through free energy minimization
• Collective homeostatic regulation through distributed control

Key Components: - Ecosystem_Simulation.py: Main simulator comparing random vs. active inference control - Biofirm_Agent.py: PyMDP-based active inference agent implementation - POMDP_ABCD.py: Generative model matrix generation (A,B,C,D matrices) - utils/: Ecological configuration files and parameters

Analysis Tools

• Free_Energy_Minimization.py: Analysis of control performance
• Noise_Control_ActiveInference_Sweep.py: Parameter sweep across noise and control levels

BioPerplexity Pipeline

1. 1_Research_Bioregions.py: County-level data collection
2. 2_Biofirm_Business_Pitch.py: Business case generation
3. 3_Biofirm_Visualization.py: Data visualization

Getting Started

1. Environment Setup: bash python Startup.py # Creates PyMDP virtual environment source venv/bin/activate

2. Configuration:

3. Adjust ecological parameters in utils/ecosystem_config.json

4. Configure agent parameters in generative model files

5. Run Simulations: bash python Scripts/Ecosystem_Simulation.py

Technical Details

See Biofirm_Generative_Model.md for comprehensive documentation of: - POMDP framework implementation - Generative model architecture - Free energy minimization approach - Control system dynamics

Project Structure

Bio_Perplexity/ # Business analysis tools Scripts/ # Core simulation code utils/ # Configuration files Outputs/ # Simulation results Stream/ # Documentation