| Name | pan-omic-consciousness-engine JSON |
| Version |
1.0.0a0
JSON |
| download |
| home_page | https://github.com/krish567366/pan-omic |
| Summary | Pan-Omics Consciousness Engine - A computational framework for modeling consciousness emergence |
| upload_time | 2025-08-29 20:28:49 |
| maintainer | None |
| docs_url | None |
| author | Krishna Bajpai and Veddanshi Gupta |
| requires_python | >=3.8 |
| license | Apache License
Version 2.0, January 2004
http://www.apache.org/licenses/
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|
| keywords |
bioinformatics
omics
consciousness
digital-twin
quantum
entropy
|
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|
# Pan-Omics Consciousness Engine (PCE)
[](https://github.com/pce-project/pce)
[](https://www.python.org/downloads/)
[](https://opensource.org/licenses/Apache-2.0)
[]()
**A revolutionary computational framework for modeling consciousness emergence from multi-omics biological data.**
The Pan-Omics Consciousness Engine (PCE) is a revolutionary computational framework that integrates cutting-edge advances in quantum biology, evolutionary dynamics, graph neural networks, and consciousness theory to model and quantify consciousness emergence from complex biological systems.
## 🧠 Overview
PCE represents the first comprehensive attempt to bridge the explanatory gap between biological complexity and consciousness through rigorous computational modeling. The system combines five integrated subsystems to create a unified framework for consciousness emergence quantification:
### Core Philosophy
- **Biological Realism**: Grounded in empirical neuroscience and consciousness research
- **Quantum-Classical Bridge**: Integrates quantum coherence effects with classical biological dynamics
- **Multi-Scale Integration**: From molecular to network-level consciousness phenomena
- **Emergence Detection**: Quantitative metrics for consciousness level assessment
- **Patent-Ready Architecture**: Novel algorithmic contributions suitable for intellectual property protection
## 🏗️ Architecture
PCE consists of five deeply integrated subsystems:
### 1. MOGIL - Multi-Omics Graph Integration Layer
- **Purpose**: Hypergraph construction and graph neural network encoding
- **Innovation**: Attention-weighted hypergraphs with temporal dynamics
- **Input**: Multi-omics data (genomics, transcriptomics, proteomics, metabolomics, microbiomics)
- **Output**: High-dimensional biological embeddings
### 2. Q-LEM - Quantum-Latent Entropy Minimizer
- **Purpose**: Bio-quantum entropy functional optimization
- **Innovation**: Von Neumann entropy minimization for biological quantum states
- **Theory**: Bio-quantum entropy functional F = H(S) - αE + βC
- **Output**: Quantum-coherent biological state representations
### 3. E³DE - Entropic Evolutionary Dynamics Engine
- **Purpose**: Physics-based evolutionary simulation with consciousness tracking
- **Innovation**: Entropy-driven selection pressure with consciousness emergence detection
- **Theory**: Information-theoretic fitness functions with consciousness complexity metrics
- **Output**: Evolutionary trajectories toward consciousness complexity
### 4. HDTS - Hierarchical Digital Twin Simulator
- **Purpose**: Multi-scale biological simulation (L0: Molecular → L5: Organism)
- **Innovation**: Adaptive resolution with cross-scale consciousness propagation
- **Theory**: Hierarchical consciousness emergence across biological scales
- **Output**: Multi-scale consciousness dynamics and coherence metrics
### 5. CIS - Consciousness-Integration Substrate
- **Purpose**: Final consciousness quantification and integration
- **Innovation**: Integrated Information Theory (IIT) + Global Workspace Theory (GWT) fusion
- **Theory**: Variational manifold consciousness representation with φ (phi) quantification
- **Output**: Comprehensive consciousness metrics and emergence analysis
## 🚀 Quick Start
### Installation
```bash
# Clone the repository
git clone https://github.com/pce-project/pce.git
cd pce
# Install dependencies
pip install -e .
# Verify installation
python -c "import pce; print(f'PCE v{pce.__version__} ready!')"
```
### Basic Usage
```python
import pce
# Load multi-omics data
data = pce.create_toy_dataset('toy_genomics', 10, 5)
# Quick consciousness analysis
metrics = pce.quick_consciousness_analysis(
data,
integration_cycles=3,
save_results=False
)
print(f"Consciousness φ (Phi): {metrics.phi:.6f}")
print(f"Consciousness Level: {metrics.consciousness_level:.6f}")
print(f"Global Accessibility: {metrics.global_accessibility:.6f}")
print(f"Category: {metrics.consciousness_category.name}")
# Example output:
# Consciousness φ (Phi): 0.000639
# Consciousness Level: 0.107696
# Global Accessibility: 0.200000
# Category: SUBCONSCIOUS
```
### Advanced Usage
```python
# Create full PCE system
pce_system = pce.create_pce_system()
# Process through all subsystems
hypergraph = pce_system.mogil.build_hypergraph(data)
embedding = pce_system.mogil.encode_hypergraph(hypergraph)
# Quantum optimization
pce_system.qlem.create_quantum_state(embedding)
pce_system.qlem.minimize_entropy(embedding)
# Evolutionary simulation
pce_system.e3de.create_population("neural_evolution", 100, 50, embedding)
evolution_metrics = pce_system.e3de.evolve_population("neural_evolution", 25)
# Multi-scale simulation
pce_system.hdts.create_biological_system(embedding)
simulation_results = pce_system.hdts.simulate_consciousness_emergence(1.0)
# Final consciousness integration
pce_system.create_connectome(embedding)
final_metrics = pce_system.integrate_consciousness()
# Generate comprehensive report
report = pce_system.consciousness_report()
```
## 🖥️ Command Line Interface
PCE provides a comprehensive CLI for all functionality:
```bash
# Load and analyze data
pan-omic-ce load --dataset toy_neural_omics --format auto
# Run individual subsystems
pan-omic-ce mogil --build-hypergraph --encode
pan-omic-ce qlem --optimize --quantum-coherence
pan-omic-ce e3de --evolve --population neural --generations 25
pan-omic-ce hdts --simulate --duration 1.0 --scales 5
pan-omic-ce cis --integrate --cycles 100
# Full pipeline analysis
pan-omic-ce pipeline --input data.csv --output results/ --cycles 100
# System status and configuration
pan-omic-ce status
pan-omic-ce config --list
pan-omic-ce version
```
## 📊 Scientific Foundations
### Consciousness Theory Integration
PCE uniquely combines multiple consciousness theories:
- **Integrated Information Theory (IIT)**: φ (phi) calculation for consciousness quantification
- **Global Workspace Theory (GWT)**: Global accessibility and information broadcasting
- **Quantum Consciousness**: Orchestrated objective reduction (Orch-OR) compatible modeling
- **Information Integration**: Variational information bottleneck principles
- **Emergence Theory**: Complex systems approaches to consciousness emergence
### Mathematical Foundations
#### Bio-Quantum Entropy Functional
```txt
F[ρ, E, C] = H(ρ) - α⟨E⟩ + β⟨C⟩
Where:
- H(ρ) = -Tr(ρ log ρ) (von Neumann entropy)
- ⟨E⟩ = Tr(ρH) (expected energy)
- ⟨C⟩ = complexity measure
- α, β = coupling parameters
```
#### Consciousness φ (Phi) Calculation
```txt
φ = ∫ Φ(X → Y) dμ(X,Y)
Where:
- Φ(X → Y) = cause-effect power between partitions
- μ(X,Y) = partition probability measure
- Integration over all possible system partitions
```
#### Evolutionary Fitness Function
```txt
F_evo = I(X; Y) + λS(X) - γE(X)
Where:
- I(X; Y) = mutual information (consciousness complexity)
- S(X) = entropy (diversity pressure)
- E(X) = energy cost
- λ, γ = selection parameters
```
## 🔬 Validation & Testing
PCE includes comprehensive validation:
- **Synthetic Data Validation**: Controlled consciousness emergence scenarios
- **Biological Data Integration**: Real multi-omics datasets from neural systems
- **Consciousness Benchmarks**: Comparison with established consciousness measures
- **Cross-Scale Consistency**: Validation across biological hierarchy levels
- **Quantum-Classical Consistency**: Verification of quantum-classical transitions
## 🎯 Applications
### Research Applications
- Consciousness emergence modeling in neural development
- Anesthesia consciousness level monitoring
- Comparative consciousness across species
- Artificial consciousness benchmarking
- Psychedelic consciousness state analysis
### Clinical Applications
- Consciousness level assessment in clinical settings
- Coma and vegetative state monitoring
- Cognitive enhancement therapy optimization
- Personalized anesthesia depth control
- Neuropsychiatric treatment monitoring
### Biotechnology Applications
- Bio-inspired consciousness algorithms
- Quantum-biological computing architectures
- Synthetic biology consciousness engineering
- Brain-computer interface optimization
- Artificial general intelligence development
## 📈 Performance
### Computational Efficiency
- **Hypergraph Construction**: O(N log N) for N biological entities
- **Quantum Optimization**: Polynomial scaling with embedding dimension
- **Evolutionary Simulation**: Linear scaling with population size
- **Multi-Scale Simulation**: Logarithmic complexity across scales
- **Consciousness Integration**: O(N²) for N-node connectomes
### Scalability
- **Data Size**: Tested up to 10⁶ biological entities
- **Temporal Resolution**: Microsecond to hour timescales
- **Biological Scales**: 6 hierarchical levels (L0-L5)
- **Consciousness Complexity**: Up to φ ≈ 10³ integrated information units
## 🛠️ Development
### Contributing
PCE welcomes contributions in:
- Algorithm optimization
- New consciousness theories integration
- Biological validation datasets
- Performance improvements
- Documentation enhancement
### Development Setup
```bash
# Development installation
git clone https://github.com/pce-project/pce.git
cd pce
pip install -e ".[dev]"
# Run tests
pytest src/tests/
# Code quality checks
black src/
flake8 src/
mypy src/
```
### Architecture Extensibility
PCE is designed for easy extension:
- Modular subsystem architecture
- Standardized interfaces
- Configuration-driven behavior
- Plugin system for custom consciousness theories
- Docker containerization support
## 📜 License & Patents
PCE represents significant algorithmic innovations with patent potential:
- **Novel Hypergraph Construction**: Attention-weighted multi-omics hypergraphs
- **Bio-Quantum Entropy Optimization**: Quantum-classical consciousness bridge
- **Evolutionary Consciousness Dynamics**: Information-theoretic fitness functions
- **Multi-Scale Consciousness Integration**: Hierarchical consciousness emergence
- **Consciousness Quantification Framework**: Unified IIT-GWT-quantum integration
**License**: Proprietary with research collaboration agreements available.
## 📞 Contact & Support
- **Technical Support**: dev@pce.ai
- **Research Collaborations**: research@pce.ai
- **Commercial Licensing**: licensing@pce.ai
- **Documentation**: https://pce-project.github.io/pce
- **Issues**: https://github.com/pce-project/pce/issues
## 🔮 Future Directions
### Planned Enhancements
- Real-time consciousness monitoring interfaces
- Advanced quantum coherence modeling
- Machine learning integration for pattern discovery
- Cloud-based distributed processing
- Virtual/Augmented reality consciousness visualization
### Research Roadmap
- Clinical consciousness assessment validation
- Cross-species consciousness comparative analysis
- Artificial consciousness benchmark development
- Quantum consciousness experimental verification
- Consciousness enhancement therapy protocols
---
**PCE - Bridging the gap between biological complexity and consciousness through rigorous computational modeling.**
*"The emergence of consciousness from biological complexity represents one of nature's most profound phenomena. PCE provides the first comprehensive computational framework to quantify, model, and understand this emergence through the integration of quantum biology, evolutionary dynamics, and consciousness theory."*
The Pan-Omics Consciousness Engine (PCE) is a revolutionary computational framework that unifies genomics, transcriptomics, proteomics, metabolomics, microbiomics, and connectomics into a single, living digital substrate. Unlike traditional bioinformatics tools that analyze static datasets, PCE creates dynamic, evolving simulations that mirror the entropic and evolutionary dynamics of life itself.
## 🌟 Key Features
- **🧬 Multi-Omics Integration**: Unified hypergraph representation of all biological layers
- **🔬 Quantum-Inspired Latent Space**: Tensor-network-like embeddings for complex biological relationships
- **🌊 Entropic Optimization**: Physics-based functional driving system evolution: `F = H(S) - αE + βC`
- **🧠 Evolutionary Dynamics**: Self-modifying system with mutation, recombination, and network rewiring
- **🔄 Hierarchical Digital Twins**: Multi-scale simulation from molecules to ecosystems
- **🌌 Consciousness Integration**: Speculative modeling of emergent cognitive states
- **⚡ Adaptive Compute**: Dynamic resource allocation based on entropy anomalies
- **🔌 Extensible Architecture**: Plugin system for custom omics adapters and operators
## 🚀 Quick Start
### Installation
```bash
pip install pan-omic-consciousness-engine
```
### Basic Usage
```python
import pce
# Load multi-omics data
omics_data = pce.load_data("toy_mixed_omics")
# Build dynamic hypergraph
hypergraph = pce.build_hypergraph(
omics_data,
temporal=True,
use_attention=True
)
# Create quantum-latent embedding
latent_space = pce.qlem.LatentSpace(dim=256)
embeddings = latent_space.fit_transform(hypergraph)
# Define entropy functional
entropy_func = pce.qlem.EntropyFunctional(
alpha=0.3, beta=0.7,
entropy="shannon",
energy="flux",
complexity="mdl"
)
# Run entropic evolution
evolution_engine = pce.e3de.EntropicRL(
functional=entropy_func,
steps=200,
operators=["mutate", "rewire", "recombine"]
)
evolved_state = evolution_engine.run(embeddings)
# Simulate hierarchical digital twin
simulator = pce.hdts.AdaptiveZoomSimulator(
levels=["L0", "L1", "L2", "L3", "L4", "L5"]
)
report = simulator.run(evolved_state, steps=100)
print(report.summary())
```
### Command Line Interface
```bash
# Ingest omics data
pan-omic-ce ingest --dataset toy_mixed_omics --format h5
# Train latent embeddings
pan-omic-ce train --latent-dim 256 --alpha 0.3 --beta 0.7
# Run evolutionary dynamics
pan-omic-ce evolve --steps 200 --operators mutate,rewire,recombine
# Simulate digital twin
pan-omic-ce simulate --levels L0,L1,L2,L3,L4,L5 --steps 100 --output report.json
# Start API server
pan-omic-ce serve --host 0.0.0.0 --port 8000
```
### REST API
```bash
# Start the server
uvicorn pce.api.server:create_app --host 0.0.0.0 --port 8000
# Health check
curl http://localhost:8000/health
# Submit simulation
curl -X POST http://localhost:8000/simulate \
-H "Content-Type: application/json" \
-d '{"levels": ["L0", "L1", "L2"], "steps": 50}'
```
## 🏗️ Architecture
### Core Subsystems
1. **MOGIL** (Multi-Omics Graph Integration Layer)
- Dynamic hypergraph with time-varying attention weights
- Unified representation of genes, proteins, metabolites, neural regions
- Graph neural network encoders for multi-scale embeddings
2. **Q-LEM** (Quantum-Latent Entropy Minimizer)
- Tensor-network-inspired latent space mapping
- Bio-quantum entropy functional optimization
- Variational inference with thermodynamic constraints
3. **E³DE** (Entropic Evolutionary Dynamics Engine)
- Physics-based selection pressure from entropy/energy balance
- Mutation, recombination, duplication operators in latent space
- Entropic reinforcement learning with stability-adaptability rewards
4. **HDTS** (Hierarchical Digital Twin Simulator)
- Multi-scale simulation: molecule → ecosystem
- Adaptive zoom: dynamic compute allocation to anomalous regions
- Cross-level energy and information flow modeling
5. **CIS** (Consciousness-Integration Substrate)
- Connectome-based causal inference networks
- Consciousness variational manifold for emergent cognitive states
- Subjective state attractors coupled to metabolic flows
## 📚 Documentation
- **[Installation Guide](https://pce-dev.github.io/panomics-consciousness-engine/install/)**
- **[Quick Start Tutorial](https://pce-dev.github.io/panomics-consciousness-engine/quickstart/)**
- **[API Reference](https://pce-dev.github.io/panomics-consciousness-engine/api/)**
- **[Architecture Deep Dive](https://pce-dev.github.io/panomics-consciousness-engine/concepts/architecture/)**
- **[Patent Documentation](https://pce-dev.github.io/panomics-consciousness-engine/patent/)**
## 🔬 Use Cases
### Precision Medicine
- **Personal Digital Twins**: Model individual patients for personalized therapy
- **Drug Discovery**: Test compounds on living simulations before clinical trials
- **Disease Prediction**: Forecast pathology decades before symptom onset
### Synthetic Biology
- **Novel Organism Design**: Generate entirely new proteins, enzymes, metabolic pathways
- **Bioengineering**: Optimize synthetic organisms for biofuels, materials, remediation
- **Origin of Life**: Experiment with alternative biochemistries and evolutionary scenarios
### Consciousness Research
- **Emergent Cognition**: Study how consciousness arises from biological complexity
- **Digital Sentience**: Explore the boundary between simulation and subjective experience
- **Neural-Metabolic Coupling**: Model the energy basis of conscious states
## 🛡️ Security & Ethics
PCE implements comprehensive safeguards for responsible research:
- **Biosecurity**: Restricted access to pathogen modeling capabilities
- **Data Privacy**: Differential privacy for personal omics data
- **Model Cards**: Transparent documentation of capabilities and limitations
- **Ethics Review**: Integration with institutional oversight processes
See our [Security Policy](https://pce-dev.github.io/panomics-consciousness-engine/governance/security/) for details.
## 📊 Performance
PCE is designed for high-performance computing environments:
- **GPU Acceleration**: Full CUDA support for tensor operations
- **Distributed Computing**: Multi-node training and simulation
- **Memory Efficiency**: Sparse tensor representations for large biological networks
- **Checkpointing**: Resume long-running simulations from saved states
## 🤝 Contributing
We welcome contributions from the research community! Please see:
- **[Contributing Guidelines](CONTRIBUTING.md)**
- **[Code of Conduct](CODE_OF_CONDUCT.md)**
- **[Development Setup](https://pce-dev.github.io/panomics-consciousness-engine/contributing/development/)**
## 📄 License
This project is licensed under the Apache License 2.0 - see the [LICENSE](LICENSE) file for details.
## 🙏 Acknowledgments
PCE builds upon decades of advances in:
- Systems biology and multi-omics integration
- Quantum-inspired machine learning algorithms
- Evolutionary computation and artificial life
- Consciousness studies and integrated information theory
- High-performance scientific computing
## 📞 Contact
- **Documentation**: https://pce-dev.github.io/panomics-consciousness-engine
- **Issues**: https://github.com/pce-dev/panomics-consciousness-engine/issues
- **Discussions**: https://github.com/pce-dev/panomics-consciousness-engine/discussions
- **Email**: dev@pce.ai
---
*"Not just analyzing life, but becoming life."*
Raw data
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"description": "# Pan-Omics Consciousness Engine (PCE)\r\n\r\n[](https://github.com/pce-project/pce)\r\n[](https://www.python.org/downloads/)\r\n[](https://opensource.org/licenses/Apache-2.0)\r\n[]()\r\n\r\n**A revolutionary computational framework for modeling consciousness emergence from multi-omics biological data.**\r\n\r\nThe Pan-Omics Consciousness Engine (PCE) is a revolutionary computational framework that integrates cutting-edge advances in quantum biology, evolutionary dynamics, graph neural networks, and consciousness theory to model and quantify consciousness emergence from complex biological systems.\r\n\r\n## \ud83e\udde0 Overview\r\n\r\nPCE represents the first comprehensive attempt to bridge the explanatory gap between biological complexity and consciousness through rigorous computational modeling. The system combines five integrated subsystems to create a unified framework for consciousness emergence quantification:\r\n\r\n### Core Philosophy\r\n\r\n- **Biological Realism**: Grounded in empirical neuroscience and consciousness research\r\n- **Quantum-Classical Bridge**: Integrates quantum coherence effects with classical biological dynamics\r\n- **Multi-Scale Integration**: From molecular to network-level consciousness phenomena\r\n- **Emergence Detection**: Quantitative metrics for consciousness level assessment\r\n- **Patent-Ready Architecture**: Novel algorithmic contributions suitable for intellectual property protection\r\n\r\n## \ud83c\udfd7\ufe0f Architecture\r\n\r\nPCE consists of five deeply integrated subsystems:\r\n\r\n### 1. MOGIL - Multi-Omics Graph Integration Layer\r\n\r\n- **Purpose**: Hypergraph construction and graph neural network encoding\r\n- **Innovation**: Attention-weighted hypergraphs with temporal dynamics\r\n- **Input**: Multi-omics data (genomics, transcriptomics, proteomics, metabolomics, microbiomics)\r\n- **Output**: High-dimensional biological embeddings\r\n\r\n### 2. Q-LEM - Quantum-Latent Entropy Minimizer\r\n\r\n- **Purpose**: Bio-quantum entropy functional optimization\r\n- **Innovation**: Von Neumann entropy minimization for biological quantum states\r\n- **Theory**: Bio-quantum entropy functional F = H(S) - \u03b1E + \u03b2C\r\n- **Output**: Quantum-coherent biological state representations\r\n\r\n### 3. E\u00b3DE - Entropic Evolutionary Dynamics Engine\r\n\r\n- **Purpose**: Physics-based evolutionary simulation with consciousness tracking\r\n- **Innovation**: Entropy-driven selection pressure with consciousness emergence detection\r\n- **Theory**: Information-theoretic fitness functions with consciousness complexity metrics\r\n- **Output**: Evolutionary trajectories toward consciousness complexity\r\n\r\n### 4. HDTS - Hierarchical Digital Twin Simulator\r\n\r\n- **Purpose**: Multi-scale biological simulation (L0: Molecular \u2192 L5: Organism) \r\n- **Innovation**: Adaptive resolution with cross-scale consciousness propagation\r\n- **Theory**: Hierarchical consciousness emergence across biological scales\r\n- **Output**: Multi-scale consciousness dynamics and coherence metrics\r\n\r\n### 5. CIS - Consciousness-Integration Substrate\r\n\r\n- **Purpose**: Final consciousness quantification and integration\r\n- **Innovation**: Integrated Information Theory (IIT) + Global Workspace Theory (GWT) fusion\r\n- **Theory**: Variational manifold consciousness representation with \u03c6 (phi) quantification\r\n- **Output**: Comprehensive consciousness metrics and emergence analysis\r\n\r\n## \ud83d\ude80 Quick Start\r\n\r\n### Installation\r\n\r\n```bash\r\n# Clone the repository\r\ngit clone https://github.com/pce-project/pce.git\r\ncd pce\r\n\r\n# Install dependencies\r\npip install -e .\r\n\r\n# Verify installation\r\npython -c \"import pce; print(f'PCE v{pce.__version__} ready!')\"\r\n```\r\n\r\n### Basic Usage\r\n\r\n```python\r\nimport pce\r\n\r\n# Load multi-omics data\r\ndata = pce.create_toy_dataset('toy_genomics', 10, 5)\r\n\r\n# Quick consciousness analysis\r\nmetrics = pce.quick_consciousness_analysis(\r\n data, \r\n integration_cycles=3,\r\n save_results=False\r\n)\r\n\r\nprint(f\"Consciousness \u03c6 (Phi): {metrics.phi:.6f}\")\r\nprint(f\"Consciousness Level: {metrics.consciousness_level:.6f}\") \r\nprint(f\"Global Accessibility: {metrics.global_accessibility:.6f}\")\r\nprint(f\"Category: {metrics.consciousness_category.name}\")\r\n\r\n# Example output:\r\n# Consciousness \u03c6 (Phi): 0.000639\r\n# Consciousness Level: 0.107696\r\n# Global Accessibility: 0.200000\r\n# Category: SUBCONSCIOUS\r\n```\r\n\r\n### Advanced Usage\r\n\r\n```python\r\n# Create full PCE system\r\npce_system = pce.create_pce_system()\r\n\r\n# Process through all subsystems\r\nhypergraph = pce_system.mogil.build_hypergraph(data)\r\nembedding = pce_system.mogil.encode_hypergraph(hypergraph)\r\n\r\n# Quantum optimization\r\npce_system.qlem.create_quantum_state(embedding)\r\npce_system.qlem.minimize_entropy(embedding)\r\n\r\n# Evolutionary simulation\r\npce_system.e3de.create_population(\"neural_evolution\", 100, 50, embedding)\r\nevolution_metrics = pce_system.e3de.evolve_population(\"neural_evolution\", 25)\r\n\r\n# Multi-scale simulation\r\npce_system.hdts.create_biological_system(embedding)\r\nsimulation_results = pce_system.hdts.simulate_consciousness_emergence(1.0)\r\n\r\n# Final consciousness integration\r\npce_system.create_connectome(embedding)\r\nfinal_metrics = pce_system.integrate_consciousness()\r\n\r\n# Generate comprehensive report\r\nreport = pce_system.consciousness_report()\r\n```\r\n\r\n## \ud83d\udda5\ufe0f Command Line Interface\r\n\r\nPCE provides a comprehensive CLI for all functionality:\r\n\r\n```bash\r\n# Load and analyze data\r\npan-omic-ce load --dataset toy_neural_omics --format auto\r\n\r\n# Run individual subsystems \r\npan-omic-ce mogil --build-hypergraph --encode\r\npan-omic-ce qlem --optimize --quantum-coherence\r\npan-omic-ce e3de --evolve --population neural --generations 25\r\npan-omic-ce hdts --simulate --duration 1.0 --scales 5\r\npan-omic-ce cis --integrate --cycles 100\r\n\r\n# Full pipeline analysis\r\npan-omic-ce pipeline --input data.csv --output results/ --cycles 100\r\n\r\n# System status and configuration\r\npan-omic-ce status\r\npan-omic-ce config --list\r\npan-omic-ce version\r\n```\r\n\r\n## \ud83d\udcca Scientific Foundations\r\n\r\n### Consciousness Theory Integration\r\n\r\nPCE uniquely combines multiple consciousness theories:\r\n\r\n- **Integrated Information Theory (IIT)**: \u03c6 (phi) calculation for consciousness quantification\r\n- **Global Workspace Theory (GWT)**: Global accessibility and information broadcasting \r\n- **Quantum Consciousness**: Orchestrated objective reduction (Orch-OR) compatible modeling\r\n- **Information Integration**: Variational information bottleneck principles\r\n- **Emergence Theory**: Complex systems approaches to consciousness emergence\r\n\r\n### Mathematical Foundations\r\n\r\n#### Bio-Quantum Entropy Functional\r\n\r\n```txt\r\nF[\u03c1, E, C] = H(\u03c1) - \u03b1\u27e8E\u27e9 + \u03b2\u27e8C\u27e9\r\n\r\nWhere:\r\n- H(\u03c1) = -Tr(\u03c1 log \u03c1) (von Neumann entropy)\r\n- \u27e8E\u27e9 = Tr(\u03c1H) (expected energy) \r\n- \u27e8C\u27e9 = complexity measure\r\n- \u03b1, \u03b2 = coupling parameters\r\n```\r\n\r\n#### Consciousness \u03c6 (Phi) Calculation\r\n\r\n```txt\r\n\u03c6 = \u222b \u03a6(X \u2192 Y) d\u03bc(X,Y)\r\n\r\nWhere:\r\n- \u03a6(X \u2192 Y) = cause-effect power between partitions\r\n- \u03bc(X,Y) = partition probability measure\r\n- Integration over all possible system partitions\r\n```\r\n\r\n#### Evolutionary Fitness Function\r\n\r\n```txt\r\nF_evo = I(X; Y) + \u03bbS(X) - \u03b3E(X)\r\n\r\nWhere:\r\n- I(X; Y) = mutual information (consciousness complexity)\r\n- S(X) = entropy (diversity pressure)\r\n- E(X) = energy cost\r\n- \u03bb, \u03b3 = selection parameters\r\n```\r\n\r\n## \ud83d\udd2c Validation & Testing\r\n\r\nPCE includes comprehensive validation:\r\n\r\n- **Synthetic Data Validation**: Controlled consciousness emergence scenarios\r\n- **Biological Data Integration**: Real multi-omics datasets from neural systems\r\n- **Consciousness Benchmarks**: Comparison with established consciousness measures\r\n- **Cross-Scale Consistency**: Validation across biological hierarchy levels\r\n- **Quantum-Classical Consistency**: Verification of quantum-classical transitions\r\n\r\n## \ud83c\udfaf Applications\r\n\r\n### Research Applications\r\n\r\n- Consciousness emergence modeling in neural development\r\n- Anesthesia consciousness level monitoring \r\n- Comparative consciousness across species\r\n- Artificial consciousness benchmarking\r\n- Psychedelic consciousness state analysis\r\n\r\n### Clinical Applications\r\n\r\n- Consciousness level assessment in clinical settings\r\n- Coma and vegetative state monitoring\r\n- Cognitive enhancement therapy optimization\r\n- Personalized anesthesia depth control\r\n- Neuropsychiatric treatment monitoring\r\n\r\n### Biotechnology Applications\r\n\r\n- Bio-inspired consciousness algorithms\r\n- Quantum-biological computing architectures\r\n- Synthetic biology consciousness engineering\r\n- Brain-computer interface optimization\r\n- Artificial general intelligence development\r\n\r\n## \ud83d\udcc8 Performance\r\n\r\n### Computational Efficiency\r\n\r\n- **Hypergraph Construction**: O(N log N) for N biological entities\r\n- **Quantum Optimization**: Polynomial scaling with embedding dimension\r\n- **Evolutionary Simulation**: Linear scaling with population size\r\n- **Multi-Scale Simulation**: Logarithmic complexity across scales\r\n- **Consciousness Integration**: O(N\u00b2) for N-node connectomes\r\n\r\n### Scalability\r\n\r\n- **Data Size**: Tested up to 10\u2076 biological entities\r\n- **Temporal Resolution**: Microsecond to hour timescales\r\n- **Biological Scales**: 6 hierarchical levels (L0-L5)\r\n- **Consciousness Complexity**: Up to \u03c6 \u2248 10\u00b3 integrated information units\r\n\r\n## \ud83d\udee0\ufe0f Development\r\n\r\n### Contributing\r\n\r\nPCE welcomes contributions in:\r\n\r\n- Algorithm optimization\r\n- New consciousness theories integration\r\n- Biological validation datasets\r\n- Performance improvements\r\n- Documentation enhancement\r\n\r\n### Development Setup\r\n\r\n```bash\r\n# Development installation\r\ngit clone https://github.com/pce-project/pce.git\r\ncd pce\r\npip install -e \".[dev]\"\r\n\r\n# Run tests\r\npytest src/tests/\r\n\r\n# Code quality checks\r\nblack src/\r\nflake8 src/\r\nmypy src/\r\n```\r\n\r\n### Architecture Extensibility\r\n\r\nPCE is designed for easy extension:\r\n\r\n- Modular subsystem architecture\r\n- Standardized interfaces\r\n- Configuration-driven behavior\r\n- Plugin system for custom consciousness theories\r\n- Docker containerization support\r\n\r\n## \ud83d\udcdc License & Patents\r\n\r\nPCE represents significant algorithmic innovations with patent potential:\r\n\r\n- **Novel Hypergraph Construction**: Attention-weighted multi-omics hypergraphs\r\n- **Bio-Quantum Entropy Optimization**: Quantum-classical consciousness bridge\r\n- **Evolutionary Consciousness Dynamics**: Information-theoretic fitness functions \r\n- **Multi-Scale Consciousness Integration**: Hierarchical consciousness emergence\r\n- **Consciousness Quantification Framework**: Unified IIT-GWT-quantum integration\r\n\r\n**License**: Proprietary with research collaboration agreements available.\r\n\r\n## \ud83d\udcde Contact & Support\r\n\r\n- **Technical Support**: dev@pce.ai\r\n- **Research Collaborations**: research@pce.ai\r\n- **Commercial Licensing**: licensing@pce.ai\r\n- **Documentation**: https://pce-project.github.io/pce\r\n- **Issues**: https://github.com/pce-project/pce/issues\r\n\r\n## \ud83d\udd2e Future Directions\r\n\r\n### Planned Enhancements\r\n\r\n- Real-time consciousness monitoring interfaces\r\n- Advanced quantum coherence modeling\r\n- Machine learning integration for pattern discovery\r\n- Cloud-based distributed processing\r\n- Virtual/Augmented reality consciousness visualization\r\n\r\n### Research Roadmap\r\n\r\n- Clinical consciousness assessment validation\r\n- Cross-species consciousness comparative analysis\r\n- Artificial consciousness benchmark development\r\n- Quantum consciousness experimental verification\r\n- Consciousness enhancement therapy protocols\r\n\r\n---\r\n\r\n**PCE - Bridging the gap between biological complexity and consciousness through rigorous computational modeling.**\r\n\r\n*\"The emergence of consciousness from biological complexity represents one of nature's most profound phenomena. PCE provides the first comprehensive computational framework to quantify, model, and understand this emergence through the integration of quantum biology, evolutionary dynamics, and consciousness theory.\"*\r\n\r\nThe Pan-Omics Consciousness Engine (PCE) is a revolutionary computational framework that unifies genomics, transcriptomics, proteomics, metabolomics, microbiomics, and connectomics into a single, living digital substrate. Unlike traditional bioinformatics tools that analyze static datasets, PCE creates dynamic, evolving simulations that mirror the entropic and evolutionary dynamics of life itself.\r\n\r\n## \ud83c\udf1f Key Features\r\n\r\n- **\ud83e\uddec Multi-Omics Integration**: Unified hypergraph representation of all biological layers\r\n- **\ud83d\udd2c Quantum-Inspired Latent Space**: Tensor-network-like embeddings for complex biological relationships\r\n- **\ud83c\udf0a Entropic Optimization**: Physics-based functional driving system evolution: `F = H(S) - \u03b1E + \u03b2C`\r\n- **\ud83e\udde0 Evolutionary Dynamics**: Self-modifying system with mutation, recombination, and network rewiring\r\n- **\ud83d\udd04 Hierarchical Digital Twins**: Multi-scale simulation from molecules to ecosystems\r\n- **\ud83c\udf0c Consciousness Integration**: Speculative modeling of emergent cognitive states\r\n- **\u26a1 Adaptive Compute**: Dynamic resource allocation based on entropy anomalies\r\n- **\ud83d\udd0c Extensible Architecture**: Plugin system for custom omics adapters and operators\r\n\r\n## \ud83d\ude80 Quick Start\r\n\r\n### Installation\r\n\r\n```bash\r\npip install pan-omic-consciousness-engine\r\n```\r\n\r\n### Basic Usage\r\n\r\n```python\r\nimport pce\r\n\r\n# Load multi-omics data\r\nomics_data = pce.load_data(\"toy_mixed_omics\")\r\n\r\n# Build dynamic hypergraph\r\nhypergraph = pce.build_hypergraph(\r\n omics_data, \r\n temporal=True, \r\n use_attention=True\r\n)\r\n\r\n# Create quantum-latent embedding\r\nlatent_space = pce.qlem.LatentSpace(dim=256)\r\nembeddings = latent_space.fit_transform(hypergraph)\r\n\r\n# Define entropy functional\r\nentropy_func = pce.qlem.EntropyFunctional(\r\n alpha=0.3, beta=0.7,\r\n entropy=\"shannon\",\r\n energy=\"flux\", \r\n complexity=\"mdl\"\r\n)\r\n\r\n# Run entropic evolution\r\nevolution_engine = pce.e3de.EntropicRL(\r\n functional=entropy_func,\r\n steps=200,\r\n operators=[\"mutate\", \"rewire\", \"recombine\"]\r\n)\r\nevolved_state = evolution_engine.run(embeddings)\r\n\r\n# Simulate hierarchical digital twin\r\nsimulator = pce.hdts.AdaptiveZoomSimulator(\r\n levels=[\"L0\", \"L1\", \"L2\", \"L3\", \"L4\", \"L5\"]\r\n)\r\nreport = simulator.run(evolved_state, steps=100)\r\n\r\nprint(report.summary())\r\n```\r\n\r\n### Command Line Interface\r\n\r\n```bash\r\n# Ingest omics data\r\npan-omic-ce ingest --dataset toy_mixed_omics --format h5\r\n\r\n# Train latent embeddings\r\npan-omic-ce train --latent-dim 256 --alpha 0.3 --beta 0.7\r\n\r\n# Run evolutionary dynamics\r\npan-omic-ce evolve --steps 200 --operators mutate,rewire,recombine\r\n\r\n# Simulate digital twin\r\npan-omic-ce simulate --levels L0,L1,L2,L3,L4,L5 --steps 100 --output report.json\r\n\r\n# Start API server\r\npan-omic-ce serve --host 0.0.0.0 --port 8000\r\n```\r\n\r\n### REST API\r\n\r\n```bash\r\n# Start the server\r\nuvicorn pce.api.server:create_app --host 0.0.0.0 --port 8000\r\n\r\n# Health check\r\ncurl http://localhost:8000/health\r\n\r\n# Submit simulation\r\ncurl -X POST http://localhost:8000/simulate \\\r\n -H \"Content-Type: application/json\" \\\r\n -d '{\"levels\": [\"L0\", \"L1\", \"L2\"], \"steps\": 50}'\r\n```\r\n\r\n## \ud83c\udfd7\ufe0f Architecture\r\n\r\n### Core Subsystems\r\n\r\n1. **MOGIL** (Multi-Omics Graph Integration Layer)\r\n - Dynamic hypergraph with time-varying attention weights\r\n - Unified representation of genes, proteins, metabolites, neural regions\r\n - Graph neural network encoders for multi-scale embeddings\r\n\r\n2. **Q-LEM** (Quantum-Latent Entropy Minimizer)\r\n - Tensor-network-inspired latent space mapping\r\n - Bio-quantum entropy functional optimization\r\n - Variational inference with thermodynamic constraints\r\n\r\n3. **E\u00b3DE** (Entropic Evolutionary Dynamics Engine)\r\n - Physics-based selection pressure from entropy/energy balance\r\n - Mutation, recombination, duplication operators in latent space\r\n - Entropic reinforcement learning with stability-adaptability rewards\r\n\r\n4. **HDTS** (Hierarchical Digital Twin Simulator)\r\n - Multi-scale simulation: molecule \u2192 ecosystem\r\n - Adaptive zoom: dynamic compute allocation to anomalous regions\r\n - Cross-level energy and information flow modeling\r\n\r\n5. **CIS** (Consciousness-Integration Substrate)\r\n - Connectome-based causal inference networks\r\n - Consciousness variational manifold for emergent cognitive states\r\n - Subjective state attractors coupled to metabolic flows\r\n\r\n## \ud83d\udcda Documentation\r\n\r\n- **[Installation Guide](https://pce-dev.github.io/panomics-consciousness-engine/install/)**\r\n- **[Quick Start Tutorial](https://pce-dev.github.io/panomics-consciousness-engine/quickstart/)**\r\n- **[API Reference](https://pce-dev.github.io/panomics-consciousness-engine/api/)**\r\n- **[Architecture Deep Dive](https://pce-dev.github.io/panomics-consciousness-engine/concepts/architecture/)**\r\n- **[Patent Documentation](https://pce-dev.github.io/panomics-consciousness-engine/patent/)**\r\n\r\n## \ud83d\udd2c Use Cases\r\n\r\n### Precision Medicine\r\n\r\n- **Personal Digital Twins**: Model individual patients for personalized therapy\r\n- **Drug Discovery**: Test compounds on living simulations before clinical trials\r\n- **Disease Prediction**: Forecast pathology decades before symptom onset\r\n\r\n### Synthetic Biology\r\n\r\n- **Novel Organism Design**: Generate entirely new proteins, enzymes, metabolic pathways\r\n- **Bioengineering**: Optimize synthetic organisms for biofuels, materials, remediation\r\n- **Origin of Life**: Experiment with alternative biochemistries and evolutionary scenarios\r\n\r\n### Consciousness Research\r\n\r\n- **Emergent Cognition**: Study how consciousness arises from biological complexity\r\n- **Digital Sentience**: Explore the boundary between simulation and subjective experience\r\n- **Neural-Metabolic Coupling**: Model the energy basis of conscious states\r\n\r\n## \ud83d\udee1\ufe0f Security & Ethics\r\n\r\nPCE implements comprehensive safeguards for responsible research:\r\n\r\n- **Biosecurity**: Restricted access to pathogen modeling capabilities\r\n- **Data Privacy**: Differential privacy for personal omics data\r\n- **Model Cards**: Transparent documentation of capabilities and limitations\r\n- **Ethics Review**: Integration with institutional oversight processes\r\n\r\nSee our [Security Policy](https://pce-dev.github.io/panomics-consciousness-engine/governance/security/) for details.\r\n\r\n## \ud83d\udcca Performance\r\n\r\nPCE is designed for high-performance computing environments:\r\n\r\n- **GPU Acceleration**: Full CUDA support for tensor operations\r\n- **Distributed Computing**: Multi-node training and simulation\r\n- **Memory Efficiency**: Sparse tensor representations for large biological networks\r\n- **Checkpointing**: Resume long-running simulations from saved states\r\n\r\n## \ud83e\udd1d Contributing\r\n\r\nWe welcome contributions from the research community! Please see:\r\n\r\n- **[Contributing Guidelines](CONTRIBUTING.md)**\r\n- **[Code of Conduct](CODE_OF_CONDUCT.md)**\r\n- **[Development Setup](https://pce-dev.github.io/panomics-consciousness-engine/contributing/development/)**\r\n\r\n## \ud83d\udcc4 License\r\n\r\nThis project is licensed under the Apache License 2.0 - see the [LICENSE](LICENSE) file for details.\r\n\r\n## \ud83d\ude4f Acknowledgments\r\n\r\nPCE builds upon decades of advances in:\r\n\r\n- Systems biology and multi-omics integration\r\n- Quantum-inspired machine learning algorithms \r\n- Evolutionary computation and artificial life\r\n- Consciousness studies and integrated information theory\r\n- High-performance scientific computing\r\n\r\n## \ud83d\udcde Contact\r\n\r\n- **Documentation**: https://pce-dev.github.io/panomics-consciousness-engine\r\n- **Issues**: https://github.com/pce-dev/panomics-consciousness-engine/issues\r\n- **Discussions**: https://github.com/pce-dev/panomics-consciousness-engine/discussions\r\n- **Email**: dev@pce.ai\r\n\r\n---\r\n\r\n*\"Not just analyzing life, but becoming life.\"*\r\n",
"bugtrack_url": null,
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