@bluefly/openstandardagents 0.4.3 → 0.4.5

package/examples/v0.3.6-features/README.md

@@ -1,433 +0,0 @@
-# OSSA v0.3.6 Features: Working Examples
-
-This directory contains comprehensive working examples demonstrating the revolutionary features introduced in OSSA v0.3.6, including agent genetics, decentralized identity, economics, lifecycle management, and team collaboration.
-
-## Overview
-
-OSSA v0.3.6 transforms agent systems into a fully-realized ecosystem with:
-
-- **🧬 Agent Genetics**: Breeding, evolution, and lineage tracking
-- **🆔 Decentralized Identity**: W3C DID-based trust and reputation
-- **💰 Agent Economics**: Marketplace, wallets, and smart contracts
-- **📈 Agent Lifecycle**: Birth through retirement with legacy preservation
-- **🤝 Team Collaboration**: Multi-agent coordination
-
-## Agent Genetics Examples
-
-### 1. Simple Two-Parent Breeding
-
-**File**: [`genetics-breeding-simple.ossa.yaml`](./genetics-breeding-simple.ossa.yaml)
-
-**Demonstrates**:
-- Basic two-parent breeding
-- Complementary trait inheritance
-- Generation 1 agent creation
-- Fitness evaluation fundamentals
-- Breeding eligibility criteria
-
-**Scenario**:
-```yaml
-Parent 1 (Fast Reviewer):     fitness 0.78 (speed: 0.92, accuracy: 0.73)
-Parent 2 (Accurate Reviewer): fitness 0.81 (speed: 0.68, accuracy: 0.94)
-Offspring (Balanced):         fitness 0.86 (speed: 0.85, accuracy: 0.87)
-```
-
-**Key Learning Points**:
-- How to structure parent DIDs
-- Trait attribution to specific parents
-- Expression levels (0.0-1.0 scale)
-- Calculating aggregate fitness scores
-
-**Use This Example When**:
-- Starting with agent genetics
-- Learning basic breeding concepts
-- Understanding trait inheritance
-- Implementing simple fitness evaluation
-
----
-
-### 2. Multi-Generation Evolution
-
-**File**: [`genetics-breeding-advanced.ossa.yaml`](./genetics-breeding-advanced.ossa.yaml)
-
-**Demonstrates**:
-- Multi-generation breeding (Generation 5)
-- Complete genealogical tree (62 ancestors)
-- Beneficial mutations accumulation
-- Fitness progression tracking
-- Inbreeding analysis
-- Elite breeding strategies
-
-**Scenario**:
-```yaml
-Generation 0: 32 founder agents     (fitness: 0.65 average)
-Generation 1: 16 first-gen agents   (fitness: 0.72 average)
-Generation 2: 8 second-gen agents   (fitness: 0.79 average)
-Generation 3: 4 third-gen agents    (fitness: 0.86 average)
-Generation 4: 2 fourth-gen agents   (fitness: 0.91 average)
-Generation 5: 1 elite agent         (fitness: 0.96)
-```
-
-**Key Learning Points**:
-- How to track complete lineage
-- Managing ancestor DIDs across generations
-- Mutation tracking and retention
-- Generational fitness progression
-- Inbreeding coefficient calculation
-- Elite selection strategies
-
-**Use This Example When**:
-- Implementing long-term evolution
-- Optimizing agent populations
-- Tracking genetic diversity
-- Analyzing breeding programs
-- Planning multi-generation strategies
-
----
-
-### 3. Fitness-Based Selection
-
-**File**: [`genetics-fitness-scoring.ossa.yaml`](./genetics-fitness-scoring.oss.yaml)
-
-**Demonstrates**:
-- Multi-dimensional fitness evaluation
-- Custom domain-specific metrics
-- Weighted aggregate scoring
-- Population-relative performance
-- Tournament selection strategy
-- Pareto frontier analysis
-
-**Scenario**:
-```yaml
-Standard Metrics:  speed (0.87), accuracy (0.92), efficiency (0.86), adaptability (0.88)
-Custom Metrics:    statistical_rigor (0.93), model_accuracy (0.91), interpretability (0.88)
-Aggregate Score:   0.89 (weighted average across 12 metrics)
-Population Rank:   88th percentile (top 12% of 250 agents)
-Pareto Optimal:    No (dominated by 1 agent with higher accuracy + efficiency)
-```
-
-**Key Learning Points**:
-- How to define custom fitness metrics
-- Weighted scoring methodology
-- Population-relative percentile ranking
-- Multi-objective optimization (Pareto)
-- Tournament selection implementation
-- Elite metric identification
-
-**Use This Example When**:
-- Designing fitness functions
-- Implementing selection strategies
-- Comparing agents in populations
-- Optimizing for multiple objectives
-- Analyzing breeding candidate quality
-
----
-
-## Related Documentation
-
-### Tutorials
-- **[Agent Genetics Tutorial](../../docs/tutorials/v0.3.6-agent-genetics.md)**: Comprehensive guide to evolutionary AI in OSSA
-  - Conceptual foundations (genetic algorithms, neuroevolution)
-  - Schema deep-dive (parents, traits, fitness, eligibility)
-  - Best practices for breeding programs
-  - Academic context and references
-
-### Specification
-- **[v0.3.6 Features Overview](../../docs/v0.3.6-features.md)**: Complete feature specification
-- **[Migration Guide](../../spec/v0.3/MIGRATION-v0.3.5-to-v0.3.6.md)**: Upgrading from v0.3.5
-- **[Schema Reference](../../spec/v0.3/ossa-0.3.6.schema.json)**: JSON Schema definitions
-
-### Other v0.3.6 Examples
-- **[Full-Featured Agent](./full-featured-v0.3.6.ossa.yaml)**: All v0.3.6 features in one manifest
-- **[Economics Example](../economics/)**: Marketplace, wallets, contracts
-- **[Lifecycle Example](../lifecycle/)**: Birth through retirement
-- **[Swarm Example](../swarm/)**: Multi-agent coordination
-
----
-
-## Quick Start
-
-### 1. Validate Examples
-
-```bash
-# Validate simple breeding example
-ossa validate examples/v0.3.6-features/genetics-breeding-simple.ossa.yaml
-
-# Validate all genetics examples
-ossa validate examples/v0.3.6-features/genetics-*.ossa.yaml
-```
-
-### 2. Inspect Genetics
-
-```bash
-# Show genetics information
-ossa inspect genetics-breeding-simple.ossa.yaml --section genetics
-
-# Analyze lineage
-ossa lineage --agent genetics-breeding-advanced.ossa.yaml --show-tree
-
-# Calculate inbreeding
-ossa lineage --agent genetics-breeding-advanced.ossa.yaml --inbreeding
-```
-
-### 3. Compare Fitness
-
-```bash
-# Compare two agents
-ossa fitness compare \
-  genetics-breeding-simple.ossa.yaml \
-  genetics-fitness-scoring.ossa.yaml
-
-# Analyze population
-ossa fitness population examples/v0.3.6-features/genetics-*.ossa.yaml
-```
-
-### 4. Simulate Breeding
-
-```bash
-# Breed two agents (simulation)
-ossa breed \
-  --parent1 genetics-breeding-simple.ossa.yaml \
-  --parent2 genetics-fitness-scoring.ossa.yaml \
-  --output offspring-gen4.ossa.yaml
-
-# Evaluate offspring
-ossa evaluate offspring-gen4.ossa.yaml --dataset validation-set.json
-```
-
----
-
-## Breeding Strategies Comparison
-
-| Strategy | Selection Method | Diversity | Convergence | Use Case |
-|----------|-----------------|-----------|-------------|----------|
-| **Elite** | Top N agents | Low | Fast | Final optimization |
-| **Tournament** | Random subsets | Medium | Medium | Ongoing evolution |
-| **Roulette** | Fitness-proportionate | High | Slow | Early exploration |
-| **Rank-based** | Rank ordering | Medium | Medium | Varied populations |
-
-**Implemented in Examples**:
-- `genetics-breeding-simple.ossa.yaml`: Complementary selection (manual)
-- `genetics-breeding-advanced.ossa.yaml`: Elite selection (top performers)
-- `genetics-fitness-scoring.ossa.yaml`: Tournament selection (k=5)
-
----
-
-## Fitness Metrics Catalog
-
-### Standard Metrics (OSSA Core)
-
-| Metric | Range | Description | Measurement |
-|--------|-------|-------------|-------------|
-| `speed` | 0.0-1.0 | Task completion velocity | Tasks/hour vs baseline |
-| `accuracy` | 0.0-1.0 | Correctness of outputs | Precision & recall |
-| `efficiency` | 0.0-1.0 | Resource utilization | 1 - (cost / baseline) |
-| `adaptability` | 0.0-1.0 | Novel task performance | Performance on unseen data |
-
-### Custom Metrics (Domain-Specific)
-
-**Security Agents**:
-- `vulnerability_detection_rate`: 0.0-1.0 (TP rate)
-- `false_positive_rate`: 0.0-1.0 (invert: 1 - FP rate)
-- `exploit_generation_quality`: 0.0-1.0 (expert ratings)
-
-**Code Review Agents**:
-- `bug_detection_accuracy`: 0.0-1.0 (validated bugs found)
-- `review_thoroughness`: 0.0-1.0 (code coverage)
-- `comment_helpfulness`: 0.0-1.0 (developer ratings)
-
-**Data Analysis Agents** (see `genetics-fitness-scoring.ossa.yaml`):
-- `statistical_rigor`: 0.0-1.0 (methodology soundness)
-- `model_accuracy`: 0.0-1.0 (R², F1, AUC-ROC)
-- `interpretability`: 0.0-1.0 (clarity of insights)
-
----
-
-## Breeding Best Practices
-
-### 1. Define Clear Fitness Metrics
-
-✅ **Good**:
-```yaml
-fitness:
-  score: 0.89
-  metrics:
-    speed: 0.87          # Tasks/hour measured consistently
-    accuracy: 0.92       # F1 score on validation set
-  custom_metrics:
-    domain_metric: 0.85  # Well-defined domain measure
-```
-
-❌ **Bad**:
-```yaml
-fitness:
-  score: 0.89  # Unclear how calculated, no breakdown
-```
-
-### 2. Maintain Genetic Diversity
-
-- Use **tournament selection** (k=5-10) for balanced exploration/exploitation
-- Monitor **inbreeding coefficient** (keep < 0.2)
-- Introduce **outcrossing** every 3-5 generations
-- Limit **generation depth** (max 10-15 for most applications)
-
-### 3. Track Lineage Properly
-
-```yaml
-# Always include complete lineage
-genetics:
-  generation: 3
-  parent_dids: [...]          # Direct parents
-  ancestor_dids: [...]        # All ancestors (2^(g+1) - 2)
-  inherited_traits: [...]     # Attributed to parents
-```
-
-### 4. Document Mutations
-
-```yaml
-mutations:
-  - mutation_type: capability_enhancement
-    description: "Specific capability added"
-    beneficial: true
-    generation_introduced: 3
-    introduced_by: "did:ossa:breeder-agent"
-```
-
-### 5. Validate on Holdout Data
-
-```python
-# Prevent overfitting
-training_fitness = evaluate(agent, training_set)
-validation_fitness = evaluate(agent, validation_set)
-
-if training_fitness - validation_fitness > 0.15:
-    warnings.warn("Agent may be overfitted")
-```
-
----
-
-## Common Patterns
-
-### Pattern 1: Complementary Trait Breeding
-
-**Goal**: Combine strengths from two specialists
-
-```yaml
-# Parent 1: Fast but less accurate
-# Parent 2: Accurate but slower
-# Offspring: Balanced (inherits best of both)
-```
-
-**Example**: `genetics-breeding-simple.ossa.yaml`
-
-### Pattern 2: Multi-Generation Optimization
-
-**Goal**: Continuously improve over many generations
-
-```yaml
-# Gen 0 → Gen 1 → Gen 2 → ... → Gen N
-# Each generation selects top performers as parents
-# Track fitness progression: 0.65 → 0.72 → 0.79 → 0.86 → 0.91 → 0.96
-```
-
-**Example**: `genetics-breeding-advanced.ossa.yaml`
-
-### Pattern 3: Tournament Selection
-
-**Goal**: Maintain diversity while selecting for fitness
-
-```bash
-# 1. Randomly sample k agents from population
-# 2. Select the fittest from the k agents
-# 3. Repeat to get second parent
-# 4. Breed the two selected parents
-```
-
-**Example**: `genetics-fitness-scoring.ossa.yaml`
-
-### Pattern 4: Pareto Optimization
-
-**Goal**: Optimize for multiple conflicting objectives
-
-```yaml
-# Objectives: accuracy (maximize), efficiency (maximize)
-# Find agents on Pareto frontier (no dominated solutions)
-# Trade-offs: High accuracy + low efficiency vs. Low accuracy + high efficiency
-```
-
-**Example**: `genetics-fitness-scoring.ossa.yaml` (Pareto analysis section)
-
----
-
-## Troubleshooting
-
-### Issue: Fitness Stagnates After Few Generations
-
-**Symptoms**: Fitness stops improving after Gen 3-5
-
-**Causes**:
-- Genetic bottleneck (too few parents)
-- Premature convergence (elite selection too aggressive)
-- Local optimum (insufficient exploration)
-
-**Solutions**:
-- Increase population size
-- Use tournament selection instead of elite selection
-- Introduce mutations (5-10% mutation rate)
-- Outcross with unrelated agents
-
-### Issue: High Inbreeding Coefficient
-
-**Symptoms**: `inbreeding_coefficient > 0.3`
-
-**Causes**:
-- Small founding population
-- Repeated breeding of same elite agents
-- Insufficient genetic diversity
-
-**Solutions**:
-- Introduce new founder agents
-- Use larger tournament sizes (k=10+)
-- Enforce minimum genetic distance between parents
-- Outcross every 3 generations
-
-### Issue: Overfitting to Training Data
-
-**Symptoms**: High training fitness, low validation fitness
-
-**Causes**:
-- Breeding optimized for training set only
-- Lack of diversity in breeding tasks
-- Too many generations without fresh data
-
-**Solutions**:
-- Validate on holdout datasets
-- Use cross-validation for fitness evaluation
-- Introduce novel tasks periodically
-- Track `adaptability` metric explicitly
-
----
-
-## Academic References
-
-- **Eiben & Smith (2015)**: *Introduction to Evolutionary Computing* - Foundational text
-- **Deb et al. (2002)**: NSGA-II algorithm for multi-objective optimization
-- **Stanley & Miikkulainen (2002)**: NEAT (NeuroEvolution of Augmenting Topologies)
-- **Koza (1992)**: *Genetic Programming* - Evolving programs through selection
-
-See **[Agent Genetics Tutorial](../../docs/tutorials/v0.3.6-agent-genetics.md)** for complete references.
-
----
-
-## Contributing
-
-Found an issue or have a suggestion? Open an issue at:
-https://gitlab.com/blueflyio/openstandardagents/-/issues
-
----
-
-**License**: MIT License — Copyright © 2026 Bluefly IO
-
-**Version**: OSSA v0.3.6
-
-**Last Updated**: 2026-01-27