symbolic-equation

The full skill.

Original instructions from the publisher’s SKILL.md

# Symbolic Equation Discovery

Discover interpretable scientific equations from data using LLM-guided evolutionary search.

## Input

- `$0` — Dataset description, variable names, and physical context

## References

- LLM-SR patterns (prompts, evolution, sampling): `~/.claude/skills/symbolic-equation/references/llmsr-patterns.md`

## Workflow (from LLM-SR)

### Step 1: Define Problem Specification
Create a specification with:
1. **Input variables**: Physical quantities with types (e.g., `x: np.ndarray`, `v: np.ndarray`)
2. **Output variable**: Target quantity to predict
3. **Evaluation function**: Fitness metric (typically negative MSE with parameter optimization)
4. **Physical context**: Domain knowledge to guide equation discovery

```python
# Example specification
@equation.evolve
def equation(x: np.ndarray, v: np.ndarray, params: np.ndarray) -> np.ndarray:
    """Describe the acceleration of a damped nonlinear oscillator."""
    return params[0] * x
```

### Step 2: Initialize Multi-Island Buffer
- Create N islands (default: 10) for population diversity
- Each island maintains independent clusters of equations
- Clusters group equations by performance signature

### Step 3: Evolutionary Search Loop
Repeat until convergence or max samples:
1. **Select island**: Random island selection
2. **Build prompt**: Sample top equations from clusters (softmax-weighted by score)
3. **LLM proposes**: Generate new equation as improved version
4. **Evaluate**: Execute on test data, compute fitness score
5. **Register**: Add to island's cluster if valid

### Step 4: Prompt Construction
Present previous equations as versioned sequence:
```python
def equation_v0(x, v, params):
    """Initial version."""
    return params[0] * x

def equation_v1(x, v, params):
    """Improved version of equation_v0."""
    return params[0] * x + params[1] * v

def equation_v2(x, v, params):
    """Improved version of equation_v1."""
    # LLM completes this
```

### Step 5: Island Reset (Diversity Maintenance)
Periodically (default: every 4 hours):
1. Sort islands by best score
2. Reset bottom 50% of islands
3. Seed each reset island with best equation from a surviving island
4. Restart cluster sampling temperature

### Step 6: Extract Best Equations
After search completes:
1. Collect best equation from each island
2. Rank by fitness score
3. Simplify if possible (algebraic simplification)
4. Report with physical interpretation

## Cluster Sampling

Temperature-scheduled softmax over cluster scores:
```
temperature = T_init * (1 - (num_programs % period) / period)
probabilities = softmax(cluster_scores / temperature)
```
- Higher temperature → more exploration
- Lower temperature → more exploitation of best clusters
- Within clusters: shorter programs are preferred (Occam's razor)

## Rules

- Equations must use only standard mathematical operations
- Parameter optimization via scipy BFGS or Adam
- Fitness = negative MSE (higher is better)
- Timeout protection for equation evaluation
- No recursive equations allowed
- Physical interpretability is preferred over pure fit

## Related Skills
- Upstream: [data-analysis](../data-analysis/), [math-reasoning](../math-reasoning/)
- Downstream: [paper-writing-section](../paper-writing-section/)
- See also: [algorithm-design](../algorithm-design/)