Sparse Autoencoder TrainingSAFE

From the repository's own README, as read at the audited commit. Badges and raw HTML are left out.

pip install sae-lens

from transformer_lens import HookedTransformer
from sae_lens import SAE

# Load model and SAE
model = HookedTransformer.from_pretrained("gpt2-small", device="cuda")
sae, cfg_dict, sparsity = SAE.from_pretrained(
release="gpt2-small-res-jb",
sae_id="blocks.8.hook_resid_pre",
device="cuda"
)

# Encode activations to sparse features
tokens = model.to_tokens("Hello world")
_, cache = model.run_with_cache(tokens)
activations = cache["resid_pre", 8]

features = sae.encode(activations)  # Sparse feature activations
reconstructed = sae.decode(features)  # Reconstructed activations

The instruction file, verbatim from the audited commit — this is the text the model reads, and the surface the audit's instruction layer examines. Quoted here so you can judge it without cloning anything.

---
name: sparse-autoencoder-training
description: Provides guidance for training and analyzing Sparse Autoencoders (SAEs) using SAELens to decompose neural network activations into interpretable features. Use when discovering interpretable features, analyzing superposition, or studying monosemantic representations in language models.
version: 1.0.0
author: Orchestra Research
license: MIT
tags: [Sparse Autoencoders, SAE, Mechanistic Interpretability, Feature Discovery, Superposition]
dependencies: [sae-lens>=6.0.0, transformer-lens>=2.0.0, torch>=2.0.0]
---

# SAELens: Sparse Autoencoders for Mechanistic Interpretability

SAELens is the primary library for training and analyzing Sparse Autoencoders (SAEs) - a technique for decomposing polysemantic neural network activations into sparse, interpretable features. Based on Anthropic's groundbreaking research on monosemanticity.

**GitHub**: [jbloomAus/SAELens](https://github.com/jbloomAus/SAELens) (1,100+ stars)

## The Problem: Polysemanticity & Superposition

Individual neurons in neural networks are **polysemantic** - they activate in multiple, semantically distinct contexts. This happens because models use **superposition** to represent more features than they have neurons, making interpretability difficult.

**SAEs solve this** by decomposing dense activations into sparse, monosemantic features - typically only a small number of features activate for any given input, and each feature corresponds to an interpretable concept.

## When to Use SAELens

**Use SAELens when you need to:**
- Discover interpretable features in model activations
- Understand what concepts a model has learned
- Study superposition and feature geometry
- Perform feature-based steering or ablation
- Analyze safety-relevant features (deception, bias, harmful content)

**Consider alternatives when:**
- You need basic activation analysis → Use **TransformerLens** directly
- You want causal intervention experiments → Use **pyvene** or **TransformerLens**
- You need production steering → Consider direct activation engineering

## Installation

```bash
pip install sae-lens
```

Requirements: Python 3.10+, transformer-lens>=2.0.0

## Core Concepts

### What SAEs Learn

SAEs are trained to reconstruct model activations through a sparse bottleneck:

```
Input Activation → Encoder → Sparse Features → Decoder → Reconstructed Activation
    (d_model)       ↓        (d_sae >> d_model)    ↓         (d_model)
                 sparsity                      reconstruction
                 penalty                          loss
```

**Loss Function**: `MSE(original, reconstructed) + L1_coefficient × L1(features)`

### Key Validation (Anthropic Research)

In "Towards Monosemanticity", human evaluators found **70% of SAE features genuinely interpretable**. Features discovered include:
- DNA sequences, legal language, HTTP requests
- Hebrew text, nutrition statements, code syntax
- Sentiment, named entities, grammatical structures

## Workflow 1: Loading and Analyzing Pre-trained SAEs

### Step-by-Step

```python
from transformer_lens import HookedTransformer
from sae_lens import SAE

# 1. Load model and pre-trained SAE
model = HookedTransformer.from_pretrained("gpt2-small", device="cuda")
sae, cfg_dict, sparsity = SAE.from_pretrained(
    release="gpt2-small-res-jb",
    sae_id="blocks.8.hook_resid_pre",
    device="cuda"
)

# 2. Get model activations
tokens = model.to_tokens("The capital of France is Paris")
_, cache = model.run_with_cache(tokens)
activations = cache["resid_pre", 8]  # [batch, pos, d_model]

# 3. Encode to SAE features
sae_features = sae.encode(activations)  # [batch, pos, d_sae]
print(f"Active features: {(sae_features > 0).sum()}")

# 4. Find top features for each position
for pos in range(tokens.shape[1]):
    top_features = sae_features[0, pos].topk(5)
    token = model.to_str_tokens(tokens[0, pos:pos+1])[0]
    print(f"Token '{token}': features {top_features.indices.tolist()}")

# 5. Reconstruct activations
reconstructed = sae.decode(sae_features)
reconstruction_error = (activations - reconstructed).norm()
```

### Available Pre-trained SAEs

| Release | Model | Layers |
|---------|-------|--------|
| `gpt2-small-res-jb` | GPT-2 Small | Multiple residual streams |
| `gemma-2b-res` | Gemma 2B | Residual streams |
| Various on HuggingFace | Search tag `saelens` | Various |

### Checklist
- [ ] Load model with TransformerLens
- [ ] Load matching SAE for target layer
- [ ] Encode activations to sparse features
- [ ] Identify top-activating features per token
- [ ] Validate reconstruction quality

## Workflow 2: Training a Custom SAE

### Step-by-Step

```python
from sae_lens import SAE, LanguageModelSAERunnerConfig, SAETrainingRunner

# 1. Configure training
cfg = LanguageModelSAERunnerConfig(
    # Model
    model_name="gpt2-small",
    hook_name="blocks.8.hook_resid_pre",
    hook_layer=8,
    d_in=768,  # Model dimension

    # SAE architecture
    architecture="standard",  # or "gated", "topk"
    d_sae=768 * 8,  # Expansion factor of 8
    activation_fn="relu",

    # Training
    lr=4e-4,
    l1_coefficient=8e-5,  # Sparsity penalty
    l1_warm_up_steps=1000,
    train_batch_size_tokens=4096,
    training_tokens=100_000_000,

    # Data
    dataset_path="monology/pile-uncopyrighted",
    context_size=128,

    # Logging
    log_to_wandb=True,
    wandb_project="sae-training",

    # Checkpointing
    checkpoint_path="checkpoints",
    n_checkpoints=5,
)

# 2. Train
trainer = SAETrainingRunner(cfg)
sae = trainer.run()

# 3. Evaluate
print(f"L0 (avg active features): {trainer.metrics['l0']}")
print(f"CE Loss Recovered: {trainer.metrics['ce_loss_score']}")
```

### Key Hyperparameters

| Parameter | Typical Value | Effect |
|-----------|---------------|--------|
| `d_sae` | 4-16× d_model | More features, higher capacity |
| `l1_coefficient` | 5e-5 to 1e-4 | Higher = sparser, less accurate |
| `lr` | 1e-4 to 1e-3 | Standard optimizer LR |
| `l1_warm_up_steps` | 500-2

SAFEgrade B · trust 89/100 Nothing in the source contradicts what it says it does. Grade A is reserved for packages that have also passed the behavioural sandbox.

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