Sparse Autoencoder Training

Sparse Autoencoder Training

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.

Skill metadata

Source	Optional — install with hermes skills install official/mlops/saelens
Path	optional-skills/mlops/saelens
Version	1.0.0
Author	Orchestra Research
License	MIT
Dependencies	sae-lens>=6.0.0, transformer-lens>=2.0.0, torch>=2.0.0
Tags	Sparse Autoencoders, SAE, Mechanistic Interpretability, Feature Discovery, Superposition

Reference: full SKILL.md

The following is the complete skill definition that Hermes loads when this skill is triggered. This is what the agent sees as instructions when the skill is active.

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 (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

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

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

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	500-2000	Prevents early feature death

Evaluation Metrics

Metric	Target	Meaning
L0	50-200	Average active features per token
CE Loss Score	80-95%	Cross-entropy recovered vs original
Dead Features	<5%	Features that never activate
Explained Variance	>90%	Reconstruction quality

Checklist

• Choose target layer and hook point
• Set expansion factor (d_sae = 4-16× d_model)
• Tune L1 coefficient for desired sparsity
• Enable L1 warm-up to prevent dead features
• Monitor metrics during training (W&B)
• Validate L0 and CE loss recovery
• Check dead feature ratio

Workflow 3: Feature Analysis and Steering

Analyzing Individual Features

from transformer_lens import HookedTransformer
from sae_lens import SAE
import torch

model = HookedTransformer.from_pretrained("gpt2-small", device="cuda")
sae, _, _ = SAE.from_pretrained(
    release="gpt2-small-res-jb",
    sae_id="blocks.8.hook_resid_pre",
    device="cuda"
)

# Find what activates a specific feature
feature_idx = 1234
test_texts = [
    "The scientist conducted an experiment",
    "I love chocolate cake",
    "The code compiles successfully",
    "Paris is beautiful in spring",
]

for text in test_texts:
    tokens = model.to_tokens(text)
    _, cache = model.run_with_cache(tokens)
    features = sae.encode(cache["resid_pre", 8])
    activation = features[0, :, feature_idx].max().item()
    print(f"{activation:.3f}: {text}")

Feature Steering

def steer_with_feature(model, sae, prompt, feature_idx, strength=5.0):
    """Add SAE feature direction to residual stream."""
    tokens = model.to_tokens(prompt)

    # Get feature direction from decoder
    feature_direction = sae.W_dec[feature_idx]  # [d_model]

    def steering_hook(activation, hook):
        # Add scaled feature direction at all positions
        activation += strength * feature_direction
        return activation

    # Generate with steering
    output = model.generate(
        tokens,
        max_new_tokens=50,
        fwd_hooks=[("blocks.8.hook_resid_pre", steering_hook)]
    )
    return model.to_string(output[0])

Feature Attribution

# Which features most affect a specific output?
tokens = model.to_tokens("The capital of France is")
_, cache = model.run_with_cache(tokens)

# Get features at final position
features = sae.encode(cache["resid_pre", 8])[0, -1]  # [d_sae]

# Get logit attribution per feature
# Feature contribution = feature_activation × decoder_weight × unembedding
W_dec = sae.W_dec  # [d_sae, d_model]
W_U = model.W_U    # [d_model, vocab]

# Contribution to "Paris" logit
paris_token = model.to_single_token(" Paris")
feature_contributions = features * (W_dec @ W_U[:, paris_token])

top_features = feature_contributions.topk(10)
print("Top features for 'Paris' prediction:")
for idx, val in zip(top_features.indices, top_features.values):
    print(f"  Feature {idx.item()}: {val.item():.3f}")

Common Issues & Solutions

Issue: High dead feature ratio

# WRONG: No warm-up, features die early
cfg = LanguageModelSAERunnerConfig(
    l1_coefficient=1e-4,
    l1_warm_up_steps=0,  # Bad!
)

# RIGHT: Warm-up L1 penalty
cfg = LanguageModelSAERunnerConfig(
    l1_coefficient=8e-5,
    l1_warm_up_steps=1000,  # Gradually increase
    use_ghost_grads=True,   # Revive dead features
)

Issue: Poor reconstruction (low CE recovery)

# Reduce sparsity penalty
cfg = LanguageModelSAERunnerConfig(
    l1_coefficient=5e-5,  # Lower = better reconstruction
    d_sae=768 * 16,       # More capacity
)

Issue: Features not interpretable

# Increase sparsity (higher L1)
cfg = LanguageModelSAERunnerConfig(
    l1_coefficient=1e-4,  # Higher = sparser, more interpretable
)
# Or use TopK architecture
cfg = LanguageModelSAERunnerConfig(
    architecture="topk",
    activation_fn_kwargs={"k": 50},  # Exactly 50 active features
)

Issue: Memory errors during training

cfg = LanguageModelSAERunnerConfig(
    train_batch_size_tokens=2048,  # Reduce batch size
    store_batch_size_prompts=4,    # Fewer prompts in buffer
    n_batches_in_buffer=8,         # Smaller activation buffer
)

Integration with Neuronpedia

Browse pre-trained SAE features at neuronpedia.org:

# Features are indexed by SAE ID
# Example: gpt2-small layer 8 feature 1234
# → neuronpedia.org/gpt2-small/8-res-jb/1234

Key Classes Reference

Class	Purpose
SAE	Sparse Autoencoder model
LanguageModelSAERunnerConfig	Training configuration
SAETrainingRunner	Training loop manager
ActivationsStore	Activation collection and batching
HookedSAETransformer	TransformerLens + SAE integration

Reference Documentation

For detailed API documentation, tutorials, and advanced usage, see the references/ folder:

File	Contents
references/README.md	Overview and quick start guide
references/api.md	Complete API reference for SAE, TrainingSAE, configurations
references/tutorials.md	Step-by-step tutorials for training, analysis, steering

External Resources

Tutorials

• Basic Loading & Analysis
• Training a Sparse Autoencoder
• ARENA SAE Curriculum

Papers

• Towards Monosemanticity - Anthropic (2023)
• Scaling Monosemanticity - Anthropic (2024)
• Sparse Autoencoders Find Highly Interpretable Features - Cunningham et al. (ICLR 2024)

Official Documentation

• SAELens Docs
• Neuronpedia - Feature browser

SAE Architectures

Architecture	Description	Use Case
Standard	ReLU + L1 penalty	General purpose
Gated	Learned gating mechanism	Better sparsity control
TopK	Exactly K active features	Consistent sparsity

# TopK SAE (exactly 50 features active)
cfg = LanguageModelSAERunnerConfig(
    architecture="topk",
    activation_fn="topk",
    activation_fn_kwargs={"k": 50},
)