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

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

Evaluation Metrics

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
how to use sparse-autoencoder-training
CursorClaude CodeClineCodexWindsurfGooseGitHub CopilotVS CodeGemini CLIKiloOpencodeKimi CLIRoo ClineAiderContinueZedBolt.newLovablev0Replit AgentSweepSmol DeveloperDevinCavemanAmpAntigravity
How to use sparse-autoencoder-training on Cursor
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Prerequisites
Before installing skills in Cursor, ensure your development environment meets these requirements:
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Execute the skills CLI command in your project's root directory to begin installation:
$npx skills add https://github.com/davila7/claude-code-templates --skill sparse-autoencoder-trainingcopy
The skills CLI fetches sparse-autoencoder-training from GitHub repository davila7/claude-code-templates and configures it for Cursor.
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Confirm successful installation by checking the skill directory location:
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